Citrus Sinensis ID: 039806

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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-------40
Protein Sequence
MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAKQGPGLASTIFPVHPTLYQRALQVYQAPDFRHGGMIPNGFSPPPPSPLFLMAPDSVTQYRGAMMNGHANFPMPLMLSNLQKPSYNYPISQPRAGQAAANNLTNGNHRAAASNENLSSMLVATSPDERKDILGQRLYPLVKKLKVITHIFVKGQFRFIFG
Secondary Structure (PSIPRED)
cccccccccccccccEEEEccccccccHHHHHHHHHccccEEEEEEEEccccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEcccccccHHHHHcccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEcccccccccccEEEEEcHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHcccccEEEEEEEEccccccccccccccccHHHHHHHHHHHcccccccccccccccccHHHcHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccHHHHHHHHHHcHHHHHHHccccccccccEEEccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccEEEEEccccccccHHHHHHHHcccccEEEEEEEEEcccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEEEccccccHHccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEEcccccccccEEEEEEEcccccHHHHHHHHHHHHHHHHccccEEEEcccccccHHHHHHHHcccccEEEEEEEEcccccccccEEEEcccHHHHHHHHHHHcccEccccEEccccEEEHHHHcHHHHHHHHHHHHHHHcHcHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccHHHHHHHHHHHHHHHHHHHcHHHHcHHcccEEEEEc
Coil and Loop (DISEMBL)
mwstpnsearLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVsqegkskgygfvqystpeSALDAIEKLQGATVERMelyvgpfirradriqegssfnnlyvknldddMTEEILVEKFSEFGKITSLVIskdangtskgfgSKVLYVARAQKKAERKAILRAQFERMRKERAELYKNINDEVDEIELKQYFsqcgtissvkimrtdrgiskghCMAIAQTKRERTSYLRIMYakqgpglastifpvhpTLYQRALQvyqapdfrhggmipngfsppppsplflmapdsvTQYRGAmmnghanfpmplmlsnlqkpsynypisqpragqaaannltngnhraaasnENLSSMLvatspderkdilgqrlyPLVKKLKVITHIFVKgqfrfifg
Flexible Loop (DISEMBL)
mwstpnseARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPfirradriqegssfnnlyvknLDDDMTEEILVEKFSEFGKITSlviskdangtskgfgskVLYVARAQKKAERKAILRAQFERMRKERAELYKNINDEVDEIELKQYfsqcgtissvkimrtdrgiskghcMAIAQTKRERTSYLRIMYAKQGPGLASTIFPVHPTLYQRALQVYQAPDFRHGGMIPNGFSPPPPSPLFLMAPDSVTQYRGAMMNGHANFPMPLMLSNLQKPSYNYPISQPRAGQAAANNLTNGNHRAAASNENLSSMLVATSPDERKDILGQRLYPLVKKLKVITHIFVKGQFRFIFG
Low Complexity Region (SEG)
MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAKQGPGLASTIFPVHPTLYQRALQVYQAPDFRHGGMIPNGfsppppsplflMAPDSVTQYRGAMMNGHANFPMPLMLSNLQKPSYNYPISQPRAGQAAANNLTNGNHRAAASNENLSSMLVATSPDERKDILGQRLYPLVKKLKVITHIFVKGQFRFIFG
Disordered region (IsUnstruct)
************GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAKQGPGLASTIFPVHPTLYQRALQVYQAPDFRHGGMI********************************************************************************************DILGQRLYPLVKKLKVITHIFVKGQFRFIF*
Disordered Region (DISOPRED)
MWS*************AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY***********************NLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKK********************LYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLR****************************************************************************************************************************************QRLYPLVKKLKVITHIFVKGQFRFIF*
Disordered Region (DISEMBL)
*********RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAKQGPGLASTIFPVHPTLYQRALQVYQAPDFRHGGMIPNGFSPPPPSPLFLMAPDSVTQYRGAMMNGHANFPMPLMLSNLQKPSYNYPISQPRAGQAAANNLTNGNHRAAASNENLSSMLVATSPDERKDILGQRLYPLVKKLKVITHIFVKGQFRFIFG
Disordered Region (DISPRO)
***********SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRI*EGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAKQGPGLASTIFPVHPTLYQRALQVYQAPDFRHGGMIPNGFSPPPPSPLFLMAPDSVTQYRGAMMNGHANFPMPLMLSNLQKPSYNYPISQPR********************ENLSSMLVATSPDERKDILGQRLYPLVKKLKVITHIFVKGQFRFIFG
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAKQGPGLASTIFPVHPTLYQRALQVYQAPDFRHGGMIPNGFSPPPPSPLFLMAPDSVTQYRGAMMNGHANFPMPLMLSNLQKPSYNYPISQPRAGQAAANNLTNGNHRAAASNENLSSMLVATSPDERKDILGQRLYPLVKKLKVITHIFVKGQFRFIFG
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	398	2.2.26 [Sep-21-2011]
Q9ZQA8	609	Probable polyadenylate-bi	yes	no	0.932	0.609	0.331	5e-56
P42731	629	Polyadenylate-binding pro	no	no	0.603	0.381	0.419	1e-48
Q05196	682	Polyadenylate-binding pro	no	no	0.924	0.539	0.304	1e-45
P31209	653	Polyadenylate-binding pro	yes	no	0.575	0.350	0.403	3e-44
Q2UK72	765	Polyadenylate-binding pro	yes	no	0.527	0.274	0.409	3e-44
Q13310	644	Polyadenylate-binding pro	yes	no	0.728	0.450	0.343	3e-44
P21187	634	Polyadenylate-binding pro	yes	no	0.665	0.417	0.353	5e-44
O64380	660	Polyadenylate-binding pro	no	no	0.613	0.369	0.364	6e-44
P29341	636	Polyadenylate-binding pro	no	no	0.952	0.595	0.299	8e-44
A1CRM1	754	Polyadenylate-binding pro	N/A	no	0.527	0.278	0.405	1e-43

>sp|Q9ZQA8|PABPX_ARATH Probable polyadenylate-binding protein At2g36660 OS=Arabidopsis thaliana GN=At2g36660 PE=3 SV=1

 Score =  218 bits (556), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 151/455 (33%), Positives = 230/455 (50%), Gaps = 84/455 (18%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS    +AR +G+GN FVKNL  ++ N  L  +F KFG+I S KV   ++GKS+GYGFV
Sbjct: 98  MWSVRAPDARRNGVGNVFVKNLPESVTNAVLQDMFKKFGNIVSCKVATLEDGKSRGYGFV 157

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEIL 120
           Q+   ++A  AI+ L    V   E+YVG F+++ DR++    + NLY+KNLD D++E++L
Sbjct: 158 QFEQEDAAHAAIQTLNSTIVADKEIYVGKFMKKTDRVKPEEKYTNLYMKNLDADVSEDLL 217

Query: 121 VEKFSEFGKITSLVISKDANGTSKG-----------------------FGSKVLYVARAQ 157
            EKF+EFGKI SL I+KD N   +G                       FGSK LYV RAQ
Sbjct: 218 REKFAEFGKIVSLAIAKDENRLCRGYAFVNFDNPEDARRAAETVNGTKFGSKCLYVGRAQ 277

Query: 158 KKAERKAILRAQFERMRKER------AELY-KNINDEVDEIELKQYFSQCGTISSVKIMR 210
           KKAER+ +LR QF+   +E+      + +Y KN+N  V E EL+++FSQCGTI+S K+M 
Sbjct: 278 KKAEREQLLREQFKEKHEEQKMIAKVSNIYVKNVNVAVTEEELRKHFSQCGTITSTKLMC 337

Query: 211 TDRGISKGH---C-------------------------MAIAQTKRERTSYLRIMY---- 238
            ++G SKG    C                         +AIAQ K +R   L++ +    
Sbjct: 338 DEKGKSKGFGFVCFSTPEEAIDAVKTFHGQMFHGKPLYVAIAQKKEDRKMQLQVQFGNRV 397

Query: 239 --------AKQGPGLASTIF--PVHPTL-YQRALQVYQAPDFRHGGMIPNGFSPPPPSPL 287
                   A   PG  + ++    HP + YQ    ++++ +   G   PN  +   P P+
Sbjct: 398 EARKSSSSASVNPGTYAPLYYTNTHPGMVYQSYPLMWKSANMI-GSSYPNSEAVTYP-PM 455

Query: 288 FLMAPDSVTQYRGAMMNGHANFPMPLMLSNLQKPSYNYPISQPRAGQAAANNLTNGNHRA 347
              AP    Q R   ++ +A   +P    N+ + +   P+S+  + Q  +     G    
Sbjct: 456 VANAPSKNRQNRIGKLDRNAVSYVP----NVYQSTQMLPLSRDFSKQQHSRTYGRGKEMK 511

Query: 348 AASNENLSSMLVATSPDERKDILGQRLYPLVKKLK 382
            +  +  S  +          +LG+ L+PLV+KL+
Sbjct: 512 KSIQQRQSETV-----GMEMQLLGELLHPLVEKLE 541

Binds the poly(A) tail of mRNA.
Arabidopsis thaliana (taxid: 3702)

>sp|P42731|PABP2_ARATH Polyadenylate-binding protein 2 OS=Arabidopsis thaliana GN=PAB2 PE=1 SV=1

 Score =  194 bits (492), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 114/272 (41%), Positives = 151/272 (55%), Gaps = 32/272 (11%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           M+S  +   R SG GN F+KNL  +ID+  LH  FS FG+I S KV V   G+SKGYGFV
Sbjct: 110 MYSHRDPSVRRSGAGNIFIKNLDESIDHKALHDTFSSFGNIVSCKVAVDSSGQSKGYGFV 169

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADR--IQEGSSFNNLYVKNLDDDMTEE 118
           QY+  ESA  AIEKL G  +   ++YVGPF+RR +R      + F N+YVKNL +  T++
Sbjct: 170 QYANEESAQKAIEKLNGMLLNDKQVYVGPFLRRQERDSTANKTKFTNVYVKNLAESTTDD 229

Query: 119 ILVEKFSEFGKITSLVISKDANGTSKGFG-----------------------SKVLYVAR 155
            L   F E+GKITS V+ KD  G SKGFG                        K  YV R
Sbjct: 230 DLKNAFGEYGKITSAVVMKDGEGKSKGFGFVNFENADDAARAVESLNGHKFDDKEWYVGR 289

Query: 156 AQKKAERKAILRAQFERMRKERAE------LY-KNINDEVDEIELKQYFSQCGTISSVKI 208
           AQKK+ER+  LR ++E+  KE A+      LY KN++  + + +LK+ FS  GT++S K+
Sbjct: 290 AQKKSERETELRVRYEQNLKEAADKFQSSNLYVKNLDPSISDEKLKEIFSPFGTVTSSKV 349

Query: 209 MRTDRGISKGHCMAIAQTKRERTSYLRIMYAK 240
           MR   G SKG       T  E T  +  +  K
Sbjct: 350 MRDPNGTSKGSGFVAFATPEEATEAMSQLSGK 381

Binds the poly(A) tail of mRNA.

Arabidopsis thaliana (taxid: 3702)

>sp|Q05196|PABP5_ARATH Polyadenylate-binding protein 5 OS=Arabidopsis thaliana GN=PAB5 PE=1 SV=3

 Score =  184 bits (467), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 152/499 (30%), Positives = 223/499 (44%), Gaps = 131/499 (26%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           M S  +   RLSG GN F+KNL ++IDN  L++ FS FG I S KV +   G+SKGYGFV
Sbjct: 132 MLSNRDPSTRLSGKGNVFIKNLDASIDNKALYETFSSFGTILSCKVAMDVVGRSKGYGFV 191

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGS----SFNNLYVKNLDDDMT 116
           Q+   E+A  AI+KL G  +   +++VG F+RR DR +  S    SF N+YVKNL  ++T
Sbjct: 192 QFEKEETAQAAIDKLNGMLLNDKQVFVGHFVRRQDRARSESGAVPSFTNVYVKNLPKEIT 251

Query: 117 EEILVEKFSEFGKITSLVISKDANGTSKGF-----------------------GSKVLYV 153
           ++ L + F ++G I+S V+ KD +G S+ F                       G  VLYV
Sbjct: 252 DDELKKTFGKYGDISSAVVMKDQSGNSRSFGFVNFVSPEAAAVAVEKMNGISLGEDVLYV 311

Query: 154 ARAQKKAERKAILRAQFERMRKERAE------LY-KNINDEVDEIELKQYFSQCGTISSV 206
            RAQKK++R+  LR +FE+ R  R E      LY KN++D V++ +LK+ FS+ G ++S 
Sbjct: 312 GRAQKKSDREEELRRKFEQERISRFEKLQGSNLYLKNLDDSVNDEKLKEMFSEYGNVTSC 371

Query: 207 KIMRTDRGISKGHC----------------------------MAIAQTKRERTSYLRIMY 238
           K+M   +G+S+G                              +A+AQ K ER ++L+ ++
Sbjct: 372 KVMMNSQGLSRGFGFVAYSNPEEALLAMKEMNGKMIGRKPLYVALAQRKEERQAHLQSLF 431

Query: 239 AK-QGPGLASTI-----------------FPVHPTLYQR-------------ALQVYQAP 267
            + + PG  S +                  P HP                    QV   P
Sbjct: 432 TQIRSPGTMSPVPSPMSGFHHHPPGGPMSGPHHPMFIGHNGQGLVPSQPMGYGYQVQFMP 491

Query: 268 DFRHGGMIPNGFSPPP------PSPLFLMAPDSVTQYRGA-------------------M 302
             R G   PN   P P      P P        V   RGA                    
Sbjct: 492 GMRPGAGPPNFMMPFPLQRQTQPGP-------RVGFRRGANNMQQQFQQQQMLQQNASRF 544

Query: 303 MNGHANFPMPLMLSNLQKPSYNYPISQPRAGQAAANNLTNGNHRAAA-SNENLSSMLVAT 361
           M G  N       + ++  +    I  P    A ++N    +H+    +   L+S L   
Sbjct: 545 MGGAGN-----RRNGMEASAPQGIIPLPLNASANSHNAPQRSHKPTPLTISKLASDLALA 599

Query: 362 SPDERKDILGQRLYPLVKK 380
           SPD+   +LG  LYPLV++
Sbjct: 600 SPDKHPRMLGDHLYPLVEQ 618

Binds the poly(A) tail of mRNA.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  179 bits (455), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 106/263 (40%), Positives = 142/263 (53%), Gaps = 34/263 (12%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  +   R  G GN F+KNL   IDN  LH  FS FG I S KV V + G +KGYGFV
Sbjct: 154 MWSQRDPSLRKMGTGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFV 213

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE----GSSFNNLYVKNLDDDMT 116
            + + ESA  AIE + G  +   ++YVG  + R +R  +     ++F N+Y+KNLD ++T
Sbjct: 214 HFDSVESANAAIEHVNGMLLNDKKVYVGHHVSRRERQSKVEALKANFTNVYIKNLDTEIT 273

Query: 117 EEILVEKFSEFGKITSLVISKDANGTSKGFG-----------------------SKVLYV 153
           E+   + F +FG+ITSL + KD N   +GFG                        K LYV
Sbjct: 274 EQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333

Query: 154 ARAQKKAERKAILRAQFERMRKERAELY-------KNINDEVDEIELKQYFSQCGTISSV 206
            RAQKK ER+  LR ++E+M+ E+   Y       KN+ DEVD+  LK  FS  GTI+S 
Sbjct: 334 GRAQKKHEREEELRKRYEQMKLEKMNKYQGVNLFIKNLQDEVDDERLKAEFSAFGTITSA 393

Query: 207 KIMRTDRGISKGHCMAIAQTKRE 229
           KIM  ++G SKG       T  E
Sbjct: 394 KIMTDEQGKSKGFGFVCYTTPEE 416

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)

>sp|Q2UK72|PABP_ASPOR Polyadenylate-binding protein, cytoplasmic and nuclear OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) GN=pab1 PE=3 SV=1

 Score =  179 bits (454), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 100/244 (40%), Positives = 140/244 (57%), Gaps = 34/244 (13%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  +   R +G GN F+KNL S IDN  LH  F+ FG+I S KV   + G SKGYGFV
Sbjct: 123 MWSQRDPALRKTGQGNVFIKNLDSAIDNKALHDTFAAFGNILSCKVAQDEFGNSKGYGFV 182

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE----GSSFNNLYVKNLDDDMT 116
            Y T E+A +AI+ + G  +   +++VG  I + DR  +     ++F N+Y+KN+D D+T
Sbjct: 183 HYETAEAANNAIKHVNGMLLNDKKVFVGHHISKKDRQSKFEEMKANFTNVYIKNIDQDVT 242

Query: 117 EEILVEKFSEFGKITSLVISKDANGTSKGFG-----------------------SKVLYV 153
           EE   E F +FG+ITS  +S+D  G S+GFG                       ++ LYV
Sbjct: 243 EEEFRELFEKFGEITSATLSRDQEGKSRGFGFVNFSTHESAQAAVDEMNEKEIRTQKLYV 302

Query: 154 ARAQKKAERKAILRAQFERMRKERAELY-------KNINDEVDEIELKQYFSQCGTISSV 206
            RAQKK ER+  LR Q+E  R E+A  Y       KN+ D+VD+ +L++ F   GTI+S 
Sbjct: 303 GRAQKKHEREEELRKQYEAARLEKASKYQGVNLYVKNLTDDVDDEKLRELFGPYGTITSA 362

Query: 207 KIMR 210
           K+MR
Sbjct: 363 KVMR 366

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.

Aspergillus oryzae (strain ATCC 42149 / RIB 40) (taxid: 510516)

>sp|Q13310|PABP4_HUMAN Polyadenylate-binding protein 4 OS=Homo sapiens GN=PABPC4 PE=1 SV=1

 Score =  179 bits (454), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 126/367 (34%), Positives = 184/367 (50%), Gaps = 77/367 (20%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  +   R SG+GN F+KNL  +IDN  L+  FS FG+I S KVV  + G SKGY FV
Sbjct: 85  MWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYAFV 143

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE----GSSFNNLYVKNLDDDMT 116
            + T E+A  AIEK+ G  +   +++VG F  R +R  E       F N+Y+KN  +++ 
Sbjct: 144 HFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVD 203

Query: 117 EEILVEKFSEFGKITSLVISKDANGTSKGFG-----------------------SKVLYV 153
           +E L E FS+FGK  S+ + +D NG SKGFG                        K+++V
Sbjct: 204 DESLKELFSQFGKTLSVKVMRDPNGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFV 263

Query: 154 ARAQKKAERKAILRAQFERMRKERAELY-------KNINDEVDEIELKQYFSQCGTISSV 206
            RAQKK ER+A L+ +FE++++ER   Y       KN++D +D+ +L++ FS  G+I+S 
Sbjct: 264 GRAQKKVERQAELKRKFEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSA 323

Query: 207 KIMRTDRGISKGH---C-------------------------MAIAQTKRERTSYLRIMY 238
           K+M  D G SKG    C                         +A+AQ K ER ++L   Y
Sbjct: 324 KVMLED-GRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQY 382

Query: 239 AKQGPGLASTIFPVHPTL--YQRALQVYQAPDFRHGGMIPNGFSPPP---PSPLFLMAPD 293
            ++  G+ +   P +  L  +Q A   Y  P       +P     PP   P+ L  M P+
Sbjct: 383 MQRVAGMRA--LPANAILNQFQPAAGGYFVP------AVPQAQGRPPYYTPNQLAQMRPN 434

Query: 294 SVTQYRG 300
              Q  G
Sbjct: 435 PRWQQGG 441

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo.

Homo sapiens (taxid: 9606)

>sp|P21187|PABP_DROME Polyadenylate-binding protein OS=Drosophila melanogaster GN=pAbp PE=1 SV=3

 Score =  179 bits (453), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 120/339 (35%), Positives = 169/339 (49%), Gaps = 74/339 (21%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  +   R SG+GN F+KNL   IDN  ++  FS FG+I S KV   ++G SKGYGFV
Sbjct: 76  MWSQRDPSLRRSGVGNVFIKNLDRAIDNKAIYDTFSAFGNILSCKVATDEKGNSKGYGFV 135

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE----GSSFNNLYVKNLDDDMT 116
            + T E+A  +I+K+ G  +   ++YVG FI R +R +E       F N+YVKN  +D  
Sbjct: 136 HFETEEAANTSIDKVNGMLLNGKKVYVGKFIPRKEREKELGEKAKLFTNVYVKNFTEDFD 195

Query: 117 EEILVEKFSEFGKITSLVISKDANGTSKGFG------------------------SKVLY 152
           +E L E F  +GKITS  +    +G SKGFG                         K LY
Sbjct: 196 DEKLKEFFEPYGKITSYKVMSKEDGKSKGFGFVAFETTEAAEAAVQALNGKDMGEGKSLY 255

Query: 153 VARAQKKAERKAILRAQFERMRKERAE------LY-KNINDEVDEIELKQYFSQCGTISS 205
           VARAQKKAER+  L+ +FE ++++R E      LY KN++D +D+  L+  FS  G I+S
Sbjct: 256 VARAQKKAERQQELKRKFEELKQKRHESVFGVNLYVKNLDDTIDDDRLRIAFSPYGNITS 315

Query: 206 VKIMRTDRGISKGH---C-------------------------MAIAQTKRERTSYLRIM 237
            K+M  + G SKG    C                         +A+AQ K ER ++L   
Sbjct: 316 AKVMTDEEGRSKGFGFVCFNAASEATCAVTELNGRVVGSKPLYVALAQRKEERKAHLASQ 375

Query: 238 YAKQGPGLASTIFPVHPTLYQRALQVYQAPDFRHGGMIP 276
           Y +   G+            Q+  Q+YQ P+   G  +P
Sbjct: 376 YMRHMTGMR----------MQQLGQIYQ-PNAASGFFVP 403

Binds the poly(A) tail of mRNA.

Drosophila melanogaster (taxid: 7227)

>sp|O64380|PABP3_ARATH Polyadenylate-binding protein 3 OS=Arabidopsis thaliana GN=PAB3 PE=2 SV=1

 Score =  178 bits (452), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 112/307 (36%), Positives = 168/307 (54%), Gaps = 63/307 (20%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           M S  +   RLSG GN F+KNL ++IDN  L + FS FG I S KV +   G+SKGYGFV
Sbjct: 122 MLSNRDPSTRLSGKGNIFIKNLDASIDNKALFETFSSFGTILSCKVAMDVTGRSKGYGFV 181

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSS----FNNLYVKNLDDDMT 116
           Q+   ESA  AI+KL G  +   +++VG FIRR +R ++ ++    F N+YVKNL  ++ 
Sbjct: 182 QFEKEESAQAAIDKLNGMLMNDKQVFVGHFIRRQERARDENTPTPRFTNVYVKNLPKEIG 241

Query: 117 EEILVEKFSEFGKITSLVISKDANGTSKGF-----------------------GSKVLYV 153
           E+ L + F +FG I+S V+ +D +G S+ F                       G  VLYV
Sbjct: 242 EDELRKTFGKFGVISSAVVMRDQSGNSRCFGFVNFECTEAAASAVEKMNGISLGDDVLYV 301

Query: 154 ARAQKKAERKAILRAQFERMRKER------AELY-KNINDEVDEIELKQYFSQCGTISSV 206
            RAQKK+ER+  LR +FE+ R  R      A LY KN++D VD+ +LK+ FS+ G ++S 
Sbjct: 302 GRAQKKSEREEELRRKFEQERINRFEKSQGANLYLKNLDDSVDDEKLKEMFSEYGNVTSS 361

Query: 207 KIMRTDRGISKGHC----------------------------MAIAQTKRERTSYLRIMY 238
           K+M   +G+S+G                              +A+AQ K +R ++L+ ++
Sbjct: 362 KVMLNPQGMSRGFGFVAYSNPEEALRALSEMNGKMIGRKPLYIALAQRKEDRRAHLQALF 421

Query: 239 AK-QGPG 244
           ++ + PG
Sbjct: 422 SQIRAPG 428

Binds the poly(A) tail of mRNA.

Arabidopsis thaliana (taxid: 3702)

>sp|P29341|PABP1_MOUSE Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2

 Score =  178 bits (451), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 147/491 (29%), Positives = 218/491 (44%), Gaps = 112/491 (22%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  +   R SG+GN F+KNL  +IDN  L+  FS FG+I S KVV  + G SKGYGFV
Sbjct: 85  MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFV 143

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE----GSSFNNLYVKNLDDDMT 116
            + T E+A  AIEK+ G  +   +++VG F  R +R  E       F N+Y+KN  +DM 
Sbjct: 144 HFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMD 203

Query: 117 EEILVEKFSEFGKITSLVISKDANGTSKGFG-----------------------SKVLYV 153
           +E L E F +FG   S+ +  D +G SKGFG                        K +YV
Sbjct: 204 DERLKELFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYV 263

Query: 154 ARAQKKAERKAILRAQFERMRKERAELY-------KNINDEVDEIELKQYFSQCGTISSV 206
            RAQKK ER+  L+ +FE+M+++R   Y       KN++D +D+  L++ FS  GTI+S 
Sbjct: 264 GRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSA 323

Query: 207 KIMRTDRGISKGH---C-------------------------MAIAQTKRERTSYLRIMY 238
           K+M  + G SKG    C                         +A+AQ K ER ++L   Y
Sbjct: 324 KVM-MEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQY 382

Query: 239 AKQGPGLASTIFPV----------------HPTLYQRA--------LQVYQAPDFRHGGM 274
            ++   + +   PV                 P    RA         Q+  +P +   G 
Sbjct: 383 MQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTAQGA 442

Query: 275 IPNGF----------SPPPP----SPLFLMAPDSVTQYRGAMMNGHANFPMPLMLSNLQK 320
            P+ F          +P PP     P     P  ++  R A  +     P P   +    
Sbjct: 443 RPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRVANTSTQTMGPRPAAAAAAAT 502

Query: 321 PS------YNYP--ISQPRAGQAAANNLTNGNHRAAASNEN--LSSMLVATSPDERKDIL 370
           P+      Y Y   +  P+    A   +T          +    +SML +  P E+K +L
Sbjct: 503 PAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQML 562

Query: 371 GQRLYPLVKKL 381
           G+RL+PL++ +
Sbjct: 563 GERLFPLIQAM 573

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Mus musculus (taxid: 10090)

>sp|A1CRM1|PABP_ASPCL Polyadenylate-binding protein, cytoplasmic and nuclear OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) GN=pab1 PE=3 SV=1

 Score =  177 bits (450), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 99/244 (40%), Positives = 140/244 (57%), Gaps = 34/244 (13%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  +   R +G GN F+KNL S IDN  LH  F+ FG+I S KV   + G SKGYGFV
Sbjct: 125 MWSQRDPALRKTGQGNVFIKNLDSAIDNKALHDTFAAFGNILSCKVAQDEFGNSKGYGFV 184

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE----GSSFNNLYVKNLDDDMT 116
            Y T E+A +AI+ + G  +   +++VG  I + DR  +     ++F N+Y+KN+D D+T
Sbjct: 185 HYETAEAANNAIKHVNGMLLNDKKVFVGHHISKKDRQSKFDEMKANFTNIYIKNIDPDVT 244

Query: 117 EEILVEKFSEFGKITSLVISKDANGTSKGFG-----------------------SKVLYV 153
           EE   + F +FG+ITS  +S+D  G S+GFG                       ++ LYV
Sbjct: 245 EEEFRKIFEQFGEITSATLSRDPEGKSRGFGFVNYSTHESAQAAVDEMHDKEVKTQKLYV 304

Query: 154 ARAQKKAERKAILRAQFERMRKERAELY-------KNINDEVDEIELKQYFSQCGTISSV 206
            RAQKK ER+  LR Q+E  R E+A  Y       KN+ D+VD+ +L++ F   GTI+S 
Sbjct: 305 GRAQKKHEREEELRKQYEAARLEKASKYQGVNLYVKNLTDDVDDEKLRELFGPYGTITSA 364

Query: 207 KIMR 210
           K+MR
Sbjct: 365 KVMR 368

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.

Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) (taxid: 344612)

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	398
225441084	634	PREDICTED: probable polyadenylate-bindin	0.949	0.596	0.405	3e-72
356548313	495	PREDICTED: probable polyadenylate-bindin	0.768	0.618	0.452	6e-71
356537017	502	PREDICTED: probable polyadenylate-bindin	0.638	0.505	0.506	2e-70
255556766	632	polyadenylate-binding protein, putative	0.944	0.594	0.393	2e-70
357510891	613	Polyadenylate binding protein [Medicago	0.952	0.618	0.407	2e-69
449440159	640	PREDICTED: probable polyadenylate-bindin	0.949	0.590	0.372	1e-67
356572504	636	PREDICTED: probable polyadenylate-bindin	0.952	0.595	0.392	7e-67
356505295	632	PREDICTED: probable polyadenylate-bindin	0.937	0.590	0.397	3e-65
357120111	714	PREDICTED: polyadenylate-binding protein	0.944	0.526	0.371	3e-60
147838149	544	hypothetical protein VITISV_008914 [Viti	0.766	0.560	0.4	1e-59

>gi|225441084|ref|XP_002264613.1| PREDICTED: probable polyadenylate-binding protein At2g36660 [Vitis vinifera] gi|297740018|emb|CBI30200.3| unnamed protein product [Vitis vinifera]

 Score =  278 bits (712), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 198/488 (40%), Positives = 259/488 (53%), Gaps = 110/488 (22%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  + +AR SGIGN FVKNL+ +IDN++L  +F KFG+I S KVVV+++GKSKGYGFV
Sbjct: 86  MWSHRDPDARRSGIGNVFVKNLSDSIDNVRLQAMFQKFGNILSCKVVVTEDGKSKGYGFV 145

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRI--QEGSSFNNLYVKNLDDDMTEE 118
           Q+ + E A  AIEKL G  ++  ++Y G F+R+ DR+     + + NLY+KNLD D+TEE
Sbjct: 146 QFESEEYANAAIEKLNGFIIDGKQIYAGKFVRKTDRVLPNPDAKYTNLYIKNLDPDVTEE 205

Query: 119 ILVEKFSEFGKITSLVISKDANGTSKGF-----------------------GSKVLYVAR 155
            L EKF EFGKI SLVISKD NG S+GF                       GSKVLYVAR
Sbjct: 206 ALREKFFEFGKIASLVISKDENGMSRGFGFVNFESPEDAKRALEALNGLQLGSKVLYVAR 265

Query: 156 AQKKAERKAILRAQFERMRKERAELYKNINDEVD-------EIELKQYFSQCGTISSVKI 208
           AQKKAER+ +LR QFE  R E+   Y+  N  V        + +L+++FS CG I+S K+
Sbjct: 266 AQKKAEREQLLRRQFEEKRNEQILKYRGSNVYVKNIDDNVNDDDLREHFSVCGKITSAKL 325

Query: 209 MRTDRGISKGH---C-------------------------MAIAQTKRERTSYLRIMYAK 240
           MR  +GISKG    C                         +AIAQ K +R + L++ YA+
Sbjct: 326 MRDQKGISKGFGFVCFSTPDEASKAVNTFHGYMFHRKPLYVAIAQRKEDRQAQLQLHYAQ 385

Query: 241 QGPGLASTIFPV----HPTLY---------QRALQVYQAPDFRHGGMIPNGFSPPPPS-- 285
           +  GLA    PV    +P LY          R   +YQ    R G    N   P  P+  
Sbjct: 386 RMAGLAGPSTPVIPGGYPPLYYTAPPGVIPPRQGLMYQPLGLRTGWRANNLIPPTRPAFQ 445

Query: 286 ----PLFLMAPDSVTQYRG------AMMNGHANFPMPLMLSNLQKP-----SYNYPISQP 330
               PL    P    Q RG          GH+   MP    +LQ+P     S    I+Q 
Sbjct: 446 PSSIPLMPNTPRQHRQNRGRTNGHIPQGGGHSTAFMP----HLQQPTQPVISPKDSINQQ 501

Query: 331 RAGQAA------ANNLTNGNH-RAAASN---------ENLSSMLVATSPDERKDILGQRL 374
           RAGQA       +  ++ G+   +AASN         E LSSML A SP+++K ILG+ L
Sbjct: 502 RAGQAKYVPNGRSYEMSKGSGIPSAASNSVGTGSQGSEMLSSMLAAASPEQQKQILGEHL 561

Query: 375 YPLVKKLK 382
           YPLV+K K
Sbjct: 562 YPLVQKQK 569

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356548313|ref|XP_003542547.1| PREDICTED: probable polyadenylate-binding protein At2g36660-like [Glycine max]

 Score =  274 bits (700), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 175/387 (45%), Positives = 216/387 (55%), Gaps = 81/387 (20%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MW   +  AR SG GN FVKNLA +IDN  LH +F K+G+I SSKVV+S++GKSKGYGFV
Sbjct: 86  MWLHRDPNARKSGRGNVFVKNLAGSIDNAGLHDLFKKYGNILSSKVVMSEDGKSKGYGFV 145

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEG--SSFNNLYVKNLDDDMTEE 118
           Q+   ESA +AIEKL G+TV   ++YVG F+R+ DRI  G  + + NLY+KNLD D+TE 
Sbjct: 146 QFEWEESANNAIEKLNGSTVGNKQIYVGKFVRKGDRILPGYDAKYTNLYIKNLDSDITEA 205

Query: 119 ILVEKFSEFGKITSLVISKDANGTSKG-----------------------FGSKVLYVAR 155
           +L EKFS FGKI SL ISKD NG SKG                       FGSK LYVAR
Sbjct: 206 LLQEKFSSFGKIISLAISKDDNGLSKGFAFVNYENPDDAKKAMEAMNGLQFGSKYLYVAR 265

Query: 156 AQKKAERKAILRAQFERMRKER------AELY-KNINDEVDEIELKQYFSQCGTISSVKI 208
           AQKKAER+ IL  QFE  RKE+      + LY KNI+D+V + EL+  FS CGTI+SVK+
Sbjct: 266 AQKKAEREQILHRQFEEKRKEQILKYQASNLYVKNIDDDVTDKELRDLFSSCGTITSVKV 325

Query: 209 MRTDRGISKGH---C-------------------------MAIAQTKRERTSYLRIMYAK 240
           MR D+GISKG    C                         +AIAQ K+ER + L + YA 
Sbjct: 326 MRDDKGISKGFGFVCFSNPEEANKAVMSFNGCTFHRKPLYIAIAQRKKERKTQLNLHYAP 385

Query: 241 QGPGLASTIFPVHP-------------TLYQRALQVYQAPDFRHGGMIPNGFSPPPPS-- 285
           Q  GL  +  PV P              ++Q  L +YQ    R  G   N F PP  S  
Sbjct: 386 QQAGLDGSSTPVIPGGVPPYFYHSVASLMFQSGL-LYQPLGLR-SGWRANDFVPPARSFQ 443

Query: 286 ----PLFLMAPDSVTQYRGAMMNGHAN 308
               P+         Q RG+ MNG+ N
Sbjct: 444 HSQVPIVPNFTRHQRQNRGSRMNGNLN 470

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356537017|ref|XP_003537028.1| PREDICTED: probable polyadenylate-binding protein At2g36660-like [Glycine max]

 Score =  273 bits (697), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 159/314 (50%), Positives = 193/314 (61%), Gaps = 60/314 (19%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS P+  AR SG GN FVKNLA +IDN  LH +F K+G+I SSKVV+S +GKSKGYGFV
Sbjct: 86  MWSHPDPSARKSGRGNVFVKNLAGSIDNAGLHDLFQKYGNILSSKVVMSGDGKSKGYGFV 145

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEG--SSFNNLYVKNLDDDMTEE 118
           Q+ + ESA +AIEKL G+TV   ++YVG F+R+ DRI  G  + + NLY+KNLD D+TE 
Sbjct: 146 QFESEESANNAIEKLNGSTVGDKQIYVGKFVRKGDRILPGYDAKYTNLYIKNLDSDITEA 205

Query: 119 ILVEKFSEFGKITSLVISKDANGTSKG-----------------------FGSKVLYVAR 155
           +L EKFS FGKI SLVISKD NG SKG                       FGSK LYVAR
Sbjct: 206 LLQEKFSSFGKIISLVISKDDNGLSKGFAFVNYENPDDARKAMEAMNGLKFGSKNLYVAR 265

Query: 156 AQKKAERKAILRAQFERMRKER------AELY-KNINDEVDEIELKQYFSQCGTISSVKI 208
           AQKKAER+ IL  QFE  RKE+      + LY KNI+D+V + EL+  FS CGTI+SVK+
Sbjct: 266 AQKKAEREQILHRQFEEKRKEQILKYQASNLYVKNIDDDVTDKELRDLFSSCGTITSVKV 325

Query: 209 MRTDRGISKGH--------------------CM--------AIAQTKRERTSYLRIMYAK 240
           MR D+GISKG                     CM        AIAQ K +R + L + YA 
Sbjct: 326 MRDDKGISKGFGFVCFSNPEEANKAVRSFNGCMFHRKPLYIAIAQRKMDRKTQLNLHYAP 385

Query: 241 QGPGLASTIFPVHP 254
           Q  GL  +  PV P
Sbjct: 386 QQTGLDGSSTPVIP 399

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556766|ref|XP_002519416.1| polyadenylate-binding protein, putative [Ricinus communis] gi|223541279|gb|EEF42830.1| polyadenylate-binding protein, putative [Ricinus communis]

 Score =  272 bits (696), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 191/486 (39%), Positives = 263/486 (54%), Gaps = 110/486 (22%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  + +AR +GIGN +VKNL+ +IDN+ L ++F +FG + S KV   ++GKSKG+GFV
Sbjct: 87  MWSHRDPDARRNGIGNVYVKNLSESIDNVGLQELFGEFGTVLSCKVATFEDGKSKGHGFV 146

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRI--QEGSSFNNLYVKNLDDDMTEE 118
           Q+ + +SA  AIEKL G+ V   ++YVG F++++DR+     + + NLYVKNLD  +TEE
Sbjct: 147 QFESEDSANSAIEKLNGSIVGDKQIYVGKFVKKSDRVLPSPDAKYTNLYVKNLDPGITEE 206

Query: 119 ILVEKFSEFGKITSLVISKDANGTSKGF-----------------------GSKVLYVAR 155
           +L EKFSEFGKI S+ I++D  G+S+GF                       GSKVLYV R
Sbjct: 207 LLQEKFSEFGKIVSVAIARDECGSSRGFGFVNFENPDDARWAMERMNGTELGSKVLYVGR 266

Query: 156 AQKKAERKAILRAQFERMRKERAELY-------KNINDEVDEIELKQYFSQCGTISSVKI 208
           AQK+AER+ ILR QFE  RKE+   +       KNI+D+V + EL+++FSQCGTI+S K+
Sbjct: 267 AQKRAEREQILRRQFEEKRKEQITKFKGSNVYVKNIDDDVTDEELREHFSQCGTITSAKL 326

Query: 209 MRTDRGISKGH---C-------------------------MAIAQTKRERTSYLRIMYAK 240
           M+ D+G SKG    C                         +AIAQ K ER + L++ YA+
Sbjct: 327 MKDDKGRSKGFGFVCFSSSEEASKAVNTFHGYMFHRKPLYVAIAQRKEERQAQLQLQYAQ 386

Query: 241 QGPGLASTIFPV-----HPTLYQRALQVYQAPDFRHG------GMIPNGFSPPP-----P 284
           +  G      PV      P  Y    QV+  P   +       G   NGF+PP      P
Sbjct: 387 RIAGFHGPSTPVIPGGYTPLYYTAPSQVHPRPGMMYQPLAMRPGWRGNGFAPPSRPVFQP 446

Query: 285 SPLFLMAPDSVTQYRGA--MMNGHANFPMPLMLSNLQKPSYNYPISQP----------RA 332
           S L +M P S  Q++     MNGH      L     Q  SY    +QP          RA
Sbjct: 447 SHLPVM-PISQRQHKQGRVRMNGHV-----LPQGGTQSVSYVQQPAQPLTSLKDPSNQRA 500

Query: 333 GQAA------ANNLTNGNHRAAAS----------NENLSSMLVATSPDERKDILGQRLYP 376
           GQA         +++ G+   +A+          +E LSSML A SPDE+K ILG++LYP
Sbjct: 501 GQAKYVPNGRTCDVSKGSGVLSAAPNSTGPVSQGSEVLSSMLAAASPDEQKQILGEQLYP 560

Query: 377 LVKKLK 382
           LV+K K
Sbjct: 561 LVRKHK 566

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357510891|ref|XP_003625734.1| Polyadenylate binding protein [Medicago truncatula] gi|355500749|gb|AES81952.1| Polyadenylate binding protein [Medicago truncatula]

 Score =  268 bits (686), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 197/484 (40%), Positives = 262/484 (54%), Gaps = 105/484 (21%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  + +AR S IGN FVKNLA +IDN  L  +F KFG+I SSKVV+S++GKSKGYGFV
Sbjct: 84  MWSRRDPDARKSCIGNVFVKNLAESIDNSGLEDMFKKFGNILSSKVVMSEDGKSKGYGFV 143

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEG--SSFNNLYVKNLDDDMTEE 118
           Q+ T ESA  AIE+L G  V   ++YVG F++++DRI  G  + + NLY+KNLD D++E 
Sbjct: 144 QFETEESANAAIERLNGYLVGDKQIYVGKFVKKSDRISSGPDTRYTNLYMKNLDLDISET 203

Query: 119 ILVEKFSEFGKITSLVISKDANGTSKGF-----------------------GSKVLYVAR 155
           +L EKFS FGKI SL ++KD+NG SKGF                       GSK+LYVAR
Sbjct: 204 LLREKFSSFGKIISLAVAKDSNGMSKGFGFVNFDNPEDAKRAMETMNGLQLGSKILYVAR 263

Query: 156 AQKKAERKAILRAQFERMRKERAELY-------KNINDEVDEIELKQYFSQCGTISSVKI 208
           AQKKAER+ IL  QFE  RKE+   Y       KNI+D V +  L+ +FS CGTI+S KI
Sbjct: 264 AQKKAEREQILHQQFEEKRKEQVLKYKGSNIYVKNIDDNVSDEGLRDHFSVCGTITSAKI 323

Query: 209 MRTDRGISKGH---C-------------------------MAIAQTKRERTSYLRIMYAK 240
           MR D+GISKG    C                         +++AQ K +R + L++ YA+
Sbjct: 324 MRDDKGISKGFGFVCFSTPEEANKAVNSFHGFMFHGKPLYVSLAQRKEDRQAQLQLQYAQ 383

Query: 241 QGPGLA---STIFP-VHPTLYQ-----------RALQVYQAPDFRHGGMIPNGFSPPP-- 283
           Q  GLA   + I P  +P  Y            RA  VYQ    R  G   NG +PP   
Sbjct: 384 QIAGLAGPSTAIVPGGYPPFYYTATGVVSHAPPRAGLVYQPMALR-PGWRANGSAPPARS 442

Query: 284 --PSPLFLMAPDSVTQYRG--AMMNGHA----NFPMPLMLSNLQKPSYNYPIS-----QP 330
              SP  +++ ++  Q+R     MNGHA    N      +   Q+ S +   S     Q 
Sbjct: 443 FQQSPTPVVSNNNTRQHRQNRGRMNGHAVSQGNTHSGTYMPQAQQASQSAISSRESSTQQ 502

Query: 331 RAGQAAANNLTNGNHR------------AAASNENLSSMLVATSPDERKDILGQRLYPLV 378
           R GQA    + +G HR             +   E L SML   +P+++K+ILG+ LY LV
Sbjct: 503 RTGQAKY--VPSGRHREMEKGSGLSSSGGSLGPEVLHSMLANATPEQQKEILGEHLYMLV 560

Query: 379 KKLK 382
           +K+K
Sbjct: 561 QKIK 564

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449440159|ref|XP_004137852.1| PREDICTED: probable polyadenylate-binding protein At2g36660-like [Cucumis sativus] gi|449521207|ref|XP_004167621.1| PREDICTED: probable polyadenylate-binding protein At2g36660-like [Cucumis sativus]

 Score =  263 bits (673), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 184/494 (37%), Positives = 257/494 (52%), Gaps = 116/494 (23%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  +++AR SGIGN FVKNL+ +I++L L ++F KFG++ SSKV  S +GKSKGYGFV
Sbjct: 88  MWSRRDADARKSGIGNVFVKNLSDSINSLGLQELFKKFGNVLSSKVATSDDGKSKGYGFV 147

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSS--FNNLYVKNLDDDMTEE 118
           Q+ + ESA  AIE L G TV   ++YVG F+R++DR+       + NLYVKNLD ++ EE
Sbjct: 148 QFESEESANAAIESLNGFTVGDKQIYVGKFVRKSDRVLANPDIKYTNLYVKNLDPEIGEE 207

Query: 119 ILVEKFSEFGKITSLVISKDANGTSKGF-----------------------GSKVLYVAR 155
            L EKFSEFGKI+S++IS+D NG S+GF                       GSKV+Y+AR
Sbjct: 208 HLQEKFSEFGKISSMIISRDENGVSRGFGFINFENSDDAKRALETLNGSQLGSKVIYIAR 267

Query: 156 AQKKAERKAILRAQFERMRKERAELY-------KNINDEVDEIELKQYFSQCGTISSVKI 208
           AQKK ER+ +LR  +E   KE+   Y       KNI+D+V + EL++ FSQ GTI+S K+
Sbjct: 268 AQKKTEREEVLRRHYEEKCKEQVLKYKGSNVYVKNIDDDVTDEELRERFSQFGTITSSKL 327

Query: 209 MRTDRGISKGH--------------------CM--------AIAQTKRERTSYLRIMYAK 240
           MR D+GI+KG                     CM        AIAQ K +R   L++ +A+
Sbjct: 328 MRDDKGINKGFGFVCFSNPDEAKRAVNTLQGCMFHGKPLYLAIAQRKEDRQMQLKLQFAQ 387

Query: 241 QG---PGLASTIF------------PVHPTLYQRALQVYQAPDFRHGGMIPNGFSPPP-- 283
           +    PG ++TIF             V P +  R   ++Q    R G   PN ++ P   
Sbjct: 388 RLAGIPGPSTTIFPGGYPPYYYPAPGVVPPVASRPGLMFQPLGMRPGWR-PNTYTSPARP 446

Query: 284 ---PSPLFLMAPDSVTQYRGAMMNGHANFPMPLMLSNLQKPSYNYPISQPRAGQAAANNL 340
              PSPL ++ P +  Q R     G  N P+    + +Q  SY             A + 
Sbjct: 447 GFQPSPLPII-PTASRQPR--QNRGKMNGPILSHQNGVQSVSYMQNSQDANQSVVTAKSS 503

Query: 341 TNG----------NHRAAASNEN----------------------LSSMLVATSPDERKD 368
           +N           N R+  +N+                       LSSML ++ PD++K 
Sbjct: 504 SNQQWTGQVKYVPNARSCETNKTSGASAAAAAFNSVGDVSQGSQILSSMLASSPPDQQKQ 563

Query: 369 ILGQRLYPLVKKLK 382
           ILG+ LYPLV+K K
Sbjct: 564 ILGEHLYPLVQKRK 577

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356572504|ref|XP_003554408.1| PREDICTED: probable polyadenylate-binding protein At2g36660-like [Glycine max]

 Score =  260 bits (665), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 192/489 (39%), Positives = 251/489 (51%), Gaps = 110/489 (22%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  + +AR S IGN FVKNL  +IDN  L  IF K+G+I SSKVV S++GKSKGYGFV
Sbjct: 86  MWSRRDPDARKSAIGNLFVKNLPESIDNAGLQDIFKKYGNILSSKVVTSEDGKSKGYGFV 145

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEG--SSFNNLYVKNLDDDMTEE 118
           Q+ + ES+  AIEKL G TV   ELYVG F++++DRI  G  + + NLY+KNLD D++E 
Sbjct: 146 QFESEESSKVAIEKLNGYTVADKELYVGKFVKKSDRILPGPDARYTNLYMKNLDLDVSEA 205

Query: 119 ILVEKFSEFGKITSLVISKDANGTSKGF-----------------------GSKVLYVAR 155
            L EKFS FGKI SLVI+KD NG SKGF                       GSK+LYVAR
Sbjct: 206 TLQEKFSSFGKIVSLVIAKDNNGMSKGFGFVNYDNPDDAKKAMEAMNGSQLGSKILYVAR 265

Query: 156 AQKKAERKAILRAQFERMRKERAELY-------KNINDEVDEIELKQYFSQCGTISSVKI 208
           AQKKAER+ IL  QFE  +KE+   Y       KNI+D V + EL+ +FS CGTI+S KI
Sbjct: 266 AQKKAEREQILHHQFEEKQKEQILKYKGSNIYVKNIDDHVSDEELRDHFSACGTITSAKI 325

Query: 209 MRTDRGISKGH---C-------------------------MAIAQTKRERTSYLRIMYAK 240
           MR D+GISKG    C                         +A+AQ K +R + L++ YA+
Sbjct: 326 MRDDKGISKGFGFVCFSTPEEANKAVNTFHGFMYHGKPLYVALAQRKEDRKAQLQLQYAQ 385

Query: 241 -----QGPGLASTIFPVHPTLYQRALQVYQAPD-----FRHGGMIP----NGFSPPP--- 283
                 GP  A       P  Y  +  +   P      ++H  + P    NGF+PP    
Sbjct: 386 QLARLSGPSTAIIPSGYPPYYYAASGVISHVPPRAGLMYQHLALRPGWGANGFAPPARSF 445

Query: 284 ---PSPLFLMAPDSVTQYRG-------AMMNGHANFPMPLMLSNLQKP--SYNYPISQPR 331
              P P          Q RG       A  N H+   +P     + +P  S     +Q R
Sbjct: 446 QQSPVPAVSNNTRQHRQNRGKLNGNSIAQGNTHSGTYLP-QAQQISQPVISSRDSSTQQR 504

Query: 332 AGQAAANNLTNGNHR------------------AAASNENLSSMLVATSPDERKDILGQR 373
            GQ  A  + +G  R                   +  +E L S+L   +P+++K+ILG+ 
Sbjct: 505 TGQ--ARYIPSGRQRDVEKGSGSSSVGSNSGRGGSQGSEMLHSLLAGAAPEQQKEILGEH 562

Query: 374 LYPLVKKLK 382
           LY LV KLK
Sbjct: 563 LYMLVHKLK 571

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505295|ref|XP_003521427.1| PREDICTED: probable polyadenylate-binding protein At2g36660-like [Glycine max]

 Score =  255 bits (651), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 195/491 (39%), Positives = 257/491 (52%), Gaps = 118/491 (24%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  + +AR + IGN FVKNL  +IDN  L  +F K+G+I SSKVV+S++GKSKGYGFV
Sbjct: 86  MWSRRDPDARKNAIGNLFVKNLPESIDNAGLQDMFKKYGNILSSKVVMSEDGKSKGYGFV 145

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEG--SSFNNLYVKNLDDDMTEE 118
           Q+ + ES+  AIEKL G+TV   +LYVG F++++DRI  G  + + NLY+KNLD D++E 
Sbjct: 146 QFESEESSNVAIEKLNGSTVGDKQLYVGKFVKKSDRILPGPDARYTNLYMKNLDLDVSEA 205

Query: 119 ILVEKFSEFGKITSLVISKDANGTSKGF-----------------------GSKVLYVAR 155
            L EKFS FGKI SLVI+KD  G SKGF                       GSK+LYVAR
Sbjct: 206 TLQEKFSSFGKIVSLVIAKDNIGMSKGFGFVNYDNPDDAKRAMEAMNGSKLGSKILYVAR 265

Query: 156 AQKKAERKAILRAQFERMRKERAELY-------KNINDEVDEIELKQYFSQCGTISSVKI 208
           AQKKAER+ IL  QFE  RKE+   Y       KNI+D V + EL+ +FS CG I+S KI
Sbjct: 266 AQKKAEREQILHHQFEEKRKEQILKYKGSNIYVKNIDDHVSDEELRDHFSACGIITSAKI 325

Query: 209 MRTDRGISKGH---C-------------------------MAIAQTKRERTSYLRIMYAK 240
           MR D+GISKG    C                         +A+AQ K +R + L++ YA+
Sbjct: 326 MRDDKGISKGFGFVCFSTPEEANKAVNTFHGFMFHGKPLYVALAQRKEDRKAQLQLQYAQ 385

Query: 241 QGPGL---ASTIFP-VHPTLYQRALQVYQAPDFRHG----------GMIPNGFSPPPPSP 286
           Q  GL   ++ I P  +P  Y  A  V      R G          G   NGF+ P  S 
Sbjct: 386 QVAGLSGPSTAIIPGGYPPYYYAATGVISHVPPRAGLMYQHLPMRPGWGANGFALPARS- 444

Query: 287 LFLMAP-----DSVTQYRG--AMMNGHANFPMPLMLSNLQKPSY---NYPISQP------ 330
            F  +P     ++  Q+R     +NG+     P+   N    +Y      ISQP      
Sbjct: 445 -FQQSPVPAVSNNTRQHRQNRGRLNGN-----PIAQGNTHSVTYLPQAQQISQPVISSST 498

Query: 331 --RAGQAAANNLTNGNHR-----------------AAASNENLSSMLVATSPDERKDILG 371
             R GQA    L +G  R                  +  +E L SML   +P+++K+ILG
Sbjct: 499 QQRTGQAKY--LPSGRQRDMEKGSGSSSSGSNSGRGSQGSEMLHSMLAGAAPEQQKEILG 556

Query: 372 QRLYPLVKKLK 382
           + LY LV KLK
Sbjct: 557 EHLYMLVHKLK 567

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357120111|ref|XP_003561773.1| PREDICTED: polyadenylate-binding protein-like [Brachypodium distachyon]

 Score =  238 bits (608), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 175/471 (37%), Positives = 244/471 (51%), Gaps = 95/471 (20%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  + +AR SG+GN FVKNL   IDN+ L ++FSKFGDI S KV  + +G S+GYGFV
Sbjct: 176 MWSNRDPDARRSGVGNVFVKNLNDHIDNVILQELFSKFGDILSCKVARNDDGTSRGYGFV 235

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADR-IQEGSSFNNLYVKNLDDDMTEEI 119
           Q++  ESA  AIE L  +  E  +L+V  FI++++R       + NLY+KNLDDDMTEE+
Sbjct: 236 QFAAQESADIAIENLNNSHFEGRQLHVAHFIKKSERSANNDDKYTNLYMKNLDDDMTEEL 295

Query: 120 LVEKFSEFGKITSLVISKDANGTSKGF-----------------------GSKVLYVARA 156
           +  KFS+FG + S+ I K  +GTSKGF                       GSK LYVARA
Sbjct: 296 IKLKFSQFGPLISVKIMKRDDGTSKGFGFVSFKSPDSAKKAKEAMNGIPLGSKSLYVARA 355

Query: 157 QKKAERKAILRAQFERMRKE------RAELY-KNINDEVDEIELKQYFSQCGTISSVKIM 209
           QKKAERK  L+   E  R E       + +Y KNI+D VD+  L++ F + G I+SVKIM
Sbjct: 356 QKKAERKQYLQLLHEEKRNEILTKSNGSNVYIKNISDRVDDETLRERFDEFGNITSVKIM 415

Query: 210 RTDRGISKG------------HC----------------MAIAQTKRERTSYLRIMYAKQ 241
           R D+GISKG             C                +AIAQ K +R + L   +A+ 
Sbjct: 416 RDDKGISKGFGFVCYNTPDEAKCAVSSMRGVMFYDKPLYVAIAQRKEDRKARLEQRFAEL 475

Query: 242 GPGLASTIFPVHPTLYQRALQVYQAPDFRHGGMIPN--GFSPPP------------PSPL 287
              +     PV PT Y      + +  F  G   P+  GF  PP            PSP 
Sbjct: 476 A-TMVGAASPVIPTGYPHVYFAHPSTHFPQG---PSRQGFMYPPMGLGQEWRQNVFPSPH 531

Query: 288 FL------MAPDSVTQY---RGAMMNGHANFPMPL-MLSNLQKPSYNYPISQPRAGQAA- 336
            +      + P++  QY   RG M      FP  +  +S+ Q       +S+ + G A  
Sbjct: 532 NIQQIHAPLMPNTPRQYRNNRGRMTGNMMTFPHTVNYVSHAQTAKDFMSMSRQQFGHAKY 591

Query: 337 --ANNLTNG---NHRAAAS--NENLSSMLVATSPDERKDILGQRLYPLVKK 380
             A+ +T+G   +H    S  N+  +S+L A  PD+++++LG RLYPLV++
Sbjct: 592 IPADVMTSGLAIHHSDPVSSVNDPFTSLLAAAPPDQQRNMLGNRLYPLVER 642

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147838149|emb|CAN74140.1| hypothetical protein VITISV_008914 [Vitis vinifera]

 Score =  236 bits (603), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 162/405 (40%), Positives = 208/405 (51%), Gaps = 100/405 (24%)

Query: 1   MWSTPNSEARLSGIGNAFVK--------------------NLASTIDNLKLHQIFSKFGD 40
           MWS  + +AR SGIGN FVK                    NL+ +IDN++L  +F KFG+
Sbjct: 86  MWSHRDPDARRSGIGNVFVKVYLFAVTSIIDAELYFLVCLNLSDSIDNVRLQAMFQKFGN 145

Query: 41  IQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRI--Q 98
           I S KVVV+++GKSKGYGFVQ+ + E A  AIEKL G  ++  ++Y G F+R+ DR+   
Sbjct: 146 ILSCKVVVTEDGKSKGYGFVQFESEEYANAAIEKLNGFIIDGKQIYAGKFVRKTDRVLPN 205

Query: 99  EGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF------------ 146
             + + NLY+KNLD D+TEE L EKF EFGKI SLVISKD NG S+GF            
Sbjct: 206 PDAKYTNLYIKNLDPDVTEEALREKFFEFGKIASLVISKDENGMSRGFGFVNFESPEDAK 265

Query: 147 -----------GSKVLYVARAQKKAERKAILRAQFERMRKERAELYKNINDEVD------ 189
                      GSKVLYVARAQKKAER+ +LR QFE  R E+   Y+  N  V       
Sbjct: 266 RALEALNGLQLGSKVLYVARAQKKAEREQLLRRQFEEKRNEQILKYRGSNVYVKNIDDNV 325

Query: 190 -EIELKQYFSQCGTISSVKIMRTDRGISKGH---C------------------------- 220
            + +L+++FS CG I+S K+MR  +GISKG    C                         
Sbjct: 326 NDDDLREHFSVCGKITSAKLMRDQKGISKGFGFVCFSTPDEASKAVNTFHGYMFHRKPLY 385

Query: 221 MAIAQTKRERTSYLRIMYAKQGPGLASTIFPV----HPTLY---------QRALQVYQAP 267
           +AIAQ K +R + L++ YA++  GLA    PV    +P LY          R   +YQ  
Sbjct: 386 VAIAQRKEDRQAQLQLHYAQRMAGLAGPSTPVIPGGYPPLYYTAPPGVIPPRQGLMYQPL 445

Query: 268 DFRHGGMIPNGFSP------PPPSPLFLMAPDSVTQYRGAMMNGH 306
             R G    N   P      P P PL    P    Q RG   NGH
Sbjct: 446 GLRTGWRANNLIPPTRPAFQPSPIPLMPNTPRQHRQNRG-RTNGH 489

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	398
TAIR|locus:2124261	629	PAB2 "AT4G34110" [Arabidopsis	0.369	0.233	0.510	1.2e-53
TAIR|locus:2040625	609	PAB7 "poly(A) binding protein	0.366	0.239	0.472	1e-52
TAIR|locus:2012161	671	PAB8 "AT1G49760" [Arabidopsis	0.369	0.219	0.489	1e-51
WB|WBGene00003903	692	pab-2 [Caenorhabditis elegans	0.404	0.232	0.443	5.4e-49
UNIPROTKB|B1ANR0	615	PABPC4 "Polyadenylate-binding	0.366	0.237	0.450	6e-49
UNIPROTKB|Q13310	644	PABPC4 "Polyadenylate-binding	0.366	0.226	0.450	9.5e-49
TAIR|locus:2199700	660	PAB3 "poly(A) binding protein	0.369	0.222	0.450	4.4e-48
UNIPROTKB|A4IFC3	645	PABPC4 "Uncharacterized protei	0.366	0.226	0.443	5.8e-48
UNIPROTKB|E1BWJ7	632	PABPC1L "Uncharacterized prote	0.366	0.231	0.443	7.9e-48
RGD|1563142	607	Pabpc1l "poly(A) binding prote	0.366	0.240	0.456	5.2e-47

TAIR|locus:2124261 PAB2 "AT4G34110" [Arabidopsis thaliana (taxid:3702)]

 Score = 372 (136.0 bits), Expect = 1.2e-53, Sum P(3) = 1.2e-53
 Identities = 76/149 (51%), Positives = 96/149 (64%)

Query:     1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
             M+S  +   R SG GN F+KNL  +ID+  LH  FS FG+I S KV V   G+SKGYGFV
Sbjct:   110 MYSHRDPSVRRSGAGNIFIKNLDESIDHKALHDTFSSFGNIVSCKVAVDSSGQSKGYGFV 169

Query:    61 QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSS--FNNLYVKNLDDDMTEE 118
             QY+  ESA  AIEKL G  +   ++YVGPF+RR +R    +   F N+YVKNL +  T++
Sbjct:   170 QYANEESAQKAIEKLNGMLLNDKQVYVGPFLRRQERDSTANKTKFTNVYVKNLAESTTDD 229

Query:   119 ILVEKFSEFGKITSLVISKDANGTSKGFG 147
              L   F E+GKITS V+ KD  G SKGFG
Sbjct:   230 DLKNAFGEYGKITSAVVMKDGEGKSKGFG 258

GO:0003723 "RNA binding" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0009651 "response to salt stress" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0006486 "protein glycosylation" evidence=RCA

GO:0006413 "translational initiation" evidence=ISS

TAIR|locus:2040625 PAB7 "poly(A) binding protein 7" [Arabidopsis thaliana (taxid:3702)]

 Score = 370 (135.3 bits), Expect = 1.0e-52, Sum P(2) = 1.0e-52
 Identities = 69/146 (47%), Positives = 99/146 (67%)

Query:     1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
             MWS    +AR +G+GN FVKNL  ++ N  L  +F KFG+I S KV   ++GKS+GYGFV
Sbjct:    98 MWSVRAPDARRNGVGNVFVKNLPESVTNAVLQDMFKKFGNIVSCKVATLEDGKSRGYGFV 157

Query:    61 QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEIL 120
             Q+   ++A  AI+ L    V   E+YVG F+++ DR++    + NLY+KNLD D++E++L
Sbjct:   158 QFEQEDAAHAAIQTLNSTIVADKEIYVGKFMKKTDRVKPEEKYTNLYMKNLDADVSEDLL 217

Query:   121 VEKFSEFGKITSLVISKDANGTSKGF 146
              EKF+EFGKI SL I+KD N   +G+
Sbjct:   218 REKFAEFGKIVSLAIAKDENRLCRGY 243

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

TAIR|locus:2012161 PAB8 "AT1G49760" [Arabidopsis thaliana (taxid:3702)]

 Score = 361 (132.1 bits), Expect = 1.0e-51, Sum P(3) = 1.0e-51
 Identities = 73/149 (48%), Positives = 95/149 (63%)

Query:     1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
             M+S  +   R SG+GN F+KNL  +ID+  LH+ FS FG I S KV V   G+SKGYGFV
Sbjct:   119 MYSVRDPSLRKSGVGNIFIKNLDKSIDHKALHETFSAFGPILSCKVAVDPSGQSKGYGFV 178

Query:    61 QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSS--FNNLYVKNLDDDMTEE 118
             QY T E+A  AI+KL G  +   ++YVGPF+ +  R   G    F N+YVKNL + +++E
Sbjct:   179 QYDTDEAAQGAIDKLNGMLLNDKQVYVGPFVHKLQRDPSGEKVKFTNVYVKNLSESLSDE 238

Query:   119 ILVEKFSEFGKITSLVISKDANGTSKGFG 147
              L + F EFG  TS VI +D  G SKGFG
Sbjct:   239 ELNKVFGEFGVTTSCVIMRDGEGKSKGFG 267

GO:0003723 "RNA binding" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0046686 "response to cadmium ion" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0006164 "purine nucleotide biosynthetic process" evidence=RCA

WB|WBGene00003903 pab-2 [Caenorhabditis elegans (taxid:6239)]

 Score = 338 (124.0 bits), Expect = 5.4e-49, Sum P(3) = 5.4e-49
 Identities = 75/169 (44%), Positives = 101/169 (59%)

Query:     1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
             MWS  +  AR +G GN F+KNL   IDN  ++  FS FG+I S KV    EG SKGYGFV
Sbjct:   131 MWSQRDPAARRAGNGNIFIKNLDRVIDNKSVYDTFSLFGNILSCKVATDDEGNSKGYGFV 190

Query:    61 QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE----GSSFNNLYVKNLDDDMT 116
              + T  SA  AIEK+ G  +   ++YVG F  RA R++E    G  + N++VKN  + + 
Sbjct:   191 HFETEHSAQTAIEKVNGMLLSDKKVYVGKFQPRAQRMKELGESGLKYTNVFVKNFGEHLD 250

Query:   117 EEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
             +E L   FS+FG+ITS V+  DA G  KGFG    +VA A + A  +A+
Sbjct:   251 QEKLSAMFSKFGEITSAVVMTDAQGKPKGFG----FVAFADQDAAGQAV 295

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

UNIPROTKB|B1ANR0 PABPC4 "Polyadenylate-binding protein 4" [Homo sapiens (taxid:9606)]

 Score = 325 (119.5 bits), Expect = 6.0e-49, Sum P(3) = 6.0e-49
 Identities = 68/151 (45%), Positives = 93/151 (61%)

Query:     1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
             MWS  +   R SG+GN F+KNL  +IDN  L+  FS FG+I S KVV  + G SKGY FV
Sbjct:    85 MWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYAFV 143

Query:    61 QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE----GSSFNNLYVKNLDDDMT 116
              + T E+A  AIEK+ G  +   +++VG F  R +R  E       F N+Y+KN  +++ 
Sbjct:   144 HFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVD 203

Query:   117 EEILVEKFSEFGKITSLVISKDANGTSKGFG 147
             +E L E FS+FGK  S+ + +D NG SKGFG
Sbjct:   204 DESLKELFSQFGKTLSVKVMRDPNGKSKGFG 234

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q13310 PABPC4 "Polyadenylate-binding protein 4" [Homo sapiens (taxid:9606)]

 Score = 325 (119.5 bits), Expect = 9.5e-49, Sum P(3) = 9.5e-49
 Identities = 68/151 (45%), Positives = 93/151 (61%)

Query:     1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
             MWS  +   R SG+GN F+KNL  +IDN  L+  FS FG+I S KVV  + G SKGY FV
Sbjct:    85 MWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYAFV 143

Query:    61 QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE----GSSFNNLYVKNLDDDMT 116
              + T E+A  AIEK+ G  +   +++VG F  R +R  E       F N+Y+KN  +++ 
Sbjct:   144 HFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVD 203

Query:   117 EEILVEKFSEFGKITSLVISKDANGTSKGFG 147
             +E L E FS+FGK  S+ + +D NG SKGFG
Sbjct:   204 DESLKELFSQFGKTLSVKVMRDPNGKSKGFG 234

GO:0000166 "nucleotide binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0008143 "poly(A) RNA binding" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0017130 "poly(C) RNA binding" evidence=IDA

GO:0006401 "RNA catabolic process" evidence=TAS

GO:0006396 "RNA processing" evidence=TAS

GO:0006412 "translation" evidence=TAS

GO:0007596 "blood coagulation" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2199700 PAB3 "poly(A) binding protein 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 318 (117.0 bits), Expect = 4.4e-48, Sum P(3) = 4.4e-48
 Identities = 68/151 (45%), Positives = 97/151 (64%)

Query:     1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
             M S  +   RLSG GN F+KNL ++IDN  L + FS FG I S KV +   G+SKGYGFV
Sbjct:   122 MLSNRDPSTRLSGKGNIFIKNLDASIDNKALFETFSSFGTILSCKVAMDVTGRSKGYGFV 181

Query:    61 QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSS----FNNLYVKNLDDDMT 116
             Q+   ESA  AI+KL G  +   +++VG FIRR +R ++ ++    F N+YVKNL  ++ 
Sbjct:   182 QFEKEESAQAAIDKLNGMLMNDKQVFVGHFIRRQERARDENTPTPRFTNVYVKNLPKEIG 241

Query:   117 EEILVEKFSEFGKITSLVISKDANGTSKGFG 147
             E+ L + F +FG I+S V+ +D +G S+ FG
Sbjct:   242 EDELRKTFGKFGVISSAVVMRDQSGNSRCFG 272

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0006397 "mRNA processing" evidence=IGI

UNIPROTKB|A4IFC3 PABPC4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 319 (117.4 bits), Expect = 5.8e-48, Sum P(3) = 5.8e-48
 Identities = 67/151 (44%), Positives = 93/151 (61%)

Query:     1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
             MWS  +   R SG+GN F+KNL  +IDN  L+  FS FG+I S KVV  + G SKGY FV
Sbjct:    85 MWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYAFV 143

Query:    61 QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE----GSSFNNLYVKNLDDDMT 116
              + T E+A  AIEK+ G  +   +++VG F  R +R  E       F N+Y+KN  +++ 
Sbjct:   144 HFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVD 203

Query:   117 EEILVEKFSEFGKITSLVISKDANGTSKGFG 147
             +E L E FS+FGK  S+ + +D +G SKGFG
Sbjct:   204 DENLKELFSQFGKTLSVKVMRDPSGKSKGFG 234

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0008266 "poly(U) RNA binding" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E1BWJ7 PABPC1L "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 306 (112.8 bits), Expect = 7.9e-48, Sum P(3) = 7.9e-48
 Identities = 67/151 (44%), Positives = 91/151 (60%)

Query:     1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
             MWS  +   R SG+GN F+KNL  +IDN  L+  FS FG+I S KVV  + G S+G+GFV
Sbjct:    85 MWSQRDPGLRKSGVGNVFIKNLDDSIDNKALYDTFSAFGNILSCKVVCDENG-SRGHGFV 143

Query:    61 QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE-GS---SFNNLYVKNLDDDMT 116
              + T E+A  AI+ + G  +   +++VG F  R +R  E G+    F N+Y+KN  DDM 
Sbjct:   144 HFETQEAATRAIQTMNGMLLNDRKVFVGHFKSRKEREAEFGARAMEFTNVYIKNFGDDMD 203

Query:   117 EEILVEKFSEFGKITSLVISKDANGTSKGFG 147
             +  L E FS FGK  S+ +  D  G SKGFG
Sbjct:   204 DNRLREIFSRFGKTLSVKVMMDHTGRSKGFG 234

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

RGD|1563142 Pabpc1l "poly(A) binding protein, cytoplasmic 1-like" [Rattus norvegicus (taxid:10116)]

 Score = 314 (115.6 bits), Expect = 5.2e-47, Sum P(4) = 5.2e-47
 Identities = 69/151 (45%), Positives = 96/151 (63%)

Query:     1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
             MWS  +   R SG+GN F+KNL ++IDN  L+  FS FG I SSKVV ++ G S+G+GFV
Sbjct:    85 MWSHRDPGLRRSGMGNIFIKNLENSIDNKALYDTFSTFGSILSSKVVYNEHG-SRGFGFV 143

Query:    61 QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE-GS---SFNNLYVKNLDDDMT 116
              + T E+A  AI  + G  +   +++VG F  R  R  E G+    F N+YVKNL  DM 
Sbjct:   144 HFETHEAAQKAINTMNGMLLNDRKVFVGHFKSRQKREAELGARALGFTNIYVKNLRVDMD 203

Query:   117 EEILVEKFSEFGKITSLVISKDANGTSKGFG 147
             E+ L + FS+FGK  S+ + +D+NG S+GFG
Sbjct:   204 EQGLQDLFSQFGKTQSVKVMRDSNGQSRGFG 234

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	398
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-87
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	5e-27
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-25
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	4e-20
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	9e-20
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-18
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-17
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	7e-17
smart00360	73	smart00360, RRM, RNA recognition motif	2e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-16
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-13
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-11
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-11
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-11
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-11
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	3e-11
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	3e-11
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	1e-10
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-10
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-10
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-10
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-10
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-10
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	3e-10
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-10
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-10
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	6e-10
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	6e-10
smart00360	73	smart00360, RRM, RNA recognition motif	1e-09
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	1e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-09
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	1e-09
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-09
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-09
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-09
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-09
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-09
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-09
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	5e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	8e-09
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	8e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	8e-09
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	8e-09
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-08
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-08
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	3e-08
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	3e-08
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	4e-08
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-08
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	4e-08
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	6e-08
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	6e-08
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	8e-08
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	8e-08
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	8e-08
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	9e-08
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-07
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-07
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-07
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-07
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-07
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-07
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-07
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-07
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-07
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-07
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-07
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	3e-07
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-07
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	3e-07
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	4e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-07
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	5e-07
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	6e-07
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	6e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	7e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	7e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	7e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	8e-07
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	8e-07
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	9e-07
smart00360	73	smart00360, RRM, RNA recognition motif	2e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-06
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-06
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-06
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	2e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-06
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-06
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-06
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-06
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	3e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	3e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	4e-06
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	4e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	5e-06
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	5e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	6e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	6e-06
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	6e-06
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	8e-06
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	8e-06
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	8e-06
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	9e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	9e-06
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	9e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-05
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	1e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	1e-05
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-05
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	1e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-05
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	1e-05
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	2e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-05
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-05
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-05
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-05
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	2e-05
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	2e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	2e-05
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	3e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	3e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	3e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	3e-05
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	3e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	3e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	4e-05
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	4e-05
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	4e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	4e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-05
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	5e-05
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	5e-05
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	5e-05
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	5e-05
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	5e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-05
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	6e-05
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	6e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	6e-05
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	7e-05
pfam00658	72	pfam00658, PABP, Poly-adenylate binding protein, u	7e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	8e-05
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	8e-05
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	8e-05
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	8e-05
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	9e-05
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	9e-05
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	9e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-04
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	1e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	1e-04
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	1e-04
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-04
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-04
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	1e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	1e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-04
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-04
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	2e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	2e-04
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	2e-04
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	2e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	3e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-04
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	3e-04
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	3e-04
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	3e-04
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	3e-04
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	4e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-04
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	4e-04
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	4e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	4e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	4e-04
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	4e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	5e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	5e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	5e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	5e-04
cd12540	105	cd12540, RRM_U2AFBPL, RNA recognition motif in U2	5e-04
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	5e-04
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	5e-04
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	5e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	5e-04
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	6e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	7e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	7e-04
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	7e-04
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	7e-04
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	7e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	7e-04
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	7e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	8e-04
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	8e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	8e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	8e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	8e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	9e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	0.001
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.001
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.001
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	0.001
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	0.001
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	0.001
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	0.001
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	0.001
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	0.001
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.001
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	0.001
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	0.001
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	0.001
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	0.001
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	0.001
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	0.001
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	0.001
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	0.001
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	0.001
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	0.001
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.002
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	0.002
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	0.002
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	0.002
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	0.002
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.002
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.002
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.002
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	0.002
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	0.002
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	0.002
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	0.002
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	0.002
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	0.002
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.003
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	0.003
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	0.003
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	0.003
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	0.003
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	0.003
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	0.003
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	0.003
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.003
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	0.003
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.003
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.003
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	0.004
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	0.004
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.004
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	0.004
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	0.004
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	0.004
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	0.004
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	0.004
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	0.004

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

 Score =  275 bits (706), Expect = 1e-87
 Identities = 138/452 (30%), Positives = 207/452 (45%), Gaps = 77/452 (17%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  +   R SG+GN FVKNL  ++DN  L   FSKFG+I S KV   + GKS+GYGFV
Sbjct: 75  MWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFV 134

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADR-IQEGSSFNNLYVKNLDDDMTEEI 119
            +   ESA  AI+K+ G  +   E+YVG FI++ +R       F NLYVKNLD  + E+ 
Sbjct: 135 HFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDK 194

Query: 120 LVEKFSEFGKITSLVISKDANGTSKGFG---------------------------SKVLY 152
           L E F++FG+ITS  + KD +G S+GF                             K LY
Sbjct: 195 LRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLY 254

Query: 153 VARAQKKAERKAILRAQFERMRKERAE------LY-KNINDEVDEIELKQYFSQCGTISS 205
           V RAQK+AER+A LR +FE +++ER        LY KN++D V + +L++ FS+CG I+S
Sbjct: 255 VGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITS 314

Query: 206 VKIMRTDRGISKGH---C-------------------------MAIAQTKRERTSYLRIM 237
            K+M  ++G+S+G    C                         +A+AQ K +R ++L+  
Sbjct: 315 AKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQ 374

Query: 238 YAKQGPG--------LASTIFPVHPTLYQRALQVYQAPDFRHGGMIPNGFSPPPPSPLFL 289
           + +  P                  P   Q   Q +         M        P  PL  
Sbjct: 375 FMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRP 434

Query: 290 MAPDSVTQYRGAMMNGHANFPMPLMLSNLQKPSYNYPISQPRAGQAAANNLTNGNHRAAA 349
                +     A      N      +  +  P     +   +      +  + G      
Sbjct: 435 NGLAPMNA-VRAPSRNAQNAAQKPPMQPVMYPPNYQSLPLSQDLPQPQSTASQGGQ---- 489

Query: 350 SNENLSSMLVATSPDERKDILGQRLYPLVKKL 381
            N+ L+ +L + +P  +K +LG+RL+PLV+ +
Sbjct: 490 -NKKLAQVLASATPQMQKQVLGERLFPLVEAI 520

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 =  102 bits (256), Expect = 5e-27
 Identities = 38/77 (49%), Positives = 52/77 (67%)

Query: 13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAI 72
          G+GN F+KNL  +IDN  L+  FS FG+I S KV   + G SKGYGFV + T E+A+ AI
Sbjct: 1  GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAI 60

Query: 73 EKLQGATVERMELYVGP 89
          EK+ G  +   +++VGP
Sbjct: 61 EKVNGMLLNDKKVFVGP 77

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

 Score =  106 bits (265), Expect = 7e-25
 Identities = 69/233 (29%), Positives = 107/233 (45%), Gaps = 44/233 (18%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK-- 74
           +V +L   +   KL+ +F  FG + S +V       +S GYG+V +  P  A  A+E   
Sbjct: 4   YVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMN 63

Query: 75  ---LQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKIT 131
              L G  +  M     P +RR       S   N++VKNLD  +  + L + FS+FG I 
Sbjct: 64  FKRLGGKPIRIMWSQRDPSLRR-------SGVGNIFVKNLDKSVDNKALFDTFSKFGNIL 116

Query: 132 SLVISKDANGTSKGFG-----------------------SKVLYVARAQKKAERKAILRA 168
           S  ++ D NG S+G+G                        K +YV R  KK ER+A    
Sbjct: 117 SCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLK 176

Query: 169 QFERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHC 220
           +F         LY KN++  V+E +L++ F++ G I+S  +M+   G S+G  
Sbjct: 177 KF-------TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFA 222

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

 Score = 83.4 bits (207), Expect = 4e-20
 Identities = 35/80 (43%), Positives = 41/80 (51%), Gaps = 23/80 (28%)

Query: 103 FNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG--------------- 147
           F N+YVKNL +DM +E L E F ++GKITS  + KD  G SKGFG               
Sbjct: 1   FTNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVE 60

Query: 148 --------SKVLYVARAQKK 159
                    K LYV RAQKK
Sbjct: 61  ELNGKEVNGKKLYVGRAQKK 80

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

 Score = 82.6 bits (205), Expect = 9e-20
 Identities = 35/73 (47%), Positives = 49/73 (67%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
          N +VKNL   +D+ KL ++F K+G I S+KV+   EGKSKG+GFV +   E+A  A+E+L
Sbjct: 3  NVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 76 QGATVERMELYVG 88
           G  V   +LYVG
Sbjct: 63 NGKEVNGKKLYVG 75

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

 Score = 79.2 bits (196), Expect = 1e-18
 Identities = 32/73 (43%), Positives = 49/73 (67%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
          N +VKNL  +ID+ +L + FS FG I S+KV+  ++G+SKG+GFV +S+PE A  A+ ++
Sbjct: 3  NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 76 QGATVERMELYVG 88
           G  +    LYV 
Sbjct: 63 NGRIIGGKPLYVA 75

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 75.3 bits (186), Expect = 3e-17
 Identities = 27/69 (39%), Positives = 38/69 (55%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV NL        L  +FSKFG I+S ++V  + G+SKG+ FV++   E A  A+E L G
Sbjct: 2  FVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNG 61

Query: 78 ATVERMELY 86
            +   EL 
Sbjct: 62 KELGGRELR 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|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 74.6 bits (184), Expect = 7e-17
 Identities = 33/77 (42%), Positives = 38/77 (49%), Gaps = 23/77 (29%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG----------------- 147
           NLYVKNLDD + +E L E+FS FG ITS  +  D  G SKGFG                 
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 148 ------SKVLYVARAQK 158
                  K LYVA AQ+
Sbjct: 63  NGRIIGGKPLYVALAQR 79

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|214636 smart00360, RRM, RNA recognition motif

 Score = 73.0 bits (180), Expect = 2e-16
 Identities = 28/71 (39%), Positives = 43/71 (60%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          FV NL       +L ++FSKFG ++S ++V  +E GKSKG+ FV++ + E A  A+E L 
Sbjct: 3  FVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALN 62

Query: 77 GATVERMELYV 87
          G  ++   L V
Sbjct: 63 GKELDGRPLKV 73

Length = 73

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

 Score = 72.3 bits (178), Expect = 3e-16
 Identities = 29/70 (41%), Positives = 45/70 (64%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV NL        L ++FSKFG+I+S ++V  ++GKSKG+ FV++ +PE A  A+E L G
Sbjct: 2  FVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNG 61

Query: 78 ATVERMELYV 87
            ++  +L V
Sbjct: 62 KELDGRKLKV 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 70.7 bits (173), Expect = 1e-13
 Identities = 48/134 (35%), Positives = 71/134 (52%), Gaps = 6/134 (4%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
           N  V  L  T+   ++  +F+  G+I+S K+V  +  G+S GYGFV Y  PE A  A+  
Sbjct: 5   NLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS 64

Query: 75  LQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGK-ITSL 133
           L G  ++   + V  + R +    +G+   NLYV  L   MT+  L   FS FG+ ITS 
Sbjct: 65  LNGLRLQNKTIKVS-YARPSSDSIKGA---NLYVSGLPKTMTQHELESIFSPFGQIITSR 120

Query: 134 VISKDANGTSKGFG 147
           ++S +  G SKG G
Sbjct: 121 ILSDNVTGLSKGVG 134

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

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

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 23/57 (40%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIE 73
          FV  L     +  L + FS+FG+I+ + V+   Q GKS+GYGFV +   ESA  A +
Sbjct: 4  FVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

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|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 = 59.2 bits (144), Expect = 2e-11
 Identities = 28/71 (39%), Positives = 43/71 (60%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          F+ +L +   +  L+Q+F+ FG++ S+KV V +  G+SK +GFV Y  PESA  AI+ + 
Sbjct: 2  FIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMN 61

Query: 77 GATVERMELYV 87
          G  V    L V
Sbjct: 62 GFQVGGKRLKV 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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 27/66 (40%), Positives = 39/66 (59%), Gaps = 1/66 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEK 74
          + FV +L+  ID   L   F+ FG+I  ++VV   Q GKSKGYGFV +   E A +AI+ 
Sbjct: 1  HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 75 LQGATV 80
          + G  +
Sbjct: 61 MNGQWL 66

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

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 24/67 (35%), Positives = 42/67 (62%), Gaps = 1/67 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
            FV NL+ ++D+  L   F KFG +  ++V+  +E G+S+G+G+V + +PE A  AIE 
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 75 LQGATVE 81
          + G  ++
Sbjct: 61 MDGKELD 67

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

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 19/40 (47%), Positives = 29/40 (72%), Gaps = 1/40 (2%)

Query: 180 LY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
           LY KN++D +D+  L++ FS  GTI+S K+M  ++G SKG
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKG 43

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|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 58.9 bits (143), Expect = 3e-11
 Identities = 23/63 (36%), Positives = 41/63 (65%), Gaps = 1/63 (1%)

Query: 18 FVKNLASTIDNLKLHQIFS-KFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
          FV +L   +D+ +L++ FS ++   + +KVV+ Q G S+GYGFV++S       A+ ++Q
Sbjct: 5  FVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTEMQ 64

Query: 77 GAT 79
          GA+
Sbjct: 65 GAS 67

This subgroup corresponds to the RRM2 of SECp43, 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. . Length = 82

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

 Score = 56.8 bits (138), Expect = 1e-10
 Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 4/61 (6%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKA 164
           N+++KNLD  +  + L + FS FG I S  ++ D NG SKG+G    +V    ++A  +A
Sbjct: 4   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYG----FVHFETEEAAVRA 59

Query: 165 I 165
           I
Sbjct: 60  I 60

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 57.2 bits (139), Expect = 1e-10
 Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE 73
             FV  L++     +L  +FSKFG ++   ++   E G+S+G+GFV + + E A  AI 
Sbjct: 2  NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 74 KLQG 77
           L G
Sbjct: 62 DLNG 65

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

 Score = 57.0 bits (138), Expect = 1e-10
 Identities = 25/73 (34%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          N  V  L   +   +L  +F   G I+S K+V  +  G+S GYGFV Y     A  AI  
Sbjct: 2  NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT 61

Query: 75 LQGATVERMELYV 87
          L G  +    L V
Sbjct: 62 LNGFEIRNKRLKV 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|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 62.4 bits (151), Expect = 1e-10
 Identities = 41/147 (27%), Positives = 71/147 (48%), Gaps = 19/147 (12%)

Query: 31  LHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG- 88
           + + F  FG I+S  +      GK KG+ FV+Y  PE+A  A+E++ G  +    + VG 
Sbjct: 124 IRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR 183

Query: 89  --------PFIRRADRIQ-EGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA 139
                   P I   D +Q E   FN +YV ++  D++E  +   F  FG+I    +++  
Sbjct: 184 PSNMPQAQPII---DMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAP 240

Query: 140 NG-TSKGFGSKVLYVARAQKKAERKAI 165
            G   KG+G    ++     +++ +AI
Sbjct: 241 TGRGHKGYG----FIEYNNLQSQSEAI 263

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

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

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 19/70 (27%), Positives = 38/70 (54%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           VKNL   +   +L + F   G++   KV+ +++GKS+ +GFV + + E A  A++    
Sbjct: 4  IVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFNK 63

Query: 78 ATVERMELYV 87
            ++  ++ V
Sbjct: 64 TFIDTSKISV 73

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

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 21/57 (36%), Positives = 37/57 (64%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
          FV NL  ++   +L ++FSK G+I   ++V + +GKSKGY +V++   ES  +A++ 
Sbjct: 3  FVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKL 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|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 56.0 bits (136), Expect = 3e-10
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 5/63 (7%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGY-GFVQYSTPESALDAIEKLQG 77
          + NL   +    LHQ+FS +G ++  K+++ +  K+ G    VQ+ + ESA +A + L G
Sbjct: 6  ISNLLYPVTVDVLHQVFSPYGAVE--KILIFE--KNTGVQALVQFDSVESAENAKKALNG 61

Query: 78 ATV 80
            +
Sbjct: 62 RNI 64

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. . Length = 85

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

 Score = 55.3 bits (134), Expect = 4e-10
 Identities = 25/61 (40%), Positives = 36/61 (59%), Gaps = 1/61 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          +V NL   I    L  IF  FG+I+  ++    E G+SKGYGF+Q++  E A  A+E+L 
Sbjct: 2  YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 77 G 77
          G
Sbjct: 62 G 62

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

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

 Score = 54.9 bits (133), Expect = 5e-10
 Identities = 22/42 (52%), Positives = 27/42 (64%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           L+V NL  D TEE L + FS+FG I S+ I +D  G SKGF 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFA 42

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

 Score = 54.9 bits (133), Expect = 6e-10
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 10/72 (13%)

Query: 18 FVKNLA--STIDNLKLHQIFSKFGDIQSSKVV------VSQEGKSKGYGFVQYSTPESAL 69
          FVKNL   +T + LK H  F K G ++S  +          +  S GYGFV++ + E+A 
Sbjct: 4  FVKNLNFKTTEETLKKH--FEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 70 DAIEKLQGATVE 81
           A+++LQG  ++
Sbjct: 62 KALKRLQGTVLD 73

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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 55.0 bits (133), Expect = 6e-10
 Identities = 26/61 (42%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          FV NL    D   L Q+FS FG + + KV+      K KGYGFV  +  E A  AI  L 
Sbjct: 5  FVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASLN 64

Query: 77 G 77
          G
Sbjct: 65 G 65

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|214636 smart00360, RRM, RNA recognition motif

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 22/44 (50%), Positives = 28/44 (63%), Gaps = 1/44 (2%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
            L+V NL  D TEE L E FS+FGK+ S+ + +D   G SKGF 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFA 44

Length = 73

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

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 21/60 (35%), Positives = 31/60 (51%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV NL   +   KL ++F   G +  + +   +EGKS+G G VQ+  P  A+ AI    G
Sbjct: 2  FVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFNG 61

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

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 26/63 (41%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          N +V NL   +    L  +F +FG++ S++V+  +E G+S+G+GFV+  T E A  AIEK
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 75 LQG 77
          L G
Sbjct: 61 LNG 63

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

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 5/71 (7%)

Query: 18 FVKNLA--STIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          F++NL   +T + LK  ++FS+FG+++ +++V  +  G SKG  FV++ T ESA   +E 
Sbjct: 4  FIRNLPFDATEEELK--ELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

Query: 75 LQGATVERMEL 85
             A    + L
Sbjct: 62 ADNAEDSGLSL 72

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|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 22/56 (39%), Positives = 35/56 (62%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
          VKNL+  + N  L Q FS+FG+++ + V+V   G+S G G V++S    A  AI++
Sbjct: 4  VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKR 59

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|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 18 FVKNLAST-IDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
          FV  L  T  D   L ++FS+ G     ++ ++  G+ +G+ FV+Y+T E A +A + L 
Sbjct: 6  FVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALN 65

Query: 77 GATVERMELYV 87
          G +++   + V
Sbjct: 66 GHSLQGSPIRV 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|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVV---VSQEGKSKGYGFVQYSTPESALDAIEK 74
          FV  L+       L ++FS++GDI+  ++V   V+  G SKGY FV+Y     AL A   
Sbjct: 7  FVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVT--GFSKGYAFVEYEHERDALRAYRD 64

Query: 75 LQGATVERMELYV 87
               ++  E++V
Sbjct: 65 AHKLVIDGSEIFV 77

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

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 6/70 (8%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          +V  LA  +D   LH  F  FGDI+  ++ +  E  K +G+ FV++  PE A  AI+ + 
Sbjct: 2  YVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMN 61

Query: 77 GATVERMELY 86
           +     EL+
Sbjct: 62 ES-----ELF 66

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

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQ 76
          FV+NL     + +L + FS+ G I+   VV  +   K +G+G+V ++  E A  A+E+ +
Sbjct: 3  FVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKK 62

Query: 77 GATVE 81
               
Sbjct: 63 KTKFG 67

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|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 = 53.1 bits (128), Expect = 3e-09
 Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKL 75
           FV+NL  T    +L ++F  FG+I    + + +E  +SKG+ FV +  PE A+ A  +L
Sbjct: 2  LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 76 QG 77
           G
Sbjct: 62 DG 63

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

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 1/70 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV NL+ + +   L + F + G++   ++    +G+SKG+G V+++T E A  A+EK  G
Sbjct: 3  FVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEK-SG 61

Query: 78 ATVERMELYV 87
            +   E+ V
Sbjct: 62 EELLGREIRV 71

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

 Score = 52.3 bits (126), Expect = 4e-09
 Identities = 23/42 (54%), Positives = 29/42 (69%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           L+V NL  D TEE L E FS+FG+I S+ I +D +G SKGF 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFA 42

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

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 21/70 (30%), Positives = 39/70 (55%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV  L  ++   +L ++F K G ++S ++V ++ GK KG  +V+Y    SA  A+ K+ G
Sbjct: 6  FVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMDG 65

Query: 78 ATVERMELYV 87
            ++   + V
Sbjct: 66 TEIKEKTISV 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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 52.6 bits (127), Expect = 4e-09
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 5/74 (6%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKS----KGYGFVQYSTPESALDAIE 73
          +V+NL   +D   L  IFSKFG+++S ++   Q+ K      G+ FV +    SA +A++
Sbjct: 4  YVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQ 63

Query: 74 KLQGATVERMELYV 87
           L G  +   ++ V
Sbjct: 64 -LNGTELGGRKISV 76

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

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

 Score = 52.3 bits (126), Expect = 5e-09
 Identities = 25/70 (35%), Positives = 39/70 (55%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV+NL  ++    L  +F + G++  + V    +G+SKG+G V + +PE A  AIE   G
Sbjct: 2  FVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFNG 61

Query: 78 ATVERMELYV 87
            +E  EL V
Sbjct: 62 YDLEGRELEV 71

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

 Score = 56.1 bits (134), Expect = 7e-09
 Identities = 46/165 (27%), Positives = 66/165 (40%), Gaps = 21/165 (12%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           FV NL   +    L ++F KFG ++  ++V  +E GKS+G+ FV++ + ESA  AIE+L 
Sbjct: 119 FVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELN 178

Query: 77  GATVERMELYVGPFIRRADRIQEGSSFN--------------------NLYVKNLDDDMT 116
           G  +E   L V      +    E S+                      NLYV NL     
Sbjct: 179 GKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTA 238

Query: 117 EEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAE 161
           EE L + F   G I    +    +G      S V   A       
Sbjct: 239 EEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALES 283

Length = 306

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

 Score = 51.9 bits (125), Expect = 8e-09
 Identities = 20/52 (38%), Positives = 35/52 (67%), Gaps = 1/52 (1%)

Query: 30 KLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQGATV 80
           L ++FS++G I+  +VV  Q+ G+S+G+GFV + + E A +A E+L G  +
Sbjct: 15 DLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEI 66

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|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 = 51.5 bits (124), Expect = 8e-09
 Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          FV N+       +L +IFS+ G + S ++V  ++ GK KGYGF ++   E+A  AI  L 
Sbjct: 2  FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 77 G 77
          G
Sbjct: 62 G 62

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

 Score = 56.8 bits (137), Expect = 8e-09
 Identities = 40/140 (28%), Positives = 66/140 (47%), Gaps = 11/140 (7%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQ 76
           FV  LA       L++ FSK G ++  + +  +   +SKG  +V++   ES + A+  L 
Sbjct: 93  FVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LT 151

Query: 77  GATVERMELYVGPFIRRADRIQEGSS--------FNNLYVKNLDDDMTEEILVEKFSEFG 128
           G  +    + V       +R  + ++        F  LYV NL  ++TE+ L + F  FG
Sbjct: 152 GQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFG 211

Query: 129 KITSLVISKDAN-GTSKGFG 147
            I  + + +D   G SKGFG
Sbjct: 212 DIEDVQLHRDPETGRSKGFG 231

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|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 = 51.5 bits (124), Expect = 8e-09
 Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 5/66 (7%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
            +V NL   +   +L + FS FG I+  +V      K KGY FV++ T E+A  AI  +
Sbjct: 2  TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVF-----KDKGYAFVRFDTHEAAATAIVAV 56

Query: 76 QGATVE 81
           G ++ 
Sbjct: 57 NGTSIN 62

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

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 50.9 bits (122), Expect = 1e-08
 Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          N  V  L   +   ++  +FS  G+I+S K++  +  G+S GYGFV Y  PE A  AI  
Sbjct: 3  NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINT 62

Query: 75 LQGATVE 81
          L G  ++
Sbjct: 63 LNGLRLQ 69

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV----SQEGKSKGYGFVQYSTPESALDAIE 73
          ++ NL S +    L ++FSK+G I+    +       +G+ +GY FV + T E A  A++
Sbjct: 3  WIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALK 62

Query: 74 KLQGATV 80
           L G T 
Sbjct: 63 SLNGKTA 69

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

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

 Score = 55.2 bits (133), Expect = 3e-08
 Identities = 38/133 (28%), Positives = 58/133 (43%), Gaps = 23/133 (17%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAERKA 164
           LYV +LD D+TE  L + F  FG + S+ + +D+    S G+G    YV         +A
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYG----YVNFQNPADAERA 58

Query: 165 ILRAQFER--------MRKERAE----------LYKNINDEVDEIELKQYFSQCGTISSV 206
           +    F+R        M  +R              KN++  VD   L   FS+ G I S 
Sbjct: 59  LETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSC 118

Query: 207 KIMRTDRGISKGH 219
           K+   + G S+G+
Sbjct: 119 KVATDENGKSRGY 131

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

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 16/37 (43%), Positives = 27/37 (72%)

Query: 182 KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
           KN+ +++D+ +LK+ F + G I+S K+M+ D G SKG
Sbjct: 7   KNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKG 43

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

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 27/72 (37%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKL 75
           FV NL  T+ + +L + FS+FG ++S  V   +E G SKGYGFV +S+ +  L+   + 
Sbjct: 2  LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRD-GLENALQK 60

Query: 76 QGATVERMELYV 87
          Q   +E  +L V
Sbjct: 61 QKHILEGNKLQV 72

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 50.2 bits (120), Expect = 3e-08
 Identities = 21/63 (33%), Positives = 35/63 (55%)

Query: 31 LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF 90
          L + FS++G ++  K+V  + G SKGYGFV + T E A   +++         +L +G  
Sbjct: 19 LRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEANRLCFRDKKLNIGQA 78

Query: 91 IRR 93
          IR+
Sbjct: 79 IRK 81

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|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 49.9 bits (120), Expect = 4e-08
 Identities = 24/53 (45%), Positives = 34/53 (64%), Gaps = 8/53 (15%)

Query: 30 KLHQIFSKFGDIQSSKVV-----VSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           L +IFSKFG     K+V     V + GK+KGY FV+++TPE A +A++ L G
Sbjct: 23 VLRKIFSKFGVG---KIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNG 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|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKLQ 76
           V NL     + +  ++ S FG ++   +V S   G+SKGYGFV+Y++  SAL A  +L 
Sbjct: 3  CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 77 GATVERMELYV 87
          G  +   +L V
Sbjct: 63 GKQIGGRKLQV 73

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

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV  +       +L   FS+FG ++  K++  + G SKGYGFV + T E A + I  +  
Sbjct: 6  FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDA-EKILAMGN 64

Query: 78 ATVERMELYVGPFIRR 93
                +L +GP IR+
Sbjct: 65 LNFRGKKLNIGPAIRK 80

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

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

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 24/60 (40%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQG 77
          V NL+   D   L ++F  FG I    +   +E G+S+G+ FV + T E A  AIEKL G
Sbjct: 4  VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

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

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

 Score = 54.1 bits (130), Expect = 6e-08
 Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           +V NL   I   +L QIF  FGDI+  ++    E G+SKG+GF+Q+   E A +A+E + 
Sbjct: 190 YVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMN 249

Query: 77  GATVERMELYVG 88
           G  +    + VG
Sbjct: 250 GFELAGRPIKVG 261

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 49.1 bits (118), Expect = 6e-08
 Identities = 18/63 (28%), Positives = 41/63 (65%), Gaps = 1/63 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V+NL  ++    L + FS +G ++  ++V +++ + +G+ FV++++PE A  A++KL G
Sbjct: 2  YVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLNG 60

Query: 78 ATV 80
            +
Sbjct: 61 LVL 63

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

>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 = 8e-08
 Identities = 24/68 (35%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAIE 73
          G  F+  L+   +   L Q+FSK+G I    VV  +E + S+G+GFV +  P+ A DA+ 
Sbjct: 1  GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 74 KLQGATVE 81
           + G +V+
Sbjct: 61 AMNGKSVD 68

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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 49.1 bits (118), Expect = 8e-08
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKL 75
           FV N+   + +  + ++  K G + S K V     GK K +GF ++  PE AL A+  L
Sbjct: 3  VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLL 62

Query: 76 QGATVERMELYV 87
           G  +   +L V
Sbjct: 63 NGLELGGKKLLV 74

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

 Score = 49.1 bits (117), Expect = 8e-08
 Identities = 23/60 (38%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEKLQ 76
          FV+NLA ++    L   FS    I+ + VV   + G+S+GYGFV ++  E A +A+ KL+
Sbjct: 3  FVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKLK 62

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

 Score = 49.2 bits (118), Expect = 9e-08
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 4/77 (5%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV--SQEGKSKGY--GFVQYSTPESALDA 71
          N +V NL   +    L Q F +FG + S K++   ++E + +    GFV +     A  A
Sbjct: 3  NLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERA 62

Query: 72 IEKLQGATVERMELYVG 88
          +++L G  V   EL +G
Sbjct: 63 LDELDGKDVMGYELKLG 79

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 48.8 bits (116), Expect = 1e-07
 Identities = 22/63 (34%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
          N +V  L  T+   +L Q+FS++G I +S+++  Q  G S+G GF+++     A +AI+ 
Sbjct: 2  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 75 LQG 77
          L G
Sbjct: 62 LNG 64

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

 Score = 50.4 bits (120), Expect = 1e-07
 Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           F+  L+   D+  L   F+ FGD+  +KV+V +E G+S+G+GFV ++   +A  AI ++ 
Sbjct: 38  FIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMD 97

Query: 77  GATVERMELYVGPFIRR 93
           G  +    + V P   R
Sbjct: 98  GKELNGRHIRVNPANDR 114

Length = 144

>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 = 48.3 bits (115), Expect = 1e-07
 Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          FV N+       +L  IFS+ G + S ++V  +E GK KGYGF +Y   E+AL A+  L 
Sbjct: 2  FVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLN 61

Query: 77 G 77
          G
Sbjct: 62 G 62

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

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 21/57 (36%), Positives = 32/57 (56%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
          VKNL   I   KL ++F  FG I   ++  +++GK + +GFV Y T E A  A++  
Sbjct: 5  VKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHF 61

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 15/39 (38%), Positives = 23/39 (58%)

Query: 182 KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHC 220
            N+  +  E +L++ FS+ G I SV+I+R   G SKG  
Sbjct: 4   GNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFA 42

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|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 22/47 (46%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 36 SKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEKLQGATVE 81
            FG I S+K ++  +  K KGYGFV + +PE+AL AIE L G  V+
Sbjct: 22 QPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGRGVQ 68

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

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

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 34 IFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQG 77
          +F  FG I+S  +    E GK KGYGF++Y  P+SA DAI  +  
Sbjct: 20 VFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNL 64

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 22/63 (34%), Positives = 28/63 (44%), Gaps = 7/63 (11%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV NL     + +L  +F K+G +    VV       K YGFV     E A DAI+ L G
Sbjct: 3  FVGNLPDATTSEELRALFEKYGTVTECDVV-------KNYGFVHMEEEEDAEDAIKALNG 55

Query: 78 ATV 80
             
Sbjct: 56 YEF 58

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 17/59 (28%), Positives = 35/59 (59%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          V+N+       +L ++FS FG ++S ++    +G  +G+ FV++ T + A +A+E L+ 
Sbjct: 5  VRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKS 63

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 24/64 (37%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDI-QSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE 73
          N F+ NL   +D   L+  FS FG I Q+ K++   + G SKG+ F+ Y + E++  AIE
Sbjct: 3  NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 74 KLQG 77
           + G
Sbjct: 63 AMNG 66

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 31 LHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQGA 78
          L  IFS+FG I+S +V+  ++ G S  Y F+++ T E   +A  K+   
Sbjct: 20 LEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNV 68

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 19/70 (27%), Positives = 39/70 (55%), Gaps = 7/70 (10%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V+NL  +    +L ++FS++G+++  +V      K K Y FV +   + A+ A+E++ G
Sbjct: 5  YVRNLPLSTTEEQLRELFSEYGEVE--RVK-----KIKDYAFVHFEERDDAVKAMEEMNG 57

Query: 78 ATVERMELYV 87
            +E   + V
Sbjct: 58 KELEGSPIEV 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|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
          V N+     +  L Q+F +FG I   +++ ++ G SKG+GFV ++    A  A EKL G 
Sbjct: 5  VSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG-SKGFGFVTFANSADADRAREKLHGT 63

Query: 79 TVE 81
           VE
Sbjct: 64 VVE 66

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|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 47.2 bits (113), Expect = 3e-07
 Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEKLQ 76
          FV +L + + +  L + FSK+   Q +KVV   + GKSKGYGFV +S P   L A++++ 
Sbjct: 10 FVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEMN 69

Query: 77 G 77
          G
Sbjct: 70 G 70

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 47.1 bits (112), Expect = 3e-07
 Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAI-EKLQ 76
          FV  L+   +   +  +F+ FG I+   V+  Q G+S+G  FV +++ + AL+AI     
Sbjct: 5  FVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMHH 64

Query: 77 GATVE 81
            T+E
Sbjct: 65 SQTME 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|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 = 4e-07
 Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKF-GDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
           VKNL +++   +L + FSK  G+I   K++ +++GKS+   F+ Y T E A  A +   
Sbjct: 4  IVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYFN 63

Query: 77 GA 78
            
Sbjct: 64 NT 65

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

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKL 75
           FV NL   I+  +L + F   GD+++ ++V  ++ G  KG+G+V + T +S   A+ KL
Sbjct: 2  VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KL 60

Query: 76 QGATVERMELYV 87
           G  ++  ++ 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|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 46.8 bits (112), Expect = 5e-07
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAERKA 164
           LYV +L  D+TE +L E FS  G + S+ + +D     S G+     YV         +A
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYA----YVNFQNPADAERA 57

Query: 165 I 165
           +
Sbjct: 58  L 58

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|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score = 46.6 bits (110), Expect = 6e-07
 Identities = 21/56 (37%), Positives = 35/56 (62%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
          VKNL+  + N  L Q FS+FG ++ + V+V   G+  G GFV+++   +A  A+E+
Sbjct: 4  VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALER 59

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

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

 Score = 46.2 bits (110), Expect = 6e-07
 Identities = 20/62 (32%), Positives = 39/62 (62%), Gaps = 1/62 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          FV NL+   D   +++ F ++G+I S ++    + G+ KG+G+V++S+ E+A  A++ L 
Sbjct: 2  FVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALG 61

Query: 77 GA 78
          G 
Sbjct: 62 GT 63

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

 Score = 46.2 bits (110), Expect = 7e-07
 Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 4/71 (5%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
           L+V NL     ++ L E F E G++  + I++D +G SKGFG    +V  A ++  +KA+
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFG----HVEFATEEGAQKAL 57

Query: 166 LRAQFERMRKE 176
            ++  E + +E
Sbjct: 58  EKSGEELLGRE 68

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

 Score = 46.1 bits (110), Expect = 7e-07
 Identities = 19/59 (32%), Positives = 31/59 (52%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          V+NL        L ++FS FG +    +    +GK KG+ FVQ+++   A  AI+ + G
Sbjct: 4  VRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNG 62

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

 Score = 46.2 bits (110), Expect = 7e-07
 Identities = 20/42 (47%), Positives = 25/42 (59%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           L+V NLD  +TEEIL E F + G +  + I KD NG  K F 
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFA 45

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 50.3 bits (120), Expect = 8e-07
 Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKLQ 76
           FV NL+   D   L Q+F  FG +Q+ K++      + KGYGFV  +  + A  AI  L 
Sbjct: 273 FVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLN 332

Query: 77  GATV 80
           G T+
Sbjct: 333 GYTL 336

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|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 = 46.1 bits (110), Expect = 8e-07
 Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEKLQ 76
          F+  L + +   ++ ++   FG +++  +V  S  G SKGY F +Y  P     AI  L 
Sbjct: 4  FIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGLN 63

Query: 77 G 77
          G
Sbjct: 64 G 64

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

 Score = 45.6 bits (108), Expect = 9e-07
 Identities = 23/70 (32%), Positives = 35/70 (50%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V NL   +    L QIF   G +Q+ K++  +  K   YGFV+Y     A  A++ L G
Sbjct: 2  YVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLNG 61

Query: 78 ATVERMELYV 87
            +E  E+ V
Sbjct: 62 RQIENNEIRV 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|214636 smart00360, RRM, RNA recognition motif

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 182 KNINDEVDEIELKQYFSQCGTISSVKIMR-TDRGISKGHC 220
            N+  +  E EL++ FS+ G + SV+++R  + G SKG  
Sbjct: 5   GNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFA 44

Length = 73

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

 Score = 48.4 bits (114), Expect = 2e-06
 Identities = 41/256 (16%), Positives = 75/256 (29%), Gaps = 45/256 (17%)

Query: 5   PNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYST 64
           P+S        +     L   +   +   +        + +V   +          +   
Sbjct: 9   PHSSFESVKPEDIESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEISPPSKKRLL 68

Query: 65  PESALDAIEKLQGATVERMELYVGPFIRR--------ADRIQEGSSFNNLYVKNLDDDMT 116
                +  E+      +    Y   F             R +     N L+V NL  D+T
Sbjct: 69  SSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVT 128

Query: 117 EEILVEKFSEFGKITSLVISKD-ANGTSKGFG-----------------------SKVLY 152
           EE L E F +FG +  + + +D   G S+GF                         + L 
Sbjct: 129 EEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLR 188

Query: 153 VARAQKKAERKA-------------ILRAQFERMRKERAELYKNINDEVDEIELKQYFSQ 199
           V +AQ  ++ ++             + R +   + K       N+  +  E EL   F  
Sbjct: 189 VQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKS 248

Query: 200 CGTISSVKIMRTDRGI 215
            G I    +  +  G 
Sbjct: 249 RGDIVRASLPPSKDGK 264

Length = 306

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

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 19/45 (42%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLV-ISKDA-NGTSKGFG 147
           NL++ NLD ++ E++L + FS FG I     I +D   G SKGF 
Sbjct: 3   NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFA 47

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 16/61 (26%), Positives = 30/61 (49%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
          V NL   +    L ++F + G+++  K+   + G+S+G   V +   E A  AI++  G 
Sbjct: 5  VSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFNGV 64

Query: 79 T 79
           
Sbjct: 65 L 65

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|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 1/66 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          N FV +L+  + +  L   FS F     ++V+   + G+S+GYGFV + + + A +AI +
Sbjct: 1  NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 75 LQGATV 80
          + G  +
Sbjct: 61 MNGKWL 66

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 = 44.4 bits (106), Expect = 2e-06
 Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 4/48 (8%)

Query: 31 LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
          L+++FS FG+++  K+      K  G+ FV++ST E+A  A++ L G 
Sbjct: 1  LYKLFSPFGNVEKIKL----LKKKPGFAFVEFSTEEAAEKAVQYLNGV 44

(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|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
          N F+ +L     + +L Q+F  FG++ S+KV V +   +SK +GFV +  P SA  AI+ 
Sbjct: 6  NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA 65

Query: 75 LQG 77
          + G
Sbjct: 66 MNG 68

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 48.9 bits (116), Expect = 2e-06
 Identities = 42/152 (27%), Positives = 73/152 (48%), Gaps = 10/152 (6%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEK 74
           N  V  L   + + +L+ +F   G I + +++   + G S GY FV + +   +  AI+ 
Sbjct: 109 NLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKN 168

Query: 75  LQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLV 134
           L G TV    L V       + I++     NLYV NL   +T++ L   F ++G+I    
Sbjct: 169 LNGITVRNKRLKVSYARPGGESIKD----TNLYVTNLPRTITDDQLDTIFGKYGQIVQKN 224

Query: 135 ISKDA-NGTSKGFGSKVLYVARAQKKAERKAI 165
           I +D   GT +G    V +V   +++  ++AI
Sbjct: 225 ILRDKLTGTPRG----VAFVRFNKREEAQEAI 252

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV  L   +   +L  +F  FG+I   K+        KG GFVQ+    +A  AI++LQG
Sbjct: 5  FVGGLDPAVTEDELRSLFGPFGEIVYVKIPPG-----KGCGFVQFVHRAAAEAAIQQLQG 59

Query: 78 ATV 80
            +
Sbjct: 60 TII 62

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

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

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 21/44 (47%), Positives = 29/44 (65%), Gaps = 1/44 (2%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
           NLYV NL  ++TEE L + F +FG++TS  +  D   G S+GFG
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFG 44

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

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 5/63 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV---SQEGKSKGYGFVQYSTPESALDAIEK 74
          FV  L  T     +  +F ++G+I+  +V +      G+SKG  FV++S+ E A  AIE 
Sbjct: 3  FVGQLPKTATEEDVRALFEEYGNIE--EVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 75 LQG 77
          L G
Sbjct: 61 LHG 63

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

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 24/64 (37%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE 73
          G  FV+NL  +     L ++FSKFG++    V + ++ GKSKG+ +V +  PE A+ A +
Sbjct: 3  GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62

Query: 74 KLQG 77
          +L G
Sbjct: 63 ELDG 66

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|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 44.6 bits (105), Expect = 3e-06
 Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEK 74
          N F+ +L     +  L Q F  FG++ S+KV +  Q   SK +GFV Y  P+SA  AI+ 
Sbjct: 6  NLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQA 65

Query: 75 LQGATVERMELYV 87
          + G  +    L V
Sbjct: 66 MNGFQIGTKRLKV 78

This subgroup corresponds to the RRM3 of Bruno protein, 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 = 79

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

 Score = 44.0 bits (104), Expect = 3e-06
 Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +     ++     + ++F   G ++   ++       + + F+ +   E+A  AIE L G
Sbjct: 3  YAGPFPTSFCLSDVKRLFETCGPVRKVTMLSR---TVQPHAFITFENLEAAQLAIETLNG 59

Query: 78 ATVERMELYV 87
          A+V+   + V
Sbjct: 60 ASVDGNCIKV 69

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 16/43 (37%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSL-VISKDANGTSKGFG 147
           L+V  L +D+TEE L E FS++G + S+ +++    G  +GF 
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFA 44

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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 16/43 (37%), Positives = 24/43 (55%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           NLY+ NL   M E+ L      +G++ S  I +D+ G S+G G
Sbjct: 2   NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVG 44

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 31 LHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKLQGATVERME 84
          L + F+ FG+IQ   VV   Q  +SKG  +V+++   SA  A+E++ G  +    
Sbjct: 19 LREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73

This subfamily corresponds to the RRM1 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 = 81

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV---SQEGKSKGYGFVQYSTPESALDA 71
          G  F++NLA T     L ++FSK+G +  S+V +       K KG+ FV Y  PE A+ A
Sbjct: 3  GRLFIRNLAYTCTEEDLEKLFSKYGPL--SEVHLPIDKLTKKPKGFAFVTYMIPEHAVKA 60

Query: 72 IEKLQGATVERMELYVGP 89
            +L G   +   L++ P
Sbjct: 61 FAELDGTVFQGRLLHLLP 78

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|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 = 43.8 bits (104), Expect = 6e-06
 Identities = 18/45 (40%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
           N L+V  L    TE+ L   FS+FG++  +++ KD   G S+GFG
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFG 46

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

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 16/33 (48%), Positives = 21/33 (63%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD 138
           LYV+NL    TEE L E FSE+G++  +   KD
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD 36

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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          N +V  L  T+   +L  +FS +G I +S+++     G S+G GF+++     A  AI+ 
Sbjct: 2  NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 75 LQGAT 79
          L G  
Sbjct: 62 LNGTI 66

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|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 43.5 bits (102), Expect = 6e-06
 Identities = 19/56 (33%), Positives = 35/56 (62%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
          V+NL+  + N  L + FS+FG ++ + V+V   G+S G G V++++  +A  A E+
Sbjct: 4  VRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAFER 59

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

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

 Score = 43.1 bits (102), Expect = 8e-06
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSL-VISKDANGTSKGFGSKVLYVARAQKKAERK 163
            L+V NL   + +E L  +F +FG +    VI+    G S+GFG    YV     +  +K
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFG----YVDFESPEDAKK 56

Query: 164 AI 165
           AI
Sbjct: 57  AI 58

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

 Score = 43.0 bits (102), Expect = 8e-06
 Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 5/70 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV NL + I   +  ++FSK+G++  S+V +++E   KG+GF++  T  +A  A  +L G
Sbjct: 5  FVGNLPNDITEEEFKELFSKYGEV--SEVFLNKE---KGFGFIRLDTRTNAEKAKAELDG 59

Query: 78 ATVERMELYV 87
             +  +L V
Sbjct: 60 IMRKGRQLRV 69

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

 Score = 42.9 bits (102), Expect = 8e-06
 Identities = 15/49 (30%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 31 LHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQGA 78
          L +IFS +G ++   + + +E    +GY +V++ +PE A  AI+ + G 
Sbjct: 15 LKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGG 63

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 43.0 bits (102), Expect = 9e-06
 Identities = 15/39 (38%), Positives = 23/39 (58%)

Query: 182 KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHC 220
            N+  +  E +LK  FS+ G I S++I+R + G SKG  
Sbjct: 4   GNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFA 42

(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|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 42.9 bits (101), Expect = 9e-06
 Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 7/70 (10%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV N+++T  + +L  +F +FG +     V       K Y FV     E AL AIE L G
Sbjct: 4  FVGNVSATCTSDELRGLFEEFGRVVECDKV-------KDYAFVHMEREEEALAAIEALNG 56

Query: 78 ATVERMELYV 87
            V+   + V
Sbjct: 57 KEVKGRRINV 66

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

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

 Score = 43.3 bits (102), Expect = 9e-06
 Identities = 19/65 (29%), Positives = 34/65 (52%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV  L       ++ ++FS +G ++   ++  +  +S+G  FV+YS+ E A  AI+ L G
Sbjct: 3  FVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALNG 62

Query: 78 ATVER 82
              R
Sbjct: 63 VYTMR 67

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
           LYV NL  ++TE+ L   F  FG+I  + + +D   G SKG+G
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYG 43

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

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEK 74
          N  +  L  T+ + +   +F   G +++ K+V   + G S G+GFV Y + E A  AI  
Sbjct: 2  NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 75 LQGATVERMELYV 87
          L G  ++   + V
Sbjct: 62 LNGLQLQNKRIKV 74

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|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 43.2 bits (101), Expect = 1e-05
 Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIE 73
           N +V  L  T+   +L Q+FS++G I +S+++V Q  G S+G GF+++     A +AI+
Sbjct: 3  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 62

Query: 74 KLQG 77
           L G
Sbjct: 63 GLNG 66

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|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKG-YGFVQYSTPESALDAIEK 74
          N +V  L+ST     L Q+FSK+G +  +K+V +        +GFV  ++ E A   I+ 
Sbjct: 1  NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60

Query: 75 L 75
          L
Sbjct: 61 L 61

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 19/48 (39%), Positives = 33/48 (68%), Gaps = 1/48 (2%)

Query: 31 LHQIFSKFGDIQSSKVV-VSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          ++  F++ G++ S K++   Q GKS GYGFV+++T E+A  A++ L G
Sbjct: 16 IYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNG 63

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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 42.8 bits (100), Expect = 1e-05
 Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
          N  V  L   +   +   +F   G+I+S K+V  +  G+S GYGFV Y  P  A  AI  
Sbjct: 5  NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 75 LQGATVERMELYV 87
          L G  ++   + V
Sbjct: 65 LNGLKLQTKTIKV 77

This subgroup corresponds to the RRM1 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 = 84

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 4/68 (5%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV+N+ S +++ +L  +F +FGDI++    +    K +G+  V Y    +A  A   LQG
Sbjct: 5  FVRNINSNVEDEELRALFEQFGDIRT----LYTACKHRGFIMVSYYDIRAARRAKRALQG 60

Query: 78 ATVERMEL 85
            +   +L
Sbjct: 61 TELGGRKL 68

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

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

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 22/64 (34%), Positives = 29/64 (45%), Gaps = 8/64 (12%)

Query: 18 FVKNLA-STIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
          FV NL    +    L +IFSK+G I    +        KGYGFVQ+   E A  A+    
Sbjct: 4  FVGNLNTDKVSKEDLEEIFSKYGKILGISL-------HKGYGFVQFDNEEDARAAVAGEN 56

Query: 77 GATV 80
          G  +
Sbjct: 57 GREI 60

This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. . Length = 68

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 22/64 (34%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIE 73
           N +V  L  T+   ++ Q+FS++G I +S+++V Q  G S+G GF+++     A +AI+
Sbjct: 2  ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIK 61

Query: 74 KLQG 77
           L G
Sbjct: 62 GLNG 65

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

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 7/70 (10%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV+NLA+T+    L + FS+FG ++  K       K K Y FV +   ++A+ A++++ G
Sbjct: 5  FVRNLATTVTEEILEKSFSEFGKLERVK-------KLKDYAFVHFEERDAAVRAMDEMNG 57

Query: 78 ATVERMELYV 87
            +E  E+ +
Sbjct: 58 KEIEGEEIEI 67

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

>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 7/70 (10%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V+          + +IFS +G ++  K++         + FV++ + ESA+ A + + G
Sbjct: 3  YVRPFPPDTSESAIREIFSPYGAVKEVKMI-------SNFAFVEFESLESAIRAKDSVHG 55

Query: 78 ATVERMELYV 87
            +    LYV
Sbjct: 56 KVLNNNPLYV 65

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

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIEKLQ 76
          +V NL  ++ N  LH+IFSK+G +    +V  +E  KSKG  F+ +   E A   ++ L 
Sbjct: 5  YVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALN 64

Query: 77 G 77
           
Sbjct: 65 N 65

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|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 31 LHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG 88
          + Q FS FG I+S  +       K KG+ FV+Y  PE+A  A+E++ G  +    + VG
Sbjct: 17 IRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKVG 75

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|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKLQ 76
          FV  +        +H  F++FG+I++  + +  + G  KGY  ++Y T + A  AIE L 
Sbjct: 10 FVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLN 69

Query: 77 GA 78
          G 
Sbjct: 70 GK 71

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|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
          N +V NL   +   +L +IF  +G+I    ++  +  G  +G  FV+Y   E A  AI  
Sbjct: 2  NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 75 LQG 77
          L G
Sbjct: 62 LNG 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|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 19/42 (45%), Positives = 25/42 (59%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           L+V NL+  + EEIL E F + G +T + I KD  G  K FG
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFG 45

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|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 19/56 (33%), Positives = 32/56 (57%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
          VKNL   + N  L + FS FG ++ + V+V   G+  G G V+++   SA  A+++
Sbjct: 4  VKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKALDR 59

This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 42.5 bits (99), Expect = 2e-05
 Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIE 73
           N +V  L  T+   +L Q+FS++G I +S+++V Q  G S+G GF+++     A +AI+
Sbjct: 6  ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 65

Query: 74 KLQG 77
           L G
Sbjct: 66 GLNG 69

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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 41.6 bits (98), Expect = 3e-05
 Identities = 17/65 (26%), Positives = 33/65 (50%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
          N ++ NL   +D   L  +   +G + S++++   +G+S+G GF +  + E   D I K 
Sbjct: 2  NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKF 61

Query: 76 QGATV 80
           G  +
Sbjct: 62 NGKYL 66

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
          N  V  L   +   +L  +FS  G+++S+K++  +  G S GYGFV Y   + A  AI  
Sbjct: 3  NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62

Query: 75 LQGATVERMELYV 87
          L G  ++   + V
Sbjct: 63 LNGLRLQSKTIKV 75

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE---GKSKGYGFVQYSTPESALDAIEKL 75
          V NL        L ++F K+G++    V + ++    +S+G+ FV++     A DA++ +
Sbjct: 3  VDNLTYRTTPDDLRRVFEKYGEV--GDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 76 QGATVERMELYV 87
           G  ++  EL V
Sbjct: 61 DGKELDGRELRV 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|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
          N  V  L   +   +L  +F   G+I+S K+V  +  G+S GYGFV Y  P+ A  AI  
Sbjct: 6  NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65

Query: 75 LQGATVERMELYV 87
          L G  ++   + V
Sbjct: 66 LNGLRLQTKTIKV 78

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 3/64 (4%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FVKNL   I   +L ++F    DI   ++   ++G SKG  ++++ T   A  A+E+ QG
Sbjct: 7  FVKNLPYNITVDELKEVFEDAVDI---RLPSGKDGSSKGIAYIEFKTEAEAEKALEEKQG 63

Query: 78 ATVE 81
          A V+
Sbjct: 64 AEVD 67

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

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V+NL   I + +L+ +F K+G I+  ++ +    +++G  FV Y     A +A + L G
Sbjct: 6  YVRNLPFKISSEELYDLFGKYGAIR--QIRIGNTKETRGTAFVVYEDIYDAKNACDHLSG 63

Query: 78 ATVERMELYVG 88
            V    L V 
Sbjct: 64 FNVANRYLVVL 74

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 4/62 (6%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
           ++V NLD  + E+ L + FS+ G+IT + + K+  G SKG+     YV    +++ ++A+
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYA----YVEFENEESVQEAL 57

Query: 166 LR 167
             
Sbjct: 58  KL 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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 9/52 (17%)

Query: 31 LHQIFSKFG-----DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          LH++F         D++         GKSKG+ +V YS P SA+ A EKL G
Sbjct: 16 LHRLFDIIPGLEYCDLKRDP----YTGKSKGFAYVTYSNPASAIYAKEKLNG 63

This subfamily corresponds to the RRM3 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 = 75

>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 = 42.0 bits (98), Expect = 4e-05
 Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIE 73
           N F+ +L     +  L Q+F  FG++ S+KV +  Q   SK +GFV Y  P SA  AI+
Sbjct: 8  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 67

Query: 74 KLQGATVERMELYV 87
           + G  +    L V
Sbjct: 68 AMNGFQIGMKRLKV 81

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 27/60 (45%), Positives = 32/60 (53%), Gaps = 7/60 (11%)

Query: 114 DMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG----SKVLYVARAQKKAER--KAIL 166
             TEE L EKF EFG I  + I KD N G SKGFG     K    A A +  ++  KA+L
Sbjct: 11  SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENCDKSFKAVL 70

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

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 12/76 (15%)

Query: 25 TIDNLKLHQIFSKFGDIQSSKVVVS-----QEGKSKGYGFVQYSTPESALDAIEKLQGAT 79
          T + LK   +FSK+G +    V VS       G  KG+ F+++ TPE A  A + L    
Sbjct: 12 THEWLK--AVFSKYGTV----VYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL-NNP 64

Query: 80 VERMELYVGPFIRRAD 95
           E      G F +   
Sbjct: 65 PETATDKPGKFPKTVA 80

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

 Score = 41.3 bits (97), Expect = 4e-05
 Identities = 18/49 (36%), Positives = 31/49 (63%), Gaps = 1/49 (2%)

Query: 30 KLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQG 77
          +L + FS+FG +++ +V  S++ G SK YGF+Q+  PE A  A + +  
Sbjct: 15 ELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNN 63

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

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 15/31 (48%), Positives = 22/31 (70%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVI 135
           NLYV NL+  +TEE+L ++F  FG + S+ I
Sbjct: 3   NLYVGNLNPKVTEEVLCQEFGRFGPLASVKI 33

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

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

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 4/60 (6%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
           L V+NL    TE  L + FS FG +  + I +  +G  KGF     +V    K    KAI
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFA----FVQFTSKADAEKAI 57

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|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 20/60 (33%), Positives = 30/60 (50%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV NL   +    L+++F + G +    +   +EGK K +GFV +   ES   AI  L G
Sbjct: 5  FVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLNG 64

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

 Score = 41.2 bits (96), Expect = 5e-05
 Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 5/60 (8%)

Query: 22 LASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE 81
          +AS +    + Q FS FG I   +V        KGY F+++ST ESA  AI  + G T+E
Sbjct: 8  IASGLTEQLMRQTFSPFGQIMEIRVF-----PEKGYSFIRFSTHESAAHAIVSVNGTTIE 62

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

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 24/57 (42%), Positives = 33/57 (57%), Gaps = 5/57 (8%)

Query: 31 LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV 87
          L + FS FG+I +    +S E K K  GFV +   ESA  AI +L G TV+ ++L V
Sbjct: 19 LKKAFSPFGNIIN----ISME-KEKNCGFVTFEKMESADRAIAELNGTTVQGVQLKV 70

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 44.5 bits (105), Expect = 6e-05
 Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
           N +V  L  T+   +L  IFS FG I +S+++     G SKG GF+++   + A  AI+ 
Sbjct: 91  NLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKT 150

Query: 75  LQGAT 79
           L G T
Sbjct: 151 LNGTT 155

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

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

 Score = 40.7 bits (96), Expect = 6e-05
 Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 5/63 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V  L       +L + F +FG I+            + Y +++Y + E+A  A E L+G
Sbjct: 2  WVGGLGPWTSLAELEREFDRFGAIRRIDYD-----PGRNYAYIEYESIEAAQAAKEALRG 56

Query: 78 ATV 80
            +
Sbjct: 57 FPL 59

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 40.7 bits (96), Expect = 6e-05
 Identities = 18/43 (41%), Positives = 28/43 (65%), Gaps = 4/43 (9%)

Query: 31 LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
          L +IFSK+GD+    VVVS   K KG   V++++ ++A  A+E
Sbjct: 21 LRKIFSKYGDVSD--VVVSS--KKKGSAIVEFASKKAAEAAVE 59

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 40.8 bits (95), Expect = 6e-05
 Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          + FV +L+  I    +   F+ FG I  ++VV     GKSKGYGFV +     A +AI++
Sbjct: 3  HVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62

Query: 75 LQG 77
          + G
Sbjct: 63 MGG 65

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 40.4 bits (95), Expect = 7e-05
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V NL  T+    L ++FS+ G I+S K++  +E  +  Y FV+Y    SA  A++ + G
Sbjct: 2  YVGNLDRTVTEDLLAELFSQIGPIKSCKLI--REHGNDPYAFVEYYDHRSAAAALQTMNG 59

Query: 78 ATVERMELYVG 88
            +   E+ V 
Sbjct: 60 RLILGQEIKVN 70

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|201378 pfam00658, PABP, Poly-adenylate binding protein, unique domain

 Score = 40.2 bits (95), Expect = 7e-05
 Identities = 13/29 (44%), Positives = 20/29 (68%)

Query: 353 NLSSMLVATSPDERKDILGQRLYPLVKKL 381
             +S L A  P E+K +LG+RLYPL++ +
Sbjct: 3   LTASALAAAPPQEQKQMLGERLYPLIQAM 31

The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family. Length = 72

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

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
           LYV  L +++ E++L   F  FG I  + I  D      +GF 
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFA 43

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

 Score = 40.4 bits (95), Expect = 8e-05
 Identities = 18/62 (29%), Positives = 30/62 (48%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV NL + +    L+++F + G ++  K+     GK K + FV +    S   AI+ L G
Sbjct: 5  FVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLNG 64

Query: 78 AT 79
            
Sbjct: 65 IR 66

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|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 40.5 bits (95), Expect = 8e-05
 Identities = 16/47 (34%), Positives = 26/47 (55%)

Query: 33 QIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGAT 79
          ++F  FG I+   ++   +G SKG  FV++S+   A  AI  L G+ 
Sbjct: 20 RLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQ 66

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 40.4 bits (94), Expect = 8e-05
 Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 6/79 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV+NL   +   KL + FS+ G +  +++ + + GKSKG G V++ +PESA  A   + G
Sbjct: 3  FVRNLPFDLTWQKLKEKFSQCGHVMFAEIKM-ENGKSKGCGTVRFDSPESAEKACRLMNG 61

Query: 78 ATVERMELYVGPFIRRADR 96
            +   E+ V     R DR
Sbjct: 62 IKINGREIDV-----RLDR 75

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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 40.5 bits (95), Expect = 9e-05
 Identities = 19/66 (28%), Positives = 37/66 (56%), Gaps = 7/66 (10%)

Query: 21 NLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAIE----KL 75
          NL ++   L+ H  F+++G +    V+V    K S+G+GF+ +S+ + A +A+E     +
Sbjct: 11 NLKTSDSGLRRH--FTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQPHSI 68

Query: 76 QGATVE 81
           G  +E
Sbjct: 69 DGNQIE 74

This subfamily corresponds to the RRM1 of hnRNP A0 which 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 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 = 79

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

 Score = 40.6 bits (95), Expect = 9e-05
 Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV  +   +D  ++   F+K+G ++  K++  + G SKGYGFV +         +E    
Sbjct: 9  FVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQKIVE--SQ 66

Query: 78 ATVERMELYVGPFIRR 93
                +L +GP IR+
Sbjct: 67 INFHGKKLKLGPAIRK 82

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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 40.3 bits (95), Expect = 9e-05
 Identities = 19/63 (30%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 18 FVKNLASTIDNLKLHQIF-SKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKL 75
          FV +LA  + +  L + F +++  ++ +KVV+    G+SKGYGFV++   +    A+ ++
Sbjct: 5  FVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTEM 64

Query: 76 QGA 78
           G 
Sbjct: 65 NGV 67

This subfamily corresponds to the RRM2 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 = 80

>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 = 39.6 bits (93), Expect = 1e-04
 Identities = 15/39 (38%), Positives = 27/39 (69%)

Query: 182 KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHC 220
            N++  V E EL++ FS+CG I+ V++++  +G SKG+ 
Sbjct: 5   SNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYA 43

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|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 4/62 (6%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
           L VKNL   ++ E+L + FS+FG++   V+  D  G S G G     V  ++K   + AI
Sbjct: 2   LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEG----IVEFSRKPGAQAAI 57

Query: 166 LR 167
            R
Sbjct: 58  KR 59

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

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESA 68
          FV  L   +    L + FS++G+++S ++V  +E GK +G+ FV +   +  
Sbjct: 3  FVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPV 54

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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGK-ITSLVISKDANGTSKGFG 147
           NLYV  L   MT++ L   FS +G+ ITS ++  +  G S+G G
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVG 45

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

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 7/64 (10%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV+NLA+T+    L + F +FG ++  K       K K Y F+ +   + A+ A+E++ G
Sbjct: 5  FVRNLANTVTEEILEKAFGQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMNG 57

Query: 78 ATVE 81
            +E
Sbjct: 58 KELE 61

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQG 77
          + NL  T    +  ++   FG+++   +V S+  G SKGYGFV+Y   +SA  A   L G
Sbjct: 4  IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 78 ATVERMELYV 87
            +    LYV
Sbjct: 64 KQLGSRTLYV 73

This subgroup corresponds to the RRM2 of raver-1, 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-1 contains 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 PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

>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 = 39.9 bits (94), Expect = 1e-04
 Identities = 20/43 (46%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
           L++  L  D TEE L E FS++G++   VI KD   G S+GFG
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFG 43

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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 7/62 (11%)

Query: 25 TIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIE----KLQGAT 79
          T ++L+ +  FSK+G++    ++     G+S+G+GFV ++ P S    +      L G  
Sbjct: 11 TEESLREY--FSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPHVLDGRE 68

Query: 80 VE 81
          ++
Sbjct: 69 ID 70

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 22/82 (26%)

Query: 10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGD---------IQSSKVVVSQE-------GK 53
          RLS      ++NL  ++D  KL ++F K            I+  K++   +       GK
Sbjct: 2  RLS------IRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGK 55

Query: 54 SKGYGFVQYSTPESALDAIEKL 75
          SKGYGFV+++  E AL A+  L
Sbjct: 56 SKGYGFVEFTNHEHALKALRAL 77

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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 6/71 (8%)

Query: 18 FVKNLA--STIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE- 73
          FV NL+  +T D L+ H  F + G I+  +++  ++ GK KG+ FV +   E A +A++ 
Sbjct: 2  FVGNLSFETTEDELRAH--FGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKG 59

Query: 74 KLQGATVERME 84
          K       R+E
Sbjct: 60 KHLNGRALRVE 70

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 12/37 (32%), Positives = 24/37 (64%)

Query: 182 KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
            N++   ++ +L+++F +CG +  V+I + D G SKG
Sbjct: 5   GNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKG 41

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 17/40 (42%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 108 VKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGF 146
           V NL +D  E+ L E F  FG I+ + ++KD   G S+GF
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGF 43

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 19/39 (48%), Positives = 22/39 (56%), Gaps = 2/39 (5%)

Query: 183 NINDEVDEIELKQYFSQCGTI-SSVKIMRT-DRGISKGH 219
           N++ EVDE  L   FS  G I  + KIMR  D G SKG 
Sbjct: 8   NLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGF 46

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

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 18/59 (30%), Positives = 34/59 (57%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          VKNL        +  +FS +G ++S +V    +  ++G+ FV++ST + AL+A+  L+ 
Sbjct: 5  VKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALKD 63

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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKLQ 76
          FV NLA   D   L Q+F  FG + + KV+      K KG+GFV  +  + A  AI  L 
Sbjct: 7  FVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLN 66

Query: 77 G 77
          G
Sbjct: 67 G 67

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|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

Query: 31 LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
          L Q F  FG+I+   +    +G +  YGFV Y     A  AIE
Sbjct: 19 LRQRFQPFGEIEEITLHFRDDGDN--YGFVTYRYACDAFRAIE 59

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 12/42 (28%), Positives = 21/42 (50%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF 146
            +YV  +  D T   L ++F  FG+I  + +    +G + GF
Sbjct: 4   VIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGF 45

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

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

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
          N  V  L   +   +   +F   G+I+S K+V  +  G+S GYGFV Y  P+ A  AI  
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 75 LQGATVERMELYV 87
          L G  ++   + V
Sbjct: 64 LNGLRLQTKTIKV 76

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 5/51 (9%)

Query: 31 LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE 81
          L ++F K+G ++    +V   GK   Y FV YS+ E A  A + L G  +E
Sbjct: 20 LLRVFEKYGTVED---LVMPPGKP--YCFVSYSSIEDAAAAYDALNGKELE 65

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

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          F+ NL  T     L + F +FG+I    + + ++G +  Y F+QY+   S + A+ K+ G
Sbjct: 6  FIGNLEKTTTYSDLREAFERFGEI--IDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDG 63

Query: 78 ATVERMELYVG 88
            +    + +G
Sbjct: 64 EYLGNNRVKLG 74

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>gnl|CDD|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 = 38.8 bits (91), Expect = 3e-04
 Identities = 16/42 (38%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 180 LYKNINDEVDEIELKQYFSQC-GTISSVKIMRTDRGISKGHC 220
           + KN+   + E ELK++FS+  G I+ VK++RT+ G S+   
Sbjct: 4   IVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIA 45

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 13/33 (39%), Positives = 23/33 (69%), Gaps = 1/33 (3%)

Query: 187 EVDEIELKQYFSQCGTISSVKIMR-TDRGISKG 218
           +++E EL+++F  CG + +V+I+R    GI KG
Sbjct: 10  DIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKG 42

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|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 5/61 (8%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKV---VVSQEGKSKGYGFVQYSTPESALDAIEK 74
          +V +L   +    L++IFS  G + S +V   +++   +S GY +V +  P  A  A++ 
Sbjct: 3  YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLIT--RRSLGYAYVNFQNPADAERALDT 60

Query: 75 L 75
          L
Sbjct: 61 L 61

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|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 38.9 bits (90), Expect = 3e-04
 Identities = 23/63 (36%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          + FV +L+  I    +   F+ FG I  ++VV     GKSKGYGFV +     A +AI  
Sbjct: 3  HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62

Query: 75 LQG 77
          + G
Sbjct: 63 MGG 65

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|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 19/43 (44%), Positives = 26/43 (60%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           NLY+ NL   M E+ L      FG++ S  I +DA+GTS+G G
Sbjct: 2   NLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVG 44

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 38.9 bits (90), Expect = 3e-04
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAIEK 74
          N +V  L+ST     L  +FSK+G +  +KVV +     ++ YGFV  ST E A   I  
Sbjct: 3  NLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINH 62

Query: 75 LQGATVERMELY 86
          L      R EL+
Sbjct: 63 LH-----RTELH 69

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE---GKSKGYGFVQYSTPESALDAIEKL 75
          ++ L        + Q  S    +    V + ++   G S+G+ FV++ + E A   ++ L
Sbjct: 7  LRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDAL 66

Query: 76 QG 77
            
Sbjct: 67 NN 68

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|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 4/70 (5%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYG-FVQYSTPESALDAIEKLQG 77
          + N+   +    L  + S +G +++ + V +   KS+     V Y +PE A  A+ KL G
Sbjct: 5  ISNIPPHVRWEDLDSLLSTYGTVKNCEQVPT---KSETATVNVTYESPEQAQQAVNKLNG 61

Query: 78 ATVERMELYV 87
             E  +L V
Sbjct: 62 HEYEGSKLKV 71

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

>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 = 38.4 bits (90), Expect = 4e-04
 Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 5/43 (11%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
            +YV NL   +TEE L   FS FG I  + + KD     KG+ 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYA 39

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 17/42 (40%), Positives = 29/42 (69%), Gaps = 5/42 (11%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           L+V NL +D+TEE   E FS++G+++ + ++K+     KGFG
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFG 40

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 4/60 (6%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V NL       +L   F K+G ++S  V V++     G+ FV++  P  A DA+  L G
Sbjct: 3  YVGNLGPRATKRELEDEFEKYGPLRS--VWVAR--NPPGFAFVEFEDPRDAEDAVRALDG 58

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|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 5/65 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSK-----VVVSQEGKSKGYGFVQYSTPESALDAI 72
          +VKNL+  +    L  IF +F D  S +     + +  EG+ KG  FV + + E A  A+
Sbjct: 5  YVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATKAL 64

Query: 73 EKLQG 77
            + G
Sbjct: 65 NLVNG 69

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 38.9 bits (91), Expect = 4e-04
 Identities = 10/38 (26%), Positives = 23/38 (60%)

Query: 102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA 139
           S  + ++  ++DD+ E  + + F +FGK  S++++  A
Sbjct: 1   SIKSFFLFGVEDDLPEYKIRDYFEQFGKSKSVIVNHRA 38

This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities. . Length = 86

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 38.9 bits (90), Expect = 4e-04
 Identities = 23/61 (37%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKLQ 76
          F+ NL    D   L Q+F  FG + + KV+      K KG+GFV  +  E A  AI  L 
Sbjct: 5  FIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASLN 64

Query: 77 G 77
          G
Sbjct: 65 G 65

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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 16/38 (42%), Positives = 24/38 (63%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTS 143
           ++V  L  D+T+E L E+FS  GKI  + + K AN T+
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTN 43

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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKLQ 76
          FV NL+   D   L Q+F  FG + + KV+      K KG+GFV  +  + A  AI  L 
Sbjct: 7  FVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLN 66

Query: 77 G 77
          G
Sbjct: 67 G 67

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

 Score = 38.3 bits (90), Expect = 5e-04
 Identities = 19/41 (46%), Positives = 26/41 (63%), Gaps = 1/41 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKG 145
           ++++NL  D TEE L E FS+FG++    I KD   G SKG
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKG 43

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 17/44 (38%), Positives = 28/44 (63%), Gaps = 1/44 (2%)

Query: 31 LHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE 73
          L + F +FGDI+   +V  +  G+SKG+G+V++  P  A  A+E
Sbjct: 17 LREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

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

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          FV  L       KL + F ++G I+  ++V  ++ GK +GY F+++        A +   
Sbjct: 5  FVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYAD 64

Query: 77 GATVE 81
          G  ++
Sbjct: 65 GKKID 69

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

 Score = 38.3 bits (89), Expect = 5e-04
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAI---- 72
          FV  L   +    L + FS+FG ++ ++V+   Q GK +G+GFV +   +SA  A     
Sbjct: 3  FVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVKF 62

Query: 73 EKLQGATVE 81
            + G  VE
Sbjct: 63 HPINGHRVE 71

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|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 16/46 (34%), Positives = 23/46 (50%)

Query: 32 HQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
             F KFG++   KV  + E   +G  +VQY + E AL A +   G
Sbjct: 46 LPEFEKFGEVVQFKVCCNYEPHLRGNVYVQYQSEEEALAAFKMFNG 91

This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif and serine/arginine rich protein 1 (U2AF1RS1), or U2 small nuclear RNA auxiliary factor 1-like 1 (U2AF1L1). Although the biological role of U2AFBPL remains unclear, it shows high sequence homology to splicing factor U2AF 35 kDa subunit (U2AF35 or U2AF1) that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. Like U2AF35, U2AFBPL contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. . Length = 105

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

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 21/70 (30%), Positives = 36/70 (51%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV NL   +   KL ++FS  G ++ + +   ++GKS+G G V +  P  A+ AI    G
Sbjct: 4  FVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFNG 63

Query: 78 ATVERMELYV 87
            +    ++V
Sbjct: 64 QFLFDRPMHV 73

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

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 5/51 (9%)

Query: 31 LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE 81
          + Q FS FG I   +V        KGY FV++++ ESA  AI  + G T+E
Sbjct: 17 MRQTFSPFGQIMEVRVF-----PDKGYSFVRFNSHESAAHAIVSVNGTTIE 62

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|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 = 38.0 bits (89), Expect = 5e-04
 Identities = 11/29 (37%), Positives = 19/29 (65%)

Query: 52 GKSKGYGFVQYSTPESALDAIEKLQGATV 80
          GKSKG+ +V++++  +A    EKL+G   
Sbjct: 39 GKSKGFAYVEFASEAAAAAVKEKLEGREF 67

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 38.2 bits (88), Expect = 5e-04
 Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKLQ 76
          FV NL+   D   L Q+F  FG + + KV+      K KG+GFV  +  + A  AI  L 
Sbjct: 5  FVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLN 64

Query: 77 G 77
          G
Sbjct: 65 G 65

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

 Score = 37.9 bits (89), Expect = 6e-04
 Identities = 17/60 (28%), Positives = 34/60 (56%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V N   + D   +  +F ++G+I S +    +  K++ + +VQ+++PESA  A+  L G
Sbjct: 4  WVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALLNG 63

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

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

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 2/66 (3%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLY-VARAQK-KAE 161
           N ++V  +  D TEE L + FS FG +  + I  D  G SKG+G         A+K  A 
Sbjct: 3   NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAM 62

Query: 162 RKAILR 167
                R
Sbjct: 63  GNLNFR 68

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

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 2/39 (5%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIM--RTDRGISKGH 219
           N+N +V E  L Q F + G ++SVKIM  RT+    +  
Sbjct: 8   NLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNR 46

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 37.8 bits (87), Expect = 7e-04
 Identities = 25/62 (40%), Positives = 32/62 (51%), Gaps = 4/62 (6%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
           L V+NL   ++ E+L E FS+FG +   V+  D  G S G G     V  A K A RKA 
Sbjct: 2   LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKG----IVEFASKPAARKAF 57

Query: 166 LR 167
            R
Sbjct: 58  ER 59

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins

 Score = 38.3 bits (90), Expect = 7e-04
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 11/73 (15%)

Query: 18 FVKNLASTI---DNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYG------FVQYSTPESA 68
          +V  L   +   + LK  + F ++G I+  K+V+++     G        +V YS  E A
Sbjct: 9  YVVGLPPRLADEEVLKKPEYFGQYGKIK--KIVINRNTSYNGSQGPSASAYVTYSRKEDA 66

Query: 69 LDAIEKLQGATVE 81
          L  I+ + G  ++
Sbjct: 67 LRCIQAVDGFYLD 79

This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T. Length = 98

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 38.2 bits (88), Expect = 7e-04
 Identities = 19/43 (44%), Positives = 24/43 (55%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           NLY+ NL   M E+ L      FG + S  I +DANG S+G G
Sbjct: 3   NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVG 45

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

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

 Score = 37.6 bits (87), Expect = 7e-04
 Identities = 17/41 (41%), Positives = 25/41 (60%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF 146
           L+V NLD  +TEE++ E F + G +  + I KD +G  K F
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQF 44

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|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 37.8 bits (87), Expect = 7e-04
 Identities = 19/67 (28%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          N +++ L     +  L ++   +G I S+K ++ +   K KGYGFV + +P +A  A+  
Sbjct: 3  NLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 62

Query: 75 LQGATVE 81
          L+ + V+
Sbjct: 63 LKASGVQ 69

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

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

 Score = 37.6 bits (88), Expect = 8e-04
 Identities = 14/36 (38%), Positives = 22/36 (61%)

Query: 182 KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISK 217
           KN+   V E  L+++F   G ++ VK+MRT  G S+
Sbjct: 6   KNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSR 41

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

 Score = 37.4 bits (87), Expect = 8e-04
 Identities = 15/42 (35%), Positives = 22/42 (52%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           ++V NLD  +  + L E F   GK+    I +D  G S+G G
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMG 42

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|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 37.6 bits (87), Expect = 8e-04
 Identities = 19/42 (45%), Positives = 26/42 (61%), Gaps = 2/42 (4%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           L+VK L +D TEE L E F   G I + +++    G+SKGFG
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSIAARIVTDRDTGSSKGFG 42

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 37.9 bits (87), Expect = 8e-04
 Identities = 19/67 (28%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          N +++ L     +  L ++   +G I S+K ++ +   K KGYGFV + +P +A  A+  
Sbjct: 9  NLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSA 68

Query: 75 LQGATVE 81
          L+ + V+
Sbjct: 69 LKASGVQ 75

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 37.7 bits (88), Expect = 8e-04
 Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
           L++  L  + T++ L   FS++G+IT  V+ KD     S+GFG
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFG 44

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|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 37.6 bits (87), Expect = 9e-04
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQG 77
          V NL  +    +  ++   +G+I+   +V S+  G SKGYGFV+Y   +SA  A  +L G
Sbjct: 4  VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63

Query: 78 ATVERMELYV 87
            +    L+ 
Sbjct: 64 KQLGESTLFA 73

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct 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. Raver-2 contains 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. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
           ++V  L    T++ L + FS+FG+I   V+  D   G S+G+G
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYG 45

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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 5/62 (8%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKKAERK 163
           +++V +L  ++  E L   F+ FG+I+   + KD   G SKG+G    +V+  +K+    
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYG----FVSFVKKEDAEN 56

Query: 164 AI 165
           AI
Sbjct: 57  AI 58

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 15/42 (35%), Positives = 25/42 (59%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           + VKNL   +TE+ L E F   G++T + + +  +G S+ FG
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFG 44

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|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 = 36.9 bits (86), Expect = 0.001
 Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 2/49 (4%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-NGTSKGFGSKVLYV 153
           L+V+NL    TEE L E F  FG+I+ + +  D     SKGF   V ++
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFA-FVSFM 49

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN 140
           +YV+NLD  + E+ L   FS+FG++ S+ I K  +
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQD 37

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 16/55 (29%), Positives = 29/55 (52%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKA 160
           ++V+NL   +T + L + F E G +    +  D +G SKGFG+ +       ++A
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRA 55

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 14/33 (42%), Positives = 22/33 (66%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD 138
           LYV+NL   +TEE L E FS +GK+  + + ++
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN 33

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

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

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 107 YVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKKAERKAI 165
           +V NL  D+ EE L + F + G + ++ I +D   G  KGFG    YV    K +   A+
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFG----YVLFKTKDSVALAL 58

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 5/61 (8%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAERKA 164
           L+V NL  D  E+ + E F E+G+I+S+ +  D + G  KGFG    YV  + ++A + A
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFG----YVEFSSQEAAQAA 56

Query: 165 I 165
           +
Sbjct: 57  L 57

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|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 16/41 (39%), Positives = 23/41 (56%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF 146
           LYV NLD  +TE++L E FS+ G I S  + ++       F
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAF 41

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

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGK--ITSLVISKD-ANGTSKGFG 147
           N L ++ LD   TEE +++  S      I  + + +D   GTS+GF 
Sbjct: 3   NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFA 49

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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
          N ++  L  T+    +  +FS+FG I +S+V+V Q  G S+G  F+++     A +AI  
Sbjct: 2  NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 75 LQG 77
            G
Sbjct: 62 FNG 64

This subgroup corresponds to the RRM2 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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 37.8 bits (87), Expect = 0.001
 Identities = 18/43 (41%), Positives = 26/43 (60%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           NLY+ NL   M E+ L      FG++ S  I +D++GTS+G G
Sbjct: 2   NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVG 44

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

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

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 20/60 (33%), Positives = 32/60 (53%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV NL   +   KL ++FS  G +  + ++  ++GKS+G G V +  P  A+ AI    G
Sbjct: 4  FVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFNG 63

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 16/56 (28%), Positives = 34/56 (60%), Gaps = 2/56 (3%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAI 72
          FV  L   +   +  + FS+FG +  ++++   + G+S+G+GFV + + ESA++ +
Sbjct: 3  FVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERV 57

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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 15/43 (34%), Positives = 28/43 (65%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
           +++  L+ + T++ L E F +FG++T   + +D A G S+GFG
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFG 43

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 = 76

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 7/70 (10%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAI---- 72
          FV  L   +    L + FS+FG +    V+   E K  +G+GF+ + + E ++D +    
Sbjct: 6  FVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFES-EDSVDQVVNEH 64

Query: 73 -EKLQGATVE 81
             + G  VE
Sbjct: 65 FHDINGKKVE 74

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|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 6/64 (9%)

Query: 18 FVKNLASTIDNLKLH----QIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
          FV +L ++  + +L     + FSK+G +   KV+  ++ + + Y FVQ++  + A +A+ 
Sbjct: 6  FVASLPASKSDDELEAAVTEHFSKYGTLVFVKVL--RDWRQRPYAFVQFTNDDDAKNALA 63

Query: 74 KLQG 77
          K QG
Sbjct: 64 KGQG 67

This subfamily corresponds to the RRM1 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 = 86

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARA 156
           L V NLD  ++++ + E F+EFG +    +  D +G S G    V++  RA
Sbjct: 3   LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTA-DVVFERRA 52

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|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 6/76 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK------SKGYGFVQYSTPESALDA 71
          FVKNL  +  N  L   F        ++V    + K      S G+GFV + T E A  A
Sbjct: 4  FVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQAA 63

Query: 72 IEKLQGATVERMELYV 87
          ++ + G  ++   L V
Sbjct: 64 LKAMDGFVLDGHTLVV 79

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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
            ++V NL  D  E +L + FS FG +T++ + +D      KG+G
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYG 46

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 12/44 (27%), Positives = 23/44 (52%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           + L+V  L   +T+E L + F + G + S+ +  + +G  KG  
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLA 46

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 13/33 (39%), Positives = 22/33 (66%)

Query: 187 EVDEIELKQYFSQCGTISSVKIMRTDRGISKGH 219
           +  E EL+ +FS+ G++  VKI+    G+SKG+
Sbjct: 13  DTTEEELRDFFSRFGSVKDVKIITDRAGVSKGY 45

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 15/42 (35%), Positives = 22/42 (52%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           L VKNL   + E+ L + F  FG IT + +    +G  + FG
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFG 44

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|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 4/62 (6%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
           L VKNL   ++ E+L + FS+FG +   V+  D  G   G G    +V  A K A RKA+
Sbjct: 2   LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKG----FVEFAAKPAARKAL 57

Query: 166 LR 167
            R
Sbjct: 58  ER 59

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

>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 = 36.1 bits (84), Expect = 0.002
 Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 1/45 (2%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
           N +++  L + ++E+ + E    FGK+ +  + KD A G SKG+ 
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYA 45

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

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 17/63 (26%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKV--VVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
          V+N+       +L ++FS FG++++ ++   ++  G  +G+GFV + T + A  A + L 
Sbjct: 5  VRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKALC 64

Query: 77 GAT 79
           +T
Sbjct: 65 HST 67

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|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 14/63 (22%), Positives = 32/63 (50%), Gaps = 5/63 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          ++ +L+  +    L  +F ++G+IQS  ++       +G  +V   T + A  A++KL+ 
Sbjct: 6  WIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP-----PRGCAYVCMETRQDAHRALQKLRN 60

Query: 78 ATV 80
            +
Sbjct: 61 VKL 63

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 2/62 (3%)

Query: 18 FVKNLASTIDNLKLHQIF-SKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKL 75
          FV +L+  ++   L  +F S+F   +S+K++     G S+GYGFV++S       A+ ++
Sbjct: 5  FVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIEM 64

Query: 76 QG 77
          QG
Sbjct: 65 QG 66

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 5/50 (10%)

Query: 31 LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATV 80
          L  +F +FG +    +V       K YG+ +Y+  ESA  AI  L G  V
Sbjct: 16 LEDVFCRFGGLIDVYLV-----PGKNYGYAKYADRESAERAITTLHGKEV 60

This subfamily corresponds to the RRM4 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 = 68

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 34 IFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQGATV 80
          +FS++G+I    +V  ++ GKSKG+ F+ Y    S + A++ L G  +
Sbjct: 29 VFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKL 76

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
           +Y+  L  ++TE  ++  FS++G+I  + + +D   G SKGF 
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFA 54

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

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE 73
          FV  L+  +    L++ FSK G ++  +++  +   +SKG  +V++   ES   A+ 
Sbjct: 3  FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG 59

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

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 4/63 (6%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           V NL S I + +L  +FS+FG+++     + +        FV++    +A  A++ L G
Sbjct: 5  LVFNLDSPISDQELRSLFSQFGEVKD----IRETPLRPSQKFVEFYDIRAAEAALDALNG 60

Query: 78 ATV 80
             
Sbjct: 61 RPF 63

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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 11/28 (39%), Positives = 18/28 (64%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMR 210
           N+  + DE  L Q FS  G +++VK++R
Sbjct: 8   NLPPDADESLLWQLFSPFGAVTNVKVIR 35

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 19/43 (44%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
           L+V+NL  D T+E L E FSE G I    + KD      +GFG
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFG 44

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

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-NGTSKGFG 147
           L+V+NL   +T+E L + FS+   I   V+  D   G S+G+G
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYG 44

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 38.8 bits (90), Expect = 0.003
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
           N +V NL  TI + +L  IF K+G I    ++  +  G  +G  FV+++  E A +AI  
Sbjct: 195 NLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISA 254

Query: 75  LQGATVE 81
           L     E
Sbjct: 255 LNNVIPE 261

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 14/34 (41%), Positives = 24/34 (70%), Gaps = 1/34 (2%)

Query: 184 INDEVDEIELKQYFSQCGTISSVKIMRTDRGISK 217
           + ++V E +L++YFSQ G + SV+I+ TD+   K
Sbjct: 7   LKEDVTEEDLREYFSQYGNVESVEIV-TDKETGK 39

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|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 24/62 (38%), Positives = 32/62 (51%), Gaps = 4/62 (6%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
           L VKNL   ++ E+L E FS FG++   V+  D  G   G G     V  A K + RKA+
Sbjct: 2   LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKG----IVEFAGKPSARKAL 57

Query: 166 LR 167
            R
Sbjct: 58  DR 59

This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 36.2 bits (83), Expect = 0.003
 Identities = 16/66 (24%), Positives = 32/66 (48%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
          N ++ NL  ++D  +L  +   FG + S++++    G S+G GF +  + E     I   
Sbjct: 2  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHF 61

Query: 76 QGATVE 81
           G  ++
Sbjct: 62 NGKFIK 67

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

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

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 14/62 (22%), Positives = 30/62 (48%), Gaps = 4/62 (6%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEKLQ 76
          FV  L+ ++    L + FS+FG +   +++     G  +G+ ++   T E+ L   +K +
Sbjct: 3  FVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQL---KKCK 59

Query: 77 GA 78
            
Sbjct: 60 ST 61

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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 36.3 bits (83), Expect = 0.003
 Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          N +++ L     +  L ++   +G I S+K ++ +   + KGYGFV + +P +A  A+  
Sbjct: 6  NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVAS 65

Query: 75 LQGATVE 81
          L+   V+
Sbjct: 66 LKANGVQ 72

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          ++ NL+S ++   L Q+F +   I  S V+V    K  GY FV       A  AIEKL G
Sbjct: 2  YIGNLSSDVNESDLRQLFEEHK-IPVSSVLV----KKGGYAFVDCPDQSWADKAIEKLNG 56

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

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

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 16/35 (45%), Positives = 25/35 (71%), Gaps = 1/35 (2%)

Query: 35 FSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESA 68
          FS+FG +   ++  S++ GKSKGY FV++ +PE A
Sbjct: 20 FSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVA 54

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 18/75 (24%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSK---VVVSQEGKSKGYGFVQ------------- 61
          FV NL  T     L ++F +FG I+S +   V V ++   K    ++             
Sbjct: 4  FVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNAY 63

Query: 62 --YSTPESALDAIEK 74
            +   ESA  A++ 
Sbjct: 64 VVFKEEESAEKALKL 78

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|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 = 35.6 bits (82), Expect = 0.004
 Identities = 16/43 (37%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT-SKGFG 147
           L++  L  D  E+ L + FS++G+I+ +V+ KD     S+GFG
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFG 45

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

 Score = 35.3 bits (82), Expect = 0.004
 Identities = 17/40 (42%), Positives = 24/40 (60%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKG 145
           L V NL  D+TEE L E F   G++  + I+ D +G S+G
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEG 42

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

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 6/83 (7%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKI-TSLVISKDANGTSKGFGSKVLYVARAQKKAERKA 164
           L+V  L  D+ E  L E FS+FG +  + VI+    G  +GFG    +V      +  KA
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFG----FVYFQNHDSADKA 57

Query: 165 ILRAQFERMRKERAELYKNINDE 187
            +  +F  +   R E+ K +  E
Sbjct: 58  AV-VKFHPINGHRVEVKKAVPKE 79

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|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 16/62 (25%), Positives = 31/62 (50%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
          N ++ NL  ++D  +L  +   FG + S++++    G S+G GF +  + E     I+  
Sbjct: 3  NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHF 62

Query: 76 QG 77
           G
Sbjct: 63 NG 64

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 11/65 (16%)

Query: 24 STIDNLKLHQIFSKFGDIQSSKVVVSQE---GKSKGYGFVQYSTPESALDAI----EKLQ 76
          +T D+LK +  FS++G+I  +  VV ++    +S+G+GFV +++      A+     K+ 
Sbjct: 11 TTDDSLKNY--FSQWGEI--TDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNARPHKVD 66

Query: 77 GATVE 81
          G  VE
Sbjct: 67 GREVE 71

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

 Score = 35.6 bits (83), Expect = 0.004
 Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSL-VISKDANGTSKGFG 147
           L+V  L   +TE  L E+FS FG ++ + +I K   G  +GF 
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFA 44

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

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 10/73 (13%)

Query: 18 FVKNLAS-TIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
          F+ NL +  +    L +IFS +G++  +++V+        YGFVQ+ +PES  +AI   Q
Sbjct: 3  FIGNLPTKRVSKEDLFRIFSTYGEL--AQIVLKN-----AYGFVQFDSPESCANAINCEQ 55

Query: 77 GATV--ERMELYV 87
          G  +   ++ L V
Sbjct: 56 GKMIRGRKLHLEV 68

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 35.6 bits (82), Expect = 0.004
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV  +   +   +L  +F + G I   ++++   G+++GY FV Y+T E A  AI  L  
Sbjct: 5  FVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRIL-- 62

Query: 78 ATVERMELYVGPFI 91
                E+  G FI
Sbjct: 63 ---NNYEIRPGKFI 73

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

 Score = 35.6 bits (83), Expect = 0.004
 Identities = 17/43 (39%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
           +YV NLD+ +TEE+L E F + G + ++ I KD      +G+G
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYG 43

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	398
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.97
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.96
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.96
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.96
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.96
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.96
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.96
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.96
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.91
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.91
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.88
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.88
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.87
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.84
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.81
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.8
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.8
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.79
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.78
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.78
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.77
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.77
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.76
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.76
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.76
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.73
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.71
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.69
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.67
KOG0122	270	consensus Translation initiation factor 3, subunit	99.61
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.6
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.59
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.58
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.58
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.58
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.57
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.56
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.56
PLN03120	260	nucleic acid binding protein; Provisional	99.54
smart00517	64	PolyA C-terminal domain of Poly(A)-binding protein	99.53
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.52
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.49
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.49
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.49
smart00362	72	RRM_2 RNA recognition motif.	99.48
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.48
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.47
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.47
PF00658	72	PABP: Poly-adenylate binding protein, unique domai	99.47
PLN03121	243	nucleic acid binding protein; Provisional	99.47
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.45
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.45
smart00360	71	RRM RNA recognition motif.	99.44
PLN03213	759	repressor of silencing 3; Provisional	99.44
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.43
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.42
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.42
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.4
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.38
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.38
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.34
smart00361	70	RRM_1 RNA recognition motif.	99.32
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.29
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.29
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.28
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.26
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.26
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.23
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.22
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.21
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.17
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.15
KOG0122	270	consensus Translation initiation factor 3, subunit	99.08
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.08
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.05
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.05
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.04
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.03
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.01
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.97
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.92
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.89
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	98.88
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.85
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.84
KOG0226	290	consensus RNA-binding proteins [General function p	98.81
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.78
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.76
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.75
PLN03120	260	nucleic acid binding protein; Provisional	98.74
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.72
PLN03121	243	nucleic acid binding protein; Provisional	98.7
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.67
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.66
smart00360	71	RRM RNA recognition motif.	98.64
smart00362	72	RRM_2 RNA recognition motif.	98.63
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.63
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	98.61
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.58
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.54
KOG4210	285	consensus Nuclear localization sequence binding pr	98.51
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.49
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.48
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.45
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.44
KOG0151	877	consensus Predicted splicing regulator, contains R	98.44
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.44
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.42
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.41
PLN03213	759	repressor of silencing 3; Provisional	98.4
smart00361	70	RRM_1 RNA recognition motif.	98.37
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.37
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	98.36
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.36
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.29
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.28
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.21
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.18
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.15
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	98.15
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.12
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.08
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.08
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.06
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.03
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.02
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.02
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.93
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.92
KOG0226	290	consensus RNA-binding proteins [General function p	97.85
KOG4210	285	consensus Nuclear localization sequence binding pr	97.76
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.74
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.73
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	97.65
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.62
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.55
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	97.51
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.5
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.48
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.47
KOG2314	698	consensus Translation initiation factor 3, subunit	97.45
KOG0151	877	consensus Predicted splicing regulator, contains R	97.45
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.4
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.38
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.31
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.25
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.2
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	97.0
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.99
KOG3152	278	consensus TBP-binding protein, activator of basal	96.88
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.83
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.74
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.71
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	96.66
KOG4660	549	consensus Protein Mei2, essential for commitment t	96.62
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.57
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.51
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.39
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.35
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	96.15
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.93
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.92
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	95.74
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.62
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.57
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.83
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.83
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.1
KOG2591	684	consensus c-Mpl binding protein, contains La domai	93.78
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	93.64
KOG2314	698	consensus Translation initiation factor 3, subunit	93.53
COG5175	480	MOT2 Transcriptional repressor [Transcription]	93.48
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	92.72
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	92.71
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	92.4
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	91.44
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	91.36
KOG2135	526	consensus Proteins containing the RNA recognition	90.63
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	90.58
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	90.37
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	89.85
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	89.49
KOG3152	278	consensus TBP-binding protein, activator of basal	89.11
KOG1996	378	consensus mRNA splicing factor [RNA processing and	89.1
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	87.74
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	86.31
PRK14548	84	50S ribosomal protein L23P; Provisional	85.31
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	84.81
KOG1995	351	consensus Conserved Zn-finger protein [General fun	84.12
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	84.0
KOG2591	684	consensus c-Mpl binding protein, contains La domai	83.55
TIGR03636	77	L23_arch archaeal ribosomal protein L23. This mode	81.18
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	80.63

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

Probab=100.00  E-value=4.4e-62  Score=506.75  Aligned_cols=238  Identities=44%  Similarity=0.746  Sum_probs=214.7

Q ss_pred             CCCCCCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCee
Q 039806            1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATV   80 (398)
Q Consensus         1 m~s~rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l   80 (398)
                      |||+||++.++++.++|||+|||.++|+++|+++|+.||.|++|+|.+|.+|+++|||||+|++.++|++||+++||..+
T Consensus        75 ~~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~  154 (562)
T TIGR01628        75 MWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLL  154 (562)
T ss_pred             ecccccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEe
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cceEeeeeccccccccc-ccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCcccc-------------
Q 039806           81 ERMELYVGPFIRRADRI-QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF-------------  146 (398)
Q Consensus        81 ~gk~i~V~~~~~~~~~~-~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf-------------  146 (398)
                      +|+.|+|..+.++.++. .....+++|||+||+.++|+++|+++|+.||.|+++++++|.+|+++||             
T Consensus       155 ~~~~i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~  234 (562)
T TIGR01628       155 NDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAK  234 (562)
T ss_pred             cCceEEEeccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHH
Confidence            99999999888777763 2233789999999999999999999999999999999999988988887             


Q ss_pred             ----------C----CchhhhHHHHHHHHHHHHHHHHHHHhhh-------hhhccccCCCcccCHHHHHHHhhcCCCeEE
Q 039806          147 ----------G----SKVLYVARAQKKAERKAILRAQFERMRK-------ERAELYKNINDEVDEIELKQYFSQCGTISS  205 (398)
Q Consensus       147 ----------~----~~~l~v~~a~~k~~~~~~~~~~~~~~~~-------~~~~~v~nL~~~vtee~L~~~F~~fG~I~s  205 (398)
                                .    +..++|.++.++.++..+++..+.....       ...++|+||++++|+++|+++|++||.|++
T Consensus       235 Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~  314 (562)
T TIGR01628       235 AVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITS  314 (562)
T ss_pred             HHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEE
Confidence                      3    6667788888887777666666554333       345888999999999999999999999999


Q ss_pred             EEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          206 VKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       206 vki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      |+|++|.+|.++|| ||+|++.++|.+|+.+++.
T Consensus       315 ~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g  348 (562)
T TIGR01628       315 AKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHG  348 (562)
T ss_pred             EEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcC
Confidence            99999999999999 9999999999999876553

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=9e-38  Score=306.60  Aligned_cols=224  Identities=29%  Similarity=0.389  Sum_probs=182.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ..+|||+|||.++|+++|+++|+.||+|.+|+|++|+ +|+++|||||+|.+.++|++||+.|||..|.|+.|.|.++.+
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            5799999999999999999999999999999999998 899999999999999999999999999999999999998865


Q ss_pred             cccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCccccCCch---------------------
Q 039806           93 RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKV---------------------  150 (398)
Q Consensus        93 ~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf~~~~---------------------  150 (398)
                      +...    ...++|||+|||.++++++|+++|+.||.|..++++.+.. +.++||+...                     
T Consensus        83 ~~~~----~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g  158 (352)
T TIGR01661        83 SSDS----IKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSG  158 (352)
T ss_pred             cccc----cccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            4432    2467899999999999999999999999999999998874 7788883211                     


Q ss_pred             ----hhhHHHHHHHHH--HHHHH-----------------------------------------------H---------
Q 039806          151 ----LYVARAQKKAER--KAILR-----------------------------------------------A---------  168 (398)
Q Consensus       151 ----l~v~~a~~k~~~--~~~~~-----------------------------------------------~---------  168 (398)
                          +.|.++......  .....                                               .         
T Consensus       159 ~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (352)
T TIGR01661       159 CTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQ  238 (352)
T ss_pred             CceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccc
Confidence                222221100000  00000                                               0         


Q ss_pred             ----HH-------------------HHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEe
Q 039806          169 ----QF-------------------ERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAI  223 (398)
Q Consensus       169 ----~~-------------------~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f  223 (398)
                          ..                   ........++|+||++++++++|+++|++||.|++|+|++|. +|.+||| ||.|
T Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F  318 (352)
T TIGR01661       239 HAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSM  318 (352)
T ss_pred             cccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEE
Confidence                00                   000011248899999999999999999999999999999998 9999999 9999


Q ss_pred             cccHHHHHHHHHHhcccc
Q 039806          224 AQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       224 ~~~~ea~~A~l~~q~~q~  241 (398)
                      .+.++|.+|+..++....
T Consensus       319 ~~~~~A~~Ai~~lnG~~~  336 (352)
T TIGR01661       319 TNYDEAAMAILSLNGYTL  336 (352)
T ss_pred             CCHHHHHHHHHHhCCCEE
Confidence            999999999999887553

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

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

Probab=100.00  E-value=7.5e-38  Score=304.49  Aligned_cols=230  Identities=41%  Similarity=0.667  Sum_probs=210.1

Q ss_pred             CCCCCCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCee
Q 039806            1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATV   80 (398)
Q Consensus         1 m~s~rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l   80 (398)
                      |||+|||+.       |||+||++++|.++|+++|+.||+|+||||.+|.+| |||| ||+|+++++|++||+.+||+.+
T Consensus        70 m~s~rd~~~-------~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll  140 (369)
T KOG0123|consen   70 MWSQRDPSL-------VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLL  140 (369)
T ss_pred             ehhccCCce-------eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCccc
Confidence            999999999       999999999999999999999999999999999999 9999 9999999999999999999999


Q ss_pred             cceEeeeecccccccccccCC----CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCcccc----------
Q 039806           81 ERMELYVGPFIRRADRIQEGS----SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF----------  146 (398)
Q Consensus        81 ~gk~i~V~~~~~~~~~~~~~~----~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf----------  146 (398)
                      .|++|+|..+.++.+|.....    ..++++|+|++.+++++.|.++|+.||.|+++.++.+..++++||          
T Consensus       141 ~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~  220 (369)
T KOG0123|consen  141 NGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPED  220 (369)
T ss_pred             CCCeeEEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhH
Confidence            999999999999888754332    688999999999999999999999999999999999999888888          


Q ss_pred             -------------CCchhhhHHHHHHHHHHHHHHHHHHHhhh-------hhhccccCCCcccCHHHHHHHhhcCCCeEEE
Q 039806          147 -------------GSKVLYVARAQKKAERKAILRAQFERMRK-------ERAELYKNINDEVDEIELKQYFSQCGTISSV  206 (398)
Q Consensus       147 -------------~~~~l~v~~a~~k~~~~~~~~~~~~~~~~-------~~~~~v~nL~~~vtee~L~~~F~~fG~I~sv  206 (398)
                                   ++..++|.+++++.++...++..+.....       ...++++||+..++++.|++.|+.||+|+++
T Consensus       221 a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~  300 (369)
T KOG0123|consen  221 AKKAVETLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSA  300 (369)
T ss_pred             HHHHHHhccCCcCCccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccceeeE
Confidence                         46678999999988888888876654433       3456779999999999999999999999999


Q ss_pred             EEeeCCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          207 KIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       207 ki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      +|+.+..|+++|| ||+|.+.++|.+|...+...
T Consensus       301 kv~~~~~g~skG~gfV~fs~~eeA~~A~~~~n~~  334 (369)
T KOG0123|consen  301 KVMVDENGKSKGFGFVEFSSPEEAKKAMTEMNGR  334 (369)
T ss_pred             EEEeccCCCccceEEEEcCCHHHHHHHHHhhChh
Confidence            9999999999999 99999999999996655543

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

Probab=100.00  E-value=1.2e-36  Score=316.21  Aligned_cols=224  Identities=25%  Similarity=0.416  Sum_probs=185.0

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRR   93 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~   93 (398)
                      .+|||+|||.++||++|+++|+.||.|.+|+|.+|. +++++|||||+|.+.++|++||+.+|+..|+|+.|+|.++.+.
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~   80 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            379999999999999999999999999999999999 7999999999999999999999999999999999999997643


Q ss_pred             ccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHH--------
Q 039806           94 ADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI--------  165 (398)
Q Consensus        94 ~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~--------  165 (398)
                      ...  .....++|||+||+.++|+++|+++|+.||.|.+|++..|.+|+++||+...+.-..+..++.....        
T Consensus        81 ~~~--~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~  158 (562)
T TIGR01628        81 PSL--RRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKE  158 (562)
T ss_pred             ccc--cccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCce
Confidence            322  1124578999999999999999999999999999999999999999996444333322222211100        


Q ss_pred             -----HHHH----HHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHH
Q 039806          166 -----LRAQ----FERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       166 -----~~~~----~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                           ....    .......+.++|+||+.++|+++|+++|++||.|++|+|++|.+|+++|| ||.|++.++|.+|+..
T Consensus       159 i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~  238 (562)
T TIGR01628       159 VYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEE  238 (562)
T ss_pred             EEEeccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHH
Confidence                 0000    00112234578899999999999999999999999999999999999999 9999999999999976


Q ss_pred             Hhccc
Q 039806          236 IMYAK  240 (398)
Q Consensus       236 ~q~~q  240 (398)
                      ++...
T Consensus       239 l~g~~  243 (562)
T TIGR01628       239 MNGKK  243 (562)
T ss_pred             hCCcE
Confidence            65443

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

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

Probab=100.00  E-value=4e-32  Score=257.11  Aligned_cols=203  Identities=20%  Similarity=0.344  Sum_probs=173.3

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCee-cceEeeeecc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATV-ERMELYVGPF   90 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l-~gk~i~V~~~   90 (398)
                      --+.|||+.||.++.|++|..+|++.|.|.+++++.|+ +|.+||||||.|.+.++|++||+.||+..| .||.|.|..+
T Consensus        82 ~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~S  161 (506)
T KOG0117|consen   82 RGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVS  161 (506)
T ss_pred             CCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEe
Confidence            35689999999999999999999999999999999997 999999999999999999999999999988 5899999887


Q ss_pred             cccccccccCCCCceEEeeCCCccccHHHHHHHHccCCC-EEEEEEeeCCC--CCccccC--------------------
Q 039806           91 IRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGK-ITSLVISKDAN--GTSKGFG--------------------  147 (398)
Q Consensus        91 ~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~-I~~~~i~~d~~--g~s~Gf~--------------------  147 (398)
                      .          ..++|||+|||.++++|+|.+.+++.++ |++|.|..+.+  .++|||.                    
T Consensus       162 v----------an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g  231 (506)
T KOG0117|consen  162 V----------ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPG  231 (506)
T ss_pred             e----------ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCC
Confidence            6          4689999999999999999999999876 77887877764  7889993                    


Q ss_pred             -----CchhhhHHHHHHHHHHHHHHHHHHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccceEEE
Q 039806          148 -----SKVLYVARAQKKAERKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMA  222 (398)
Q Consensus       148 -----~~~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGffV~  222 (398)
                           +..+.|.||..+.+-.      .+....-+.|+|+||+.++|||.|+++|++||.|+.|+.++|     -+ ||.
T Consensus       232 ~~klwgn~~tVdWAep~~e~d------ed~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-----Ya-FVH  299 (506)
T KOG0117|consen  232 KIKLWGNAITVDWAEPEEEPD------EDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-----YA-FVH  299 (506)
T ss_pred             ceeecCCcceeeccCcccCCC------hhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-----ee-EEe
Confidence                 3344555554433321      122344567888999999999999999999999999999977     22 999


Q ss_pred             ecccHHHHHHHHHHh
Q 039806          223 IAQTKRERTSYLRIM  237 (398)
Q Consensus       223 f~~~~ea~~A~l~~q  237 (398)
                      |+++++|.+|...+.
T Consensus       300 f~eR~davkAm~~~n  314 (506)
T KOG0117|consen  300 FAEREDAVKAMKETN  314 (506)
T ss_pred             ecchHHHHHHHHHhc
Confidence            999999999998543

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

Probab=100.00  E-value=2.9e-33  Score=248.02  Aligned_cols=221  Identities=29%  Similarity=0.434  Sum_probs=182.1

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ..+|.|.-||...|+|||+.+|...|+|++||+++|+ +|.|-|||||.|.+++||++||..|||..|..|.|+|.++.+
T Consensus        41 kTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARP  120 (360)
T KOG0145|consen   41 KTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARP  120 (360)
T ss_pred             cceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccC
Confidence            4689999999999999999999999999999999999 999999999999999999999999999999999999999887


Q ss_pred             cccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCccccC------------------------
Q 039806           93 RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG------------------------  147 (398)
Q Consensus        93 ~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf~------------------------  147 (398)
                      .++..    +..||||++||...|..||+.+|++||.|...+|..|.. |.+||.+                        
T Consensus       121 Ss~~I----k~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g  196 (360)
T KOG0145|consen  121 SSDSI----KDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSG  196 (360)
T ss_pred             Chhhh----cccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCC
Confidence            65443    567999999999999999999999999998888888874 8888762                        


Q ss_pred             -CchhhhHHHHHHHH--HHHHHHHHH---------------HHh-----------------------------------h
Q 039806          148 -SKVLYVARAQKKAE--RKAILRAQF---------------ERM-----------------------------------R  174 (398)
Q Consensus       148 -~~~l~v~~a~~k~~--~~~~~~~~~---------------~~~-----------------------------------~  174 (398)
                       ...|.|+++..-..  ..+.+...+               .+.                                   .
T Consensus       197 ~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~  276 (360)
T KOG0145|consen  197 CTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPG  276 (360)
T ss_pred             CCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCC
Confidence             12233333321110  001111100               000                                   0


Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ..-+++|.||..+.+|..|+.+|.+||.|++|||++|- +.++||| ||...+.+||..|+..+..
T Consensus       277 ~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNG  342 (360)
T KOG0145|consen  277 GGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNG  342 (360)
T ss_pred             CeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcC
Confidence            01246779999999999999999999999999999998 6999999 9999999999999987654

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

Probab=100.00  E-value=8.6e-32  Score=273.45  Aligned_cols=209  Identities=20%  Similarity=0.287  Sum_probs=166.2

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec-ceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE-RMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~-gk~i~V~~~~~   92 (398)
                      .++|||+|||.++||++|+++|++||.|.+|+|++|.+|++||||||+|.+.|+|++||+.||+..|. |+.|.|..+. 
T Consensus        58 ~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~-  136 (578)
T TIGR01648        58 GCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV-  136 (578)
T ss_pred             CCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc-
Confidence            47999999999999999999999999999999999999999999999999999999999999999885 7888776653 


Q ss_pred             cccccccCCCCceEEeeCCCccccHHHHHHHHccCCC-EEEEEEeeCC--CCCccccCCchhhhHHHHHHHHHHHHHHH-
Q 039806           93 RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGK-ITSLVISKDA--NGTSKGFGSKVLYVARAQKKAERKAILRA-  168 (398)
Q Consensus        93 ~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~-I~~~~i~~d~--~g~s~Gf~~~~l~v~~a~~k~~~~~~~~~-  168 (398)
                               ..++|||+|||.++|+++|.+.|++++. ++++.+....  .++++||+...+.-..+..++.+...... 
T Consensus       137 ---------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki  207 (578)
T TIGR01648       137 ---------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRI  207 (578)
T ss_pred             ---------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccce
Confidence                     3578999999999999999999999964 4555444332  36788996544433333322221110000 


Q ss_pred             ------------------HHHHhhhhhhccccCCCcccCHHHHHHHhhcC--CCeEEEEEeeCCCCCccce-EEEecccH
Q 039806          169 ------------------QFERMRKERAELYKNINDEVDEIELKQYFSQC--GTISSVKIMRTDRGISKGH-CMAIAQTK  227 (398)
Q Consensus       169 ------------------~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~f--G~I~svki~~d~~g~skGf-fV~f~~~~  227 (398)
                                        ..+.....++++|+||+.++||++|+++|++|  |+|++|+++       ++| ||+|++.+
T Consensus       208 ~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~-------rgfAFVeF~s~e  280 (578)
T TIGR01648       208 QLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-------RDYAFVHFEDRE  280 (578)
T ss_pred             EecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee-------cCeEEEEeCCHH
Confidence                              00011224678899999999999999999999  999999987       446 99999999


Q ss_pred             HHHHHHHHHhcc
Q 039806          228 RERTSYLRIMYA  239 (398)
Q Consensus       228 ea~~A~l~~q~~  239 (398)
                      +|.+|+.+++..
T Consensus       281 ~A~kAi~~lnG~  292 (578)
T TIGR01648       281 DAVKAMDELNGK  292 (578)
T ss_pred             HHHHHHHHhCCC
Confidence            999999876543

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

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

Probab=99.97  E-value=2.8e-30  Score=262.93  Aligned_cols=217  Identities=16%  Similarity=0.193  Sum_probs=167.2

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHh--cCCeecceEeeeeccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL--QGATVERMELYVGPFI   91 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~l--ng~~l~gk~i~V~~~~   91 (398)
                      ++.|||+|||.++|+++|+++|+.||.|.+|+|++     +||||||+|++.++|++||+.+  |+..|.|+.|+|.++.
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 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP-----GKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYST   76 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC-----CCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecC
Confidence            67899999999999999999999999999999986     5689999999999999999864  7899999999999987


Q ss_pred             cccccccc--------CCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCcccc----------------C
Q 039806           92 RRADRIQE--------GSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF----------------G  147 (398)
Q Consensus        92 ~~~~~~~~--------~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf----------------~  147 (398)
                      .+......        .....+|||+||++.+|+++|+++|+.||.|.+|.|+++.. ...||                +
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~-~~~afVef~~~~~A~~A~~~Ln  155 (481)
T TIGR01649        77 SQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN-VFQALVEFESVNSAQHAKAALN  155 (481)
T ss_pred             CcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC-ceEEEEEECCHHHHHHHHHHhc
Confidence            54322111        11345799999999999999999999999999999988653 33466                1


Q ss_pred             Cc-------h----------hhhHHHHHHH----------HHHHHHHH----HHH-------------------------
Q 039806          148 SK-------V----------LYVARAQKKA----------ERKAILRA----QFE-------------------------  171 (398)
Q Consensus       148 ~~-------~----------l~v~~a~~k~----------~~~~~~~~----~~~-------------------------  171 (398)
                      +.       .          |.|.++.++.          +++..+..    ...                         
T Consensus       156 g~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  235 (481)
T TIGR01649       156 GADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPL  235 (481)
T ss_pred             CCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCcc
Confidence            11       1          2222222221          00000000    000                         


Q ss_pred             -----------------------------------HhhhhhhccccCCCc-ccCHHHHHHHhhcCCCeEEEEEeeCCCCC
Q 039806          172 -----------------------------------RMRKERAELYKNIND-EVDEIELKQYFSQCGTISSVKIMRTDRGI  215 (398)
Q Consensus       172 -----------------------------------~~~~~~~~~v~nL~~-~vtee~L~~~F~~fG~I~svki~~d~~g~  215 (398)
                                                         ....+.+++|+||++ .+|+++|+++|+.||.|++|+|+++.   
T Consensus       236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~---  312 (481)
T TIGR01649       236 AGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK---  312 (481)
T ss_pred             cccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC---
Confidence                                               011345788899997 69999999999999999999999873   


Q ss_pred             ccce-EEEecccHHHHHHHHHHhccc
Q 039806          216 SKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       216 skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                       +|| ||+|.+.++|.+|+..++...
T Consensus       313 -~g~afV~f~~~~~A~~Ai~~lng~~  337 (481)
T TIGR01649       313 -KETALIEMADPYQAQLALTHLNGVK  337 (481)
T ss_pred             -CCEEEEEECCHHHHHHHHHHhCCCE
Confidence             678 999999999999998888654

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=99.96  E-value=6.9e-29  Score=252.03  Aligned_cols=224  Identities=22%  Similarity=0.327  Sum_probs=172.6

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+|+.|. +|+++|||||+|.+.++|.+||. |||..|.|+.|.|..+.
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            46789999999999999999999999999999999998 89999999999999999999997 89999999999998765


Q ss_pred             cccccccc--------CCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCcccc----------------
Q 039806           92 RRADRIQE--------GSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGF----------------  146 (398)
Q Consensus        92 ~~~~~~~~--------~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf----------------  146 (398)
                      ....+...        ....++|||+||+.++|+++|+++|+.||.|.+|.+.+|.. |+++||                
T Consensus       167 ~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~  246 (457)
T TIGR01622       167 AEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALE  246 (457)
T ss_pred             hhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHH
Confidence            44332211        11358899999999999999999999999999999999986 688888                


Q ss_pred             -------CCchhhhHHHHHHHHH------------------------HHHHHHHH---H---------------------
Q 039806          147 -------GSKVLYVARAQKKAER------------------------KAILRAQF---E---------------------  171 (398)
Q Consensus       147 -------~~~~l~v~~a~~k~~~------------------------~~~~~~~~---~---------------------  171 (398)
                             .++.|.|.++.+....                        ...+....   .                     
T Consensus       247 ~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  326 (457)
T TIGR01622       247 VMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQ  326 (457)
T ss_pred             hcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccc
Confidence                   3445555553211000                        00000000   0                     


Q ss_pred             -------------------------------HhhhhhhccccCCCcccC----------HHHHHHHhhcCCCeEEEEEee
Q 039806          172 -------------------------------RMRKERAELYKNINDEVD----------EIELKQYFSQCGTISSVKIMR  210 (398)
Q Consensus       172 -------------------------------~~~~~~~~~v~nL~~~vt----------ee~L~~~F~~fG~I~svki~~  210 (398)
                                                     .....+++++.||-...+          .++|+++|++||.|++|.|..
T Consensus       327 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~  406 (457)
T TIGR01622       327 RDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDT  406 (457)
T ss_pred             ccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeC
Confidence                                           001223445566643333          378999999999999999973


Q ss_pred             CCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          211 TDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       211 d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                         ..+.|+ ||.|.+.++|.+|+..++..-
T Consensus       407 ---~~~~G~~fV~F~~~e~A~~A~~~lnGr~  434 (457)
T TIGR01622       407 ---KNSAGKIYLKFSSVDAALAAFQALNGRY  434 (457)
T ss_pred             ---CCCceeEEEEECCHHHHHHHHHHhcCcc
Confidence               345677 999999999999999888643

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.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.96  E-value=6.1e-29  Score=240.86  Aligned_cols=154  Identities=19%  Similarity=0.310  Sum_probs=127.5

Q ss_pred             ccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806            9 ARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus         9 ~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      ...+..++|||+|||.++|+++|+++|+.||.|.+|+|++|. ++++||||||+|.++++|++||+.||+..|.+++|+|
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            345567899999999999999999999999999999999998 9999999999999999999999999999999999999


Q ss_pred             ecccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHHHH
Q 039806           88 GPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILR  167 (398)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~~~  167 (398)
                      .++.+..+.    ...+                                                               
T Consensus       182 ~~a~p~~~~----~~~~---------------------------------------------------------------  194 (346)
T TIGR01659       182 SYARPGGES----IKDT---------------------------------------------------------------  194 (346)
T ss_pred             ecccccccc----cccc---------------------------------------------------------------
Confidence            886532110    0122                                                               


Q ss_pred             HHHHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          168 AQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       168 ~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                                +++|.|||.++||++|+++|++||.|++|+|++|. +|++||| ||+|+++++|.+|+.++...
T Consensus       195 ----------~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~  258 (346)
T TIGR01659       195 ----------NLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNV  258 (346)
T ss_pred             ----------eeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence                      35556666666666667777777777777777766 7888888 99999999999999987754

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).

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

Probab=99.96  E-value=3e-29  Score=242.47  Aligned_cols=223  Identities=24%  Similarity=0.370  Sum_probs=186.0

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRR   93 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~   93 (398)
                      .+|||++||++++.++|.++|+.+|.|..|.++++. ++.++|||||.|.-.||+++|+..+++..+.|+.|.|..+.++
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            799999999999999999999999999999999999 8899999999999999999999999999999999999998866


Q ss_pred             ccccc-c---------------------CCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCcccc-----
Q 039806           94 ADRIQ-E---------------------GSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF-----  146 (398)
Q Consensus        94 ~~~~~-~---------------------~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf-----  146 (398)
                      ...+. +                     +....+|.|.|||+.+.+++|..+|+.||.|.+++|.+..+|+-.||     
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~f  165 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQF  165 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEE
Confidence            53320 0                     01256799999999999999999999999999999999989888899     


Q ss_pred             ------------------CCchhhhHHHHHHHHHHH--------HH--------HH------------------------
Q 039806          147 ------------------GSKVLYVARAQKKAERKA--------IL--------RA------------------------  168 (398)
Q Consensus       147 ------------------~~~~l~v~~a~~k~~~~~--------~~--------~~------------------------  168 (398)
                                        +|+.+.|.||..+..-+.        ..        ..                        
T Consensus       166 k~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~  245 (678)
T KOG0127|consen  166 KEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEET  245 (678)
T ss_pred             eeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccc
Confidence                              456666666543321100        00        00                        


Q ss_pred             ------------------HH---------------------HHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEe
Q 039806          169 ------------------QF---------------------ERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIM  209 (398)
Q Consensus       169 ------------------~~---------------------~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~  209 (398)
                                        ..                     +....+.++||+||++++||++|.++|++||.|.++.|+
T Consensus       246 D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV  325 (678)
T KOG0127|consen  246 DGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIV  325 (678)
T ss_pred             cccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEE
Confidence                              00                     000012467889999999999999999999999999999


Q ss_pred             eCC-CCCccce-EEEecccHHHHHHHHHHh
Q 039806          210 RTD-RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       210 ~d~-~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      .++ +|.++|. ||.|.+..++..++..+.
T Consensus       326 ~~k~T~~skGtAFv~Fkt~~~~~~ci~~As  355 (678)
T KOG0127|consen  326 KDKDTGHSKGTAFVKFKTQIAAQNCIEAAS  355 (678)
T ss_pred             eccCCCCcccceEEEeccHHHHHHHHHhcC
Confidence            998 9999999 999999999999998763

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

Probab=99.96  E-value=6.6e-29  Score=252.89  Aligned_cols=223  Identities=18%  Similarity=0.212  Sum_probs=169.4

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecc--eEeeeecc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVER--MELYVGPF   90 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g--k~i~V~~~   90 (398)
                      ...+|||+||+.++|+++|+++|+.||.|++|+|.++.   .+|+|||+|++.++|.+|++.|||..|.+  ..|+|.++
T Consensus        95 ~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~---~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~s  171 (481)
T TIGR01649        95 KVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN---NVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYA  171 (481)
T ss_pred             ceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC---CceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEe
Confidence            34589999999999999999999999999999998865   34799999999999999999999999965  46777665


Q ss_pred             cccc--------------------ccc----------cc-----------------------------------------
Q 039806           91 IRRA--------------------DRI----------QE-----------------------------------------   99 (398)
Q Consensus        91 ~~~~--------------------~~~----------~~-----------------------------------------   99 (398)
                      ....                    ++.          ..                                         
T Consensus       172 k~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  251 (481)
T TIGR01649       172 KPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRY  251 (481)
T ss_pred             cCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCcccccccCCCcccCCCCC
Confidence            5211                    000          00                                         


Q ss_pred             --------------------CCCCceEEeeCCCc-cccHHHHHHHHccCCCEEEEEEeeCCCCCcccc------------
Q 039806          100 --------------------GSSFNNLYVKNLDD-DMTEEILVEKFSEFGKITSLVISKDANGTSKGF------------  146 (398)
Q Consensus       100 --------------------~~~~~~lfV~nLp~-~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf------------  146 (398)
                                          ....++|||+||++ .+|+++|+++|+.||.|.+|+++++..  ..||            
T Consensus       252 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~--g~afV~f~~~~~A~~A  329 (481)
T TIGR01649       252 RPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKK--ETALIEMADPYQAQLA  329 (481)
T ss_pred             cccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC--CEEEEEECCHHHHHHH
Confidence                                01346899999998 699999999999999999999998742  2233            


Q ss_pred             ---------CCchhhhHHHHHHHHHHHH-------HH--HHHHH-----------------hhhhhhccccCCCcccCHH
Q 039806          147 ---------GSKVLYVARAQKKAERKAI-------LR--AQFER-----------------MRKERAELYKNINDEVDEI  191 (398)
Q Consensus       147 ---------~~~~l~v~~a~~k~~~~~~-------~~--~~~~~-----------------~~~~~~~~v~nL~~~vtee  191 (398)
                               .|+.|+|.++.........       ..  ..+..                 ....++++|+|||.++|++
T Consensus       330 i~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee  409 (481)
T TIGR01649       330 LTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEE  409 (481)
T ss_pred             HHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHH
Confidence                     4666666654332110000       00  00000                 1134578899999999999


Q ss_pred             HHHHHhhcCCC--eEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          192 ELKQYFSQCGT--ISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       192 ~L~~~F~~fG~--I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      +|+++|+.||.  |++|+++.+.++ ++|| ||+|.+.++|.+|+..++....
T Consensus       410 ~L~~lF~~~G~~~i~~ik~~~~~~~-~~~~gfVeF~~~e~A~~Al~~ln~~~l  461 (481)
T TIGR01649       410 DLKELFAENGVHKVKKFKFFPKDNE-RSKMGLLEWESVEDAVEALIALNHHQL  461 (481)
T ss_pred             HHHHHHHhcCCccceEEEEecCCCC-cceeEEEEcCCHHHHHHHHHHhcCCcc
Confidence            99999999998  899999865544 4677 9999999999999999987654

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).

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

Probab=99.96  E-value=7e-29  Score=241.72  Aligned_cols=209  Identities=28%  Similarity=0.433  Sum_probs=182.4

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRA   94 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~~   94 (398)
                      ..|||+   +++|+..|+++|+.+|.|++++|.+|. + |-|||||.|.++++|++||+++|...+.|++|+|-|+.+..
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            468999   999999999999999999999999999 6 99999999999999999999999999999999999987543


Q ss_pred             cccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCcccc----------------------CCchhh
Q 039806           95 DRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF----------------------GSKVLY  152 (398)
Q Consensus        95 ~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf----------------------~~~~l~  152 (398)
                               +-+||+||++++|..+|.++|+.||+|.||++..|.+| ++||                      .++.++
T Consensus        77 ---------~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~FV~f~~e~~a~~ai~~~ng~ll~~kki~  146 (369)
T KOG0123|consen   77 ---------SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGYFVQFESEESAKKAIEKLNGMLLNGKKIY  146 (369)
T ss_pred             ---------ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceeeEEEeCCHHHHHHHHHHhcCcccCCCeeE
Confidence                     22999999999999999999999999999999999998 8887                      455566


Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHH
Q 039806          153 VARAQKKAERKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERT  231 (398)
Q Consensus       153 v~~a~~k~~~~~~~~~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~  231 (398)
                      |+....+.++.+....   ........+++|+..+++++.|.++|+.||.|+++.|+++..|+++|| ||.|++.++|.+
T Consensus       147 vg~~~~~~er~~~~~~---~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~  223 (369)
T KOG0123|consen  147 VGLFERKEEREAPLGE---YKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKK  223 (369)
T ss_pred             Eeeccchhhhcccccc---hhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHH
Confidence            6666655555433322   223334566799999999999999999999999999999999999999 999999999999


Q ss_pred             HHHHHhcccc
Q 039806          232 SYLRIMYAKQ  241 (398)
Q Consensus       232 A~l~~q~~q~  241 (398)
                      |...+.....
T Consensus       224 av~~l~~~~~  233 (369)
T KOG0123|consen  224 AVETLNGKIF  233 (369)
T ss_pred             HHHhccCCcC
Confidence            9988876543

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

Probab=99.96  E-value=5.9e-29  Score=234.57  Aligned_cols=133  Identities=29%  Similarity=0.430  Sum_probs=122.0

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCC-eecc--eEee
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGA-TVER--MELY   86 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~-~l~g--k~i~   86 (398)
                      ..+.-++||+-+|+.++|+||+++|++||.|.+|.|++|+ ++.++|||||.|.+.++|.+|+.+|++. .|-|  ..|.
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvq  110 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQ  110 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCccee
Confidence            3566789999999999999999999999999999999999 9999999999999999999999999876 4544  7899


Q ss_pred             eecccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCcccc
Q 039806           87 VGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF  146 (398)
Q Consensus        87 V~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf  146 (398)
                      |++++...+|..   ..++|||+-|++.+||.|++++|++||.|++|.|++|.++.|||+
T Consensus       111 vk~Ad~E~er~~---~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGc  167 (510)
T KOG0144|consen  111 VKYADGERERIV---EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGC  167 (510)
T ss_pred             ecccchhhhccc---cchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccce
Confidence            999887766642   357899999999999999999999999999999999999999999

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

Probab=99.96  E-value=3.3e-28  Score=217.28  Aligned_cols=192  Identities=21%  Similarity=0.369  Sum_probs=152.4

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      .+-++|||+||+.+|||+-|..+|+..|.|.+|||+.|                                  +|+|.++.
T Consensus         4 ~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~----------------------------------e~~v~wa~   49 (321)
T KOG0148|consen    4 DEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD----------------------------------ELKVNWAT   49 (321)
T ss_pred             CCCceEEeeccChhhHHHHHHHHHHhccccccceeehh----------------------------------hhcccccc
Confidence            34579999999999999999999999999999999876                                  34454544


Q ss_pred             ccccccccCC-CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCcccc-----------------------
Q 039806           92 RRADRIQEGS-SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGF-----------------------  146 (398)
Q Consensus        92 ~~~~~~~~~~-~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf-----------------------  146 (398)
                      .......... ..-.+||+.|..+++.|+|++.|.+||+|.+++|++|.. ++||||                       
T Consensus        50 ~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWl  129 (321)
T KOG0148|consen   50 APGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWL  129 (321)
T ss_pred             CcccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeee
Confidence            3322222221 356799999999999999999999999999999999986 999999                       


Q ss_pred             CCchhhhHHHHHHHHHHHHHHH----HHHHhhhhh-hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-E
Q 039806          147 GSKVLYVARAQKKAERKAILRA----QFERMRKER-AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-C  220 (398)
Q Consensus       147 ~~~~l~v~~a~~k~~~~~~~~~----~~~~~~~~~-~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-f  220 (398)
                      +++.|...||.+|..+......    -+.+....+ +++++||...++|++||+.|++||.|.+|+|++|     +|| |
T Consensus       130 G~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-----qGYaF  204 (321)
T KOG0148|consen  130 GRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-----QGYAF  204 (321)
T ss_pred             ccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-----cceEE
Confidence            4556666666666533222222    233344444 4555999999999999999999999999999966     899 9


Q ss_pred             EEecccHHHHHHHHHHhccccC
Q 039806          221 MAIAQTKRERTSYLRIMYAKQG  242 (398)
Q Consensus       221 V~f~~~~ea~~A~l~~q~~q~~  242 (398)
                      |.|.++|.|.+|+.++......
T Consensus       205 VrF~tkEaAahAIv~mNntei~  226 (321)
T KOG0148|consen  205 VRFETKEAAAHAIVQMNNTEIG  226 (321)
T ss_pred             EEecchhhHHHHHHHhcCceeC
Confidence            9999999999999998876543

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

Probab=99.95  E-value=3.5e-27  Score=240.17  Aligned_cols=135  Identities=25%  Similarity=0.479  Sum_probs=120.2

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      +..++|||+||+.++|+++|+++|+.||.|.+|+|+.|+ +|++||||||+|++.++|++||+.|||..|+|+.|+|.+.
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            356799999999999999999999999999999999998 9999999999999999999999999999999999999865


Q ss_pred             cccccc-------cccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCcccc
Q 039806           91 IRRADR-------IQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGF  146 (398)
Q Consensus        91 ~~~~~~-------~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf  146 (398)
                      ......       ..+....++|||+||+.++++++|+++|+.||.|++++|.+|.. ++++||
T Consensus       185 ~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGf  248 (612)
T TIGR01645       185 SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGY  248 (612)
T ss_pred             ccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCe
Confidence            432211       11112568999999999999999999999999999999999986 788888

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

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

Probab=99.95  E-value=5.9e-28  Score=248.43  Aligned_cols=224  Identities=19%  Similarity=0.228  Sum_probs=161.3

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhcc------------CCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCe
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKF------------GDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGAT   79 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~------------G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~   79 (398)
                      ...++|||+|||.++|+++|.++|+.+            +.|.+|.+     +.++|||||+|.+.|+|..||+ |||..
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~-----~~~kg~afVeF~~~e~A~~Al~-l~g~~  246 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI-----NKEKNFAFLEFRTVEEATFAMA-LDSII  246 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE-----CCCCCEEEEEeCCHHHHhhhhc-CCCeE
Confidence            346789999999999999999999975            23444444     3468999999999999999995 99999


Q ss_pred             ecceEeeeeccccccccc-----------------c--------cCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEE
Q 039806           80 VERMELYVGPFIRRADRI-----------------Q--------EGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLV  134 (398)
Q Consensus        80 l~gk~i~V~~~~~~~~~~-----------------~--------~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~  134 (398)
                      |.|+.|+|..........                 .        .....++|||+|||..+|+++|+++|+.||.|..+.
T Consensus       247 ~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~  326 (509)
T TIGR01642       247 YSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFN  326 (509)
T ss_pred             eeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE
Confidence            999999997543221000                 0        011357899999999999999999999999999999


Q ss_pred             EeeCCC-CCccccCCch-----------------------hhhHHHHHHHHH-----HH------HHHHHHH------Hh
Q 039806          135 ISKDAN-GTSKGFGSKV-----------------------LYVARAQKKAER-----KA------ILRAQFE------RM  173 (398)
Q Consensus       135 i~~d~~-g~s~Gf~~~~-----------------------l~v~~a~~k~~~-----~~------~~~~~~~------~~  173 (398)
                      +++|.. |.++||+...                       |.|.++......     ..      .......      ..
T Consensus       327 ~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  406 (509)
T TIGR01642       327 LIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGG  406 (509)
T ss_pred             EEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhccccC
Confidence            999874 8899984322                       333222110000     00      0000000      01


Q ss_pred             hhhhhccccCCCcc----------cCHHHHHHHhhcCCCeEEEEEeeCC----CCCccce-EEEecccHHHHHHHHHHhc
Q 039806          174 RKERAELYKNINDE----------VDEIELKQYFSQCGTISSVKIMRTD----RGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       174 ~~~~~~~v~nL~~~----------vtee~L~~~F~~fG~I~svki~~d~----~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ...+++++.||...          ...++|+++|++||.|++|+|+++.    ++..+|| ||.|++.++|.+|+.+++.
T Consensus       407 ~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnG  486 (509)
T TIGR01642       407 KPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNG  486 (509)
T ss_pred             CCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCC
Confidence            12345666777532          1236899999999999999999763    3556787 9999999999999999886


Q ss_pred             ccc
Q 039806          239 AKQ  241 (398)
Q Consensus       239 ~q~  241 (398)
                      ...
T Consensus       487 r~~  489 (509)
T TIGR01642       487 RKF  489 (509)
T ss_pred             CEE
Confidence            553

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

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

Probab=99.91  E-value=2.9e-24  Score=192.09  Aligned_cols=136  Identities=31%  Similarity=0.543  Sum_probs=121.3

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ..-|||+.|...|+.++|++.|..||+|.++||++|. +++|||||||.|.+.++|++||..+||..|.+|.|+-.|+.+
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            4469999999999999999999999999999999999 999999999999999999999999999999999999999998


Q ss_pred             ccccccc------------CCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhH
Q 039806           93 RADRIQE------------GSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVA  154 (398)
Q Consensus        93 ~~~~~~~------------~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~  154 (398)
                      |..+...            ....++|||+|++..+||++|++.|+.||.|.+|+|.+|+     ||.+..+...
T Consensus       142 Kp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q-----GYaFVrF~tk  210 (321)
T KOG0148|consen  142 KPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ-----GYAFVRFETK  210 (321)
T ss_pred             CccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc-----ceEEEEecch
Confidence            8754221            1267889999999999999999999999999999999884     6654333333

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

Probab=99.91  E-value=1.2e-23  Score=194.94  Aligned_cols=133  Identities=26%  Similarity=0.495  Sum_probs=119.4

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      .|+|||+.+.+++.|+.|+..|..||.|.+|.+..|+ ++++||||||+|+-+|.|+-|++.+||..++||.|+|+....
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            4789999999999999999999999999999999999 999999999999999999999999999999999999985432


Q ss_pred             cccc-------cccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCcccc
Q 039806           93 RADR-------IQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGF  146 (398)
Q Consensus        93 ~~~~-------~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf  146 (398)
                      -..-       ..+..++++|||..+..+.+|+||+.+|+.||+|.+|.+-++.+ +..|||
T Consensus       193 mpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGy  254 (544)
T KOG0124|consen  193 MPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGY  254 (544)
T ss_pred             CcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccce
Confidence            1110       11223789999999999999999999999999999999999997 667887

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

Probab=99.88  E-value=6.5e-22  Score=191.85  Aligned_cols=223  Identities=22%  Similarity=0.360  Sum_probs=165.3

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRR   93 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~   93 (398)
                      .-+|.|+|||+++.+.+|..+|+.||.|.+|.|++..+|+-.|||||+|.+..+|..||+.+|+..|.|++|-|.|+..+
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            45899999999999999999999999999999998889988899999999999999999999999999999999998743


Q ss_pred             ccc-------------------------------------------c--c---------------------cC-C-----
Q 039806           94 ADR-------------------------------------------I--Q---------------------EG-S-----  101 (398)
Q Consensus        94 ~~~-------------------------------------------~--~---------------------~~-~-----  101 (398)
                      ..-                                           +  .                     .. +     
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            300                                           0  0                     00 0     


Q ss_pred             --------------CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCcccc--------------------
Q 039806          102 --------------SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGF--------------------  146 (398)
Q Consensus       102 --------------~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf--------------------  146 (398)
                                    -..+|||.|||+++||++|.+.|++||.|..+.|+.+++ +.++|.                    
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                          014599999999999999999999999999999999986 888876                    


Q ss_pred             ---------CCchhhhHHHHHHHHHHHH-HH--------------------------------------HHH----HHhh
Q 039806          147 ---------GSKVLYVARAQKKAERKAI-LR--------------------------------------AQF----ERMR  174 (398)
Q Consensus       147 ---------~~~~l~v~~a~~k~~~~~~-~~--------------------------------------~~~----~~~~  174 (398)
                               .|+.|.|..|..+.+.... .+                                      ..+    ....
T Consensus       357 a~e~g~~ll~GR~Lkv~~Av~RkeA~dmeqkk~~Kk~~gkrNLyLa~EG~I~~gt~aAeglS~~Dm~kRer~~~~k~k~l  436 (678)
T KOG0127|consen  357 ASEDGSVLLDGRLLKVTLAVTRKEAADMEQKKKRKKPKGKRNLYLAREGLIRDGTPAAEGLSATDMAKRERIAERKRKKL  436 (678)
T ss_pred             cCCCceEEEeccEEeeeeccchHHHHHHHHHhhhhccCCccceeeeccCccccCChhhcccchhhHHHHHHHHHHHHHhh
Confidence                     2333444333222211111 00                                      000    0000


Q ss_pred             h-------hhhccccCCCcccCHHHHHHHhhc----C-CCe-EEEEEeeCC----CCCccce-EEEecccHHHHHHHHHH
Q 039806          175 K-------ERAELYKNINDEVDEIELKQYFSQ----C-GTI-SSVKIMRTD----RGISKGH-CMAIAQTKRERTSYLRI  236 (398)
Q Consensus       175 ~-------~~~~~v~nL~~~vtee~L~~~F~~----f-G~I-~svki~~d~----~g~skGf-fV~f~~~~ea~~A~l~~  236 (398)
                      .       -+.+.|.|||..+++..|..+.-.    | +.+ ..|+.+++.    .+.+.|| |+.|...+.|.+|..-.
T Consensus       437 knpnlhlSrtRL~i~Nlpramn~KqL~~Ll~~Av~~~at~~kk~~R~~~~le~~~k~~s~g~aF~~f~EhEhalkalk~~  516 (678)
T KOG0127|consen  437 KNPNLHLSRTRLVIRNLPRAMNPKQLNRLLRDAVTGFATKVKKCIRQIKFLEEEKKNYSEGYAFVGFTEHEHALKALKVL  516 (678)
T ss_pred             cCCceeeehhhhhhhcCccccCHHHHHHHHHHHHhhhhhhcchhhhhhhhHHhhhhcccccccccCccHHHHHHHhhhcc
Confidence            0       123556999999999999888743    3 333 335666654    4556777 99999999988886544

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.88  E-value=2.4e-22  Score=197.26  Aligned_cols=138  Identities=28%  Similarity=0.439  Sum_probs=117.7

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecc--eEeeeec
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVER--MELYVGP   89 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g--k~i~V~~   89 (398)
                      ..++|||+|||.++++++|+++|+.||.|..+++..+. ++.++|||||+|++.++|++||+.|||..+.|  .+|.|.+
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~  167 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKF  167 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            45689999999999999999999999999999999998 88999999999999999999999999998877  6788877


Q ss_pred             ccccccccc---------------c-------------------------------------------------------
Q 039806           90 FIRRADRIQ---------------E-------------------------------------------------------   99 (398)
Q Consensus        90 ~~~~~~~~~---------------~-------------------------------------------------------   99 (398)
                      +........               .                                                       
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            653321000               0                                                       


Q ss_pred             ------------------CCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCC-CCCccccCCch
Q 039806          100 ------------------GSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-NGTSKGFGSKV  150 (398)
Q Consensus       100 ------------------~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~-~g~s~Gf~~~~  150 (398)
                                        .....+|||+|||+++++++|+++|++||.|++++|++|. ++.++||+...
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~  317 (352)
T TIGR01661       248 ATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVS  317 (352)
T ss_pred             cccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEE
Confidence                              0012269999999999999999999999999999999998 59999997443

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

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

Probab=99.87  E-value=2.9e-22  Score=169.83  Aligned_cols=136  Identities=28%  Similarity=0.421  Sum_probs=121.4

Q ss_pred             ccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806            9 ARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus         9 ~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      ...+...+|||+||+..++++-|+++|-+.|+|+++++.+|. +...+|||||+|.++|+|+-||+-||...|.||+|+|
T Consensus         4 ~~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv   83 (203)
T KOG0131|consen    4 IERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRV   83 (203)
T ss_pred             cccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEE
Confidence            345567899999999999999999999999999999999999 8899999999999999999999999999999999999


Q ss_pred             ecccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEE-EEEeeCCC-CCccccC
Q 039806           88 GPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITS-LVISKDAN-GTSKGFG  147 (398)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~-~~i~~d~~-g~s~Gf~  147 (398)
                      ..+....   .......++||+||.++++|.-|.+.|+.||.+.+ -.+++|.+ |.++||+
T Consensus        84 ~kas~~~---~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g  142 (203)
T KOG0131|consen   84 NKASAHQ---KNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFG  142 (203)
T ss_pred             Eeccccc---ccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCe
Confidence            9887221   12225689999999999999999999999999876 47889987 8888885

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

Probab=99.84  E-value=3.4e-21  Score=196.28  Aligned_cols=187  Identities=21%  Similarity=0.236  Sum_probs=140.0

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCC-eeEEEEEEcC--CCCceeEEEEEecCHHHHHHHHHHhcC--CeecceEeee
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGD-IQSSKVVVSQ--EGKSKGYGFVQYSTPESALDAIEKLQG--ATVERMELYV   87 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~-I~~vki~~d~--~g~skg~aFV~F~~~e~A~~Ai~~lng--~~l~gk~i~V   87 (398)
                      +.++|||+|||.++|+++|++.|++++. ++++.+....  .++++|||||+|++.++|..|+++|+.  ..++|+.|.|
T Consensus       137 ~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~V  216 (578)
T TIGR01648       137 DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAV  216 (578)
T ss_pred             cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEE
Confidence            4679999999999999999999999874 5555544332  578899999999999999999998864  4688999999


Q ss_pred             ecccccccccccC-CCCceEEeeCCCccccHHHHHHHHccC--CCEEEEEEeeCCCCCcccc------------------
Q 039806           88 GPFIRRADRIQEG-SSFNNLYVKNLDDDMTEEILVEKFSEF--GKITSLVISKDANGTSKGF------------------  146 (398)
Q Consensus        88 ~~~~~~~~~~~~~-~~~~~lfV~nLp~~~tee~L~~~F~~f--G~I~~~~i~~d~~g~s~Gf------------------  146 (398)
                      .++.++.+...+. ...++|||+||++++|+++|+++|+.|  |+|++|.++++     .+|                  
T Consensus       217 dwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~rg-----fAFVeF~s~e~A~kAi~~lnG  291 (578)
T TIGR01648       217 DWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD-----YAFVHFEDREDAVKAMDELNG  291 (578)
T ss_pred             EeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeecC-----eEEEEeCCHHHHHHHHHHhCC
Confidence            9988765443222 256789999999999999999999999  99999987754     233                  


Q ss_pred             ---CCchhhhHHHHHHHHHHHH--------------HHH-HH--HHhhhhhhccccCCCcccCHHHHHHHhhcCCCeE
Q 039806          147 ---GSKVLYVARAQKKAERKAI--------------LRA-QF--ERMRKERAELYKNINDEVDEIELKQYFSQCGTIS  204 (398)
Q Consensus       147 ---~~~~l~v~~a~~k~~~~~~--------------~~~-~~--~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~  204 (398)
                         +++.|.|.++..+....-.              .+. .+  .......++.+.|+++..+++.+.++|..+|.|.
T Consensus       292 ~~i~Gr~I~V~~Akp~~~~~~~~~~rg~gg~~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~~~~~~~~~f~~~g~~~  369 (578)
T TIGR01648       292 KELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAPSLHFPRMPGPIR  369 (578)
T ss_pred             CEECCEEEEEEEccCCCcccccccccccCCCcccccccccccCcccCccccccccccccccccccchhhccccCcccc
Confidence               4555666655432211000              000 00  0011345678899999999999999999999854

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.

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

Probab=99.81  E-value=3.9e-20  Score=165.31  Aligned_cols=236  Identities=21%  Similarity=0.240  Sum_probs=154.6

Q ss_pred             CCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCC-eecc-
Q 039806            5 PNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA-TVER-   82 (398)
Q Consensus         5 rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~-~l~g-   82 (398)
                      -|++.|..+.++|||+-|.+.-.|||++.+|..||.|.+|.+.+..+|.|||+|||.|.+.-+|+.||..|+|. .+-| 
T Consensus        10 adsesrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGA   89 (371)
T KOG0146|consen   10 ADSESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGA   89 (371)
T ss_pred             cccccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCC
Confidence            36667777889999999999999999999999999999999999999999999999999999999999999997 3333 


Q ss_pred             -eEeeeecccccccccccCC----------CCceEEe-----------------------eCCCccccHH----HHHHHH
Q 039806           83 -MELYVGPFIRRADRIQEGS----------SFNNLYV-----------------------KNLDDDMTEE----ILVEKF  124 (398)
Q Consensus        83 -k~i~V~~~~~~~~~~~~~~----------~~~~lfV-----------------------~nLp~~~tee----~L~~~F  124 (398)
                       ..+.|++++..+||....-          +.-.+-+                       .-|...++..    +....+
T Consensus        90 SSSLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~  169 (371)
T KOG0146|consen   90 SSSLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAAL  169 (371)
T ss_pred             ccceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHH
Confidence             6788999887777632110          0000101                       1122222211    111223


Q ss_pred             ccCCCEEEEEEeeCCC----C-------------Ccccc-------CC----chhhhH-------------------HHH
Q 039806          125 SEFGKITSLVISKDAN----G-------------TSKGF-------GS----KVLYVA-------------------RAQ  157 (398)
Q Consensus       125 ~~fG~I~~~~i~~d~~----g-------------~s~Gf-------~~----~~l~v~-------------------~a~  157 (398)
                      +--|-+..-++.....    +             .-.||       ++    ..+|-+                   .+.
T Consensus       170 ~angl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g  249 (371)
T KOG0146|consen  170 NANGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAG  249 (371)
T ss_pred             hhcccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhh
Confidence            3222221111110000    0             01222       00    001000                   000


Q ss_pred             HHHHH------HHHHH----------HHHHHhh-hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce
Q 039806          158 KKAER------KAILR----------AQFERMR-KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH  219 (398)
Q Consensus       158 ~k~~~------~~~~~----------~~~~~~~-~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf  219 (398)
                      .....      ...+.          ....++. ..+.++|..||.+..|.+|...|-+||.|+|.||+.|. ++.||+|
T Consensus       250 ~~~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCF  329 (371)
T KOG0146|consen  250 VQQYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCF  329 (371)
T ss_pred             HHHHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccce
Confidence            00000      00000          0111222 24567889999999999999999999999999999999 9999999


Q ss_pred             -EEEecccHHHHHHHHHHhccc
Q 039806          220 -CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       220 -fV~f~~~~ea~~A~l~~q~~q  240 (398)
                       ||.|++...+..|+.++..-|
T Consensus       330 GFVSfDNp~SaQaAIqAMNGFQ  351 (371)
T KOG0146|consen  330 GFVSFDNPASAQAAIQAMNGFQ  351 (371)
T ss_pred             eeEecCCchhHHHHHHHhcchh
Confidence             999999999999998876554

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

Probab=99.80  E-value=1.6e-19  Score=160.85  Aligned_cols=145  Identities=29%  Similarity=0.428  Sum_probs=122.1

Q ss_pred             ccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecc--e
Q 039806            7 SEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVER--M   83 (398)
Q Consensus         7 ~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g--k   83 (398)
                      |+...-...+|||.+||+..|.+||+++|+.||.|...+|+.|. +|.|||.|||.|+..++|+.||+.|||..-.|  .
T Consensus       120 PSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~te  199 (360)
T KOG0145|consen  120 PSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTE  199 (360)
T ss_pred             CChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCC
Confidence            44444456799999999999999999999999999999999999 99999999999999999999999999987765  5


Q ss_pred             Eeeeeccccccccc--------------------------c---------------------------------cCCCCc
Q 039806           84 ELYVGPFIRRADRI--------------------------Q---------------------------------EGSSFN  104 (398)
Q Consensus        84 ~i~V~~~~~~~~~~--------------------------~---------------------------------~~~~~~  104 (398)
                      +|.|+.+...+...                          .                                 ......
T Consensus       200 pItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~  279 (360)
T KOG0145|consen  200 PITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGW  279 (360)
T ss_pred             CeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCee
Confidence            68886665221100                          0                                 000236


Q ss_pred             eEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCccccCCchh
Q 039806          105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVL  151 (398)
Q Consensus       105 ~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf~~~~l  151 (398)
                      +|||.||..+++|.-|..+|.+||.|++++|++|-+ .++|||++..+
T Consensus       280 ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtM  327 (360)
T KOG0145|consen  280 CIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTM  327 (360)
T ss_pred             EEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEe
Confidence            799999999999999999999999999999999987 99999976554

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

Probab=99.80  E-value=9.8e-20  Score=172.48  Aligned_cols=146  Identities=23%  Similarity=0.321  Sum_probs=121.3

Q ss_pred             CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCccccCCchhhhHHHHHHHHHHHHHHH------------
Q 039806          102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAERKAILRA------------  168 (398)
Q Consensus       102 ~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf~~~~l~v~~a~~k~~~~~~~~~------------  168 (398)
                      +.-++||+.+|..++|.||+++|++||.|.+|.|++|+. +.++|+.+.+.+...+..+....--...            
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk  112 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVK  112 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeec
Confidence            567899999999999999999999999999999999995 9999997666665554444332111000            


Q ss_pred             --HHHHhh--hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccccCC
Q 039806          169 --QFERMR--KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQGP  243 (398)
Q Consensus       169 --~~~~~~--~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~~~  243 (398)
                        ..++++  .+++++|+-|+..+||.+++++|++||.|++|.|++|+.|.|||| ||.|.+++-|..|+..++..+.+.
T Consensus       113 ~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tme  192 (510)
T KOG0144|consen  113 YADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTME  192 (510)
T ss_pred             ccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeec
Confidence              112222  378899999999999999999999999999999999999999999 999999999999999999998877


Q ss_pred             CCCC
Q 039806          244 GLAS  247 (398)
Q Consensus       244 ~~~~  247 (398)
                      +.-.
T Consensus       193 Gcs~  196 (510)
T KOG0144|consen  193 GCSQ  196 (510)
T ss_pred             cCCC
Confidence            6633

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

Probab=99.79  E-value=1.4e-19  Score=163.64  Aligned_cols=112  Identities=27%  Similarity=0.447  Sum_probs=104.7

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRA   94 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~~   94 (398)
                      .+|||+|||..+++.+|+.+|++||+|++|.|+++       ||||+.++...|+.||.+|||-.|+|..|.|+.++.|+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN-------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN-------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc-------cceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            46999999999999999999999999999999764       99999999999999999999999999999999988763


Q ss_pred             cccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCC
Q 039806           95 DRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA  139 (398)
Q Consensus        95 ~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~  139 (398)
                      .      ..++|+|+||.+.++.+||+..|.+||.|.+|.|.+|-
T Consensus        76 k------~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkdy  114 (346)
T KOG0109|consen   76 K------ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKDY  114 (346)
T ss_pred             C------CccccccCCCCccccCHHHhhhhcccCCceeeeeecce
Confidence            2      47899999999999999999999999999999999874

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

Probab=99.78  E-value=2.7e-19  Score=182.77  Aligned_cols=139  Identities=20%  Similarity=0.301  Sum_probs=109.4

Q ss_pred             CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCccccCCchhhhHHHHHHHHHH-----------------
Q 039806          102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAERK-----------------  163 (398)
Q Consensus       102 ~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf~~~~l~v~~a~~k~~~~-----------------  163 (398)
                      ..++|||+||++++++++|+++|+.||.|.+|++++|.. |+++||++..+....+..++...                 
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            568899999999999999999999999999999999974 99999954443333332222110                 


Q ss_pred             ------HHHHHHHHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHH
Q 039806          164 ------AILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       164 ------~~~~~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                            .............++++|+||+.++++++|+++|+.||.|++|+|.+|. +|++||| ||+|.+.++|.+|+..
T Consensus       186 ~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~a  265 (612)
T TIGR01645       186 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  265 (612)
T ss_pred             cccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHH
Confidence                  0000000111234578899999999999999999999999999999997 7889999 9999999999999998


Q ss_pred             Hhccc
Q 039806          236 IMYAK  240 (398)
Q Consensus       236 ~q~~q  240 (398)
                      +....
T Consensus       266 mNg~e  270 (612)
T TIGR01645       266 MNLFD  270 (612)
T ss_pred             hCCCe
Confidence            87553

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.

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

Probab=99.78  E-value=3.6e-19  Score=168.13  Aligned_cols=134  Identities=28%  Similarity=0.532  Sum_probs=122.6

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      +.++|||++|+.++|+|.|++.|+.||.|.+|+|++|+ +++++||+||+|++.+...+++.. ..+.|+|+.|.+..+.
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            67899999999999999999999999999999999999 999999999999999999999973 5778999999999999


Q ss_pred             ccccccccCC--CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCccccC
Q 039806           92 RRADRIQEGS--SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG  147 (398)
Q Consensus        92 ~~~~~~~~~~--~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf~  147 (398)
                      ++.+......  ...+|||+.|+.++++++++++|++||.|..+.++.|.+ .+++||+
T Consensus        84 ~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFg  142 (311)
T KOG4205|consen   84 SREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFG  142 (311)
T ss_pred             CcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccce
Confidence            8876644332  467899999999999999999999999999999999986 8899994

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

Probab=99.77  E-value=4.3e-18  Score=175.30  Aligned_cols=127  Identities=23%  Similarity=0.382  Sum_probs=106.6

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...+|||+|||.++|+++|+++|+.||.|..|+|+.+. +|.++|||||+|.+.++|..||+.|||..|.|+.|.|.++.
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            45789999999999999999999999999999999998 99999999999999999999999999999999999998875


Q ss_pred             ccccccc------------------------cCCCCceEEeeCCCcc----------ccHHHHHHHHccCCCEEEEEEee
Q 039806           92 RRADRIQ------------------------EGSSFNNLYVKNLDDD----------MTEEILVEKFSEFGKITSLVISK  137 (398)
Q Consensus        92 ~~~~~~~------------------------~~~~~~~lfV~nLp~~----------~tee~L~~~F~~fG~I~~~~i~~  137 (398)
                      .......                        .......|+|.|+...          ...++|+++|++||.|++|+|.+
T Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~  453 (509)
T TIGR01642       374 VGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPR  453 (509)
T ss_pred             cCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeec
Confidence            3221100                        0013466889998532          12468999999999999999998


Q ss_pred             CC
Q 039806          138 DA  139 (398)
Q Consensus       138 d~  139 (398)
                      +.
T Consensus       454 ~~  455 (509)
T TIGR01642       454 PN  455 (509)
T ss_pred             cC
Confidence            63

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

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

Probab=99.77  E-value=2.9e-18  Score=162.57  Aligned_cols=225  Identities=17%  Similarity=0.154  Sum_probs=176.3

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhc-cCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSK-FGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~-~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      .+.+||.|||+++...||+++|.. -|.|..|.++.|.+|++||+|.|+|+++|.+++|+++||...+.|++|.|+....
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            345999999999999999999965 8999999999999999999999999999999999999999999999999976432


Q ss_pred             ccccccc--CCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHHHHHHH
Q 039806           93 RADRIQE--GSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQF  170 (398)
Q Consensus        93 ~~~~~~~--~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~~~~~~  170 (398)
                      .......  -..-.+.|+.++...+-...|...|+--|.+....+.+|.+..|++-+..++.-.........---+...+
T Consensus       124 ~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~F  203 (608)
T KOG4212|consen  124 EQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASF  203 (608)
T ss_pred             hhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhh
Confidence            1111100  01456799999999999999999999889888888899999888876433322111111111000011111


Q ss_pred             HH------hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          171 ER------MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       171 ~~------~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      .+      .......++.||+..+..+.|++.|.--|.|++|.+-.|+.|.++|| -++|...-+|-.|+..+.-
T Consensus       204 lr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~  278 (608)
T KOG4212|consen  204 LRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDR  278 (608)
T ss_pred             hhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhcc
Confidence            11      12234567899999999999999999999999999999999999999 7789999999999887664

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

Probab=99.76  E-value=8.1e-19  Score=175.62  Aligned_cols=223  Identities=23%  Similarity=0.329  Sum_probs=165.1

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ...-|+|+|||..+..++|.+.|..||.|..+-+.  +.|.   -++|+|.+..+|+.|++.|+...+..-.+++.++-.
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--PGGT---GAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPE  458 (725)
T ss_pred             hcceeeeccCccccccHHHHHHhhcccccceeecC--cccc---eeeeeecCccchHHHHHHhchhhhccCccccccChh
Confidence            34679999999999999999999999999988443  5444   399999999999999999999888887777755431


Q ss_pred             cc-----------------------ccc----------cc------------CC-CCceEEeeCCCccccHHHHHHHHcc
Q 039806           93 RA-----------------------DRI----------QE------------GS-SFNNLYVKNLDDDMTEEILVEKFSE  126 (398)
Q Consensus        93 ~~-----------------------~~~----------~~------------~~-~~~~lfV~nLp~~~tee~L~~~F~~  126 (398)
                      ..                       ++.          .+            .. ..+.|||+||++++|.++|...|..
T Consensus       459 dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k  538 (725)
T KOG0110|consen  459 DVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSK  538 (725)
T ss_pred             hhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHh
Confidence            00                       000          00            00 2234999999999999999999999


Q ss_pred             CCCEEEEEEeeCCCC----CccccCCchhhhHHHHHHHHHHHH---------------------HHHHHHHhhhhhhccc
Q 039806          127 FGKITSLVISKDANG----TSKGFGSKVLYVARAQKKAERKAI---------------------LRAQFERMRKERAELY  181 (398)
Q Consensus       127 fG~I~~~~i~~d~~g----~s~Gf~~~~l~v~~a~~k~~~~~~---------------------~~~~~~~~~~~~~~~v  181 (398)
                      .|.|.++.|....+.    .|.||++..+.-........+.-.                     ..+..........|+|
T Consensus       539 ~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlV  618 (725)
T KOG0110|consen  539 QGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKILV  618 (725)
T ss_pred             cCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccccccccccccceeee
Confidence            999999988766654    366886444333322222211100                     0011111122346788


Q ss_pred             cCCCcccCHHHHHHHhhcCCCeEEEEEeeC-CCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          182 KNINDEVDEIELKQYFSQCGTISSVKIMRT-DRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       182 ~nL~~~vtee~L~~~F~~fG~I~svki~~d-~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +|||+..+-.+++++|+.||.|.+|+|... ..+.++|| ||.|-+.+||.+|.-++...+
T Consensus       619 RNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STH  679 (725)
T KOG0110|consen  619 RNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTH  679 (725)
T ss_pred             eccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccc
Confidence            999999999999999999999999999876 36667999 999999999999998777433

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

Probab=99.76  E-value=1.3e-18  Score=169.86  Aligned_cols=134  Identities=29%  Similarity=0.466  Sum_probs=119.5

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++||+--|.-.++.-||+++|+.+|.|.+|.++.|. ++.+||.|||+|.+.++.-.||. |+|..+.|.+|.|...
T Consensus       177 Rd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~s  255 (549)
T KOG0147|consen  177 RDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLS  255 (549)
T ss_pred             HhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEeccc
Confidence            456788998999999999999999999999999999999 99999999999999999999995 9999999999999887


Q ss_pred             cccccccccCC----------CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCC-CCCcccc
Q 039806           91 IRRADRIQEGS----------SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-NGTSKGF  146 (398)
Q Consensus        91 ~~~~~~~~~~~----------~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~-~g~s~Gf  146 (398)
                      ...+.+.....          +...|||+||.+++||++|+.+|++||.|..+.+.+|. +|.++||
T Consensus       256 Eaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgf  322 (549)
T KOG0147|consen  256 EAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGF  322 (549)
T ss_pred             HHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCc
Confidence            65555422211          34449999999999999999999999999999999998 6999999

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

Probab=99.76  E-value=3.8e-18  Score=145.57  Aligned_cols=83  Identities=29%  Similarity=0.549  Sum_probs=78.4

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ..+++|||+||+.++|+++|+++|++||.|.+|+|+.|. +++++|||||+|++.++|++||+.||+..|+|+.|+|.++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            446789999999999999999999999999999999998 9999999999999999999999999999999999999998


Q ss_pred             cccc
Q 039806           91 IRRA   94 (398)
Q Consensus        91 ~~~~   94 (398)
                      ..+.
T Consensus       112 ~~~~  115 (144)
T PLN03134        112 NDRP  115 (144)
T ss_pred             CcCC
Confidence            7554

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

Probab=99.73  E-value=1.9e-17  Score=157.71  Aligned_cols=126  Identities=25%  Similarity=0.346  Sum_probs=112.0

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCC-eeEEEEEEcC--CCCceeEEEEEecCHHHHHHHHHHhc-C-CeecceEeee
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGD-IQSSKVVVSQ--EGKSKGYGFVQYSTPESALDAIEKLQ-G-ATVERMELYV   87 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~-I~~vki~~d~--~g~skg~aFV~F~~~e~A~~Ai~~ln-g-~~l~gk~i~V   87 (398)
                      .+++|||+|+|++.++++|.+-|++.+. |++|.|..++  ..++||||||+|++...|..|-.+|- + ..|+|..+.|
T Consensus       163 an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tV  242 (506)
T KOG0117|consen  163 ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITV  242 (506)
T ss_pred             ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCccee
Confidence            4679999999999999999999999885 8888888887  56899999999999999999998873 3 3789999999


Q ss_pred             ecccccccccccCC-CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeC
Q 039806           88 GPFIRRADRIQEGS-SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD  138 (398)
Q Consensus        88 ~~~~~~~~~~~~~~-~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d  138 (398)
                      .|+.+..+...+.- +-.-|||+||+.++|||.|+++|+.||.|+.|+..+|
T Consensus       243 dWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD  294 (506)
T KOG0117|consen  243 DWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD  294 (506)
T ss_pred             eccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc
Confidence            99999887755432 5677999999999999999999999999999999977

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

Probab=99.71  E-value=5.4e-17  Score=162.66  Aligned_cols=138  Identities=27%  Similarity=0.436  Sum_probs=117.0

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCC----ceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK----SKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~----skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      +|||+||+.++|.++|.+.|+..|.|++|.|.+.+++.    |.|||||+|.+.++|++|++.|+|+.|+|+.|.|..+.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            39999999999999999999999999999998877553    66999999999999999999999999999999999887


Q ss_pred             ccccccc-----cCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCccccCCchhhh
Q 039806           92 RRADRIQ-----EGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYV  153 (398)
Q Consensus        92 ~~~~~~~-----~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf~~~~l~v  153 (398)
                      .+.....     .....++|.|+|||+..+..+++++|..||.|.+|+|.+-.. +.++||++..+..
T Consensus       597 ~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t  664 (725)
T KOG0110|consen  597 NKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLT  664 (725)
T ss_pred             CccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccC
Confidence            2221111     111457999999999999999999999999999999998743 7788986554443

>PF00076 RRM_1: RNA recognition motif

Probab=99.69  E-value=1.9e-16  Score=117.74  Aligned_cols=70  Identities=37%  Similarity=0.663  Sum_probs=67.9

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806           17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus        17 lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      |||+|||.++|+++|+++|+.||.|..|++..+.++.++|||||+|++.++|++|++.+||..++|++|+
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            7999999999999999999999999999999998899999999999999999999999999999999885

(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 ....

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

Probab=99.67  E-value=1.5e-16  Score=161.79  Aligned_cols=139  Identities=24%  Similarity=0.249  Sum_probs=108.2

Q ss_pred             CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCccccCCchhhhHHHHHHHHHH-----------------
Q 039806          102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAERK-----------------  163 (398)
Q Consensus       102 ~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf~~~~l~v~~a~~k~~~~-----------------  163 (398)
                      ..++|||+|||.++|+++|+++|++||.|.+|.+++|.. ++++||+...+.......++...                 
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~~  167 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQA  167 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecch
Confidence            467899999999999999999999999999999999975 88999965444333322222110                 


Q ss_pred             -----HHHHHHH-HHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHH
Q 039806          164 -----AILRAQF-ERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       164 -----~~~~~~~-~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                           ....... ......++++|+||+..+++++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+..
T Consensus       168 ~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~  247 (457)
T TIGR01622       168 EKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV  247 (457)
T ss_pred             hhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHh
Confidence                 0000000 000114678899999999999999999999999999999988 6799999 9999999999999987


Q ss_pred             Hhccc
Q 039806          236 IMYAK  240 (398)
Q Consensus       236 ~q~~q  240 (398)
                      +....
T Consensus       248 l~g~~  252 (457)
T TIGR01622       248 MNGFE  252 (457)
T ss_pred             cCCcE
Confidence            77643

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.

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

Probab=99.61  E-value=1.9e-15  Score=134.15  Aligned_cols=83  Identities=25%  Similarity=0.361  Sum_probs=79.4

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      +++.++|-|.||+.+++|++|.++|..||.|..|.|.+|+ +|.+||||||.|.+.++|.+||+.|||.-++.--|.|+|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            4578899999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             cccc
Q 039806           90 FIRR   93 (398)
Q Consensus        90 ~~~~   93 (398)
                      +.++
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            8764

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.60  E-value=5.2e-15  Score=110.36  Aligned_cols=70  Identities=29%  Similarity=0.648  Sum_probs=65.4

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806           17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus        17 lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      |||+|||.++|+++|.++|+.||.|..+++..++++.++|+|||+|.+.++|.+|++.+++..++|+.|+
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            7999999999999999999999999999999998899999999999999999999999998999999885

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 ....

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

Probab=99.59  E-value=2.2e-14  Score=134.05  Aligned_cols=127  Identities=31%  Similarity=0.468  Sum_probs=110.0

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc-
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI-   91 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~-   91 (398)
                      .++|||+|||.++|+++|.++|+.||.|..|++..|. +|+++|||||+|.+.++|..|++.+++..|.|+.|.|.+.. 
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 99999999999999999999999999999999999999953 


Q ss_pred             ---ccccccc----------------cCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC
Q 039806           92 ---RRADRIQ----------------EGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN  140 (398)
Q Consensus        92 ---~~~~~~~----------------~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~  140 (398)
                         .+.....                .......+++.+++..++++++...|..+|.+....+.....
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKD  262 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCC
Confidence               2222220                011567799999999999999999999999996666655543

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

Probab=99.58  E-value=3.8e-15  Score=137.21  Aligned_cols=84  Identities=27%  Similarity=0.456  Sum_probs=78.6

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      .++.-++|+|.|||....+-||+..|.+||+|++|.|+.++.| |||||||.|++.+||++|-++|||..+.||+|.|..
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~  170 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTVVEGRKIEVNN  170 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhcceeeceEEEEec
Confidence            4566789999999999999999999999999999999999866 899999999999999999999999999999999999


Q ss_pred             ccccc
Q 039806           90 FIRRA   94 (398)
Q Consensus        90 ~~~~~   94 (398)
                      +..+-
T Consensus       171 ATarV  175 (376)
T KOG0125|consen  171 ATARV  175 (376)
T ss_pred             cchhh
Confidence            87653

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.58  E-value=7.3e-15  Score=142.77  Aligned_cols=81  Identities=30%  Similarity=0.445  Sum_probs=75.0

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecc--eEeeeec
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVER--MELYVGP   89 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g--k~i~V~~   89 (398)
                      ...+|||+|||.++|+++|+++|++||.|.+|+|+.|. +|++||||||+|++.++|++||+.||+..+.+  ++|.|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            45789999999999999999999999999999999998 99999999999999999999999999998876  6888887


Q ss_pred             cccc
Q 039806           90 FIRR   93 (398)
Q Consensus        90 ~~~~   93 (398)
                      +..+
T Consensus       272 a~~~  275 (346)
T TIGR01659       272 AEEH  275 (346)
T ss_pred             CCcc
Confidence            7643

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).

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

Probab=99.58  E-value=1.3e-14  Score=123.66  Aligned_cols=127  Identities=20%  Similarity=0.258  Sum_probs=106.1

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..+++|||+|||.+|.++||.++|.+||.|.+|.+...+ + .-+||||+|++..+|+.||..-+|..++|..|.|+...
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~-g-~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP-G-PPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC-C-CCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            357899999999999999999999999999998875433 2 34799999999999999999999999999999998875


Q ss_pred             ccccc---c-------------------ccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC
Q 039806           92 RRADR---I-------------------QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN  140 (398)
Q Consensus        92 ~~~~~---~-------------------~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~  140 (398)
                      .-...   .                   ....+...+.|.+||..-+++||++...+-|.|.-..+.+|..
T Consensus        82 ggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rDg~  152 (241)
T KOG0105|consen   82 GGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRDGV  152 (241)
T ss_pred             CCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecccc
Confidence            32100   0                   0000456799999999999999999999999999999998864

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

Probab=99.57  E-value=4.1e-15  Score=131.58  Aligned_cols=80  Identities=26%  Similarity=0.431  Sum_probs=72.7

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      .+-..+|||++|++.+..|+|+++|++||+|++.+|+.|+ +|+|||||||.|++.|+|.+|++. -+-.|+||+..+..
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnl   87 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNL   87 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccch
Confidence            3446789999999999999999999999999999999999 999999999999999999999985 45688999887776


Q ss_pred             cc
Q 039806           90 FI   91 (398)
Q Consensus        90 ~~   91 (398)
                      +.
T Consensus        88 A~   89 (247)
T KOG0149|consen   88 AS   89 (247)
T ss_pred             hh
Confidence            64

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

Probab=99.56  E-value=1.6e-15  Score=143.41  Aligned_cols=133  Identities=25%  Similarity=0.397  Sum_probs=102.1

Q ss_pred             CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCccccCCchhhhHHHH---------HHHHHHHHHHHHHH
Q 039806          102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQ---------KKAERKAILRAQFE  171 (398)
Q Consensus       102 ~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf~~~~l~v~~a~---------~k~~~~~~~~~~~~  171 (398)
                      ..++|||++|+|++|+|.|+++|+.||+|.+|++++|.. ++++||++..+......         ....+..+.+....
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            468899999999999999999999999999999999986 99999954433211110         00111111111111


Q ss_pred             Hh--------hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHH
Q 039806          172 RM--------RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       172 ~~--------~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      +.        ...+++++++|+.++++++|+++|++||.|.++.++.|. +.+++|| ||.|.+.+.+.++..
T Consensus        85 r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~  157 (311)
T KOG4205|consen   85 REDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL  157 (311)
T ss_pred             cccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc
Confidence            11        124578889999999999999999999999999999998 8899999 999998888877755

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

Probab=99.56  E-value=9.6e-14  Score=134.44  Aligned_cols=222  Identities=15%  Similarity=0.197  Sum_probs=157.5

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ...-|.+++||+++|++||+++|+.++ |.++++.++ +|+..|-|||+|.++|++++|++ .+-+.+..+.|.|-.+..
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~-~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR-NGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGG   85 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc-CCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCC
Confidence            345688999999999999999999994 887555443 69999999999999999999998 488899999999977654


Q ss_pred             ccccc-----ccC--CCCceEEeeCCCccccHHHHHHHHccCCCEEE-EEEeeCCCCCccccCCch--------------
Q 039806           93 RADRI-----QEG--SSFNNLYVKNLDDDMTEEILVEKFSEFGKITS-LVISKDANGTSKGFGSKV--------------  150 (398)
Q Consensus        93 ~~~~~-----~~~--~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~-~~i~~d~~g~s~Gf~~~~--------------  150 (398)
                      .....     ...  .....|.+.+||+.+|++||.++|+..-.+.. +.+..|..+++.|-..+.              
T Consensus        86 ~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~rh  165 (510)
T KOG4211|consen   86 AEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGRH  165 (510)
T ss_pred             ccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHHH
Confidence            33221     111  15567889999999999999999997766665 566777777777663111              


Q ss_pred             --------hhhHHHHHHHHHHHHHH--H------HHHH-----h---------------h--------------------
Q 039806          151 --------LYVARAQKKAERKAILR--A------QFER-----M---------------R--------------------  174 (398)
Q Consensus       151 --------l~v~~a~~k~~~~~~~~--~------~~~~-----~---------------~--------------------  174 (398)
                              |.|-++.....+...-.  .      .++.     .               +                    
T Consensus       166 re~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~  245 (510)
T KOG4211|consen  166 RENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDY  245 (510)
T ss_pred             HHhhccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccc
Confidence                    11111111111111000  0      0000     0               0                    


Q ss_pred             -------------------h------------hhh-ccc--cCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-
Q 039806          175 -------------------K------------ERA-ELY--KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-  219 (398)
Q Consensus       175 -------------------~------------~~~-~~v--~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-  219 (398)
                                         .            ... .++  ++||++.++.++.++|+..-.+ .|+|-..++|+..|- 
T Consensus       246 ~~~gs~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~dGr~TGEA  324 (510)
T KOG4211|consen  246 GNFGSYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGPDGRATGEA  324 (510)
T ss_pred             ccccccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCCCCccCCcc
Confidence                               0            000 111  7899999999999999987666 788888889999988 


Q ss_pred             EEEecccHHHHHHHHHHhc
Q 039806          220 CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       220 fV~f~~~~ea~~A~l~~q~  238 (398)
                      +|+|++.+||..|...-..
T Consensus       325 dveF~t~edav~Amskd~a  343 (510)
T KOG4211|consen  325 DVEFATGEDAVGAMGKDGA  343 (510)
T ss_pred             eeecccchhhHhhhccCCc
Confidence            9999999999999875443

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.54  E-value=3e-14  Score=130.27  Aligned_cols=78  Identities=22%  Similarity=0.324  Sum_probs=71.7

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ..++|||+||++++|+++|+++|+.||.|.+|.|..|..  ++|||||+|+++++|+.||. |||..|.|+.|.|.++..
T Consensus         3 ~~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          3 QVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            357999999999999999999999999999999998863  57999999999999999996 999999999999998764


Q ss_pred             c
Q 039806           93 R   93 (398)
Q Consensus        93 ~   93 (398)
                      .
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            3

>smart00517 PolyA C-terminal domain of Poly(A)-binding protein

Probab=99.53  E-value=2.4e-15  Score=107.43  Aligned_cols=33  Identities=36%  Similarity=0.561  Sum_probs=31.5

Q ss_pred             ChHHHhhhhhcccchhhhccccceeceeeeeee
Q 039806          362 SPDERKDILGQRLYPLVKKLKVITHIFVKGQFR  394 (398)
Q Consensus       362 ~p~~qk~mLGe~Lyplv~~~~~~~~~~~~~~~~  394 (398)
                      +|++||+||||+|||+|++++|++|+|||||+-
T Consensus         1 ~p~~qkq~LGE~Lyp~V~~~~p~~A~KITGMLL   33 (64)
T smart00517        1 PPQEQKQALGERLYPKVQALEPELAGKITGMLL   33 (64)
T ss_pred             CHHHHHHHHhHHHhHHHHhhCcccCCcCeeeee
Confidence            689999999999999999999999999999973

Present also in Drosophila hyperplastics discs protein. Involved in homodimerisation (either directly or indirectly)

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

Probab=99.52  E-value=2.7e-14  Score=114.65  Aligned_cols=80  Identities=21%  Similarity=0.337  Sum_probs=75.0

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ..+++|||+||+..++||.|+++|+.+|.|..|.+-.|+ +-...|||||+|-+.++|+.|++.+||..|+++.|.|.+.
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            457899999999999999999999999999999999998 6778899999999999999999999999999999999875


Q ss_pred             c
Q 039806           91 I   91 (398)
Q Consensus        91 ~   91 (398)
                      .
T Consensus       114 ~  114 (153)
T KOG0121|consen  114 A  114 (153)
T ss_pred             c
Confidence            4

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

Probab=99.49  E-value=2.4e-13  Score=120.21  Aligned_cols=124  Identities=23%  Similarity=0.377  Sum_probs=105.7

Q ss_pred             cceEEEcCCCCCCcHHHHHH----HHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           14 IGNAFVKNLASTIDNLKLHQ----IFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~----~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      +++|||.||...+..++|+.    +|+.||.|++|...+  +.+.+|-|||.|.+.+.|..|+..|+|..+.||.++|.+
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k--t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqy   86 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK--TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQY   86 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC--CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheec
Confidence            44999999999999999877    999999999887755  568999999999999999999999999999999999988


Q ss_pred             cccccccccc----------------------------------------------CCCCceEEeeCCCccccHHHHHHH
Q 039806           90 FIRRADRIQE----------------------------------------------GSSFNNLYVKNLDDDMTEEILVEK  123 (398)
Q Consensus        90 ~~~~~~~~~~----------------------------------------------~~~~~~lfV~nLp~~~tee~L~~~  123 (398)
                      +..++.....                                              ......+|+.|||.+++.+.+..+
T Consensus        87 A~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~l  166 (221)
T KOG4206|consen   87 AKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDL  166 (221)
T ss_pred             ccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHH
Confidence            8755432100                                              113456899999999999999999


Q ss_pred             HccCCCEEEEEEeeCC
Q 039806          124 FSEFGKITSLVISKDA  139 (398)
Q Consensus       124 F~~fG~I~~~~i~~d~  139 (398)
                      |..|.-...++++...
T Consensus       167 f~qf~g~keir~i~~~  182 (221)
T KOG4206|consen  167 FEQFPGFKEIRLIPPR  182 (221)
T ss_pred             HhhCcccceeEeccCC
Confidence            9999988888887654

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

Probab=99.49  E-value=3.2e-14  Score=132.57  Aligned_cols=137  Identities=20%  Similarity=0.362  Sum_probs=111.4

Q ss_pred             CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCcccc-----------------------CCchhhhHHHH
Q 039806          102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGF-----------------------GSKVLYVARAQ  157 (398)
Q Consensus       102 ~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf-----------------------~~~~l~v~~a~  157 (398)
                      --+++||+.|++++.|+.|+..|.+||.|.|+.+..|.- ++.+||                       +|+.|.|++..
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            357899999999999999999999999999999999984 999999                       56666666554


Q ss_pred             HHHHHHHHHHHHHHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCC-CCccce-EEEecccHHHHHHHHH
Q 039806          158 KKAERKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDR-GISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       158 ~k~~~~~~~~~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~-g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                      .-...+.....-.+..+.-+.+++..+..+.+|+||+.+|+.||+|.+|++.++++ +..||| |++|++......|+..
T Consensus       192 NmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAias  271 (544)
T KOG0124|consen  192 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  271 (544)
T ss_pred             CCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhh
Confidence            43333333333333444455678899999999999999999999999999999994 568999 9999999888888776


Q ss_pred             Hhc
Q 039806          236 IMY  238 (398)
Q Consensus       236 ~q~  238 (398)
                      +.+
T Consensus       272 MNl  274 (544)
T KOG0124|consen  272 MNL  274 (544)
T ss_pred             cch
Confidence            654

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

Probab=99.49  E-value=4.3e-15  Score=126.23  Aligned_cols=84  Identities=20%  Similarity=0.399  Sum_probs=78.7

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ..+++-|||+|||.+.||.||.-.||+||.|.+|.+++|+ ||+|+||||+.|++..+..-|+.+|||..|.|+.|+|..
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeee
Confidence            3567889999999999999999999999999999999999 999999999999999999999999999999999999987


Q ss_pred             ccccc
Q 039806           90 FIRRA   94 (398)
Q Consensus        90 ~~~~~   94 (398)
                      .....
T Consensus       112 v~~Yk  116 (219)
T KOG0126|consen  112 VSNYK  116 (219)
T ss_pred             ccccc
Confidence            65443

>smart00362 RRM_2 RNA recognition motif

Probab=99.48  E-value=2.3e-13  Score=100.49  Aligned_cols=72  Identities=40%  Similarity=0.637  Sum_probs=68.1

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      +|+|+|||.++++++|.++|+.||.|..+++..+. +.++|+|||+|.+.++|++|++.+++..+.|+.|.|.
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            58999999999999999999999999999999887 7889999999999999999999999999999998873

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

Probab=99.48  E-value=8e-14  Score=118.01  Aligned_cols=80  Identities=29%  Similarity=0.463  Sum_probs=73.9

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...++|||+||+..+++.||+..|..||.|.+|.|..+    ..|||||+|++..+|+.|+..|+|..|+|..|.|+.+.
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            45789999999999999999999999999999999885    46899999999999999999999999999999999987


Q ss_pred             cccc
Q 039806           92 RRAD   95 (398)
Q Consensus        92 ~~~~   95 (398)
                      -...
T Consensus        84 G~~r   87 (195)
T KOG0107|consen   84 GRPR   87 (195)
T ss_pred             CCcc
Confidence            5544

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

Probab=99.47  E-value=1.9e-13  Score=124.69  Aligned_cols=87  Identities=25%  Similarity=0.393  Sum_probs=80.6

Q ss_pred             CCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecce
Q 039806            5 PNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERM   83 (398)
Q Consensus         5 rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk   83 (398)
                      .|+..-....+||||.-|+.+++|..|+..|+.||.|..|+|+.|. +|+++|||||+|+++.+...|.+..+|..|+|+
T Consensus        92 ~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgr  171 (335)
T KOG0113|consen   92 NDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGR  171 (335)
T ss_pred             CCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCc
Confidence            3555556778999999999999999999999999999999999998 999999999999999999999999999999999


Q ss_pred             Eeeeeccc
Q 039806           84 ELYVGPFI   91 (398)
Q Consensus        84 ~i~V~~~~   91 (398)
                      .|.|.+-.
T Consensus       172 ri~VDvER  179 (335)
T KOG0113|consen  172 RILVDVER  179 (335)
T ss_pred             EEEEEecc
Confidence            99997643

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

Probab=99.47  E-value=5.6e-13  Score=116.92  Aligned_cols=220  Identities=15%  Similarity=0.179  Sum_probs=126.8

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC--CCCceeEEEEEecCHHHHHHHHHHhcCCeec---ceEe
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ--EGKSKGYGFVQYSTPESALDAIEKLQGATVE---RMEL   85 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~--~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~---gk~i   85 (398)
                      ....++|||.+||.++.-.+|+.+|..|-.-+.+.+....  +...+-+|||.|.+..+|..|++.|||+.++   +..+
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            3458999999999999999999999998877777776544  2345679999999999999999999999996   6788


Q ss_pred             eeecccccccccccCC-----CCceEEeeCCCcccc----HHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHH-
Q 039806           86 YVGPFIRRADRIQEGS-----SFNNLYVKNLDDDMT----EEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVAR-  155 (398)
Q Consensus        86 ~V~~~~~~~~~~~~~~-----~~~~lfV~nLp~~~t----ee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~-  155 (398)
                      +++.++++.++.....     ...-+-+.+-.....    ++.+..+...+ ++..       -+..........+-.. 
T Consensus       111 hiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~-~l~~-------~~~a~al~~~~~t~~~~  182 (284)
T KOG1457|consen  111 HIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPD-ELQE-------PGNADALKENDTTKSEA  182 (284)
T ss_pred             EeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCcc-ccCC-------ccccccCCCccccchhh
Confidence            8888876655433221     122222222221111    01000000000 0000       0110000000000000 


Q ss_pred             --HH-HH---HHHHHHHHHHH-HHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccceEEEecccHH
Q 039806          156 --AQ-KK---AERKAILRAQF-ERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKR  228 (398)
Q Consensus       156 --a~-~k---~~~~~~~~~~~-~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGffV~f~~~~e  228 (398)
                        +. .+   ++..-...++. ...+...+++|-||..++|||+|+.+|+.|-.....||. .+.|..-. ||+|...+.
T Consensus       183 l~a~~~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~-~~~g~~va-f~~~~~~~~  260 (284)
T KOG1457|consen  183 LSAPDSKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIR-ARGGMPVA-FADFEEIEQ  260 (284)
T ss_pred             hhhhhhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEe-cCCCcceE-eecHHHHHH
Confidence              00 00   00000111111 223445678999999999999999999999877777774 12222211 566666666


Q ss_pred             HHHHHHHHhccc
Q 039806          229 ERTSYLRIMYAK  240 (398)
Q Consensus       229 a~~A~l~~q~~q  240 (398)
                      |..|...+|..+
T Consensus       261 at~am~~lqg~~  272 (284)
T KOG1457|consen  261 ATDAMNHLQGNL  272 (284)
T ss_pred             HHHHHHHhhcce
Confidence            666655555444

>PF00658 PABP: Poly-adenylate binding protein, unique domain; InterPro: IPR002004 The polyadenylate-binding protein (PABP) has a conserved C-terminal domain (PABC), which is also found in the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains (IPR000569 from INTERPRO) []

Probab=99.47  E-value=3.8e-15  Score=110.33  Aligned_cols=41  Identities=37%  Similarity=0.569  Sum_probs=39.8

Q ss_pred             hHHhhhhcCChHHHhhhhhcccchhhhccccceeceeeeee
Q 039806          353 NLSSMLVATSPDERKDILGQRLYPLVKKLKVITHIFVKGQF  393 (398)
Q Consensus       353 ~~~s~la~a~p~~qk~mLGe~Lyplv~~~~~~~~~~~~~~~  393 (398)
                      .+++.||++++++||++|||+|||+|.+++|++|+|||||+
T Consensus         3 ~~~~~la~~~~~~qk~~LGe~Ly~~V~~~~p~~A~KITGML   43 (72)
T PF00658_consen    3 LTASALASASPEQQKQILGERLYPLVQAIYPELAGKITGML   43 (72)
T ss_dssp             TSHHHHHTSCHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred             chHHHHhcCCHHHHHHHHhccccHHHHHhCcchhHHHHHHH
Confidence            57899999999999999999999999999999999999997

PABP recognises the 3' mRNA poly(A) tail and plays an essential role in eukaryotic translation initiation and mRNA stabilisation/degradation. PABC domains of PABP are peptide-binding domains that mediate PABP homo-oligomerisation and protein-protein interactions. In mammals, the PABC domain of PABP functions to recruit several different translation factors to the mRNA poly(A) tail [].; GO: 0003723 RNA binding; PDB: 3KUR_E 1JH4_A 2RQH_B 3KUI_A 3KUS_A 3KUJ_A 3KTR_A 2X04_A 3PTH_A 1JGN_A ....

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.47  E-value=2.2e-13  Score=122.64  Aligned_cols=77  Identities=22%  Similarity=0.303  Sum_probs=70.4

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      +..+|||+||+.++|+++|+++|+.||+|.+|+|.+|  +.++|||||+|+++++|+.|+. |||..|.|+.|.|.....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D--~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS--GEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC--CCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            4469999999999999999999999999999999988  4566899999999999999996 999999999999987553

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

Probab=99.45  E-value=8.6e-14  Score=112.75  Aligned_cols=81  Identities=25%  Similarity=0.395  Sum_probs=76.3

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      .=-|||.++...+||++|++.|..||.|.++++..|. +|-.||||+|+|++.++|++||+.+||..|.|.+|.|.|+-.
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            3459999999999999999999999999999999999 999999999999999999999999999999999999999764


Q ss_pred             cc
Q 039806           93 RA   94 (398)
Q Consensus        93 ~~   94 (398)
                      +.
T Consensus       152 ~g  153 (170)
T KOG0130|consen  152 KG  153 (170)
T ss_pred             cC
Confidence            43

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

Probab=99.45  E-value=1.8e-13  Score=118.59  Aligned_cols=85  Identities=24%  Similarity=0.416  Sum_probs=79.5

Q ss_pred             ccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEe
Q 039806            7 SEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMEL   85 (398)
Q Consensus         7 ~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i   85 (398)
                      +-.+-.+..+|.|-||..-++.++|..+|++||.|-+|.|..|. ++.++|||||.|....+|+.|++.|+|.+|+|++|
T Consensus         6 ~PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRel   85 (256)
T KOG4207|consen    6 PPPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGREL   85 (256)
T ss_pred             CCCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeecccee
Confidence            34455788999999999999999999999999999999999999 99999999999999999999999999999999999


Q ss_pred             eeeccc
Q 039806           86 YVGPFI   91 (398)
Q Consensus        86 ~V~~~~   91 (398)
                      .|..+.
T Consensus        86 rVq~ar   91 (256)
T KOG4207|consen   86 RVQMAR   91 (256)
T ss_pred             eehhhh
Confidence            997654

>smart00360 RRM RNA recognition motif

Probab=99.44  E-value=5.1e-13  Score=98.21  Aligned_cols=70  Identities=39%  Similarity=0.658  Sum_probs=66.4

Q ss_pred             EcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        19 V~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      |+|||.++++++|+++|+.||.|.+|++..+. ++.++|||||+|.+.++|.+|++.+++..+.|+.|.|.
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            68999999999999999999999999999988 68999999999999999999999999999999998873

>PLN03213 repressor of silencing 3; Provisional

Probab=99.44  E-value=3e-13  Score=130.55  Aligned_cols=77  Identities=17%  Similarity=0.293  Sum_probs=71.1

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCH--HHHHHHHHHhcCCeecceEeeeeccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTP--ESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~--e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      .-+|||+||++++|++||...|+.||.|.+|.|++ .+|  ||||||+|.+.  +++.+||+.|||..+.|+.|+|..+.
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR-ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR-TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec-ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            46899999999999999999999999999999993 367  89999999987  78999999999999999999999887


Q ss_pred             cc
Q 039806           92 RR   93 (398)
Q Consensus        92 ~~   93 (398)
                      +.
T Consensus        87 P~   88 (759)
T PLN03213         87 EH   88 (759)
T ss_pred             HH
Confidence            53

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

Probab=99.43  E-value=1.3e-13  Score=117.46  Aligned_cols=137  Identities=27%  Similarity=0.338  Sum_probs=103.1

Q ss_pred             CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCccccCCchhhhHHHHHHHHHHHHHHHHH----------
Q 039806          102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAERKAILRAQF----------  170 (398)
Q Consensus       102 ~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf~~~~l~v~~a~~k~~~~~~~~~~~----------  170 (398)
                      ...+|||+||+..++++.|.++|-+.|.|.++++.+|.- ...+||++.+...+...+=+-+--..-+-+          
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            567999999999999999999999999999999999985 678888654443332221111000000000          


Q ss_pred             ---HHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEE-EEEeeCC-CCCccce-EEEecccHHHHHHHHHHhc
Q 039806          171 ---ERMRKERAELYKNINDEVDEIELKQYFSQCGTISS-VKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       171 ---~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~s-vki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                         ........++++||+++++|..|.+.|+.||.|.+ -+|++|+ +|.++|| ||.|++.+.+.+|+..+..
T Consensus        88 ~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ng  161 (203)
T KOG0131|consen   88 AHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNG  161 (203)
T ss_pred             cccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhcc
Confidence               11223456788999999999999999999999987 4899998 6889988 9999999888888766543

>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=99.42  E-value=1.8e-12  Score=96.16  Aligned_cols=74  Identities=35%  Similarity=0.591  Sum_probs=69.7

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      +|+|+|||..+++++|.++|+.+|.|..+++..+..+..+|+|||+|.+.++|..|++.+++..++|+.+.|.+
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            48999999999999999999999999999999988667899999999999999999999999999999998863

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).

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

Probab=99.42  E-value=3.9e-13  Score=132.63  Aligned_cols=83  Identities=31%  Similarity=0.463  Sum_probs=79.4

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRR   93 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~   93 (398)
                      +.|||||+|+++++++|.++|+..|.|.+++++.|+ +|+.|||||++|.+.++|..|++.|||..+.|++|+|.++...
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            899999999999999999999999999999999999 9999999999999999999999999999999999999998866


Q ss_pred             cccc
Q 039806           94 ADRI   97 (398)
Q Consensus        94 ~~~~   97 (398)
                      ..+.
T Consensus        99 ~~~~  102 (435)
T KOG0108|consen   99 KNAE  102 (435)
T ss_pred             chhH
Confidence            6543

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

Probab=99.40  E-value=1.1e-12  Score=101.59  Aligned_cols=84  Identities=21%  Similarity=0.308  Sum_probs=74.2

Q ss_pred             ccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806            9 ARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus         9 ~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      +....++-|||+|||++||.|+..++|.+||.|..|+|-..+  ..+|.|||.|++..+|++|++.|+|..+.++.+.|.
T Consensus        13 lppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k--~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vl   90 (124)
T KOG0114|consen   13 LPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK--ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVL   90 (124)
T ss_pred             CChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc--CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEE
Confidence            344456789999999999999999999999999999996544  467999999999999999999999999999999998


Q ss_pred             cccccc
Q 039806           89 PFIRRA   94 (398)
Q Consensus        89 ~~~~~~   94 (398)
                      +..+..
T Consensus        91 yyq~~~   96 (124)
T KOG0114|consen   91 YYQPED   96 (124)
T ss_pred             ecCHHH
Confidence            876544

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

Probab=99.38  E-value=2.3e-13  Score=119.00  Aligned_cols=85  Identities=24%  Similarity=0.397  Sum_probs=79.6

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++|||++|..++||.-|+..|-.||.|.+|+++.|- +++.||||||+|+..|+|..||.++|+..|.||.|+|.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            345799999999999999999999999999999999998 9999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      .+.+..
T Consensus        88 kP~kik   93 (298)
T KOG0111|consen   88 KPEKIK   93 (298)
T ss_pred             CCcccc
Confidence            865543

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

Probab=99.38  E-value=3.2e-13  Score=122.74  Aligned_cols=110  Identities=20%  Similarity=0.301  Sum_probs=89.4

Q ss_pred             ceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCcccc---------------------CCchhhhHHHHHHHHH
Q 039806          104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF---------------------GSKVLYVARAQKKAER  162 (398)
Q Consensus       104 ~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf---------------------~~~~l~v~~a~~k~~~  162 (398)
                      .+|||+|||.++++.+|+.+|++||+|.+|.|+++-     ||                     ++..|.|+.+..|   
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKNY-----gFVHiEdktaaedairNLhgYtLhg~nInVeaSksK---   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKNY-----GFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK---   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeeccc-----ceEEeecccccHHHHhhcccceecceEEEEEecccc---
Confidence            469999999999999999999999999999998652     44                     2333333333222   


Q ss_pred             HHHHHHHHHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          163 KAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                                +....+++++||.+.++.++|++.|++||.|+.|+|++|       | ||.|.-.++|..|+..+..
T Consensus        75 ----------sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd-------y~fvh~d~~eda~~air~l~~  134 (346)
T KOG0109|consen   75 ----------SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD-------YAFVHFDRAEDAVEAIRGLDN  134 (346)
T ss_pred             ----------CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc-------eeEEEEeeccchHHHHhcccc
Confidence                      345678899999999999999999999999999999954       4 8999999999999954443

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

Probab=99.34  E-value=4e-11  Score=121.75  Aligned_cols=108  Identities=17%  Similarity=0.225  Sum_probs=85.9

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      .++||||+.|++++++.||.++|+.||.|.+|+++.     ++|||||...+..+|.+|+.+|++..+.++.|+|.|+..
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 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP-----PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeecc-----CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            478999999999999999999999999999999976     679999999999999999999999999999999999987


Q ss_pred             cccccccCC-CCceEEeeCCCccccHHHHHHHHc
Q 039806           93 RADRIQEGS-SFNNLYVKNLDDDMTEEILVEKFS  125 (398)
Q Consensus        93 ~~~~~~~~~-~~~~lfV~nLp~~~tee~L~~~F~  125 (398)
                      +.-+..-.. -..++=|.-||++.-.++|+.+.+
T Consensus       495 ~G~kse~k~~wD~~lGVt~IP~~kLt~dl~~~~e  528 (894)
T KOG0132|consen  495 KGPKSEYKDYWDVELGVTYIPWEKLTDDLEAWCE  528 (894)
T ss_pred             CCcchhhhhhhhcccCeeEeehHhcCHHHHHhhh
Confidence            766541110 112233455666544444554443

>smart00361 RRM_1 RNA recognition motif

Probab=99.32  E-value=7.2e-12  Score=93.50  Aligned_cols=60  Identities=18%  Similarity=0.386  Sum_probs=55.2

Q ss_pred             HHHHHHHHh----ccCCeeEEE-EEEcC-C--CCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           28 NLKLHQIFS----KFGDIQSSK-VVVSQ-E--GKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        28 e~~L~~~F~----~~G~I~~vk-i~~d~-~--g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      +++|+++|+    .||.|.+|. |..++ +  +.++|||||+|.+.++|.+|++.|||..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            678999998    999999995 77766 5  899999999999999999999999999999999976

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

Probab=99.29  E-value=4e-12  Score=113.48  Aligned_cols=72  Identities=22%  Similarity=0.464  Sum_probs=66.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRR   93 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~   93 (398)
                      ..|||++|++.+.++||..+|..||.|.+|.+       ..||+||+|++.-+|..||..||+..|.+..+.|+++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~m-------k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADM-------KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhcccccccee-------ecccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            46999999999999999999999999999988       4589999999999999999999999999988888888743

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

Probab=99.29  E-value=3e-12  Score=115.10  Aligned_cols=84  Identities=31%  Similarity=0.430  Sum_probs=78.7

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ..+.|+|||-.||.+..+.||...|-.||.|.+.||..|+ +..||+||||.|+|..+|+.||..+||..|+=|+++|..
T Consensus       282 GPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQL  361 (371)
T KOG0146|consen  282 GPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQL  361 (371)
T ss_pred             CCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhh
Confidence            4578999999999999999999999999999999999999 999999999999999999999999999999999999987


Q ss_pred             ccccc
Q 039806           90 FIRRA   94 (398)
Q Consensus        90 ~~~~~   94 (398)
                      -.+|.
T Consensus       362 KRPkd  366 (371)
T KOG0146|consen  362 KRPKD  366 (371)
T ss_pred             cCccc
Confidence            65544

>PF13893 RRM_5: RNA recognition motif

Probab=99.28  E-value=1.4e-11  Score=87.67  Aligned_cols=56  Identities=34%  Similarity=0.611  Sum_probs=50.6

Q ss_pred             HHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           31 LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        31 L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      |+++|++||+|.++++..+.    +++|||+|.+.++|++|++.|||..++|+.|+|.++
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            78999999999999996643    589999999999999999999999999999999875

(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 ....

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

Probab=99.26  E-value=9.2e-11  Score=109.31  Aligned_cols=184  Identities=17%  Similarity=0.140  Sum_probs=122.0

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCee--------EEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEe
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQ--------SSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMEL   85 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~--------~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i   85 (398)
                      +.+|||.|||.+||.+++.++|++||-|.        .||+.++..|.-||=|.+.|-..|+..-||+-|++..|.|++|
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~  213 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKKL  213 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcEE
Confidence            55799999999999999999999999773        5899999999999999999999999999999999999999999


Q ss_pred             eeecccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHH
Q 039806           86 YVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI  165 (398)
Q Consensus        86 ~V~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~  165 (398)
                      +|+.+.=............         .-...+++.+-+.               +.++|+-               ..
T Consensus       214 rVerAkfq~Kge~~~~~k~---------k~k~~~~kk~~k~---------------q~k~~dw---------------~p  254 (382)
T KOG1548|consen  214 RVERAKFQMKGEYDASKKE---------KGKCKDKKKLKKQ---------------QQKLLDW---------------RP  254 (382)
T ss_pred             EEehhhhhhccCcCccccc---------ccccccHHHHHHH---------------HHhhccc---------------CC
Confidence            9988752221111100000         0000011111000               0000000               00


Q ss_pred             HHHHHHHhhhhhhccccCCCc----ccC-------HHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHH
Q 039806          166 LRAQFERMRKERAELYKNIND----EVD-------EIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSY  233 (398)
Q Consensus       166 ~~~~~~~~~~~~~~~v~nL~~----~vt-------ee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~  233 (398)
                      .+......+.+++++++|+=.    ..+       .++|++.+++||.|.+|.|.-.   .+.|- -|.|.+.++|..++
T Consensus       255 d~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~---hPdGvvtV~f~n~eeA~~ci  331 (382)
T KOG1548|consen  255 DRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR---HPDGVVTVSFRNNEEADQCI  331 (382)
T ss_pred             CccccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc---CCCceeEEEeCChHHHHHHH
Confidence            000011223345555555421    111       4788999999999999999732   34454 58999999999999


Q ss_pred             HHHhcc
Q 039806          234 LRIMYA  239 (398)
Q Consensus       234 l~~q~~  239 (398)
                      ..++..
T Consensus       332 q~m~GR  337 (382)
T KOG1548|consen  332 QTMDGR  337 (382)
T ss_pred             HHhcCe
Confidence            877753

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

Probab=99.26  E-value=2.2e-11  Score=121.05  Aligned_cols=183  Identities=20%  Similarity=0.273  Sum_probs=123.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ..+|||++||..++++.+.|+...||.+...+++.|. +|.+|||||.+|.+......|+..|||+.+.++++.|..+..
T Consensus       289 ~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~  368 (500)
T KOG0120|consen  289 PNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIV  368 (500)
T ss_pred             cchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhc
Confidence            4679999999999999999999999999999999999 899999999999999999999999999999999999988764


Q ss_pred             cccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHHHHHHHHH
Q 039806           93 RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFER  172 (398)
Q Consensus        93 ~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~~~~~~~~  172 (398)
                      -........+....-|..|+..        .+..-|..+.+.+..+             .|....-++            
T Consensus       369 g~~~~~~~~~~~~~~~~~i~~~--------~~q~~g~~t~Vl~L~n-------------~Vt~deLkd------------  415 (500)
T KOG0120|consen  369 GASNANVNFNISQSQVPGIPLL--------MTQMAGIPTEVLCLTN-------------VVTPDELKD------------  415 (500)
T ss_pred             cchhccccCCccccccccchhh--------hcccCCCcchhhhhhh-------------cCCHHHhcc------------
Confidence            3332111100000000111100        0011122222111111             000000000            


Q ss_pred             hhhhhhccccCCCcccC--HHHHHHHhhcCCCeEEEEEeeC-CCC---Cccce-EEEecccHHHHHHHHHHhcccc
Q 039806          173 MRKERAELYKNINDEVD--EIELKQYFSQCGTISSVKIMRT-DRG---ISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vt--ee~L~~~F~~fG~I~svki~~d-~~g---~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                                  +.+++  -|+++..+++||.|.+|+|.++ ..+   ...|- ||+|++.+++.+|+.++...+-
T Consensus       416 ------------d~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF  479 (500)
T KOG0120|consen  416 ------------DEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKF  479 (500)
T ss_pred             ------------hHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCcee
Confidence                        00111  2788999999999999999988 322   22333 9999999999999998876653

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

Probab=99.23  E-value=5e-12  Score=124.20  Aligned_cols=137  Identities=21%  Similarity=0.255  Sum_probs=106.1

Q ss_pred             CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCcccc----------------------CCchhhhHHHHH
Q 039806          102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGF----------------------GSKVLYVARAQK  158 (398)
Q Consensus       102 ~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf----------------------~~~~l~v~~a~~  158 (398)
                      ..+++|+--|+..++.-||.++|+.+|+|.++.++.|.. ++++|.                      .+..+.|.....
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sEa  257 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSEA  257 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecccHH
Confidence            567788888999999999999999999999999999986 778876                      233334433322


Q ss_pred             HHHHHHHHHHHHHH---hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHH
Q 039806          159 KAERKAILRAQFER---MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSY  233 (398)
Q Consensus       159 k~~~~~~~~~~~~~---~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~  233 (398)
                      ...+.+........   ..+-..++++||.+.++|++|+.+|++||.|..|.+++|. +|.++|| ||+|.+.++|++|+
T Consensus       258 eknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~  337 (549)
T KOG0147|consen  258 EKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKAL  337 (549)
T ss_pred             HHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHH
Confidence            22222222222211   1111227889999999999999999999999999999997 9999999 99999999999998


Q ss_pred             HHHhc
Q 039806          234 LRIMY  238 (398)
Q Consensus       234 l~~q~  238 (398)
                      .++..
T Consensus       338 e~lng  342 (549)
T KOG0147|consen  338 EQLNG  342 (549)
T ss_pred             HHhcc
Confidence            88776

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

Probab=99.22  E-value=4.4e-12  Score=120.95  Aligned_cols=123  Identities=20%  Similarity=0.115  Sum_probs=107.2

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRR   93 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~   93 (398)
                      -.++|++++...+-.+-|...|+--|.+..-.+.+|.++.|++..++.|++.-.+..++.-.+......+.+.+ .+   
T Consensus       136 g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~Flr~~h~-f~---  211 (608)
T KOG4212|consen  136 GGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASFLRSLHI-FS---  211 (608)
T ss_pred             cCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhhhhhccC-CC---
Confidence            46899999999999999999999999888888999999999999999999999999999866666666666554 11   


Q ss_pred             ccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCcccc
Q 039806           94 ADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF  146 (398)
Q Consensus        94 ~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf  146 (398)
                            ..-..++||.||...+..+.|++.|.--|.|+++.+-.|+.|.++||
T Consensus       212 ------pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~  258 (608)
T KOG4212|consen  212 ------PPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGF  258 (608)
T ss_pred             ------CCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCe
Confidence                  11456799999999999999999999999999999999999999999

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

Probab=99.21  E-value=3.7e-12  Score=111.50  Aligned_cols=126  Identities=25%  Similarity=0.317  Sum_probs=108.6

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...++|||.||...+||+-|.++|-.-|.|..|+|..+.+++.| ||||.|+++-+..-|++-+||..+.+.++.|....
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            34679999999999999999999999999999999999988888 99999999999999999999999999998876532


Q ss_pred             ccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchh
Q 039806           92 RRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVL  151 (398)
Q Consensus        92 ~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l  151 (398)
                      -.+-             .-|...++++.+.+.|+.-|.|+.+++.++.+|+.+.|+.+++
T Consensus        86 G~sh-------------apld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~  132 (267)
T KOG4454|consen   86 GNSH-------------APLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTY  132 (267)
T ss_pred             CCCc-------------chhhhhcchhhheeeecccCCCCCccccccccCCccCccchhh
Confidence            1110             1166778999999999999999999999999988888765443

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

Probab=99.17  E-value=2.1e-10  Score=108.88  Aligned_cols=221  Identities=19%  Similarity=0.221  Sum_probs=147.1

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecc--eEeeeecc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVER--MELYVGPF   90 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g--k~i~V~~~   90 (398)
                      ..-+++|.|+-.-|+-|-|+.+|++||.|+.|......+|-   -|.|+|.+.+.|+.|...|+|..|.+  ..++|.++
T Consensus       149 ~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn~F---QALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~S  225 (492)
T KOG1190|consen  149 PVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNNGF---QALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFS  225 (492)
T ss_pred             eeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEecccch---hhhhhccchhhHHHHHHhccCCcccCceeEEEeehh
Confidence            34578999999999999999999999999987666554332   38999999999999999999987754  44555444


Q ss_pred             c----------cccccc------cc-----------------------------------------CCC--CceEEeeCC
Q 039806           91 I----------RRADRI------QE-----------------------------------------GSS--FNNLYVKNL  111 (398)
Q Consensus        91 ~----------~~~~~~------~~-----------------------------------------~~~--~~~lfV~nL  111 (398)
                      .          .|+..-      ..                                         ...  ...|.|.||
T Consensus       226 klt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnl  305 (492)
T KOG1190|consen  226 KLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNL  305 (492)
T ss_pred             hcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecC
Confidence            3          111100      00                                         001  345788888


Q ss_pred             Cc-cccHHHHHHHHccCCCEEEEEEeeCCC-CC----cccc--------------CCchhhhHHHHHHHH-------HHH
Q 039806          112 DD-DMTEEILVEKFSEFGKITSLVISKDAN-GT----SKGF--------------GSKVLYVARAQKKAE-------RKA  164 (398)
Q Consensus       112 p~-~~tee~L~~~F~~fG~I~~~~i~~d~~-g~----s~Gf--------------~~~~l~v~~a~~k~~-------~~~  164 (398)
                      .. .+|.+.|..+|+-||+|..++|+.++. ..    +.++              .++.|.|........       +..
T Consensus       306 n~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~egq~d~  385 (492)
T KOG1190|consen  306 NEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREGQEDQ  385 (492)
T ss_pred             chhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccCCCCCCccc
Confidence            65 589999999999999999999998764 22    2222              233333332211000       000


Q ss_pred             HHHHHHHH-----------------hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEeccc
Q 039806          165 ILRAQFER-----------------MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQT  226 (398)
Q Consensus       165 ~~~~~~~~-----------------~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~  226 (398)
                      .+.+.+..                 -.+..++...|||.+++||+|++.|..-|-..+.....   ++.+-+ .+.+.+.
T Consensus       386 glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff---~kd~kmal~q~~sv  462 (492)
T KOG1190|consen  386 GLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF---QKDRKMALPQLESV  462 (492)
T ss_pred             cccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeec---CCCcceeecccCCh
Confidence            00111100                 01234566699999999999999999998876665542   222333 7889999


Q ss_pred             HHHHHHHHHHhcc
Q 039806          227 KRERTSYLRIMYA  239 (398)
Q Consensus       227 ~ea~~A~l~~q~~  239 (398)
                      +||..|...++..
T Consensus       463 eeA~~ali~~hnh  475 (492)
T KOG1190|consen  463 EEAIQALIDLHNH  475 (492)
T ss_pred             hHhhhhccccccc
Confidence            9999887766543

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

Probab=99.15  E-value=7.1e-11  Score=100.82  Aligned_cols=65  Identities=12%  Similarity=0.207  Sum_probs=59.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ..++++|+||+.+++|++|+++|++||.|++|+|++|. +++++|| ||+|++.++|.+|+..+...
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~   99 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGK   99 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC
Confidence            35678999999999999999999999999999999987 8999999 99999999999999876543

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

Probab=99.08  E-value=1.4e-10  Score=103.43  Aligned_cols=64  Identities=20%  Similarity=0.352  Sum_probs=59.9

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      .+.++.|.||+.+++|++|+++|.+||.|.+|.|.+|+ +|.+||| ||+|.++++|.+|+..+..
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG  253 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNG  253 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccC
Confidence            45679999999999999999999999999999999998 9999999 9999999999999987654

>PF00076 RRM_1: RNA recognition motif

Probab=99.08  E-value=2.7e-10  Score=84.24  Aligned_cols=61  Identities=30%  Similarity=0.434  Sum_probs=56.8

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ++|+|||.++|+++|+++|++||.|.+++++.+.++.++|| ||.|.+.++|.+|+..++..
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~   62 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGK   62 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCC
Confidence            46799999999999999999999999999999888899999 99999999999999888764

(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 ....

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

Probab=99.05  E-value=2.6e-10  Score=106.37  Aligned_cols=84  Identities=25%  Similarity=0.343  Sum_probs=78.3

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      +....-|||=-|.+-+|.+||+-+||.||.|.+|.|++|. +|.|-.||||+|++.+++++|.-++++.+|+++.|.|..
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            3456689999999999999999999999999999999999 999999999999999999999999999999999999988


Q ss_pred             ccccc
Q 039806           90 FIRRA   94 (398)
Q Consensus        90 ~~~~~   94 (398)
                      +.+-+
T Consensus       316 SQSVs  320 (479)
T KOG0415|consen  316 SQSVS  320 (479)
T ss_pred             hhhhh
Confidence            87543

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

Probab=99.05  E-value=2.2e-10  Score=101.84  Aligned_cols=59  Identities=19%  Similarity=0.271  Sum_probs=55.5

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHH
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      -.+++|++|+.++.+|+|+++|++||+|+++.|+.|+ +|+|||| ||+|.+.+.|.||..
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~   72 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACK   72 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhc
Confidence            3567889999999999999999999999999999998 9999999 999999999999976

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

Probab=99.04  E-value=7.6e-09  Score=97.41  Aligned_cols=221  Identities=18%  Similarity=0.135  Sum_probs=151.2

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec-c-eEeeeecccccc
Q 039806           17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE-R-MELYVGPFIRRA   94 (398)
Q Consensus        17 lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~-g-k~i~V~~~~~~~   94 (398)
                      +-|-|--+.||-+-|+.+....|.|+.|.|.+. +|.   -|.|+|++.+.|++|.++|||..|. | ..|+|+++++.+
T Consensus       125 ~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ngV---QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  125 FTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NGV---QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             EEeecCccccchhhhhhhcCCCCceEEEEEEec-cce---eeEEeechhHHHHHHHhhcccccccccceeEEEEecCcce
Confidence            344455589999999999999999999999886 454   4999999999999999999998774 3 678887776332


Q ss_pred             ccccc---------------------------------------------------------------------------
Q 039806           95 DRIQE---------------------------------------------------------------------------   99 (398)
Q Consensus        95 ~~~~~---------------------------------------------------------------------------   99 (398)
                      -+...                                                                           
T Consensus       201 lnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~  280 (494)
T KOG1456|consen  201 LNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGRGYAS  280 (494)
T ss_pred             eeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccccCCCCCC
Confidence            11000                                                                           


Q ss_pred             ---CCCCceEEeeCCCcc-ccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHH-----------------
Q 039806          100 ---GSSFNNLYVKNLDDD-MTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQK-----------------  158 (398)
Q Consensus       100 ---~~~~~~lfV~nLp~~-~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~-----------------  158 (398)
                         ......+.|.+|... .+-+.|.++|=-||.|+.++.|+.+.|...---+....|+++..                 
T Consensus       281 p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~S  360 (494)
T KOG1456|consen  281 PGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVS  360 (494)
T ss_pred             CCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeec
Confidence               001233778888765 56778999999999999999998876532211111112222211                 


Q ss_pred             --------------------------HHHHH--HHHHHHHHHhhhhhhccccCCCcccCHHHHHHHhhcCCC-eEEEEEe
Q 039806          159 --------------------------KAERK--AILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGT-ISSVKIM  209 (398)
Q Consensus       159 --------------------------k~~~~--~~~~~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~-I~svki~  209 (398)
                                                +..|-  .+...+..-.-+++++.|.|.|..+|||.|.++|..-+. -++|+|+
T Consensus       361 kQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvF  440 (494)
T KOG1456|consen  361 KQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVF  440 (494)
T ss_pred             cccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEee
Confidence                                      00000  000000000113456777999999999999999987654 5788988


Q ss_pred             eCCCCC-ccceEEEecccHHHHHHHHHHhccccC
Q 039806          210 RTDRGI-SKGHCMAIAQTKRERTSYLRIMYAKQG  242 (398)
Q Consensus       210 ~d~~g~-skGffV~f~~~~ea~~A~l~~q~~q~~  242 (398)
                      .-++-+ +.| .++|++.++|..|+....+.+..
T Consensus       441 p~kserSssG-llEfe~~s~Aveal~~~NH~pi~  473 (494)
T KOG1456|consen  441 PLKSERSSSG-LLEFENKSDAVEALMKLNHYPIE  473 (494)
T ss_pred             cccccccccc-eeeeehHHHHHHHHHHhcccccc
Confidence            766444 456 79999999999999888776654

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.03  E-value=3.2e-08  Score=93.58  Aligned_cols=222  Identities=15%  Similarity=0.190  Sum_probs=149.0

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEE-EEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccccc
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKFGDIQSS-KVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRA   94 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~G~I~~v-ki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~~   94 (398)
                      -|..++||+.-++.+|..+|+-.....-- .+..+..|+..|.|.|.|.+.|.-+-|++. +.+.+.++.|.|-.+...+
T Consensus        62 vvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkR-hkhh~g~ryievYka~ge~  140 (508)
T KOG1365|consen   62 VVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKR-HKHHMGTRYIEVYKATGEE  140 (508)
T ss_pred             EEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHh-hhhhccCCceeeeccCchh
Confidence            45667999999999999999764221111 122223677889999999999999999985 7778888999887665433


Q ss_pred             cccc------cC------CCCceEEeeCCCccccHHHHHHHHccC----CCEEEEEEeeCCCCCccccCCchhhhH----
Q 039806           95 DRIQ------EG------SSFNNLYVKNLDDDMTEEILVEKFSEF----GKITSLVISKDANGTSKGFGSKVLYVA----  154 (398)
Q Consensus        95 ~~~~------~~------~~~~~lfV~nLp~~~tee~L~~~F~~f----G~I~~~~i~~d~~g~s~Gf~~~~l~v~----  154 (398)
                      --..      +.      .+.--|.+++||++.|+.|+.++|..-    |.++.+-.++..+|+..|-.+..+...    
T Consensus       141 f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq  220 (508)
T KOG1365|consen  141 FLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQ  220 (508)
T ss_pred             heEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHH
Confidence            1110      00      023447788999999999999999732    345667667777777776532222111    


Q ss_pred             HHHHH-----------------HHHHHHHHHHHH---------------------HhhhhhhccccCCCcccCHHHHHHH
Q 039806          155 RAQKK-----------------AERKAILRAQFE---------------------RMRKERAELYKNINDEVDEIELKQY  196 (398)
Q Consensus       155 ~a~~k-----------------~~~~~~~~~~~~---------------------~~~~~~~~~v~nL~~~vtee~L~~~  196 (398)
                      .+-.|                 ++-...+++...                     ..+...++.+++||++.+.|+|-++
T Consensus       221 ~aL~khrq~iGqRYIElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~F  300 (508)
T KOG1365|consen  221 FALRKHRQNIGQRYIELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDF  300 (508)
T ss_pred             HHHHHHHHHHhHHHHHHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHH
Confidence            11111                 111111111110                     0111334566999999999999999


Q ss_pred             hhcCCC-eEE--EEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          197 FSQCGT-ISS--VKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       197 F~~fG~-I~s--vki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      |..|-+ |.-  |.++.+..|+..|- ||+|.+.++|+.|....+-
T Consensus       301 lgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk  346 (508)
T KOG1365|consen  301 LGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHK  346 (508)
T ss_pred             HHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHH
Confidence            999965 444  88888889999998 9999999998888765544

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

Probab=99.01  E-value=6.7e-10  Score=96.95  Aligned_cols=79  Identities=22%  Similarity=0.343  Sum_probs=71.9

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhcc-CCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKF-GDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~-G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      .+-++|+.+|.-+.+.+|..+|.+| |.|+.+++.++. ||.|||||||+|+++|.|.-|-+.||+.++.++-|.+...-
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmp  128 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMP  128 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeC
Confidence            4568999999999999999999998 778888888888 99999999999999999999999999999999999887654


Q ss_pred             c
Q 039806           92 R   92 (398)
Q Consensus        92 ~   92 (398)
                      +
T Consensus       129 p  129 (214)
T KOG4208|consen  129 P  129 (214)
T ss_pred             c
Confidence            3

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

Probab=98.97  E-value=1.1e-09  Score=107.61  Aligned_cols=82  Identities=30%  Similarity=0.403  Sum_probs=76.1

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      +.+-.++|||.+|+..+...||+.+|++||.|+-.||+++. +--.+|||||.+.+.++|.+||+.|+...|.|+-|.|+
T Consensus       401 rs~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVE  480 (940)
T KOG4661|consen  401 RSTLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVE  480 (940)
T ss_pred             ccccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeee
Confidence            34556899999999999999999999999999999999998 66789999999999999999999999999999999998


Q ss_pred             ccc
Q 039806           89 PFI   91 (398)
Q Consensus        89 ~~~   91 (398)
                      .+.
T Consensus       481 kaK  483 (940)
T KOG4661|consen  481 KAK  483 (940)
T ss_pred             ecc
Confidence            776

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

Probab=98.92  E-value=1.3e-08  Score=96.87  Aligned_cols=117  Identities=22%  Similarity=0.260  Sum_probs=95.8

Q ss_pred             cceEEEcCCC-CCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLA-STIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp-~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      +..|.|.||. ..||.+.|+.+|..||+|..|||..++.    --|.|++.+...|+-|++.|+|..|.||+|+|.+++.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC----cceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            5788999998 5789999999999999999999998752    3599999999999999999999999999999988763


Q ss_pred             ccc-----cccc-------------------C-------CCCceEEeeCCCccccHHHHHHHHccCCCEEEEE
Q 039806           93 RAD-----RIQE-------------------G-------SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLV  134 (398)
Q Consensus        93 ~~~-----~~~~-------------------~-------~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~  134 (398)
                      ..-     ...+                   .       ....++...|+|.+++||++++.|..-|-..+..
T Consensus       373 ~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkaf  445 (492)
T KOG1190|consen  373 TNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAF  445 (492)
T ss_pred             ccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEee
Confidence            221     0000                   0       0234577899999999999999999888665543

>PF14259 RRM_6: RNA recognition motif (a

Probab=98.89  E-value=4.9e-09  Score=77.84  Aligned_cols=59  Identities=17%  Similarity=0.412  Sum_probs=53.0

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHh
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ++++|||.++++++|+++|+.||.|..+++..+++|.++|+ ||+|.+.++|.+|+...+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~   60 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLN   60 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCC
Confidence            46799999999999999999999999999999888889999 999999999999988765

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

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

Probab=98.88  E-value=2e-09  Score=99.83  Aligned_cols=67  Identities=18%  Similarity=0.274  Sum_probs=60.7

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ...+.+.|.|||+..-|-||+..|.+||.|.+|.|+.++.| |||| ||+|++.+||.||+.+++....
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~V  161 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTVV  161 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhccee
Confidence            34567899999999999999999999999999999988665 7999 9999999999999999998753

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

Probab=98.85  E-value=7.8e-09  Score=96.66  Aligned_cols=76  Identities=22%  Similarity=0.363  Sum_probs=68.6

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHh-cCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL-QGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~l-ng~~l~gk~i~V~~~   90 (398)
                      ..+.+|||++|-..++|.+|+++|.+||.|.++.+..     .+++|||+|.+.++|+.|.+++ |...|+|++|+|.|.
T Consensus       226 ~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~-----~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg  300 (377)
T KOG0153|consen  226 TSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILP-----RKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWG  300 (377)
T ss_pred             cceeEEEecccccchhHHHHHHHHhhcCCeeeEEeec-----ccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeC
Confidence            3467999999999999999999999999999999987     4579999999999999998864 666889999999998


Q ss_pred             cc
Q 039806           91 IR   92 (398)
Q Consensus        91 ~~   92 (398)
                      .+
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            87

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

Probab=98.84  E-value=9e-09  Score=94.11  Aligned_cols=83  Identities=19%  Similarity=0.340  Sum_probs=76.4

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      +...+|.|.|||..|+++||+++|..||.+..+-|-.|++|.|.|.|-|.|...++|..|++.+||..|+|+.+.+....
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            44578999999999999999999999999999999999999999999999999999999999999999999999887765


Q ss_pred             ccc
Q 039806           92 RRA   94 (398)
Q Consensus        92 ~~~   94 (398)
                      +..
T Consensus       161 ~~~  163 (243)
T KOG0533|consen  161 SPS  163 (243)
T ss_pred             Ccc
Confidence            443

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

Probab=98.81  E-value=4.3e-09  Score=94.52  Aligned_cols=89  Identities=25%  Similarity=0.399  Sum_probs=80.2

Q ss_pred             CCccc--cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeec
Q 039806            5 PNSEA--RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVE   81 (398)
Q Consensus         5 rd~~~--~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~   81 (398)
                      .||++  -+....+||.+.|..+++++.|-..|++|-.....++++|. +|+||||+||.|.+.+++.+|+.++||..++
T Consensus       179 edPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVg  258 (290)
T KOG0226|consen  179 EDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVG  258 (290)
T ss_pred             CCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccc
Confidence            45554  35667899999999999999999999999999999999999 9999999999999999999999999999999


Q ss_pred             ceEeeeeccccc
Q 039806           82 RMELYVGPFIRR   93 (398)
Q Consensus        82 gk~i~V~~~~~~   93 (398)
                      .+.|+...+.-+
T Consensus       259 srpiklRkS~wk  270 (290)
T KOG0226|consen  259 SRPIKLRKSEWK  270 (290)
T ss_pred             cchhHhhhhhHH
Confidence            999998766543

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

Probab=98.78  E-value=1.3e-08  Score=100.23  Aligned_cols=77  Identities=27%  Similarity=0.423  Sum_probs=68.9

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      .++|||+|||.+++.++|+++|+.||.|....|.... .+++.+||||+|++.++++.||++ +-..|+++++.|+.-.
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            4459999999999999999999999999999888866 666669999999999999999996 6889999999997643

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.76  E-value=4.5e-10  Score=115.54  Aligned_cols=220  Identities=17%  Similarity=0.119  Sum_probs=162.5

Q ss_pred             ceEEEcCCCCCCcHH-HHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           15 GNAFVKNLASTIDNL-KLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        15 ~~lfV~nLp~~vte~-~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ....+.|+.+...++ .....|..+|.|..|++.... .-.+.-++++.+....+++.|.. .++..+.++...|..+.+
T Consensus       572 ~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~~av~~ad~  650 (881)
T KOG0128|consen  572 REKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAGGALANRSAAVGLADA  650 (881)
T ss_pred             hhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhccc-ccccccCCccccCCCCCc
Confidence            456777888777666 577889999999999998744 22222389999999999999997 588999999999988887


Q ss_pred             cccccccCC------CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCC-CCCccccCCchhhhHHHHHHHHHHHH
Q 039806           93 RADRIQEGS------SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-NGTSKGFGSKVLYVARAQKKAERKAI  165 (398)
Q Consensus        93 ~~~~~~~~~------~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~-~g~s~Gf~~~~l~v~~a~~k~~~~~~  165 (398)
                      +.......-      ...++||+||+....++||...|+.+|.+..+.+.... .++.+|++    |+.+-.......+.
T Consensus       651 ~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~----Y~~F~~~~~~~aaV  726 (881)
T KOG0128|consen  651 EEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKA----YVEFLKPEHAGAAV  726 (881)
T ss_pred             hhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccce----eeEeecCCchhhhh
Confidence            664322111      23568999999999999999999999999887766332 36777764    33222222111111


Q ss_pred             HHHHHHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          166 LRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       166 ~~~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ... ....-....+++.|+|+..|+++|+.+|+++|++++.+++....|+.+|- ||.|.+..++.++........
T Consensus       727 ~f~-d~~~~gK~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~  801 (881)
T KOG0128|consen  727 AFR-DSCFFGKISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAG  801 (881)
T ss_pred             hhh-hhhhhhhhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhh
Confidence            000 00011134577799999999999999999999999999998889999998 999999999888876555543

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

Probab=98.75  E-value=3.9e-08  Score=96.00  Aligned_cols=133  Identities=16%  Similarity=0.239  Sum_probs=90.4

Q ss_pred             CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHH--HHHHHH---------
Q 039806          102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKA--ILRAQF---------  170 (398)
Q Consensus       102 ~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~--~~~~~~---------  170 (398)
                      ...-|-+.+|||+.|++||.++|+.++ |+++.+.++ +|+..|-...++.-+....++.+..  ...+.+         
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~-~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR-NGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc-CCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCc
Confidence            344577889999999999999999986 777655554 5677666433322222221111110  000000         


Q ss_pred             ------HH-----hhhhhhccccCCCcccCHHHHHHHhhcCCCeEE-EEEeeCCCCCccce-EEEecccHHHHHHHHHH
Q 039806          171 ------ER-----MRKERAELYKNINDEVDEIELKQYFSQCGTISS-VKIMRTDRGISKGH-CMAIAQTKRERTSYLRI  236 (398)
Q Consensus       171 ------~~-----~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~s-vki~~d~~g~skGf-fV~f~~~~ea~~A~l~~  236 (398)
                            ..     ......+.+++||+.||+++|.++|+..-.|.. |-+..|..|+++|- ||+|++.+.|++|+..-
T Consensus        87 e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~rh  165 (510)
T KOG4211|consen   87 EADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGRH  165 (510)
T ss_pred             cccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHHH
Confidence                  00     012334566999999999999999998877766 55677789999988 99999999999998743

>PLN03120 nucleic acid binding protein; Provisional

Probab=98.74  E-value=1.7e-08  Score=92.82  Aligned_cols=61  Identities=20%  Similarity=0.288  Sum_probs=53.9

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      .++++|+||++++||++|+++|+.||.|++|+|.+|..  ++|| ||+|.+.++|..|++ +...
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~All-LnG~   65 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETALL-LSGA   65 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHHH-hcCC
Confidence            46789999999999999999999999999999998763  5788 999999999999996 4433

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.72  E-value=7.4e-08  Score=94.66  Aligned_cols=132  Identities=20%  Similarity=0.265  Sum_probs=96.8

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC--CC--Ccee---EEEEEecCHHHHHHHHHHhcCCeecceE
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ--EG--KSKG---YGFVQYSTPESALDAIEKLQGATVERME   84 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~--~g--~skg---~aFV~F~~~e~A~~Ai~~lng~~l~gk~   84 (398)
                      .-+++|||++||.+++|+.|...|..||.+. |......  .+  ..+|   |+|+.|+++.+...-|.++.-   .+.+
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~---~~~~  332 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE---GEGN  332 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh---cccc
Confidence            3468899999999999999999999999874 4444222  22  3466   999999999999988876532   3333


Q ss_pred             eeeecccccccc-------------------cccCCCCceEEeeCCCccccHHHHHHHHc-cCCCEEEEEEeeCCC-CCc
Q 039806           85 LYVGPFIRRADR-------------------IQEGSSFNNLYVKNLDDDMTEEILVEKFS-EFGKITSLVISKDAN-GTS  143 (398)
Q Consensus        85 i~V~~~~~~~~~-------------------~~~~~~~~~lfV~nLp~~~tee~L~~~F~-~fG~I~~~~i~~d~~-g~s  143 (398)
                      .++..+.+....                   ...-+..++|||++||.-++.++|..+|+ -||.|..+-|-.|.+ +..
T Consensus       333 ~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYP  412 (520)
T KOG0129|consen  333 YYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYP  412 (520)
T ss_pred             eEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCC
Confidence            333222221111                   01112678999999999999999999999 899999999999965 667


Q ss_pred             cccC
Q 039806          144 KGFG  147 (398)
Q Consensus       144 ~Gf~  147 (398)
                      +|-+
T Consensus       413 kGaG  416 (520)
T KOG0129|consen  413 KGAG  416 (520)
T ss_pred             CCcc
Confidence            7765

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.70  E-value=2.6e-08  Score=90.09  Aligned_cols=56  Identities=23%  Similarity=0.405  Sum_probs=50.7

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHH
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      .+++|+||++++||++|+++|+.||+|++|+|.+|  +..+|| ||+|.+.+++..|++
T Consensus         6 ~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D--~et~gfAfVtF~d~~aaetAll   62 (243)
T PLN03121          6 YTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS--GEYACTAYVTFKDAYALETAVL   62 (243)
T ss_pred             eEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC--CCcceEEEEEECCHHHHHHHHh
Confidence            57888999999999999999999999999999988  455567 999999999998875

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

Probab=98.67  E-value=3.1e-08  Score=90.91  Aligned_cols=68  Identities=19%  Similarity=0.329  Sum_probs=62.2

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccccC
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAKQG  242 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q~~  242 (398)
                      +=+++||.-|+.+++|.+|+.+|+.||.|+.|+|++|. +|+++|| ||+|....+...|..++...+..
T Consensus       100 Py~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Id  169 (335)
T KOG0113|consen  100 PYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKID  169 (335)
T ss_pred             ccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceec
Confidence            34689999999999999999999999999999999997 9999999 99999999999999888865543

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

Probab=98.66  E-value=1.7e-08  Score=99.91  Aligned_cols=78  Identities=22%  Similarity=0.348  Sum_probs=70.1

Q ss_pred             CCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceE
Q 039806            5 PNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERME   84 (398)
Q Consensus         5 rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~   84 (398)
                      ++|+......++|+|-|||.+|++++|+.+|+.||+|..|+.-.    ..+|..||+|-+..+|++|+++||+..+.|+.
T Consensus        66 ~np~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~----~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~  141 (549)
T KOG4660|consen   66 DNPSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP----NKRGIVFVEFYDVRDAERALKALNRREIAGKR  141 (549)
T ss_pred             CCCCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc----ccCceEEEEEeehHhHHHHHHHHHHHHhhhhh
Confidence            45666677889999999999999999999999999999866533    46789999999999999999999999999999


Q ss_pred             ee
Q 039806           85 LY   86 (398)
Q Consensus        85 i~   86 (398)
                      |+
T Consensus       142 ~k  143 (549)
T KOG4660|consen  142 IK  143 (549)
T ss_pred             hc
Confidence            88

>smart00360 RRM RNA recognition motif

Probab=98.64  E-value=1e-07  Score=69.50  Aligned_cols=57  Identities=28%  Similarity=0.459  Sum_probs=52.2

Q ss_pred             ccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHh
Q 039806          181 YKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       181 v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ++||+..+++++|+++|++||.|.++++..+. +++++|+ ||.|.+.++|.+|+..++
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~   59 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALN   59 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcC
Confidence            36899999999999999999999999999887 6889999 999999999999987665

>smart00362 RRM_2 RNA recognition motif

Probab=98.63  E-value=1.1e-07  Score=69.66  Aligned_cols=58  Identities=29%  Similarity=0.414  Sum_probs=53.0

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHh
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      +++.|||..+++++|+++|++||.|.++++.++. +.++|+ ||+|.+.++|.+|...++
T Consensus         2 v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~   60 (72)
T smart00362        2 LFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALN   60 (72)
T ss_pred             EEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhC
Confidence            5779999999999999999999999999999887 778888 999999999999987655

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

Probab=98.63  E-value=2.9e-08  Score=86.59  Aligned_cols=65  Identities=15%  Similarity=0.184  Sum_probs=60.7

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ..|+|.||-+.++.++|+.+|++||.|-+|.|.+|. ++.++|| ||.|..+.||..|..++.....
T Consensus        14 ~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~l   80 (256)
T KOG4207|consen   14 TSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVL   80 (256)
T ss_pred             eeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceee
Confidence            468899999999999999999999999999999999 9999999 9999999999999998876653

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

Probab=98.61  E-value=7e-08  Score=78.06  Aligned_cols=66  Identities=18%  Similarity=0.245  Sum_probs=58.3

Q ss_pred             HHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHH
Q 039806          171 ERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRI  236 (398)
Q Consensus       171 ~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~  236 (398)
                      +..+.+.+++|+||++.++||.|.++|+++|.|..|-+-.|. +-..+|| ||+|.++++|..|..-.
T Consensus        31 ~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryi   98 (153)
T KOG0121|consen   31 EALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYI   98 (153)
T ss_pred             HHHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHh
Confidence            345567889999999999999999999999999999988888 6779999 99999999999886543

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

Probab=98.58  E-value=6.1e-08  Score=88.83  Aligned_cols=82  Identities=21%  Similarity=0.294  Sum_probs=75.7

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      .-+...+||+|++..+|.+++...|+.||.|..+.|..|. +|.+|||+||+|.+.+.+.+|+. ||+..|.|+.+.|.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            4466789999999999999999999999999999999999 77899999999999999999999 999999999999987


Q ss_pred             cccc
Q 039806           90 FIRR   93 (398)
Q Consensus        90 ~~~~   93 (398)
                      ..-+
T Consensus       177 ~r~~  180 (231)
T KOG4209|consen  177 KRTN  180 (231)
T ss_pred             eeee
Confidence            6544

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

Probab=98.54  E-value=6.6e-07  Score=70.43  Aligned_cols=77  Identities=16%  Similarity=0.261  Sum_probs=65.8

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhc--cCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeec----ceEeee
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSK--FGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVE----RMELYV   87 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~--~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~----gk~i~V   87 (398)
                      +||.|+|||...|.++|.+++..  .|...-+-++.|. ++.+.|||||.|.+.++|.+-.+..+|..+.    .|.+.|
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            58999999999999999998865  5677778888888 8889999999999999999999999998775    355566


Q ss_pred             eccc
Q 039806           88 GPFI   91 (398)
Q Consensus        88 ~~~~   91 (398)
                      .++.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            5554

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

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.51  E-value=1.4e-07  Score=89.33  Aligned_cols=135  Identities=24%  Similarity=0.287  Sum_probs=107.0

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcC-CeecceEeeeec
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQG-ATVERMELYVGP   89 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng-~~l~gk~i~V~~   89 (398)
                      ...+++|++++...+.+.++..++..+|.+..+...... +..++|+++|+|...+.+..|+.. ++ ..+.+..+....
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~-s~~~~~~~~~~~~dl  164 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEE-SGSKVLDGNKGEKDL  164 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHh-hhccccccccccCcc
Confidence            457899999999999999999999999988888777766 889999999999999999999984 55 355555555444


Q ss_pred             ccccccc------cccCCCCceEE-eeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCccccC
Q 039806           90 FIRRADR------IQEGSSFNNLY-VKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG  147 (398)
Q Consensus        90 ~~~~~~~------~~~~~~~~~lf-V~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf~  147 (398)
                      ...+..+      ........++| |+++++++++++|+..|..+|.|+.+++..+.. +.++||+
T Consensus       165 ~~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a  230 (285)
T KOG4210|consen  165 NTRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFA  230 (285)
T ss_pred             cccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhh
Confidence            3333211      11111334444 999999999999999999999999999998886 8899985

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

Probab=98.49  E-value=3.1e-08  Score=84.77  Aligned_cols=56  Identities=21%  Similarity=0.311  Sum_probs=49.7

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHH
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRER  230 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~  230 (398)
                      .+.-++++|||++.||.+|.-+|++||+|++|.++||+ ||+|+|| |.+|.+.....
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTI   91 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTI   91 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceE
Confidence            34567889999999999999999999999999999998 9999999 99997765433

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

Probab=98.48  E-value=2.4e-07  Score=79.61  Aligned_cols=132  Identities=15%  Similarity=0.201  Sum_probs=90.2

Q ss_pred             CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCcccc---------------------CCchhhhHHHHHHH
Q 039806          102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF---------------------GSKVLYVARAQKKA  160 (398)
Q Consensus       102 ~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf---------------------~~~~l~v~~a~~k~  160 (398)
                      ..+.|||+|||.++-|.||.++|.+||.|.+|.+......-.-.|                     ++..|.|+++.--.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr   84 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGR   84 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCC
Confidence            567899999999999999999999999999998865442222222                     12222332221100


Q ss_pred             HHHHHHHH----------------HHHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccceEEEec
Q 039806          161 ERKAILRA----------------QFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIA  224 (398)
Q Consensus       161 ~~~~~~~~----------------~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGffV~f~  224 (398)
                      ... ....                .-...+.+..+.|.+||.+-++.+|+++..+-|.|-...+.+|-+|     -|+|.
T Consensus        85 ~s~-~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rDg~G-----vV~~~  158 (241)
T KOG0105|consen   85 SSS-DRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRDGVG-----VVEYL  158 (241)
T ss_pred             ccc-ccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecccce-----eeeee
Confidence            000 0000                0011123345667999999999999999999999999999988654     59999


Q ss_pred             ccHHHHHHHHHHhcc
Q 039806          225 QTKRERTSYLRIMYA  239 (398)
Q Consensus       225 ~~~ea~~A~l~~q~~  239 (398)
                      ..++-.-|+.++.-+
T Consensus       159 r~eDMkYAvr~ld~~  173 (241)
T KOG0105|consen  159 RKEDMKYAVRKLDDQ  173 (241)
T ss_pred             ehhhHHHHHHhhccc
Confidence            999888887766543

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.45  E-value=1.7e-08  Score=104.17  Aligned_cols=114  Identities=25%  Similarity=0.303  Sum_probs=98.1

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEE-cCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~-d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..+++||+||+..+.++||.+.|+.+|.+..+.+.- ..+++-+|+|||.|.++++|.+||.....+.+ |         
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~-g---------  735 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF-G---------  735 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh-h---------
Confidence            356799999999999999999999999988887773 33788999999999999999999985443333 3         


Q ss_pred             ccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccC
Q 039806           92 RRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG  147 (398)
Q Consensus        92 ~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~  147 (398)
                                 ...++|.|.|+..|.++++.+++.+|.+++..++...+|+.+|-.
T Consensus       736 -----------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a  780 (881)
T KOG0128|consen  736 -----------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKA  780 (881)
T ss_pred             -----------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccce
Confidence                       236899999999999999999999999999999988888888863

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

Probab=98.44  E-value=3.5e-07  Score=85.18  Aligned_cols=65  Identities=17%  Similarity=0.343  Sum_probs=60.9

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..+++|+||+.++++++|+++|.+||.|.+|+|..|. +|+++|| ||.|.+.+++..|+..++...
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~  181 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKE  181 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCe
Confidence            5889999999999999999999999999999999996 9999999 999999999999999888443

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

Probab=98.44  E-value=5.3e-07  Score=91.44  Aligned_cols=80  Identities=28%  Similarity=0.433  Sum_probs=72.3

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC----CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ----EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~----~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      .-.+||||+||+++++++.|..+|..||+|.++||+.-.    ..+-+-+|||-|-+..+|++|++.|+|.++.+.++++
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~  251 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKL  251 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeee
Confidence            346899999999999999999999999999999998765    2345669999999999999999999999999999999


Q ss_pred             eccc
Q 039806           88 GPFI   91 (398)
Q Consensus        88 ~~~~   91 (398)
                      .|..
T Consensus       252 gWgk  255 (877)
T KOG0151|consen  252 GWGK  255 (877)
T ss_pred             cccc
Confidence            9884

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=98.44  E-value=7.7e-07  Score=65.38  Aligned_cols=61  Identities=23%  Similarity=0.359  Sum_probs=54.8

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      +++.|||..+++++|+++|+.||.|..+++..++.+..+|+ ||+|.+.++|..|....+..
T Consensus         2 i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~   63 (74)
T cd00590           2 LFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGK   63 (74)
T ss_pred             EEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            56799999999999999999999999999998886677777 99999999999998876654

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).

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.42  E-value=1.2e-06  Score=83.15  Aligned_cols=135  Identities=16%  Similarity=0.186  Sum_probs=100.9

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhc----cCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSK----FGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~----~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      .+.--|..++||+++|+.|+.++|..    -|....|-+++..+|+-.|-|||.|..+++|+.||.+ |...|+-|.|.+
T Consensus       159 ~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIEl  237 (508)
T KOG1365|consen  159 ENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIEL  237 (508)
T ss_pred             ccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHH
Confidence            33456778899999999999999963    2345677777877999999999999999999999986 666666666655


Q ss_pred             eccccccc-----cc----------------------ccCCCCceEEeeCCCccccHHHHHHHHccCCCEEE---EEEee
Q 039806           88 GPFIRRAD-----RI----------------------QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITS---LVISK  137 (398)
Q Consensus        88 ~~~~~~~~-----~~----------------------~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~---~~i~~  137 (398)
                      -.+....-     |.                      ....+..+|.+++||++.|.|||.++|..|..-..   +.+..
T Consensus       238 FRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~  317 (508)
T KOG1365|consen  238 FRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVL  317 (508)
T ss_pred             HHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEE
Confidence            44332110     00                      00114678999999999999999999999975433   67777


Q ss_pred             CCCCCccccC
Q 039806          138 DANGTSKGFG  147 (398)
Q Consensus       138 d~~g~s~Gf~  147 (398)
                      +..|+..|-.
T Consensus       318 N~qGrPSGeA  327 (508)
T KOG1365|consen  318 NGQGRPSGEA  327 (508)
T ss_pred             cCCCCcChhh
Confidence            7778877764

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

Probab=98.41  E-value=4.4e-06  Score=79.08  Aligned_cols=124  Identities=19%  Similarity=0.154  Sum_probs=97.7

Q ss_pred             CcceEEEcCCCC-CCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLAS-TIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~-~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..+-+.|-+|+. .++.+.|..+|..||+|+.||+++.+.    |.|.|+..+..+.++|+..||+..+.|.+|.|..+.
T Consensus       286 ~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~----gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~Sk  361 (494)
T KOG1456|consen  286 PGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKP----GTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSK  361 (494)
T ss_pred             CCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeeccc----ceeEEEcCcHHHHHHHHHHhccCccccceEEEeecc
Confidence            456789999995 567888999999999999999998753    579999999999999999999999999999997765


Q ss_pred             ccc------------------------cccccC---------CCCceEEeeCCCccccHHHHHHHHccCCC-EEEEEEee
Q 039806           92 RRA------------------------DRIQEG---------SSFNNLYVKNLDDDMTEEILVEKFSEFGK-ITSLVISK  137 (398)
Q Consensus        92 ~~~------------------------~~~~~~---------~~~~~lfV~nLp~~~tee~L~~~F~~fG~-I~~~~i~~  137 (398)
                      ...                        .|-...         ..++.|..-|.|..+|||.|.++|..-+. -++++|..
T Consensus       362 Q~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp  441 (494)
T KOG1456|consen  362 QNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFP  441 (494)
T ss_pred             ccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeec
Confidence            221                        110000         04456888899999999999999986654 35666665


Q ss_pred             CCC
Q 039806          138 DAN  140 (398)
Q Consensus       138 d~~  140 (398)
                      .++
T Consensus       442 ~ks  444 (494)
T KOG1456|consen  442 LKS  444 (494)
T ss_pred             ccc
Confidence            544

>PLN03213 repressor of silencing 3; Provisional

Probab=98.40  E-value=5.3e-07  Score=87.92  Aligned_cols=62  Identities=16%  Similarity=0.247  Sum_probs=54.5

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEeccc--HHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQT--KRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~--~ea~~A~l~~q~~q  240 (398)
                      ...++|+||++++++++|+..|+.||.|.+|.|+++ +|  ||| ||+|...  +++.+|+..+....
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAE   74 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCV   74 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCe
Confidence            456888999999999999999999999999999954 66  999 9999988  68899988776554

>smart00361 RRM_1 RNA recognition motif

Probab=98.37  E-value=9e-07  Score=65.81  Aligned_cols=51  Identities=10%  Similarity=0.259  Sum_probs=43.5

Q ss_pred             HHHHHHHhh----cCCCeEEEE-EeeCC-C--CCccce-EEEecccHHHHHHHHHHhccc
Q 039806          190 EIELKQYFS----QCGTISSVK-IMRTD-R--GISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       190 ee~L~~~F~----~fG~I~svk-i~~d~-~--g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +++|+++|+    +||.|.+|. |..|. +  |.++|| ||.|.+.++|.+|+..++...
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~   61 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRY   61 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            678888888    999999995 66654 5  899999 999999999999998877543

>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=98.37  E-value=1.6e-06  Score=65.24  Aligned_cols=71  Identities=21%  Similarity=0.276  Sum_probs=48.5

Q ss_pred             ceEEEcCCCCCCcHHHHH----HHHhccC-CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           15 GNAFVKNLASTIDNLKLH----QIFSKFG-DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~----~~F~~~G-~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ..|+|.|||.+.+-..|+    .++..+| .|++|         +.+.|+|.|.+.|.|++|.+.|+|..+.|.+|.|.+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v---------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV---------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE---------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            469999999999887754    5666776 67766         346799999999999999999999999999999988


Q ss_pred             ccccc
Q 039806           90 FIRRA   94 (398)
Q Consensus        90 ~~~~~   94 (398)
                      .....
T Consensus        74 ~~~~r   78 (90)
T PF11608_consen   74 SPKNR   78 (90)
T ss_dssp             S--S-
T ss_pred             cCCcc
Confidence            75433

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

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

Probab=98.36  E-value=7.7e-07  Score=69.44  Aligned_cols=63  Identities=16%  Similarity=0.238  Sum_probs=53.2

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      .++.++|+|||+++|.|+..++|.+||+|..|+|-.+..  -+|- ||.|++..+|++|...+...
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~--TrGTAFVVYedi~dAk~A~dhlsg~   80 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE--TRGTAFVVYEDIFDAKKACDHLSGY   80 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC--cCceEEEEehHhhhHHHHHHHhccc
Confidence            356788899999999999999999999999999975543  3454 99999999999998766543

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

Probab=98.36  E-value=1e-06  Score=78.43  Aligned_cols=136  Identities=18%  Similarity=0.244  Sum_probs=93.9

Q ss_pred             CceEEeeCCCccccHHHHHH----HHccCCCEEEEEEeeCCCCCcccc---------------------CCchhhhHHHH
Q 039806          103 FNNLYVKNLDDDMTEEILVE----KFSEFGKITSLVISKDANGTSKGF---------------------GSKVLYVARAQ  157 (398)
Q Consensus       103 ~~~lfV~nLp~~~tee~L~~----~F~~fG~I~~~~i~~d~~g~s~Gf---------------------~~~~l~v~~a~  157 (398)
                      +.+|||.||+..+..++|+.    +|+.||+|.+|...+-..-+...|                     -|+.+.+..|.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~   88 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAK   88 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheeccc
Confidence            44999999999999999988    999999999998775543222222                     34555555544


Q ss_pred             HHHHHHHH----------------HH---------HH--------------HHHhhhhhhccccCCCcccCHHHHHHHhh
Q 039806          158 KKAERKAI----------------LR---------AQ--------------FERMRKERAELYKNINDEVDEIELKQYFS  198 (398)
Q Consensus       158 ~k~~~~~~----------------~~---------~~--------------~~~~~~~~~~~v~nL~~~vtee~L~~~F~  198 (398)
                      .+...-..                +.         ..              ......+..+++.|||.+++.+.|..+|+
T Consensus        89 s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~lf~  168 (221)
T KOG4206|consen   89 SDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDLFE  168 (221)
T ss_pred             CccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHHHh
Confidence            33221110                00         00              01123455677799999999999999999


Q ss_pred             cCCCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHHhcccc
Q 039806          199 QCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       199 ~fG~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      +|..-..|+++..   ++-.-||+|.+...+..|+..++....
T Consensus       169 qf~g~keir~i~~---~~~iAfve~~~d~~a~~a~~~lq~~~i  208 (221)
T KOG4206|consen  169 QFPGFKEIRLIPP---RSGIAFVEFLSDRQASAAQQALQGFKI  208 (221)
T ss_pred             hCcccceeEeccC---CCceeEEecchhhhhHHHhhhhcccee
Confidence            9999999998843   333339999999888888777765443

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

Probab=98.29  E-value=5.1e-06  Score=84.27  Aligned_cols=130  Identities=15%  Similarity=0.063  Sum_probs=99.5

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ++.+.+-+++.+.+.++.|++++|... .|.++.|..+. .+...|-++|.|....++++|++. |.+..-++.+.|...
T Consensus       309 ~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~  386 (944)
T KOG4307|consen  309 SDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPP  386 (944)
T ss_pred             chhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCC
Confidence            566778889999999999999999754 47777777777 555589999999999999999985 777777888888655


Q ss_pred             ccccc-----------------------------cc------ccCCCCceEEeeCCCccccHHHHHHHHccCCCEEE-EE
Q 039806           91 IRRAD-----------------------------RI------QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITS-LV  134 (398)
Q Consensus        91 ~~~~~-----------------------------~~------~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~-~~  134 (398)
                      .....                             +.      .......+|||..||..+++.++-+.|..--.|++ |.
T Consensus       387 g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~  466 (944)
T KOG4307|consen  387 GNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIE  466 (944)
T ss_pred             CccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeE
Confidence            42210                             00      00013467999999999999999999998888887 66


Q ss_pred             EeeCCCCCc
Q 039806          135 ISKDANGTS  143 (398)
Q Consensus       135 i~~d~~g~s  143 (398)
                      |.+..+++.
T Consensus       467 lt~~P~~~~  475 (944)
T KOG4307|consen  467 LTRLPTDLL  475 (944)
T ss_pred             eccCCcccc
Confidence            666665443

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

Probab=98.28  E-value=3e-07  Score=80.98  Aligned_cols=66  Identities=17%  Similarity=0.220  Sum_probs=60.5

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|++|-++|||..|...|-+||.|++|++..|. +++.||| ||+|...+||..|+..+.-+.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesE   76 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESE   76 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhh
Confidence            45789999999999999999999999999999999987 9999999 999999999999998665544

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

Probab=98.21  E-value=1.7e-06  Score=85.98  Aligned_cols=61  Identities=20%  Similarity=0.255  Sum_probs=57.6

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHh
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      +.++|+||+++++|++|.++|+..|.|.+++++.|. +|+.+|| |++|.+.+++.+|...+.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lN   81 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLN   81 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcC
Confidence            678899999999999999999999999999999998 9999999 999999999999988554

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

Probab=98.18  E-value=2.3e-06  Score=85.70  Aligned_cols=127  Identities=24%  Similarity=0.368  Sum_probs=102.9

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhcc-----------C-CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKF-----------G-DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE   81 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~-----------G-~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~   81 (398)
                      ...++|++++..++++....+|+.-           | .|++|.+..     .+.|||++|.+.++|..|.. +++..+.
T Consensus       175 ~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~-----~~nfa~ie~~s~~~at~~~~-~~~~~f~  248 (500)
T KOG0120|consen  175 ARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNL-----EKNFAFIEFRSISEATEAMA-LDGIIFE  248 (500)
T ss_pred             hhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecc-----cccceeEEecCCCchhhhhc-ccchhhC
Confidence            5679999999999999999998763           3 378888755     56899999999999999997 7899999


Q ss_pred             ceEeeeecccccccc-------------------cccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-C
Q 039806           82 RMELYVGPFIRRADR-------------------IQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-G  141 (398)
Q Consensus        82 gk~i~V~~~~~~~~~-------------------~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g  141 (398)
                      |..+++........-                   .........+||++|+...++++++++...||.+....+..|.. |
T Consensus       249 g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g  328 (500)
T KOG0120|consen  249 GRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATG  328 (500)
T ss_pred             CCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccc
Confidence            988877443322111                   00011456799999999999999999999999999999999986 8


Q ss_pred             Ccccc
Q 039806          142 TSKGF  146 (398)
Q Consensus       142 ~s~Gf  146 (398)
                      .++||
T Consensus       329 ~skg~  333 (500)
T KOG0120|consen  329 NSKGF  333 (500)
T ss_pred             cccce
Confidence            99999

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.15  E-value=1.2e-05  Score=75.56  Aligned_cols=74  Identities=20%  Similarity=0.282  Sum_probs=65.9

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccC--CeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKFG--DIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~G--~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ++||+||-+.+|++||.+.....|  .|.++|+..++ +|+|||||+|...+..+.++.++-|-.+.|.|..-.|..
T Consensus        82 ~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen   82 CCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             EEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeec
Confidence            689999999999999999998877  58899999999 999999999999999999999998888888887655543

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

Probab=98.15  E-value=2.7e-06  Score=72.75  Aligned_cols=63  Identities=16%  Similarity=0.219  Sum_probs=55.8

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      .++.++|+||+..+++.||..+|..||.|.+|-|.+.    .-|| ||+|++..||..|.-.+.....
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn----PPGfAFVEFed~RDA~DAvr~LDG~~~   72 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN----PPGFAFVEFEDPRDAEDAVRYLDGKDI   72 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec----CCCceEEeccCcccHHHHHhhcCCccc
Confidence            3567888999999999999999999999999999865    4688 9999999999999988876653

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

Probab=98.12  E-value=7.4e-05  Score=77.06  Aligned_cols=57  Identities=18%  Similarity=0.355  Sum_probs=51.5

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHh
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      +++|+|+.|+..++|.||.++|+.||.|.||.++     .++|| ||....+.+|.+|+.++.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li-----~~R~cAfI~M~~RqdA~kalqkl~  478 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI-----PPRGCAFIKMVRRQDAEKALQKLS  478 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeec-----cCCceeEEEEeehhHHHHHHHHHh
Confidence            5678899999999999999999999999999997     34666 999999999999998765

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.08  E-value=1.9e-06  Score=82.74  Aligned_cols=110  Identities=20%  Similarity=0.344  Sum_probs=92.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCC-eecceEeeeeccccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA-TVERMELYVGPFIRR   93 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~-~l~gk~i~V~~~~~~   93 (398)
                      ..+||+||.+.++-.||..+|...-.-.+-.++.     ..||+||.+.+..-|.+|++.++|. .+.|+.+.|..+.++
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~-----k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~k   76 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-----KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK   76 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee-----ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH
Confidence            4689999999999999999997642111111111     3489999999999999999999997 789999999999888


Q ss_pred             ccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEE
Q 039806           94 ADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVI  135 (398)
Q Consensus        94 ~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i  135 (398)
                      ..+      .+.+-|.|++....++-|..+...||.++.|..
T Consensus        77 kqr------srk~Qirnippql~wevld~Ll~qyg~ve~~eq  112 (584)
T KOG2193|consen   77 KQR------SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQ  112 (584)
T ss_pred             HHH------hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhh
Confidence            776      456889999999999999999999999999865

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

Probab=98.08  E-value=2.4e-06  Score=80.27  Aligned_cols=67  Identities=18%  Similarity=0.264  Sum_probs=61.4

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ..+++.++|..|.+-+++++|.-+|+.||+|.+|.|++|. +|-+-.| ||+|.+.++..+|.-++...
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNv  304 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNV  304 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcce
Confidence            3457889999999999999999999999999999999997 8988888 99999999999999887754

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

Probab=98.06  E-value=4.5e-06  Score=68.28  Aligned_cols=64  Identities=16%  Similarity=0.245  Sum_probs=58.2

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      .++|.++..+.+|+++.+.|+.||.|..+.+-.|. +|-.||| .|+|++.++|..|+.++..+..
T Consensus        74 Ii~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~l  139 (170)
T KOG0130|consen   74 IIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAEL  139 (170)
T ss_pred             EEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhh
Confidence            46779999999999999999999999999999887 9999999 9999999999999988775543

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

Probab=98.03  E-value=4.8e-06  Score=73.79  Aligned_cols=68  Identities=24%  Similarity=0.392  Sum_probs=56.0

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATV   80 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l   80 (398)
                      .-+-..+|||-||..++||++|+.+|+.|....-.||.. +.|  -..|||+|++.+.|..|+..|.|..|
T Consensus       206 ~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~-~~g--~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  206 GARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA-RGG--MPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             cchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec-CCC--cceEeecHHHHHHHHHHHHHhhccee
Confidence            334567899999999999999999999998766555533 233  35899999999999999999988776

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

Probab=98.02  E-value=3.2e-06  Score=88.05  Aligned_cols=121  Identities=16%  Similarity=0.209  Sum_probs=102.0

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ....+++||++||+..+++.+|+..|..+|.|.+|.|-+-.-+.-..||||.|.+.+.+-+|.-.+.+..|..-.+.+.+
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            34457799999999999999999999999999999887766555557999999999999999999999888766666655


Q ss_pred             ccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEe
Q 039806           90 FIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVIS  136 (398)
Q Consensus        90 ~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~  136 (398)
                      ...+      ....+.+++++|...+....|...|..||.|..|.+-
T Consensus       448 G~~k------st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~  488 (975)
T KOG0112|consen  448 GQPK------STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR  488 (975)
T ss_pred             cccc------cccceeeccCCCCCCChHHHHHHHhhccCcceeeecc
Confidence            4331      1257889999999999999999999999999987653

>PF13893 RRM_5: RNA recognition motif

Probab=98.02  E-value=1.3e-05  Score=56.55  Aligned_cols=44  Identities=18%  Similarity=0.388  Sum_probs=36.9

Q ss_pred             HHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          193 LKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       193 L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      |+++|++||+|+++++..+.    +++ ||+|.+.++|++|...++...
T Consensus         1 L~~~f~~fG~V~~i~~~~~~----~~~a~V~f~~~~~A~~a~~~l~~~~   45 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK----RGFAFVEFASVEDAQKAIEQLNGRQ   45 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHTTSE
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCE
Confidence            78999999999999998553    466 999999999999998887544

(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 ....

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

Probab=97.93  E-value=1.1e-05  Score=76.38  Aligned_cols=88  Identities=26%  Similarity=0.263  Sum_probs=78.9

Q ss_pred             ccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCe--------eEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcC
Q 039806            7 SEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDI--------QSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQG   77 (398)
Q Consensus         7 ~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I--------~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng   77 (398)
                      +...++...+|||-+|+.++++++|.++|.++|.|        -.|+|.+|+ ++..||-|.|.|++...|+.||+.+++
T Consensus        59 ~~~~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~ag  138 (351)
T KOG1995|consen   59 SMADKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAG  138 (351)
T ss_pred             ccccccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcc
Confidence            34457788899999999999999999999999977        346788888 999999999999999999999999999


Q ss_pred             CeecceEeeeecccccc
Q 039806           78 ATVERMELYVGPFIRRA   94 (398)
Q Consensus        78 ~~l~gk~i~V~~~~~~~   94 (398)
                      ..+.+..|+|..+.++.
T Consensus       139 kdf~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  139 KDFCGNTIKVSLAERRT  155 (351)
T ss_pred             ccccCCCchhhhhhhcc
Confidence            99999999998887655

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

Probab=97.92  E-value=2.7e-05  Score=79.21  Aligned_cols=79  Identities=15%  Similarity=0.202  Sum_probs=69.7

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCe-eEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDI-QSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I-~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      +.+.+-|-+.|+|++++-+||.++|+.|-.+ .+|.+..+.+|+-.|-|.|-|++.|+|.+|...|++..|..++|++..
T Consensus       864 ~pGp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  864 SPGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            4455579999999999999999999999765 456677777999999999999999999999999999999999998753

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

Probab=97.85  E-value=2.8e-05  Score=70.34  Aligned_cols=134  Identities=16%  Similarity=0.321  Sum_probs=107.2

Q ss_pred             cceEEEcCCCCCCcHHH-H--HHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           14 IGNAFVKNLASTIDNLK-L--HQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~-L--~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      .-..++.|+-..+..+- |  ...|+.+-.....+++++.-+..++++|+.|.....-.++-..-+++.+.-..|+..-.
T Consensus        96 vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~g  175 (290)
T KOG0226|consen   96 VFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAG  175 (290)
T ss_pred             cccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccc
Confidence            34567777777765554 3  77899888888889999988889999999999888877777777778887777777665


Q ss_pred             cccccccccC--CCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC-CCccccC
Q 039806           91 IRRADRIQEG--SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG  147 (398)
Q Consensus        91 ~~~~~~~~~~--~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~-g~s~Gf~  147 (398)
                      ....+....+  ....+||.+.|..+++++-|...|++|-.-...++++|+. |+++||+
T Consensus       176 tswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgyg  235 (290)
T KOG0226|consen  176 TSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYG  235 (290)
T ss_pred             cccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccce
Confidence            5544432222  2678899999999999999999999999999999999985 9999995

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.76  E-value=1.4e-05  Score=75.84  Aligned_cols=84  Identities=23%  Similarity=0.323  Sum_probs=75.4

Q ss_pred             CCcceEE-EcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           12 SGIGNAF-VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        12 ~~~~~lf-V~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ....++| |+||+.++++++|++.|..+|.|..+++..++ ++.++|||||.|.+..++..++.. +...+.++.+.+..
T Consensus       182 ~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  260 (285)
T KOG4210|consen  182 GPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEE  260 (285)
T ss_pred             CccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCccccccc
Confidence            4456677 99999999999999999999999999999999 999999999999999999999987 88899999999988


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      ...+..+
T Consensus       261 ~~~~~~~  267 (285)
T KOG4210|consen  261 DEPRPKS  267 (285)
T ss_pred             CCCCccc
Confidence            7665443

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

Probab=97.74  E-value=2e-05  Score=70.88  Aligned_cols=71  Identities=24%  Similarity=0.356  Sum_probs=62.5

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      -.+.|.|.||+..+...+|.+.|+.||.+....+       ..+++||+|.+.++|.+|++.|++..+.++.|.+...
T Consensus        98 s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen   98 THFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             ccceeeeccchhhhhHHHHhhhhcccCCCchhhh-------hccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            3567999999999999999999999999954443       4578999999999999999999999999999999443

>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=97.73  E-value=5.7e-05  Score=60.76  Aligned_cols=59  Identities=27%  Similarity=0.438  Sum_probs=38.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCC
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA   78 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~   78 (398)
                      +-|+|.+++..++-++|++.|+.||.|..|.+....     .-|||.|.+.++|+.|++++...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~-----~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD-----TEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC-----CEEEEEECCcchHHHHHHHHHhc
Confidence            458999999999999999999999999888775422     36999999999999999977543

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

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

Probab=97.65  E-value=4.9e-05  Score=71.65  Aligned_cols=61  Identities=21%  Similarity=0.314  Sum_probs=51.8

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      +..-++++|++|.+.++|.+|+++|.+||.|.++.++..     +++ ||+|.++..|.+|..+.--
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n  286 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFN  286 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcc
Confidence            334567888999999999999999999999999999843     334 9999999999999887654

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.62  E-value=0.00015  Score=69.34  Aligned_cols=161  Identities=16%  Similarity=0.185  Sum_probs=101.5

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCC----CCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE----GKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~----g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      -+-|.|.||++++|.+.++.+|...|.|.+++|.-+.+    ......|||.|.+...+..|-. |-+..+-|+-|.|-+
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p   85 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRP   85 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEe
Confidence            34799999999999999999999999999999887542    2456799999999999998876 666666666666654


Q ss_pred             ccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCcccc--------------CCchhhhHH
Q 039806           90 FIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF--------------GSKVLYVAR  155 (398)
Q Consensus        90 ~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf--------------~~~~l~v~~  155 (398)
                      ...-.                     -.+..  .|..++.-+.+--..-.+|..-+-              ..-.|.-..
T Consensus        86 ~~~~~---------------------~p~r~--af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~  142 (479)
T KOG4676|consen   86 YGDEV---------------------IPDRF--AFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQA  142 (479)
T ss_pred             cCCCC---------------------CccHH--HHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHh
Confidence            32111                     11111  333333222221111111110000              000011111


Q ss_pred             HHHHHHHHHHHHHHHHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEee
Q 039806          156 AQKKAERKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMR  210 (398)
Q Consensus       156 a~~k~~~~~~~~~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~  210 (398)
                      +..+-            ....+++.+.+|...+...++.+.|..+|.|...++.-
T Consensus       143 ~A~kl------------eeirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~as  185 (479)
T KOG4676|consen  143 AAKKL------------EEIRRTREVQSLISAAILPESGESFERKGEVSYAHTAS  185 (479)
T ss_pred             hhhhh------------HHHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhc
Confidence            11111            12237788899999999999999999999998877753

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

Probab=97.55  E-value=0.00013  Score=67.02  Aligned_cols=62  Identities=16%  Similarity=0.191  Sum_probs=58.1

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ..+.|.||+..|++++|+++|..||.++.+-|.+|+.|.+.|. =|.|...+||.+|+.+.+.
T Consensus        84 ~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~g  146 (243)
T KOG0533|consen   84 TKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNG  146 (243)
T ss_pred             ceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcC
Confidence            4577799999999999999999999999999999999999998 8999999999999988876

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

Probab=97.51  E-value=0.00021  Score=62.98  Aligned_cols=63  Identities=22%  Similarity=0.310  Sum_probs=54.9

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcC-CCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHh
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQC-GTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~f-G~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ......+..++.-+.+.+|..+|.+| |+|+.+++-|+. ||.|||| ||+|.+.+.|.-|.-.|.
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMN  113 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMN  113 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhh
Confidence            34456669999999999999999999 788888888887 9999999 999999999998876655

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.50  E-value=0.00036  Score=69.22  Aligned_cols=131  Identities=15%  Similarity=0.197  Sum_probs=86.8

Q ss_pred             CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCC-C--CCccc---cCCchhhhHHHHHHHHHHHHH---------
Q 039806          102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-N--GTSKG---FGSKVLYVARAQKKAERKAIL---------  166 (398)
Q Consensus       102 ~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~-~--g~s~G---f~~~~l~v~~a~~k~~~~~~~---------  166 (398)
                      -.++|||++||++++|++|...|..||.+.-=.=.+.. .  --.+|   |-    +.-+...++.+.-..         
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~Yv----flvFe~E~sV~~Ll~aC~~~~~~~  333 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYV----FLVFEDERSVQSLLSACSEGEGNY  333 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEE----EEEecchHHHHHHHHHHhhcccce
Confidence            56789999999999999999999999976421111111 1  12344   41    110111111100000         


Q ss_pred             ---------H-------------H-----HHHHhhhhhhccccCCCcccCHHHHHHHhh-cCCCeEEEEEeeCC-CCCcc
Q 039806          167 ---------R-------------A-----QFERMRKERAELYKNINDEVDEIELKQYFS-QCGTISSVKIMRTD-RGISK  217 (398)
Q Consensus       167 ---------~-------------~-----~~~~~~~~~~~~v~nL~~~vtee~L~~~F~-~fG~I~svki~~d~-~g~sk  217 (398)
                               +             .     .....+..++++|++||.-++.++|-.+|+ -||.|..|-|-.|+ =+-.+
T Consensus       334 yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPk  413 (520)
T KOG0129|consen  334 YFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPK  413 (520)
T ss_pred             EEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCC
Confidence                     0             0     011234567889999999999999999998 69999999999884 45566


Q ss_pred             ce-EEEecccHHHHHHHHHH
Q 039806          218 GH-CMAIAQTKRERTSYLRI  236 (398)
Q Consensus       218 Gf-fV~f~~~~ea~~A~l~~  236 (398)
                      |- -|+|.+...-.+|+.+.
T Consensus       414 GaGRVtFsnqqsYi~AIsar  433 (520)
T KOG0129|consen  414 GAGRVTFSNQQAYIKAISAR  433 (520)
T ss_pred             CcceeeecccHHHHHHHhhh
Confidence            66 89999988888887654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.48  E-value=0.00023  Score=66.87  Aligned_cols=77  Identities=18%  Similarity=0.327  Sum_probs=61.7

Q ss_pred             ceEEEcCCCCCCcHHHH------HHHHhccCCeeEEEEEEcC-C-CCceeEE--EEEecCHHHHHHHHHHhcCCeecceE
Q 039806           15 GNAFVKNLASTIDNLKL------HQIFSKFGDIQSSKVVVSQ-E-GKSKGYG--FVQYSTPESALDAIEKLQGATVERME   84 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L------~~~F~~~G~I~~vki~~d~-~-g~skg~a--FV~F~~~e~A~~Ai~~lng~~l~gk~   84 (398)
                      .-+||-+|+..+..|+.      +++|.+||.|..|.|.+.- + ....+.+  ||.|.+.|+|.+||..++|..++||-
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            34899999998877662      5799999999988776544 1 2223333  99999999999999999999999999


Q ss_pred             eeeeccc
Q 039806           85 LYVGPFI   91 (398)
Q Consensus        85 i~V~~~~   91 (398)
                      |+..+-.
T Consensus       195 lkatYGT  201 (480)
T COG5175         195 LKATYGT  201 (480)
T ss_pred             EeeecCc
Confidence            9987755

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

Probab=97.47  E-value=2.2e-05  Score=69.42  Aligned_cols=120  Identities=24%  Similarity=0.348  Sum_probs=85.9

Q ss_pred             CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHH--HH-HHHHHHhhhhhh
Q 039806          102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKA--IL-RAQFERMRKERA  178 (398)
Q Consensus       102 ~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~--~~-~~~~~~~~~~~~  178 (398)
                      ..++|||.|+...+|||-|.++|-.-|.|..+.|..+.+++.+ |.    +|.+.......-+  .+ ...........+
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa----~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~   82 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FA----YVFFPNENSVQLAGQLENGDDLEEDEEQRT   82 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-ee----eeecccccchhhhhhhcccchhccchhhcc
Confidence            4578999999999999999999999999999999999988777 52    2322221111100  00 001111222233


Q ss_pred             ccccC----CCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEeccc
Q 039806          179 ELYKN----INDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQT  226 (398)
Q Consensus       179 ~~v~n----L~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~  226 (398)
                      .+-+|    |+..++++.+.+.|+.-|.|..+++.++.+|+++-| |+.+...
T Consensus        83 ~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~  135 (267)
T KOG4454|consen   83 LRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRL  135 (267)
T ss_pred             cccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhh
Confidence            44466    999999999999999999999999999888888776 6665443

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

Probab=97.45  E-value=0.00024  Score=70.96  Aligned_cols=80  Identities=26%  Similarity=0.395  Sum_probs=65.1

Q ss_pred             CCcceEEEcCCCC--CCc----HHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec-ceE
Q 039806           12 SGIGNAFVKNLAS--TID----NLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE-RME   84 (398)
Q Consensus        12 ~~~~~lfV~nLp~--~vt----e~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~-gk~   84 (398)
                      .-...|+|.|.|-  ...    ..-|..+|+++|.|....++-++.|.++||.|++|.+..+|+.|++.|||..|+ ...
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            4456799999994  222    234667899999999999999997779999999999999999999999999875 456


Q ss_pred             eeeeccc
Q 039806           85 LYVGPFI   91 (398)
Q Consensus        85 i~V~~~~   91 (398)
                      ..|..+.
T Consensus       136 f~v~~f~  142 (698)
T KOG2314|consen  136 FFVRLFK  142 (698)
T ss_pred             EEeehhh
Confidence            6665544

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

Probab=97.45  E-value=0.00035  Score=71.52  Aligned_cols=65  Identities=25%  Similarity=0.227  Sum_probs=55.9

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC------CCCccceEEEecccHHHHHHHHHHhccccC
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD------RGISKGHCMAIAQTKRERTSYLRIMYAKQG  242 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~------~g~skGffV~f~~~~ea~~A~l~~q~~q~~  242 (398)
                      +.++++||+.+++++.|...|..||.|.+|+||...      .+..|| ||.|-+++||.+|...+|..-.+
T Consensus       175 TNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cg-fvafmnR~D~era~k~lqg~iv~  245 (877)
T KOG0151|consen  175 TNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCG-FVAFMNRADAERALKELQGIIVM  245 (877)
T ss_pred             cceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccc-eeeehhhhhHHHHHHHhcceeee
Confidence            446679999999999999999999999999998643      455677 79999999999999988876544

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

Probab=97.40  E-value=0.001  Score=62.96  Aligned_cols=82  Identities=17%  Similarity=0.229  Sum_probs=65.3

Q ss_pred             cccCCCcceEEEcCCCC----CCc-------HHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhc
Q 039806            8 EARLSGIGNAFVKNLAS----TID-------NLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ   76 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~----~vt-------e~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~ln   76 (398)
                      ..+.+..++|.|+||=.    ..+       .++|.+--++||.|.+|.|.-..   ..|.+-|.|.+.++|..||+.|+
T Consensus       259 ~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~h---PdGvvtV~f~n~eeA~~ciq~m~  335 (382)
T KOG1548|consen  259 PSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRH---PDGVVTVSFRNNEEADQCIQTMD  335 (382)
T ss_pred             cccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccC---CCceeEEEeCChHHHHHHHHHhc
Confidence            34556678999999852    223       34455567889999999887655   55789999999999999999999


Q ss_pred             CCeecceEeeeecccc
Q 039806           77 GATVERMELYVGPFIR   92 (398)
Q Consensus        77 g~~l~gk~i~V~~~~~   92 (398)
                      |..+.|++|.......
T Consensus       336 GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  336 GRWFDGRQLTASIWDG  351 (382)
T ss_pred             CeeecceEEEEEEeCC
Confidence            9999999999876543

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

Probab=97.38  E-value=6.9e-05  Score=68.06  Aligned_cols=63  Identities=17%  Similarity=0.199  Sum_probs=53.3

Q ss_pred             HHHHHHHh-ccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           29 LKLHQIFS-KFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        29 ~~L~~~F~-~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      +||+..|+ +||.|.+++|..+..-.-+|-.||.|..+|+|++|++.||+..+.|++|..+.+.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            34555555 7999999988877655578899999999999999999999999999999987653

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

Probab=97.31  E-value=0.00022  Score=70.76  Aligned_cols=59  Identities=17%  Similarity=0.193  Sum_probs=51.6

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHH
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRI  236 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~  236 (398)
                      .++++|||.++++++|+++|+.||.|+...|..-. .+++.+| ||+|.+..++..|+.+.
T Consensus       290 ~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As  350 (419)
T KOG0116|consen  290 GIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS  350 (419)
T ss_pred             ceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC
Confidence            47889999999999999999999999999987644 5555566 99999999999998877

>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=97.25  E-value=0.00071  Score=53.68  Aligned_cols=76  Identities=21%  Similarity=0.220  Sum_probs=50.9

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEE-EEEc-------CCCCceeEEEEEecCHHHHHHHHHHhcCCeecceE
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSK-VVVS-------QEGKSKGYGFVQYSTPESALDAIEKLQGATVERME   84 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vk-i~~d-------~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~   84 (398)
                      ..+-|.|-+.|.+.+ ..+.+.|++||+|++.. +.++       +......+-.|.|+++.+|.+||. .||+.|.|.-
T Consensus         5 ~~~wVtVFGfp~~~~-~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPSAS-NQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GGGH-HHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHHHH-HHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            345699999999954 56889999999998875 1111       101123478899999999999998 4999998854


Q ss_pred             e-eeecc
Q 039806           85 L-YVGPF   90 (398)
Q Consensus        85 i-~V~~~   90 (398)
                      + -|.+.
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            4 45554

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

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

Probab=97.20  E-value=0.00089  Score=46.73  Aligned_cols=52  Identities=19%  Similarity=0.314  Sum_probs=42.2

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHH
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAI   72 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai   72 (398)
                      +.|-|.+.+.+..+. +...|+.||.|..+.+..     .+-+.||.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~-----~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPE-----STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCC-----CCcEEEEEECCHHHHHhhC
Confidence            468888998777654 556999999999988852     3458999999999999985

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

Probab=97.00  E-value=0.00094  Score=66.78  Aligned_cols=66  Identities=11%  Similarity=0.189  Sum_probs=56.1

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..+.++|.+|...+-..+|+.+|++||+|+-+||+.+. +-..++| ||+..+..+|.+++..++-..
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTE  471 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTE  471 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhh
Confidence            34568889999999999999999999999999999876 3344555 999999999999998877654

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

Probab=96.99  E-value=0.00062  Score=66.00  Aligned_cols=77  Identities=27%  Similarity=0.283  Sum_probs=62.5

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEc---C---CCCc--------eeEEEEEecCHHHHHHHHHHhcCC
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS---Q---EGKS--------KGYGFVQYSTPESALDAIEKLQGA   78 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d---~---~g~s--------kg~aFV~F~~~e~A~~Ai~~lng~   78 (398)
                      .+++|.+-|||.+-..+.|.++|+.+|.|.+|+|+.-   +   .+..        +-+|+|+|+..+.|.+|.+.+|..
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            5789999999999999999999999999999999876   3   2222        457999999999999999988665


Q ss_pred             eecceEeeeec
Q 039806           79 TVERMELYVGP   89 (398)
Q Consensus        79 ~l~gk~i~V~~   89 (398)
                      ..+..-++|..
T Consensus       310 ~~wr~glkvkL  320 (484)
T KOG1855|consen  310 QNWRMGLKVKL  320 (484)
T ss_pred             hhhhhcchhhh
Confidence            55444444433

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

Probab=96.88  E-value=0.00097  Score=60.62  Aligned_cols=72  Identities=18%  Similarity=0.380  Sum_probs=62.0

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-C--------CCceeE----EEEEecCHHHHHHHHHHhcCCe
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-E--------GKSKGY----GFVQYSTPESALDAIEKLQGAT   79 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~--------g~skg~----aFV~F~~~e~A~~Ai~~lng~~   79 (398)
                      ..+-||+++||+..+-.-|+++|+.||.|-.|.+.... +        |.++++    |+|+|.+...|.++.+.||+..
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            56789999999999999999999999999988877655 3        333332    6799999999999999999999


Q ss_pred             ecceE
Q 039806           80 VERME   84 (398)
Q Consensus        80 l~gk~   84 (398)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99975

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

Probab=96.83  E-value=7.3e-05  Score=72.27  Aligned_cols=62  Identities=19%  Similarity=0.299  Sum_probs=52.0

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeC---C---CCCccce---------EEEecccHHHHHHHHHH
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRT---D---RGISKGH---------CMAIAQTKRERTSYLRI  236 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d---~---~g~skGf---------fV~f~~~~ea~~A~l~~  236 (398)
                      ..+++++.|||.+..-+.|.++|+.+|.|.+|+|+..   +   .|..++|         +|+|...+.|++|..-+
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            4567778999999999999999999999999999875   2   3445555         89999999999997654

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.74  E-value=0.0016  Score=59.32  Aligned_cols=77  Identities=26%  Similarity=0.364  Sum_probs=66.7

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCC----eecceEeeeecc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA----TVERMELYVGPF   90 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~----~l~gk~i~V~~~   90 (398)
                      +.|+|.||..-+.++.|++.|+.||.|....+..|..++..+-++|.|.+.-.|.+|+..++-.    ...+..+-|.+.
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            7899999999999999999999999999999999999999999999999999999999987533    334566666554


Q ss_pred             c
Q 039806           91 I   91 (398)
Q Consensus        91 ~   91 (398)
                      .
T Consensus       112 e  112 (275)
T KOG0115|consen  112 E  112 (275)
T ss_pred             h
Confidence            4

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

Probab=96.71  E-value=0.0026  Score=51.14  Aligned_cols=58  Identities=17%  Similarity=0.331  Sum_probs=37.5

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHHhcc
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~q~~  239 (398)
                      .++|.+++..++-++|++.|+.||.|..|.+.   .|...| ||.|.+.+.|.+|..+....
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~---~G~~~g-~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFS---RGDTEG-YVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE-----TT-SEE-EEEESS---HHHHHHHHHHT
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEec---CCCCEE-EEEECCcchHHHHHHHHHhc
Confidence            45678899999999999999999999998886   445556 89999999999998877655

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

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

Probab=96.66  E-value=0.0013  Score=60.37  Aligned_cols=68  Identities=18%  Similarity=0.260  Sum_probs=58.8

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      .-..+.++|+|+++.++.+++..+|+.||.|..|.|..|. .|.+||| ||+|.+.+.+..|+. +.....
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i  167 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEI  167 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccc
Confidence            4445678889999999999999999999999999999998 6679999 999999999999977 555443

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

Probab=96.62  E-value=0.0014  Score=65.63  Aligned_cols=63  Identities=11%  Similarity=0.147  Sum_probs=51.6

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      +...++++|-|||.+|++++|+.+|+.||+|..|+--+.    .+|- ||+|.+..+|.+|..++...
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~----~~~~~~v~FyDvR~A~~Alk~l~~~  135 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN----KRGIVFVEFYDVRDAERALKALNRR  135 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc----cCceEEEEEeehHhHHHHHHHHHHH
Confidence            445688999999999999999999999999998665432    3444 99999999999888765543

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

Probab=96.57  E-value=0.0081  Score=50.64  Aligned_cols=72  Identities=21%  Similarity=0.221  Sum_probs=52.6

Q ss_pred             CcceEEEcCCC-----CCCcH----HHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecce
Q 039806           13 GIGNAFVKNLA-----STIDN----LKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERM   83 (398)
Q Consensus        13 ~~~~lfV~nLp-----~~vte----~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk   83 (398)
                      ..++|.|.=+.     .+.-.    .+|.+.|+.||.+.-+++..+       --+|.|.+-++|-+|++ ++|..++|+
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~-------~mwVTF~dg~sALaals-~dg~~v~g~   97 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD-------TMWVTFRDGQSALAALS-LDGIQVNGR   97 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT-------CEEEEESSCHHHHHHHH-GCCSEETTE
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC-------eEEEEECccHHHHHHHc-cCCcEECCE
Confidence            34577776555     22222    367889999999888888653       48999999999999998 899999999


Q ss_pred             Eeeeecccc
Q 039806           84 ELYVGPFIR   92 (398)
Q Consensus        84 ~i~V~~~~~   92 (398)
                      .|.|..-.+
T Consensus        98 ~l~i~LKtp  106 (146)
T PF08952_consen   98 TLKIRLKTP  106 (146)
T ss_dssp             EEEEEE---
T ss_pred             EEEEEeCCc
Confidence            999977543

; PDB: 1UFW_A 2DNR_A.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.51  E-value=0.0072  Score=55.14  Aligned_cols=79  Identities=29%  Similarity=0.320  Sum_probs=64.3

Q ss_pred             HHHHHHHHhcCCeecceEeeeecccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCcccc
Q 039806           67 SALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF  146 (398)
Q Consensus        67 ~A~~Ai~~lng~~l~gk~i~V~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf  146 (398)
                      -|..|-..|.+....++.+.|.++.           ...|||.||+..++.|.+...|+.||.|...+++.|..++..+-
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~-----------~a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~e   74 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAM-----------HAELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTRE   74 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeec-----------cceEEEEecchhhhhHHHHHhhhhcCccchheeeeccccccccc
Confidence            4566666788999999999999875           26799999999999999999999999999999999987776655


Q ss_pred             CCchhhhHHHHHHH
Q 039806          147 GSKVLYVARAQKKA  160 (398)
Q Consensus       147 ~~~~l~v~~a~~k~  160 (398)
                      +    .|.++++..
T Consensus        75 g----~v~~~~k~~   84 (275)
T KOG0115|consen   75 G----IVEFAKKPN   84 (275)
T ss_pred             c----hhhhhcchh
Confidence            4    444444333

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.39  E-value=0.017  Score=43.72  Aligned_cols=54  Identities=19%  Similarity=0.266  Sum_probs=41.2

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ   76 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~ln   76 (398)
                      .-.+|. +|+.....||.++|+.||.|. |..+.|-      -|||...+.+.|..|+..++
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT------EEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC------cEEEEeecHHHHHHHHHHhc
Confidence            345555 999999999999999999984 6666543      49999999999999998775

; 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.

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

Probab=96.35  E-value=0.0047  Score=43.05  Aligned_cols=50  Identities=10%  Similarity=0.117  Sum_probs=35.3

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccceEEEecccHHHHHHH
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSY  233 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGffV~f~~~~ea~~A~  233 (398)
                      +.|.+.+.+.. +.+.++|..||+|+++.+.    ....-+||.|+++.+|.+|+
T Consensus         4 I~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~----~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    4 ISVSGFPPDLA-EEVLEHFASFGEIVDIYVP----ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             EEEEeECchHH-HHHHHHHHhcCCEEEEEcC----CCCcEEEEEECCHHHHHhhC
Confidence            33445554444 4555699999999998885    12233499999999999984

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

Probab=96.15  E-value=0.015  Score=45.81  Aligned_cols=63  Identities=11%  Similarity=0.056  Sum_probs=52.8

Q ss_pred             hhccccCCCcccCHHHHHHHhhcC--CCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQC--GTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~f--G~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      .++.++|||...|.++|.+++...  |...-+.+..|- ++.+.|| ||.|.+.+.+.+-....+..
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~   68 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGK   68 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCC
Confidence            356779999999999999999664  777778888886 8889999 99999999998877666644

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

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

Probab=95.93  E-value=0.022  Score=52.95  Aligned_cols=62  Identities=16%  Similarity=0.194  Sum_probs=50.6

Q ss_pred             HHHHHHHhccCCeeEEEEEEcCCC-Cce-eEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           29 LKLHQIFSKFGDIQSSKVVVSQEG-KSK-GYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        29 ~~L~~~F~~~G~I~~vki~~d~~g-~sk-g~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      +++.+-..+||.|..|.|..+++. ... ---||+|+..++|.+|+-.|||..++|+.+...+.
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            456677889999999999988722 111 13799999999999999999999999999887654

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

Probab=95.92  E-value=0.0078  Score=60.84  Aligned_cols=82  Identities=18%  Similarity=0.181  Sum_probs=65.3

Q ss_pred             CCccc-cCCCcceEEEcCCCCCCcHHHHHHHHhc-cCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCee--
Q 039806            5 PNSEA-RLSGIGNAFVKNLASTIDNLKLHQIFSK-FGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATV--   80 (398)
Q Consensus         5 rd~~~-~~~~~~~lfV~nLp~~vte~~L~~~F~~-~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l--   80 (398)
                      |+|+. |+.-+.-|+|.||-.-.|...|++++.. .|.|.+..|  |   +-|..|||.|.+.++|.+.+++|||..+  
T Consensus       434 RvpSPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--D---kIKShCyV~yss~eEA~atr~AlhnV~WP~  508 (718)
T KOG2416|consen  434 RVPSPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--D---KIKSHCYVSYSSVEEAAATREALHNVQWPP  508 (718)
T ss_pred             cCCCCCCCCccceEeeecccccchHHHHHHHHhhccCchHHHHH--H---HhhcceeEecccHHHHHHHHHHHhccccCC
Confidence            44443 6666788999999999999999999985 666766622  3   2566899999999999999999999876  


Q ss_pred             -cceEeeeeccc
Q 039806           81 -ERMELYVGPFI   91 (398)
Q Consensus        81 -~gk~i~V~~~~   91 (398)
                       +.|.|.+.+..
T Consensus       509 sNPK~L~adf~~  520 (718)
T KOG2416|consen  509 SNPKHLIADFVR  520 (718)
T ss_pred             CCCceeEeeecc
Confidence             56777776654

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=95.74  E-value=0.028  Score=58.72  Aligned_cols=11  Identities=9%  Similarity=0.311  Sum_probs=4.4

Q ss_pred             HHHHHHHHhcc
Q 039806           28 NLKLHQIFSKF   38 (398)
Q Consensus        28 e~~L~~~F~~~   38 (398)
                      .+++.+.|...
T Consensus        85 ~~e~~~~F~~~   95 (1102)
T KOG1924|consen   85 SNEVLELFELM   95 (1102)
T ss_pred             HHHHHHHHHHH
Confidence            33344444433

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.62  E-value=0.0073  Score=57.30  Aligned_cols=79  Identities=15%  Similarity=0.209  Sum_probs=61.0

Q ss_pred             ceEEEcCCCCCCcHHHHH---HHHhccCCeeEEEEEEcCC--CCc--eeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           15 GNAFVKNLASTIDNLKLH---QIFSKFGDIQSSKVVVSQE--GKS--KGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~---~~F~~~G~I~~vki~~d~~--g~s--kg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      .-+||-+|+.....+++.   +.|..||.|.+|.+..+.+  ..+  -.-++|.|+..|+|..||...+|..++|+.++.
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            357888999877555554   4899999999998888662  111  123899999999999999999999999998777


Q ss_pred             eccccc
Q 039806           88 GPFIRR   93 (398)
Q Consensus        88 ~~~~~~   93 (398)
                      .+...+
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            665443

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.57  E-value=0.066  Score=38.43  Aligned_cols=52  Identities=15%  Similarity=0.240  Sum_probs=42.4

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhcc----CCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHh
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKF----GDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL   75 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~----G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~l   75 (398)
                      .|+|++++. .+-+||+.+|..|    + ...|..+-|.      -|-|.|.+.+.|.+||.+|
T Consensus         7 avhirGvd~-lsT~dI~~y~~~y~~~~~-~~~IEWIdDt------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    7 AVHIRGVDE-LSTDDIKAYFSEYFDEEG-PFRIEWIDDT------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eEEEEcCCC-CCHHHHHHHHHHhcccCC-CceEEEecCC------cEEEEECCHHHHHHHHHcC
Confidence            699999965 6777899999998    4 4467777664      3889999999999999764

>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=94.83  E-value=0.032  Score=49.22  Aligned_cols=70  Identities=10%  Similarity=0.168  Sum_probs=46.5

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhc-cCCe---eEEE--EEEcCC-CCceeEEEEEecCHHHHHHHHHHhcCCeecc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSK-FGDI---QSSK--VVVSQE-GKSKGYGFVQYSTPESALDAIEKLQGATVER   82 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~-~G~I---~~vk--i~~d~~-g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g   82 (398)
                      ...+|-|++||++.|++++.+.++. ++.-   ..+.  +..... -..-.-|||.|.+.+++..-.+.++|..+.+
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D   82 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVD   82 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEEC
Confidence            4458999999999999999998777 6655   3333  222221 1233469999999999999999999987754

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

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

Probab=94.83  E-value=0.017  Score=61.14  Aligned_cols=132  Identities=17%  Similarity=0.180  Sum_probs=87.4

Q ss_pred             CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCC--CCccccCCchhhhHHH--HHHHHHH------HHHHHHHH
Q 039806          102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN--GTSKGFGSKVLYVARA--QKKAERK------AILRAQFE  171 (398)
Q Consensus       102 ~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~--g~s~Gf~~~~l~v~~a--~~k~~~~------~~~~~~~~  171 (398)
                      ..++||++||+..+++.+|+..|..+|.|+++.|.+-.-  +...+|-  .+....+  ..+.+..      -..+..+.
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~--~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFV--SLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhh--hhhccccCcccchhhcCCccccCccccccc
Confidence            346699999999999999999999999999998876643  3344441  1100000  0000000      00111111


Q ss_pred             --HhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHHhcc
Q 039806          172 --RMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       172 --~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~q~~  239 (398)
                        .....+.+++++|..-+....|...|..||.|..|.+-   .|.+-- ||.+.+...+..|.-.+...
T Consensus       449 ~~kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~---hgq~ya-yi~yes~~~aq~a~~~~rga  514 (975)
T KOG0112|consen  449 QPKSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR---HGQPYA-YIQYESPPAAQAATHDMRGA  514 (975)
T ss_pred             ccccccceeeccCCCCCCChHHHHHHHhhccCcceeeecc---cCCcce-eeecccCccchhhHHHHhcC
Confidence              23345567779999999999999999999999987773   333332 89999988877776655544

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

Probab=94.10  E-value=0.17  Score=47.36  Aligned_cols=74  Identities=18%  Similarity=0.266  Sum_probs=54.7

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecce-Eeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERM-ELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk-~i~V~~~~~   92 (398)
                      ..=|-|-+++..-.. -|..+|+.||+|++....  .+|   -+-+|.|.+.-+|++||.+ ||++|+|. -|-|..+..
T Consensus       197 D~WVTVfGFppg~~s-~vL~~F~~cG~Vvkhv~~--~ng---NwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQVS-IVLNLFSRCGEVVKHVTP--SNG---NWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             cceEEEeccCccchh-HHHHHHHhhCeeeeeecC--CCC---ceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecCC
Confidence            344667788876554 477899999999866543  333   3789999999999999985 99999874 455666555


Q ss_pred             cc
Q 039806           93 RA   94 (398)
Q Consensus        93 ~~   94 (398)
                      +.
T Consensus       270 ks  271 (350)
T KOG4285|consen  270 KS  271 (350)
T ss_pred             HH
Confidence            44

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=93.78  E-value=0.12  Score=52.28  Aligned_cols=68  Identities=10%  Similarity=0.152  Sum_probs=55.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhc--cCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcC--CeecceEeee
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSK--FGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG--ATVERMELYV   87 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~--~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng--~~l~gk~i~V   87 (398)
                      .|-|.|+.||..+-.|+++.+|+.  +-++.+|....+.      -=||.|++..||+.|.+.|..  +.|.||.|..
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            456788999999999999999976  7789999987764      258999999999999987754  3667776644

>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=93.64  E-value=0.43  Score=34.79  Aligned_cols=56  Identities=7%  Similarity=0.156  Sum_probs=45.0

Q ss_pred             CCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           24 STIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        24 ~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      ..++-+|++..+..|+-   .+|..|.+|     =||.|.+.++|++|....||..+.+..+.+
T Consensus        10 ~~~~v~d~K~~Lr~y~~---~~I~~d~tG-----fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYRW---DRIRDDRTG-----FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CCccHHHHHHHHhcCCc---ceEEecCCE-----EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            35678899999999963   345556544     379999999999999999999998877665

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

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

Probab=93.53  E-value=0.082  Score=53.44  Aligned_cols=50  Identities=18%  Similarity=0.232  Sum_probs=45.0

Q ss_pred             HHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          191 IELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       191 e~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..|..+|+++|+|+...+..|+.|+.+|| |++|++..+|..|...+...+
T Consensus        79 ~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~  129 (698)
T KOG2314|consen   79 KVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKR  129 (698)
T ss_pred             HHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccce
Confidence            35778999999999999999999999999 999999999999998777654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=93.48  E-value=0.21  Score=47.50  Aligned_cols=59  Identities=17%  Similarity=0.271  Sum_probs=43.4

Q ss_pred             cCCCcccCHHH----H--HHHhhcCCCeEEEEEeeCC-----CCCccceEEEecccHHHHHHHHHHhccc
Q 039806          182 KNINDEVDEIE----L--KQYFSQCGTISSVKIMRTD-----RGISKGHCMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       182 ~nL~~~vtee~----L--~~~F~~fG~I~svki~~d~-----~g~skGffV~f~~~~ea~~A~l~~q~~q  240 (398)
                      -+|+..+-+|+    |  .++|.+||.|..|.|-+..     +...-|.||+|.+.+||++++.+....-
T Consensus       120 igi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~  189 (480)
T COG5175         120 IGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSL  189 (480)
T ss_pred             ecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccc
Confidence            56666665554    3  4789999999998886543     1223566999999999999998776543

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=92.72  E-value=0.054  Score=55.76  Aligned_cols=70  Identities=20%  Similarity=0.229  Sum_probs=63.4

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ...-+|||+|+...+..+-+..+...+|.|.+|+...        |||.+|....-+.+|+..++-..++|+++.+..
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            3456899999999999999999999999999998754        999999999999999999999999998887755

>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=92.71  E-value=1.3  Score=35.82  Aligned_cols=65  Identities=14%  Similarity=0.143  Sum_probs=47.9

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccC-CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecc
Q 039806           17 AFVKNLASTIDNLKLHQIFSKFG-DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVER   82 (398)
Q Consensus        17 lfV~nLp~~vte~~L~~~F~~~G-~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g   82 (398)
                      +-+-..|..++.++|..+.+.+- .|..++|++|... ++--+.+.|++.++|++..+..||+.++.
T Consensus        16 ~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p-nrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   16 CCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP-NRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             EEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC-ceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            33444455566667766666654 5778999987643 45568899999999999999999988754

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>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=92.40  E-value=0.3  Score=43.31  Aligned_cols=61  Identities=23%  Similarity=0.149  Sum_probs=45.5

Q ss_pred             cHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhc--CCeecceEeeeecccc
Q 039806           27 DNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ--GATVERMELYVGPFIR   92 (398)
Q Consensus        27 te~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~ln--g~~l~gk~i~V~~~~~   92 (398)
                      ..+.|+++|+.|+.+.+..+++.     -+-..|.|.+.++|.+|...|+  +..+.|+.++|.++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s-----FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS-----FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT-----TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC-----CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            34789999999999988877763     3558999999999999999999  8999999999987743

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.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=91.44  E-value=0.078  Score=51.74  Aligned_cols=131  Identities=17%  Similarity=0.198  Sum_probs=77.1

Q ss_pred             ceEEeeCCCccccHHHHHHHHccCCC-EEEEEEeeCCCCCccccCCchh-hhHHHHHHHHH---HHH-------HHHHHH
Q 039806          104 NNLYVKNLDDDMTEEILVEKFSEFGK-ITSLVISKDANGTSKGFGSKVL-YVARAQKKAER---KAI-------LRAQFE  171 (398)
Q Consensus       104 ~~lfV~nLp~~~tee~L~~~F~~fG~-I~~~~i~~d~~g~s~Gf~~~~l-~v~~a~~k~~~---~~~-------~~~~~~  171 (398)
                      +.+|++||.+.++..||..+|..--. ...-.+++.      ||.+... .-.|+.+..+.   ..+       ......
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 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVKS------GYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeeec------ceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            46899999999999999999985411 011112211      2211110 11222221111   111       111223


Q ss_pred             HhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEee-CCCCCccceEEEecccHHHHHHHHHHhccccC
Q 039806          172 RMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMR-TDRGISKGHCMAIAQTKRERTSYLRIMYAKQG  242 (398)
Q Consensus       172 ~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~-d~~g~skGffV~f~~~~ea~~A~l~~q~~q~~  242 (398)
                      .....+.+-+.|++...-++.|..+...||++++|.... |..-.--  -|++..++.++.|+..++..|..
T Consensus        76 kkqrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavv--nvty~~~~~~~~ai~kl~g~Q~e  145 (584)
T KOG2193|consen   76 KKQRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVV--NVTYSAQQQHRQAIHKLNGPQLE  145 (584)
T ss_pred             HHHHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHH--HHHHHHHHHHHHHHHhhcchHhh
Confidence            333456678899999999999999999999999997642 3211001  36677777777777776665543

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=91.36  E-value=0.57  Score=39.31  Aligned_cols=72  Identities=21%  Similarity=0.187  Sum_probs=52.6

Q ss_pred             CCcceEEEcCCCCCC----cHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           12 SGIGNAFVKNLASTI----DNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        12 ~~~~~lfV~nLp~~v----te~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      ...++|.|+=|.++.    +-+.+...++.||+|.+|...-      +--|.|.|++..+|=+|+.+... ..-|..+..
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qC  156 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG------RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQC  156 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC------CceEEEEehhhHHHHHHHHhhcC-CCCCceEEe
Confidence            456788887666554    4445666789999999998842      34699999999999999998754 445566665


Q ss_pred             ecc
Q 039806           88 GPF   90 (398)
Q Consensus        88 ~~~   90 (398)
                      .|-
T Consensus       157 sWq  159 (166)
T PF15023_consen  157 SWQ  159 (166)
T ss_pred             ecc
Confidence            553

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

Probab=90.63  E-value=0.14  Score=50.76  Aligned_cols=71  Identities=18%  Similarity=0.148  Sum_probs=56.1

Q ss_pred             EEEcCCCCCC-cHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccccc
Q 039806           17 AFVKNLASTI-DNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRR   93 (398)
Q Consensus        17 lfV~nLp~~v-te~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~   93 (398)
                      |-+.-.+... |-++|...|.+||.|..|.|-..     --.|.|.|.+..+|-+|.. ..+..|+++.|+|.|....
T Consensus       375 l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-----~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  375 LALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-----SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             hhhhccCCCCchHhhhhhhhhhcCccccccccCc-----hhhheeeeeccccccchhc-cccceecCceeEEEEecCC
Confidence            3333344333 67889999999999999988443     2358999999999988876 5899999999999998753

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=90.58  E-value=0.082  Score=51.12  Aligned_cols=128  Identities=12%  Similarity=-0.039  Sum_probs=82.6

Q ss_pred             CccccCCCcceEEEcCCCCCC-cHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceE
Q 039806            6 NSEARLSGIGNAFVKNLASTI-DNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERME   84 (398)
Q Consensus         6 d~~~~~~~~~~lfV~nLp~~v-te~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~   84 (398)
                      |++.-..-.++.||++++..+ +-+++...|-..+..+-|....+.. .--.|||+.|.+......++. -+|.++....
T Consensus        44 ~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~~~~-~p~r~af~~l~~~navprll~-pdg~Lp~~~~  121 (479)
T KOG4676|consen   44 DDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYGDEV-IPDRFAFVELADQNAVPRLLP-PDGVLPGDRP  121 (479)
T ss_pred             CCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecCCCC-CccHHHHHhcCcccccccccC-CCCccCCCCc
Confidence            333334456789999999755 5555555555445444343333331 123469999999888887776 5787777777


Q ss_pred             eeeecccccccc------------cccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEe
Q 039806           85 LYVGPFIRRADR------------IQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVIS  136 (398)
Q Consensus        85 i~V~~~~~~~~~------------~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~  136 (398)
                      +...-+.+...-            ..+. -.++++|.+|...+...++-+.|..+|+|.....-
T Consensus       122 lt~~nh~p~ailktP~Lp~~~~A~klee-irRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a  184 (479)
T KOG4676|consen  122 LTKINHSPNAILKTPELPPQAAAKKLEE-IRRTREVQSLISAAILPESGESFERKGEVSYAHTA  184 (479)
T ss_pred             cccccCCccceecCCCCChHhhhhhhHH-HHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhh
Confidence            644333222111            0011 23679999999999999999999999998876554

>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=90.37  E-value=0.36  Score=37.31  Aligned_cols=68  Identities=19%  Similarity=0.230  Sum_probs=45.5

Q ss_pred             EEEEecCHHHHHHHHHHh-cCCeecceEeee--eccccccccc---ccCCCCceEEeeCCCccccHHHHHHHHc
Q 039806           58 GFVQYSTPESALDAIEKL-QGATVERMELYV--GPFIRRADRI---QEGSSFNNLYVKNLDDDMTEEILVEKFS  125 (398)
Q Consensus        58 aFV~F~~~e~A~~Ai~~l-ng~~l~gk~i~V--~~~~~~~~~~---~~~~~~~~lfV~nLp~~~tee~L~~~F~  125 (398)
                      |.|.|++++-|++.++.- +...+++..+.|  .+.....-.+   ....+.++|.|.|||...++|+|++..+
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeEE
Confidence            689999999999999742 223555555444  3333222111   1122678899999999999999987654

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>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=89.85  E-value=0.28  Score=38.97  Aligned_cols=59  Identities=14%  Similarity=0.109  Sum_probs=35.5

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEE-EeeCCCCC--------ccceEEEecccHHHHHHHHHH
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVK-IMRTDRGI--------SKGHCMAIAQTKRERTSYLRI  236 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svk-i~~d~~g~--------skGffV~f~~~~ea~~A~l~~  236 (398)
                      ..+.|.+.|.. ....+.++|++||+|.+.. +.++..|.        .-...|.|+++.+|.||+.+.
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~N   74 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKN   74 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTT
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhC
Confidence            34555667776 5567888999999998875 22221111        111189999999999998653

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.

>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=89.49  E-value=1.3  Score=32.99  Aligned_cols=59  Identities=17%  Similarity=0.245  Sum_probs=37.0

Q ss_pred             CCCcHHHHHHHHhccC-----CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           24 STIDNLKLHQIFSKFG-----DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        24 ~~vte~~L~~~F~~~G-----~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ..++..+|..++..-+     .|-.|.|..       .|+||+-.. +.|..+++.|++..+.|++|.|+.+
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~-------~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFD-------NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-S-------S-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEee-------eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            4678889999997754     366777743       489998775 5899999999999999999999764

; PDB: 2G0C_A 3MOJ_B.

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

Probab=89.11  E-value=0.27  Score=45.13  Aligned_cols=67  Identities=16%  Similarity=0.184  Sum_probs=54.1

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-C--------CCccce-----EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-R--------GISKGH-----CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~--------g~skGf-----fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ....+++.|||+..+-..||++|+.||.|-.|.+.... .        |.+++.     .|+|.+...|.+....+...+
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            44677889999999999999999999999999997654 2        333333     899999999998887777665


Q ss_pred             c
Q 039806          241 Q  241 (398)
Q Consensus       241 ~  241 (398)
                      .
T Consensus       153 I  153 (278)
T KOG3152|consen  153 I  153 (278)
T ss_pred             c
Confidence            4

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

Probab=89.10  E-value=1.7  Score=40.70  Aligned_cols=50  Identities=12%  Similarity=0.071  Sum_probs=39.5

Q ss_pred             CHHHHHHHhhcCCCeEEEEEeeCCCCC---ccceEEEecccHHHHHHHHHHhc
Q 039806          189 DEIELKQYFSQCGTISSVKIMRTDRGI---SKGHCMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       189 tee~L~~~F~~fG~I~svki~~d~~g~---skGffV~f~~~~ea~~A~l~~q~  238 (398)
                      -++++++.+++||+|..|-|+.++.-.   ..-.||+|...++|.+|...+..
T Consensus       299 lede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnG  351 (378)
T KOG1996|consen  299 LEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNG  351 (378)
T ss_pred             HHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCC
Confidence            357889999999999999998775221   22229999999999999887654

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=87.74  E-value=7.4  Score=37.47  Aligned_cols=43  Identities=19%  Similarity=0.226  Sum_probs=36.5

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCC--CeEEEEEeeCC-CCCccce
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCG--TISSVKIMRTD-RGISKGH  219 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG--~I~svki~~d~-~g~skGf  219 (398)
                      -+.+|+||-.-+||+||.+....-|  .|.++|++.+. +|.||||
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~  126 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGY  126 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccce
Confidence            4567799999999999999988776  46778888777 8999999

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=86.31  E-value=2.9  Score=31.86  Aligned_cols=50  Identities=16%  Similarity=0.223  Sum_probs=35.8

Q ss_pred             cCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHHh
Q 039806          182 KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       182 ~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~q  237 (398)
                      -..|.++...||.++|+.||.|. |.-+.|     .-.||.+.+++.+..+.....
T Consensus        14 ltFPkeWK~~DI~qlFspfG~I~-VsWi~d-----TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   14 LTFPKEWKTSDIYQLFSPFGQIY-VSWIND-----TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             EE--TT--HHHHHHHCCCCCCEE-EEEECT-----TEEEEEECCCHHHHHHHHHHT
T ss_pred             EeCchHhhhhhHHHHhccCCcEE-EEEEcC-----CcEEEEeecHHHHHHHHHHhc
Confidence            45889999999999999999985 444433     233999999999998776554

; 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.

>PRK14548 50S ribosomal protein L23P; Provisional

Probab=85.31  E-value=3.5  Score=31.56  Aligned_cols=59  Identities=10%  Similarity=0.258  Sum_probs=47.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhc-cC-CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHh
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSK-FG-DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL   75 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~-~G-~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~l   75 (398)
                      .+-|+-..+...+..+|++.++. || .|.+|+...-..+..  =|||.+...++|.+....+
T Consensus        21 ~n~y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT~~~~~~~K--KA~V~L~~g~~A~~va~ki   81 (84)
T PRK14548         21 ENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPKGEK--KAYVKLAEEYDAEEIASRL   81 (84)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCCCcE--EEEEEeCCCCcHHHHHHhh
Confidence            35677778999999999999988 77 588888887765444  3999999999999877654

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=84.81  E-value=3.6  Score=40.97  Aligned_cols=68  Identities=10%  Similarity=0.144  Sum_probs=57.0

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccC-CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFG-DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVER   82 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G-~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g   82 (398)
                      +..|.|=-+|...|-.||..|...+- .|.+++|++|..+. +=-..|.|.+.++|..-.+.+||..++.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pn-rymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPN-RYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCc-eEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            67899999999999999999887654 59999999965332 2246899999999999999999998764

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

Probab=84.12  E-value=1.1  Score=43.26  Aligned_cols=61  Identities=21%  Similarity=0.348  Sum_probs=49.8

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEE--------EEEeeCC-CCCccce-EEEecccHHHHHHHHH
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISS--------VKIMRTD-RGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~s--------vki~~d~-~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                      ...++++-+|++.+++++|.++|.++|.|..        |+|-+|. |+++||- -|+|.+...|..|+.-
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~  135 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEW  135 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhh
Confidence            3457888999999999999999999998854        5555555 7888877 8999999888888763

>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=84.00  E-value=1.6  Score=33.37  Aligned_cols=53  Identities=17%  Similarity=0.195  Sum_probs=35.0

Q ss_pred             hccccCCCcccCH----HHHHHHhhcC-CCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHHhc
Q 039806          178 AELYKNINDEVDE----IELKQYFSQC-GTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       178 ~~~v~nL~~~vte----e~L~~~F~~f-G~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~q~  238 (398)
                      .++|.|||.+.+-    ..|+.++..+ |.|.+|.       ..+. .|.|.+.+.|+||+..+..
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~-------~~tA-ilrF~~~~~A~RA~KRmeg   61 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS-------GGTA-ILRFPNQEFAERAQKRMEG   61 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE---------TT-E-EEEESSHHHHHHHHHHHTT
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe-------CCEE-EEEeCCHHHHHHHHHhhcc
Confidence            4677999988775    4577777788 5676662       1223 7999999999999998874

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

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=83.55  E-value=1  Score=45.80  Aligned_cols=54  Identities=11%  Similarity=0.254  Sum_probs=45.4

Q ss_pred             ccccCCCcccCHHHHHHHhhc--CCCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHHh
Q 039806          179 ELYKNINDEVDEIELKQYFSQ--CGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~--fG~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~q  237 (398)
                      ++++.|+..+-+|+++.+|+.  +-.+++|....     +.++||+|.+..||..|...++
T Consensus       178 vilREIpettp~e~Vk~lf~~encPk~iscefa~-----N~nWyITfesd~DAQqAykylr  233 (684)
T KOG2591|consen  178 VILREIPETTPIEVVKALFKGENCPKVISCEFAH-----NDNWYITFESDTDAQQAYKYLR  233 (684)
T ss_pred             EEEeecCCCChHHHHHHHhccCCCCCceeeeeee-----cCceEEEeecchhHHHHHHHHH
Confidence            344999999999999999965  78899999864     3567999999999999977544

>TIGR03636 L23_arch archaeal ribosomal protein L23

Probab=81.18  E-value=6.9  Score=29.42  Aligned_cols=59  Identities=12%  Similarity=0.258  Sum_probs=47.0

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhc-cC-CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHh
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSK-FG-DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL   75 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~-~G-~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~l   75 (398)
                      .+-|+-..+...+..+|++.++. || .|.+|+...-+.+..  =|||.+...++|.+.-.++
T Consensus        14 ~n~y~F~V~~~anK~eIK~avE~lf~VkV~~Vnt~~~~~~~K--KA~VtL~~g~~a~~va~k~   74 (77)
T TIGR03636        14 ENKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITPRGEK--KAYVKLAEEYAAEEIASRL   74 (77)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCCCce--EEEEEECCCCcHHHHHHhh
Confidence            36778888999999999999988 77 588888777664433  3999999999998876654

This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=80.63  E-value=1.2  Score=37.82  Aligned_cols=108  Identities=14%  Similarity=0.016  Sum_probs=71.9

Q ss_pred             CCCcHHHHHHHHhc-cCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccccccccccCC-
Q 039806           24 STIDNLKLHQIFSK-FGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGS-  101 (398)
Q Consensus        24 ~~vte~~L~~~F~~-~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~~~~~~~~~-  101 (398)
                      ..++-..|.+.+.. ++....+++..-    ..++..++|.++++++++++. ....+++..+.+..-.+......... 
T Consensus        27 ~~~~~~~l~~~l~~~W~~~~~~~i~~l----~~~~fl~~F~~~~d~~~vl~~-~p~~~~~~~~~l~~W~~~~~~~~~~~~  101 (153)
T PF14111_consen   27 KPISLSALEQELAKIWKLKGGVKIRDL----GDNLFLFQFESEEDRQRVLKG-GPWNFNGHFLILQRWSPDFNPSEVKFE  101 (153)
T ss_pred             CCCCHHHHHHHHHHHhCCCCcEEEEEe----CCCeEEEEEEeccceeEEEec-ccccccccchhhhhhccccccccccee
Confidence            34667777776655 443323333221    447899999999999999983 45567777777766554332221111 


Q ss_pred             -CCceEEeeCCCcc-ccHHHHHHHHccCCCEEEEEEe
Q 039806          102 -SFNNLYVKNLDDD-MTEEILVEKFSEFGKITSLVIS  136 (398)
Q Consensus       102 -~~~~lfV~nLp~~-~tee~L~~~F~~fG~I~~~~i~  136 (398)
                       ..--|-|.|||.. .+++-++.+-+.+|++.++...
T Consensus       102 ~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~  138 (153)
T PF14111_consen  102 HIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDEN  138 (153)
T ss_pred             ccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcC
Confidence             2233677899987 7888999999999999887544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	398
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		8e-19
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		3e-08
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		9e-19
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		3e-08
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		2e-17
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		5e-16
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		2e-11
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		2e-06
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-10
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-09
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-09
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		3e-09
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		6e-09
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-08
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		1e-08
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		2e-07
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		8e-07
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-06
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-06
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		6e-06
2nlw_A	105	Solution Structure Of The Rrm Domain Of Human Eukar		1e-05
2krb_A	81	Solution Structure Of Eif3b-Rrm Bound To Eif3j Pept		2e-05
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		2e-05
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		2e-05
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		7e-05
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		9e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		1e-04
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		2e-04
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		2e-04
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		3e-04
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		4e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		5e-04
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		6e-04
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		6e-04
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		6e-04
2dhg_A	104	Solution Structure Of The C-Terminal Rna Recognitio		7e-04
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		7e-04
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		7e-04
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		7e-04
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		8e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		8e-04

>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 = 91.3 bits (225), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 47/99 (47%), Positives = 62/99 (62%), Gaps = 1/99 (1%)
Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  +   R SG+GN F+KNL  +IDN  L+  FS FG+I S KVV  + G SKGYGFV
Sbjct: 85  MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFV 143
Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE 99
            + T E+A  AIEK+ G  +   +++VG F  R +R  E
Sbjct: 144 HFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 182

>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 = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 47/158 (29%), Positives = 76/158 (48%), Gaps = 18/158 (11%)
Query: 14  IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTP---ESAL 69
           + + +V +L   +    L++ FS  G I S +V       +S GY +V +  P   E AL
Sbjct: 10  MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 69
Query: 70  DAI--EKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEF 127
           D +  + ++G  V  M     P +R+       S   N+++KNLD  +  + L + FS F
Sbjct: 70  DTMNFDVIKGKPVRIMWSQRDPSLRK-------SGVGNIFIKNLDKSIDNKALYDTFSAF 122
Query: 128 GKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
           G I S  +  D NG SKG+G    +V    ++A  +AI
Sbjct: 123 GNILSCKVVCDENG-SKGYG----FVHFETQEAAERAI 155

>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 = 91.3 bits (225), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 50/114 (43%), Positives = 68/114 (59%), Gaps = 2/114 (1%)
Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  +   R SG+GN F+KNL  +IDN  L+  FS FG+I S KVV  + G SKGYGFV
Sbjct: 90  MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFV 148
Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE-GSSFNNLYVKNLDD 113
            + T E+A  AIEK+ G  +   +++VG F  R +R  E G+     Y  ++ D
Sbjct: 149 HFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPD 202

>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 = 56.2 bits (134), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 47/158 (29%), Positives = 76/158 (48%), Gaps = 18/158 (11%)
Query: 14  IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTP---ESAL 69
           + + +V +L   +    L++ FS  G I S +V       +S GY +V +  P   E AL
Sbjct: 15  MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 70  DAI--EKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEF 127
           D +  + ++G  V  M     P +R+       S   N+++KNLD  +  + L + FS F
Sbjct: 75  DTMNFDVIKGKPVRIMWSQRDPSLRK-------SGVGNIFIKNLDKSIDNKALYDTFSAF 127
Query: 128 GKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
           G I S  +  D NG SKG+G    +V    ++A  +AI
Sbjct: 128 GNILSCKVVCDENG-SKGYG----FVHFETQEAAERAI 160

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 86.7 bits (213), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 47/103 (45%), Positives = 62/103 (60%), Gaps = 5/103 (4%)
Query: 13  GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAI 72
           G GN F+KNL  +IDN  L+  FS FG+I S KVV  + G SKGYGFV + T E+A  AI
Sbjct: 4   GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAI 62
Query: 73  EKLQGATVERMELYVGPFIRRADRIQE----GSSFNNLYVKNL 111
           EK+ G  +   +++VG F  R +R  E       F N+Y+KN 
Sbjct: 63  EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNF 105

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 82.0 bits (201), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 44/90 (48%), Positives = 58/90 (64%), Gaps = 1/90 (1%)
Query: 10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESAL 69
          R SG+GN F+KNL  +IDN  L+  FS FG+I S KVV  + G SKGYGFV + T E+A 
Sbjct: 7  RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAE 65
Query: 70 DAIEKLQGATVERMELYVGPFIRRADRIQE 99
           AIEK+ G  +   +++VG F  R +R  E
Sbjct: 66 RAIEKMNGMLLNDRKVFVGRFKSRKEREAE 95

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 38/87 (43%), Positives = 55/87 (63%), Gaps = 2/87 (2%)
Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
           N +VKNL   ID+ +L + FS FG I S+KV++ + G+SKG+GFV +S+PE A  A+ ++
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM-EGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 76  QGATVERMELYVGPFIRRADRIQEGSS 102
            G  V    LYV    R+ +R Q G S
Sbjct: 76  NGRIVATKPLYVALAQRKEER-QSGPS 101

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 34/83 (40%), Positives = 43/83 (51%), Gaps = 24/83 (28%)
Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG----------------- 147
           NLYVKNLDD + +E L + FS FG ITS  +  +  G SKGFG                 
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 148 ------SKVLYVARAQKKAERKA 164
                 +K LYVA AQ+K ER++
Sbjct: 76  NGRIVATKPLYVALAQRKEERQS 98

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 44/134 (32%), Positives = 68/134 (50%), Gaps = 6/134 (4%)
Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
           N  V  L   +   +   +F   GDI+S K+V  +  G+S GYGFV YS P  A  AI  
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 75  LQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGK-ITSL 133
           L G  ++   + V      +  I++     NLYV  L   M+++ + + FS++G+ ITS 
Sbjct: 66  LNGLKLQTKTIKVSYARPSSASIRDA----NLYVSGLPKTMSQKEMEQLFSQYGRIITSR 121
Query: 134 VISKDANGTSKGFG 147
           ++   A G S+G G
Sbjct: 122 ILLDQATGVSRGVG 135

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 43/134 (32%), Positives = 67/134 (50%), Gaps = 6/134 (4%)
Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
           N  V  L   +   +   +F   G+I+S K+V  +  G+S GYGFV Y  P+ A  AI  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 75  LQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGK-ITSL 133
           L G  ++   + V      +  I++     NLYV  L   MT++ L + FS++G+ ITS 
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASIRDA----NLYVSGLPKTMTQKELEQLFSQYGRIITSR 119
Query: 134 VISKDANGTSKGFG 147
           ++     G S+G G
Sbjct: 120 ILVDQVTGVSRGVG 133

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 41/148 (27%), Positives = 74/148 (50%), Gaps = 13/148 (8%)
Query: 11  LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESAL 69
           L+ +   +V ++   +    + Q F+ FG I+S  +   S   K KG+ FV+Y  PE+A 
Sbjct: 10  LAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQ 69
Query: 70  DAIEKLQGATVERMELYVG---------PFIRRADRIQEGSSFNNLYVKNLDDDMTEEIL 120
            A+E++    +    + VG         P I +    +E  +FN +YV ++  D++++ +
Sbjct: 70  LALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQL--AEEARAFNRIYVASVHQDLSDDDI 127
Query: 121 VEKFSEFGKITSLVISKD-ANGTSKGFG 147
              F  FGKI S  +++D   G  KG+G
Sbjct: 128 KSVFEAFGKIKSCTLARDPTTGKHKGYG 155

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 42/156 (26%), Positives = 76/156 (48%), Gaps = 13/156 (8%)
Query: 3   STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQ 61
           S    +  L+ +   +V ++   +    + Q F+ FG I+S  +   S   K KG+ FV+
Sbjct: 17  SAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVE 76
Query: 62  YSTPESALDAIEKLQGATVERMELYVG---------PFIRRADRIQEGSSFNNLYVKNLD 112
           Y  PE+A  A+E++    +    + VG         P I +    +E  +FN +YV ++ 
Sbjct: 77  YEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQL--AEEARAFNRIYVASVH 134
Query: 113 DDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
            D++++ +   F  FGKI S  +++D   G  KG+G
Sbjct: 135 QDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYG 170

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 58.5 bits (140), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 40/141 (28%), Positives = 69/141 (48%), Gaps = 13/141 (9%)
Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQS-SKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
           +V ++   +    + Q F+ FG I+S      S   K KG+ FV+Y  PE+A  A+E+  
Sbjct: 16  YVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXN 75
Query: 77  GATVERMELYVG---------PFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEF 127
              +    + VG         P I +    +E  +FN +YV ++  D++++ +   F  F
Sbjct: 76  SVXLGGRNIKVGRPSNIGQAQPIIDQL--AEEARAFNRIYVASVHQDLSDDDIKSVFEAF 133
Query: 128 GKITSLVISKD-ANGTSKGFG 147
           GKI S  +++D   G  KG+G
Sbjct: 134 GKIKSCTLARDPTTGKHKGYG 154

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 42/135 (31%), Positives = 68/135 (50%), Gaps = 6/135 (4%)
Query: 13  GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDA 71
           G  N  V  L   +   +L  +FS  G+++S+K++  +  G S GYGFV Y T + A  A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 72  IEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGK-I 130
           I  L G  ++   + V      ++ I++     NLY+  L   MT++ + + FS FG+ I
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSEVIKDA----NLYISGLPRTMTQKDVEDMFSRFGRII 116
Query: 131 TSLVISKDANGTSKG 145
            S V+     G S+G
Sbjct: 117 NSRVLVDQTTGLSRG 131

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 42/135 (31%), Positives = 68/135 (50%), Gaps = 6/135 (4%)
Query: 13  GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDA 71
           G  N  V  L   +   +L  +FS  G+++S+K++  +  G S GYGFV Y T + A  A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 72  IEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGK-I 130
           I  L G  ++   + V      ++ I++     NLY+  L   MT++ + + FS FG+ I
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSEVIKDA----NLYISGLPRTMTQKDVEDMFSRFGRII 116
Query: 131 TSLVISKDANGTSKG 145
            S V+     G S+G
Sbjct: 117 NSRVLVDQTTGLSRG 131

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAIEK 74
           N  V  + +T+D ++L Q+F ++G I+S K+V  +E + S+GYGFV++ +  SA  AI  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 75  LQGATVERMELYV 87
           L G  +    L V
Sbjct: 104 LNGFNILNKRLKV 116

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 51.6 bits (122), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 42/151 (27%), Positives = 72/151 (47%), Gaps = 19/151 (12%)
Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           FV NL + I      ++F ++G  + S+V ++   + +G+GF++  +   A  A  +L G
Sbjct: 26  FVGNLPTDITEEDFKRLFERYG--EPSEVFIN---RDRGFGFIRLESRTLAEIAKAELDG 80
Query: 78  ATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISK 137
             ++   L          RI+  +    L VKNL   ++ E+L + FS+FG +   V+  
Sbjct: 81  TILKSRPL----------RIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV 130
Query: 138 DANGTSKGFGSKVLYVARAQKKAERKAILRA 168
           D  G + G G    +V  A K   RKA+ R 
Sbjct: 131 DDRGRATGKG----FVEFAAKPPARKALERC 157

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/151 (28%), Positives = 72/151 (47%), Gaps = 19/151 (12%)
Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           FV NL   I   ++ ++F K+G  ++ +V +    K KG+GF++          +E    
Sbjct: 26  FVGNLPPDITEEEMRKLFEKYG--KAGEVFIH---KDKGFGFIR----------LETRTL 70
Query: 78  ATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISK 137
           A + ++EL   P   +  R++      +L V+NL   ++ E+L E FS FG++   V+  
Sbjct: 71  AEIAKVELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIV 130
Query: 138 DANGTSKGFGSKVLYVARAQKKAERKAILRA 168
           D  G   G G     V  + K A RKA+ R 
Sbjct: 131 DDRGRPSGKG----IVEFSGKPAARKALDRC 157

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEKLQ 76
           +V +L   I    L  IF  FG I+S ++++ S+ G+SKGYGF+ +S  E A  A+E+L 
Sbjct: 30  YVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLN 89
Query: 77  GATVERMELYVGPFIRRAD 95
           G  +    + VG    R D
Sbjct: 90  GFELAGRPMKVGHVTERTD 108

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 30/80 (37%), Positives = 43/80 (53%), Gaps = 4/80 (5%)
Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK----SKGYGFVQYSTPES 67
          SG    F+KNL  +     L  +FSK G I+S  +   +       S G+GFV+Y  PE 
Sbjct: 3  SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 68 ALDAIEKLQGATVERMELYV 87
          A  A+++LQG TV+  +L V
Sbjct: 63 AQKALKQLQGHTVDGHKLEV 82

>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic Initiation Factor 3b Length = 105

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 20/56 (35%), Positives = 38/56 (67%), Gaps = 1/56 (1%)
Query: 31 LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY 86
          +H+IFSKFG I ++     ++GK+KGY F++Y++P  A+DA++   G  +++   +
Sbjct: 38 IHKIFSKFGKI-TNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 92

>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide Length = 81

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 20/56 (35%), Positives = 38/56 (67%), Gaps = 1/56 (1%)
Query: 31 LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY 86
          +H+IFSKFG I ++     ++GK+KGY F++Y++P  A+DA++   G  +++   +
Sbjct: 24 IHKIFSKFGKI-TNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 78

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/125 (32%), Positives = 64/125 (51%), Gaps = 12/125 (9%)
Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG-------SKVLYVARAQ 157
           +++  L+ D TE+ L E F ++G +T L I KD A G S+GFG       S V  V + Q
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 158 KKAERKAI--LRAQFERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIM-RTDR 213
              + K I   RA     + +  +++   I  +V   E +++FSQ GTI   ++M   D 
Sbjct: 66  HILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDT 125
Query: 214 GISKG 218
           G S+G
Sbjct: 126 GQSRG 130

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/133 (28%), Positives = 66/133 (49%), Gaps = 7/133 (5%)
Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           +V NL   I    L Q F   G I + K+++ +  K+  Y FV+Y     A  A++ L G
Sbjct: 4   YVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNG 63
Query: 78  ATVERMELYVGPFIRRADRIQEGSSFN--NLYVKNLDDDMTEEILVEKFSEF-GKITSLV 134
             +E   +     I  A + Q+ SS +  NL+V +L+ ++ +E L   F +F   ++  V
Sbjct: 64  KQIENNIVK----INWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHV 119
Query: 135 ISKDANGTSKGFG 147
           +     G+S+G+G
Sbjct: 120 MWDMQTGSSRGYG 132

>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 = 46.6 bits (109), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/63 (39%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          + FV N+       +L  IFS+ G + S ++V  +E GK KGYGF +Y   E+AL A+  
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 75 LQG 77
          L G
Sbjct: 70 LNG 72

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 30/85 (35%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALD 70
          SG    +V +L   I    L  IF  FG I +  ++  S  G+SKGYGF+ +S  E A  
Sbjct: 3  SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 71 AIEKLQGATVERMELYVGPFIRRAD 95
          A+E+L G  +    + VG    R D
Sbjct: 63 ALEQLNGFELAGRPMRVGHVTERLD 87

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 44.7 bits (104), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIE 73
          G  FV  L+   +   L Q+FSK+G I    VV  +E  +S+G+GFV +   + A DA+ 
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
Query: 74 KLQGATVERMELYV 87
           + G +V+  ++ V
Sbjct: 73 AMNGKSVDGRQIRV 86

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
          N  V  L   +   +   +F   GDI+S K+V  +  G+S GYGFV YS P  A  AI  
Sbjct: 6  NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 75 LQGATVERMELYV 87
          L G  ++   + V
Sbjct: 66 LNGLKLQTKTIKV 78

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 19  VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
           V N+     +  L Q+F +FG I   +++ ++ G SKG+GFV +     A  A EKL G 
Sbjct: 34  VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 92
Query: 79  TVERMELYV 87
            VE  ++ V
Sbjct: 93  VVEGRKIEV 101

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
          V N+     +  L Q+F +FG I   +++ ++ G SKG+GFV +     A  A EKL G 
Sbjct: 20 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGT 78
Query: 79 TVERMELYV 87
           VE  ++ V
Sbjct: 79 VVEGRKIEV 87

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEK 74
          N F+ +L     +  L Q+F  FG++ S+KV +  Q   SK +GFV Y  P SA  AI+ 
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 75 LQGATVERMELYV 87
          + G  +    L V
Sbjct: 87 MNGFQIGMKRLKV 99

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-QEGKSKGYGFVQYSTPESALDAIEK 74
          N FV +L   +D+  L   F  F    S  V+   Q G S+GYGFV +++ + A +A++ 
Sbjct: 3  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 75 LQG 77
          +QG
Sbjct: 63 MQG 65

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEK 74
          N +V  L  T+   ++ Q+FS++G I +S++++ Q  G S+G GF+++     A +AI+ 
Sbjct: 3  NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 75 LQG 77
          L G
Sbjct: 63 LNG 65

>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 = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 40/139 (28%), Positives = 61/139 (43%), Gaps = 21/139 (15%)
Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT-SKGFGSKVLYV--- 153
           +E      L++  L  + T+E L   F ++G +T  V+ +D N   S+GFG  V Y    
Sbjct: 9   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF-VTYATVE 67
Query: 154 -------ARAQKKAER-----KAILRAQFERMRKE---RAELYKNINDEVDEIELKQYFS 198
                  AR  K   R     +A+ R   +R       +      I ++ +E  L+ YF 
Sbjct: 68  EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 127
Query: 199 QCGTISSVKIMRTDRGISK 217
           Q G I  ++IM TDRG  K
Sbjct: 128 QYGKIEVIEIM-TDRGSGK 145

>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 = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 40/139 (28%), Positives = 61/139 (43%), Gaps = 21/139 (15%)
Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT-SKGFGSKVLYV--- 153
           +E      L++  L  + T+E L   F ++G +T  V+ +D N   S+GFG  V Y    
Sbjct: 7   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF-VTYATVE 65
Query: 154 -------ARAQKKAER-----KAILRAQFERMRKE---RAELYKNINDEVDEIELKQYFS 198
                  AR  K   R     +A+ R   +R       +      I ++ +E  L+ YF 
Sbjct: 66  EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 125
Query: 199 QCGTISSVKIMRTDRGISK 217
           Q G I  ++IM TDRG  K
Sbjct: 126 QYGKIEVIEIM-TDRGSGK 143

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 40/139 (28%), Positives = 61/139 (43%), Gaps = 21/139 (15%)
Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT-SKGFGSKVLYV--- 153
           +E      L++  L  + T+E L   F ++G +T  V+ +D N   S+GFG  V Y    
Sbjct: 8   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF-VTYATVE 66
Query: 154 -------ARAQKKAER-----KAILRAQFERMRKE---RAELYKNINDEVDEIELKQYFS 198
                  AR  K   R     +A+ R   +R       +      I ++ +E  L+ YF 
Sbjct: 67  EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 126
Query: 199 QCGTISSVKIMRTDRGISK 217
           Q G I  ++IM TDRG  K
Sbjct: 127 QYGKIEVIEIM-TDRGSGK 144

>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif In Trna Selenocysteine Associated Protein Length = 104

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 18 FVKNLASTIDNLKLHQIFSK-FGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
          FV +L   +D+  L++ F K +   +  KVV+ Q G SKGYGFV+++       A+ + Q
Sbjct: 13 FVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQ 72
Query: 77 GA 78
          GA
Sbjct: 73 GA 74

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 40/139 (28%), Positives = 61/139 (43%), Gaps = 21/139 (15%)
Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT-SKGFGSKVLYV--- 153
           +E      L++  L  + T+E L   F ++G +T  V+ +D N   S+GFG  V Y    
Sbjct: 6   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF-VTYATVE 64
Query: 154 -------ARAQKKAER-----KAILRAQFERMRKE---RAELYKNINDEVDEIELKQYFS 198
                  AR  K   R     +A+ R   +R       +      I ++ +E  L+ YF 
Sbjct: 65  EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 124
Query: 199 QCGTISSVKIMRTDRGISK 217
           Q G I  ++IM TDRG  K
Sbjct: 125 QYGKIEVIEIM-TDRGSGK 142

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 5/64 (7%)
Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +   +AS + +  + Q FS FG I   +V        KGY FV++ST ESA  AI  + G
Sbjct: 29 YCGGIASGLTDQLMRQTFSPFGQIMEIRVF-----PEKGYSFVRFSTHESAAHAIVSVNG 83
Query: 78 ATVE 81
           T+E
Sbjct: 84 TTIE 87

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 40/139 (28%), Positives = 61/139 (43%), Gaps = 21/139 (15%)
Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT-SKGFGSKVLYV--- 153
           +E      L++  L  + T+E L   F ++G +T  V+ +D N   S+GFG  V Y    
Sbjct: 8   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF-VTYATVE 66
Query: 154 -------ARAQKKAER-----KAILRAQFERMRKE---RAELYKNINDEVDEIELKQYFS 198
                  AR  K   R     +A+ R   +R       +      I ++ +E  L+ YF 
Sbjct: 67  EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 126
Query: 199 QCGTISSVKIMRTDRGISK 217
           Q G I  ++IM TDRG  K
Sbjct: 127 QYGKIEVIEIM-TDRGSGK 144

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 40/139 (28%), Positives = 61/139 (43%), Gaps = 21/139 (15%)
Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT-SKGFGSKVLYV--- 153
           +E      L++  L  + T+E L   F ++G +T  V+ +D N   S+GFG  V Y    
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF-VTYATVE 59
Query: 154 -------ARAQKKAER-----KAILRAQFERMRKE---RAELYKNINDEVDEIELKQYFS 198
                  AR  K   R     +A+ R   +R       +      I ++ +E  L+ YF 
Sbjct: 60  EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 119
Query: 199 QCGTISSVKIMRTDRGISK 217
           Q G I  ++IM TDRG  K
Sbjct: 120 QYGKIEVIEIM-TDRGSGK 137

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDA 71
          G  N  V  L   +   +L  +FS  G+++S+K++  +  G S GYGFV Y T + A  A
Sbjct: 3  GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 72 IEKLQG 77
          I  L G
Sbjct: 63 INTLNG 68

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	398
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-54
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-38
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-20
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-50
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-47
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-20
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-17
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-44
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-27
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-21
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-41
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-22
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-20
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-41
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-25
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-18
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-38
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-26
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-22
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-37
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-15
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-07
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-37
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	7e-27
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-23
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-33
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-33
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-19
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-04
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-33
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-23
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-22
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-31
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-27
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-19
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-04
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-30
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-17
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-29
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	7e-16
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-26
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-10
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-24
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-16
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-11
1x5o_A	114	RNA binding motif, single-stranded interacting pro	7e-23
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-16
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-14
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-22
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	9e-11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-06
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-22
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-18
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-09
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-21
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-14
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-06
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-21
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-19
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-21
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-15
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-09
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	6e-21
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-15
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-07
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-20
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-16
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	8e-07
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-20
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	7e-12
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-20
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-20
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-19
1x4e_A	85	RNA binding motif, single-stranded interacting pro	8e-11
1x4e_A	85	RNA binding motif, single-stranded interacting pro	8e-06
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-19
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	9e-15
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-09
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	5e-19
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-16
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-08
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-19
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-14
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-08
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	7e-19
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-16
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-06
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	7e-19
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-13
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	8e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	4e-18
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	4e-16
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	4e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-18
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-10
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-05
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-17
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-14
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-17
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-10
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-17
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-17
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-05
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-17
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-09
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-17
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-09
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-04
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	9e-17
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-05
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-16
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-15
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-12
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-16
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-10
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	6e-06
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-16
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	7e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	5e-06
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-16
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-08
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-04
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-16
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-12
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-11
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-16
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	8e-10
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-04
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-16
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-08
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	6e-04
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-16
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-08
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-16
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-11
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	6e-04
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-16
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-09
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-05
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-16
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-09
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-16
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-11
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-04
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-16
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-07
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	7e-16
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-09
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-05
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	9e-16
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	5e-04
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-16
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-15
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-05
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-15
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	9e-08
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-04
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-15
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	6e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-05
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-15
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	9e-09
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-05
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-15
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-10
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-04
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-15
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-07
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-15
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-15
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	6e-10
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	7e-05
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-15
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-15
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-09
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-04
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-15
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-10
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	7e-04
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-15
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-08
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-14
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-08
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-14
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	7e-08
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-04
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-07
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-04
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-14
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-08
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-14
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-07
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-14
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-08
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-04
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	5e-14
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-09
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-04
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-14
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-08
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-04
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	7e-14
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-07
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	9e-14
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-07
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-13
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-08
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	7e-04
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	6e-07
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-13
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-13
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-05
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-13
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	9e-05
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-13
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-07
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-08
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-04
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
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	7e-13
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	8e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-05
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	9e-13
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-08
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	8e-05
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-12
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-07
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-12
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-06
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	4e-04
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-12
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-09
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	9e-07
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-12
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	6e-10
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	6e-04
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-06
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-04
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-11
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	9e-06
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-11
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	6e-05
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-08
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-04
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-05
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-11
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	7e-11
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-07
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-04
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-09
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-04
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	4e-11
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-06
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-11
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	6e-07
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	4e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-06
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	5e-11
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-04
2div_A	99	TRNA selenocysteine associated protein; structural	5e-11
2div_A	99	TRNA selenocysteine associated protein; structural	5e-07
2div_A	99	TRNA selenocysteine associated protein; structural	3e-04
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	6e-11
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-06
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	7e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-04
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-10
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-08
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	9e-06
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-04
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-10
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-04
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-10
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-04
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-10
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	7e-10
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	7e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-09
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-09
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-08
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	6e-05
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-09
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-07
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-05
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-09
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-06
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-09
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-06
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-05
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	3e-09
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-04
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-09
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-09
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-06
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	8e-04
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-09
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	4e-09
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	6e-06
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	4e-09
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	6e-09
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-04
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	6e-09
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	6e-09
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-05
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-09
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-04
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	9e-09
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	8e-05
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-08
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	4e-05
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-08
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	5e-06
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-08
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-05
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-07
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	5e-04
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	6e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	5e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	3e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-06
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-04
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	5e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-05
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-05
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	8e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-04
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-06
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	4e-06
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	5e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-06
1nmr_A	85	Poly(A)-binding protein; all helical domain, pepti	3e-06
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-06
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-05
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	5e-06
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	5e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	8e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	4e-05
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	6e-05
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	6e-05
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	9e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	5e-04

>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 =  179 bits (456), Expect = 8e-54
 Identities = 39/249 (15%), Positives = 82/249 (32%), Gaps = 49/249 (19%)

Query: 1   MWS---TPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGY 57
             +      +  R   +    VKNL  + +  K+++ F   G I     V     K+  +
Sbjct: 25  GLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVD-VADSLKKNFRF 83

Query: 58  GFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTE 117
             ++++  + AL AI K     V + E+ V              +   L++ N     T+
Sbjct: 84  ARIEFARYDGALAAITKTHK-VVGQNEIIVSHL-----------TECTLWMTNFPPSYTQ 131

Query: 118 EILVEKFSEFGKIT-SLVISKDANGTSKGFG-----------------------SKVLYV 153
             + +   +   +  S+ +      TS+ F                           L  
Sbjct: 132 RNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVT 191

Query: 154 ARAQKKAERKAILRAQFERMRKERAELY-KNINDEV-DEIELKQYFSQCGTISSVKIMRT 211
             +    + K     + +    E  E+  +N++ E+ DE  L++ F   G+I  + I   
Sbjct: 192 KVSNPLEKSK-----RTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAG 246

Query: 212 DR--GISKG 218
            +    +  
Sbjct: 247 QKEHSFNNC 255

>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 =  138 bits (351), Expect = 2e-38
 Identities = 27/173 (15%), Positives = 57/173 (32%), Gaps = 29/173 (16%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
             ++ N   +     +  +      +  S  + S     S+ + ++  ++ E A   +EK
Sbjct: 119 TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 178

Query: 75  LQGATVERMELYVG---PFIRRADRIQEGSSFNNLYVKNLDDDMTEE-ILVEKFSEFGKI 130
           L G  +E   L      P  +             + ++NL  ++ +E +L E F  FG I
Sbjct: 179 LNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSI 238

Query: 131 TSLVISKD--ANGTSKGFG----------------------SKVLYVARAQKK 159
             + I      +  +                          ++ + V+ A KK
Sbjct: 239 EKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKK 291

>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 = 89.7 bits (223), Expect = 2e-20
 Identities = 21/176 (11%), Positives = 47/176 (26%), Gaps = 23/176 (13%)

Query: 54  SKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDD 113
           S  YG       +  LD           +         +  + +        + VKNL  
Sbjct: 1   SMEYGHHARPDSKRPLDEGSPAAAGLTSK---------KANEALTRNRELTTVLVKNLPK 51

Query: 114 DMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFERM 173
              +  + + F   G I  + ++      +  F      +  A+      AI +      
Sbjct: 52  SYNQNKVYKYFKHCGPIIHVDVADS-LKKNFRFA----RIEFARYDGALAAITKTHKVVG 106

Query: 174 RKE-------RAELY-KNINDEVDEIELKQYFSQCGTI-SSVKIMRTDRGISKGHC 220
           + E          L+  N      +  ++        +  S+++       S+   
Sbjct: 107 QNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFA 162

>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 =  170 bits (434), Expect = 1e-50
 Identities = 43/244 (17%), Positives = 75/244 (30%), Gaps = 53/244 (21%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
                 +E +        ++ L   + N ++H + S +  ++   V      K KG  FV
Sbjct: 11  RLEH--TERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----DKYKGTAFV 62

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEIL 120
                E A  AI     + +   EL V          Q   +   L V NL   +T++  
Sbjct: 63  TLLNGEQAEAAINAFHQSRLRERELSV----------QLQPTDALLCVANLPPSLTQQQF 112

Query: 121 VEKFSEFGKITSLVISKD-ANGTSKGFG-----------------------SKVLYVARA 156
            E    FG +    +      G SKG+G                        + LYV   
Sbjct: 113 EELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT 172

Query: 157 QKKAERKAILRAQFERMRKERAELY-KNINDEVDEIE-LKQYFSQCGTISSVKIMRTDRG 214
                  A+L             L    +    ++++ L +  S   + +  ++     G
Sbjct: 173 DAGQLTPALLH---------SRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDG 223

Query: 215 ISKG 218
             KG
Sbjct: 224 QLKG 227

>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 =  162 bits (413), Expect = 1e-47
 Identities = 37/187 (19%), Positives = 59/187 (31%), Gaps = 26/187 (13%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
              V NL  ++   +  ++   FG ++   +V S+  G+SKGYGF +Y   +SA  A   
Sbjct: 97  LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156

Query: 75  LQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTE-EILVEKFSEFGKITSL 133
           L G  +    LYV                  L V  L     + + L    S     T  
Sbjct: 157 LLGKPLGPRTLYVHWTDAGQLT-PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFC 215

Query: 134 VISKDANGTSKGFG-----------------------SKVLYVARAQKKAERKAILRAQF 170
            ++   +G  KGF                           L V+        +++L A  
Sbjct: 216 QLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALI 275

Query: 171 ERMRKER 177
                  
Sbjct: 276 AAQATAL 282

>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 = 89.7 bits (223), Expect = 1e-20
 Identities = 18/100 (18%), Positives = 35/100 (35%), Gaps = 2/100 (2%)

Query: 2   WSTPNSEA-RLSGIGNAFVKNLASTIDNL-KLHQIFSKFGDIQSSKVVVSQEGKSKGYGF 59
           W+        L       V  L    +++  L +  S        ++   Q+G+ KG+  
Sbjct: 171 WTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAV 230

Query: 60  VQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE 99
           ++Y T E A +A ++  G ++    L V            
Sbjct: 231 LEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSM 270

>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 = 78.9 bits (195), Expect = 9e-17
 Identities = 20/139 (14%), Positives = 51/139 (36%), Gaps = 21/139 (15%)

Query: 91  IRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKV 150
            R     ++  +   + ++ L  D+T + + +  S++  +    +        KG     
Sbjct: 10  KRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----DKYKGTA--- 60

Query: 151 LYVARAQKKAERKAIL---------RAQFERMRKERAELY-KNINDEVDEIELKQYFSQC 200
            +V     +    AI          R    +++   A L   N+   + + + ++     
Sbjct: 61  -FVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPF 119

Query: 201 GTISSVKIMRTDR-GISKG 218
           G++    ++ ++R G SKG
Sbjct: 120 GSLERCFLVYSERTGQSKG 138

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

 Score =  151 bits (383), Expect = 5e-44
 Identities = 41/180 (22%), Positives = 75/180 (41%), Gaps = 32/180 (17%)

Query: 12  SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALD 70
           + +   +V ++   +    + Q F+ FG I+S  +   S   K KG+ FV+Y  PE+A  
Sbjct: 26  AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL 85

Query: 71  AIEKLQGATVERMELYVGPFIRRADR-------IQEGSSFNNLYVKNLDDDMTEEILVEK 123
           A+E++    +    + VG                +E  +FN +YV ++  D++++ +   
Sbjct: 86  ALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSV 145

Query: 124 FSEFGKITSLVISKDA-NGTSKGFG-----------------------SKVLYVARAQKK 159
           F  FGKI S  +++D   G  KG+G                        + L V +A   
Sbjct: 146 FEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

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

 Score =  105 bits (265), Expect = 6e-27
 Identities = 30/168 (17%), Positives = 62/168 (36%), Gaps = 30/168 (17%)

Query: 77  GATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVIS 136
            +     ++  G   +R       +  + +YV ++  ++ E+ + + F+ FG I S+ +S
Sbjct: 5   ASMTGGQQMGRGSAAQRQ---GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMS 61

Query: 137 KD-ANGTSKGFG-----------------------SKVLYVARAQKKAERKAILRAQFER 172
            D      KGF                         + + V R     + + I+    E 
Sbjct: 62  WDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEE 121

Query: 173 MRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMR-TDRGISKG 218
            R     +Y  +++ ++ + ++K  F   G I S  + R    G  KG
Sbjct: 122 ARAF-NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKG 168

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

 Score = 89.7 bits (223), Expect = 5e-21
 Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 1/92 (1%)

Query: 3   STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQ 61
                          +V ++   + +  +  +F  FG I+S+ +      GK KGYGF++
Sbjct: 114 IIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIE 173

Query: 62  YSTPESALDAIEKLQGATVERMELYVGPFIRR 93
           Y   +S+ DA+  +    +    L VG  +  
Sbjct: 174 YEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

>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 =  143 bits (364), Expect = 1e-41
 Identities = 34/175 (19%), Positives = 61/175 (34%), Gaps = 30/175 (17%)

Query: 9   ARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESA 68
           +  +   N F+ NL       +L    S+        VV  + G ++ +G+V + + E  
Sbjct: 8   SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDL 67

Query: 69  LDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFG 128
             A+E L G  V   E+ +     R  +         L  KNL  ++TE+ L E F +  
Sbjct: 68  EKALE-LTGLKVFGNEIKLEKPKGRDSKKVRA--ARTLLAKNLSFNITEDELKEVFEDAL 124

Query: 129 KITSLVISKDANGTSKGFG-----------------------SKVLYVARAQKKA 160
           +I  +      +G SKG                          + + +    +K 
Sbjct: 125 EIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 175

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 93.1 bits (232), Expect = 1e-22
 Identities = 32/143 (22%), Positives = 53/143 (37%), Gaps = 25/143 (17%)

Query: 93  RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLY 152
                 E ++  NL++ NL+ + +   L    SE      L +     GT++ FG    Y
Sbjct: 3   HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFG----Y 58

Query: 153 VARAQKKAERKAI-----------LRAQFERMRKERAE-----LY-KNINDEVDEIELKQ 195
           V     +   KA+           ++ +  + R  +       L  KN++  + E ELK+
Sbjct: 59  VDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKE 118

Query: 196 YFSQCGTISSVKIMRTDRGISKG 218
            F     I  V       G SKG
Sbjct: 119 VFEDALEIRLVS----QDGKSKG 137

>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 = 87.7 bits (218), Expect = 1e-20
 Identities = 20/94 (21%), Positives = 41/94 (43%), Gaps = 4/94 (4%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
                    ++        KNL+  I   +L ++F    +I     +VSQ+GKSKG  ++
Sbjct: 86  EKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI----RLVSQDGKSKGIAYI 141

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRA 94
           ++ +   A   +E+ QGA ++   + +     + 
Sbjct: 142 EFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 175

>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 =  141 bits (359), Expect = 6e-41
 Identities = 31/139 (22%), Positives = 52/139 (37%), Gaps = 3/139 (2%)

Query: 12  SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVV---VSQEGKSKGYGFVQYSTPESA 68
           S     FV  +  T     L ++F ++G +    V+        +SKG  FV + T ++A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 69  LDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFG 128
           L+A   L    V     +                   L++  +    TE  +   FS FG
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG 120

Query: 129 KITSLVISKDANGTSKGFG 147
           +I    I +  +G S+G  
Sbjct: 121 QIEECRILRGPDGLSRGCA 139

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  101 bits (253), Expect = 1e-25
 Identities = 24/141 (17%), Positives = 51/141 (36%), Gaps = 35/141 (24%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANG---TSKGFG-------------- 147
            ++V  +    +E+ L E F ++G +  + + +D +     SKG                
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 148 ---------SKVLYVARAQKKAERKAILRAQFERMRKERAELY-KNINDEVDEIELKQYF 197
                      + +  + +     K            E  +L+   I+ +  E +++  F
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADSEK--------NNAVEDRKLFIGMISKKCTENDIRVMF 116

Query: 198 SQCGTISSVKIMRTDRGISKG 218
           S  G I   +I+R   G+S+G
Sbjct: 117 SSFGQIEECRILRGPDGLSRG 137

>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 = 80.3 bits (199), Expect = 3e-18
 Identities = 16/65 (24%), Positives = 31/65 (47%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
             F+  ++       +  +FS FG I+  +++   +G S+G  FV ++T   A  AI+ +
Sbjct: 97  KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 156

Query: 76  QGATV 80
             A  
Sbjct: 157 HQAQT 161

>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 =  134 bits (340), Expect = 3e-38
 Identities = 41/152 (26%), Positives = 69/152 (45%), Gaps = 10/152 (6%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
           N  V  L   + + +L+ +F   G I + +++   + G S GY FV +++   +  AI+ 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 75  LQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLV 134
           L G TV    L V      A    E     NLYV NL   +T++ L   F ++G I    
Sbjct: 65  LNGITVRNKRLKVS----YARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 120

Query: 135 ISKD-ANGTSKGFGSKVLYVARAQKKAERKAI 165
           I +D   G  +G      +V   +++  ++AI
Sbjct: 121 ILRDKLTGRPRGVA----FVRYNKREEAQEAI 148

>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 =  102 bits (256), Expect = 3e-26
 Identities = 33/144 (22%), Positives = 50/144 (34%), Gaps = 38/144 (26%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG------------ 147
           +S  NL V  L  DMT+  L   F   G I +  I +D   G S G+             
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60

Query: 148 -----------SKVLYVARAQKKAERKAILRAQFERMRKERAELY-KNINDEVDEIELKQ 195
                      +K L V+ A+   E              +   LY  N+   + + +L  
Sbjct: 61  AIKVLNGITVRNKRLKVSYARPGGE------------SIKDTNLYVTNLPRTITDDQLDT 108

Query: 196 YFSQCGTISSVKIMR-TDRGISKG 218
            F + G+I    I+R    G  +G
Sbjct: 109 IFGKYGSIVQKNILRDKLTGRPRG 132

>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 = 92.6 bits (231), Expect = 1e-22
 Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGF 59
            ++ P  E+      N +V NL  TI + +L  IF K+G I    ++  +  G+ +G  F
Sbjct: 78  SYARPGGES--IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAF 135

Query: 60  VQYSTPESALDAIEKLQGATVE 81
           V+Y+  E A +AI  L     E
Sbjct: 136 VRYNKREEAQEAISALNNVIPE 157

>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 =  130 bits (328), Expect = 3e-37
 Identities = 48/111 (43%), Positives = 63/111 (56%), Gaps = 5/111 (4%)

Query: 12  SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDA 71
            G GN F+KNL  +IDN  L+  FS FG+I S KVV   E  SKGYGFV + T E+A  A
Sbjct: 3   LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERA 61

Query: 72  IEKLQGATVERMELYVGPFIRRADRIQEGSS----FNNLYVKNLDDDMTEE 118
           IEK+ G  +   +++VG F  R +R  E  +    F N+Y+KN     T  
Sbjct: 62  IEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRA 112

>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 = 71.5 bits (176), Expect = 1e-15
 Identities = 29/114 (25%), Positives = 46/114 (40%), Gaps = 29/114 (25%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG------------- 147
               N+++KNLD  +  + L + FS FG I S  +  D NG SKG+G             
Sbjct: 3   LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERA 61

Query: 148 ----------SKVLYVARAQKKAERKAILRAQFERMRKERAELY-KNINDEVDE 190
                      + ++V R + + ER+A L A+ +        +Y KN       
Sbjct: 62  IEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTN----VYIKNFGPGSTR 111

>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 = 47.2 bits (113), Expect = 5e-07
 Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 1/37 (2%)

Query: 182 KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
           KN++  +D   L   FS  G I S K++  D   SKG
Sbjct: 11  KNLDKSIDNKALYDTFSAFGNILSCKVVC-DENGSKG 46

>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 =  134 bits (339), Expect = 4e-37
 Identities = 42/264 (15%), Positives = 84/264 (31%), Gaps = 80/264 (30%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
                  E   +     FV NL + I      ++F ++G+     +      + +G+GF+
Sbjct: 9   KSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN-----RDRGFGFI 63

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEIL 120
           +  +   A  A  +L G  ++   L +    R A           L VKNL   ++ E+L
Sbjct: 64  RLESRTLAEIAKAELDGTILKSRPLRI----RFATH------GAALTVKNLSPVVSNELL 113

Query: 121 VEKFSEFGKITSLVISKDANGTSKGFG---------------------------SKVLYV 153
            + FS+FG +   V+  D  G + G G                            + + V
Sbjct: 114 EQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV 173

Query: 154 ARAQKKAERKAILRAQFERMRKER--------------------------AELYKNINDE 187
              ++  +   +     ++ ++                             E+ K   ++
Sbjct: 174 EPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRWKALDEMEKQQREQ 233

Query: 188 VD------------EIELKQYFSQ 199
           VD            E+E  ++  Q
Sbjct: 234 VDRNIREAKEKLEAEMEAARHEHQ 257

>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 =  107 bits (268), Expect = 7e-27
 Identities = 32/142 (22%), Positives = 59/142 (41%), Gaps = 13/142 (9%)

Query: 84  ELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTS 143
            + +  F++  ++    +    L+V NL  D+TEE     F  +G+ + + I++D     
Sbjct: 5   TIDIKSFLKPGEK--TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD----- 57

Query: 144 KGFG----SKVLYVARAQKKAERKAILRAQFERMRKER-AELY-KNINDEVDEIELKQYF 197
           +GFG            A+ + +   +             A L  KN++  V    L+Q F
Sbjct: 58  RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAF 117

Query: 198 SQCGTISSVKIMRTDRGISKGH 219
           SQ G +    ++  DRG + G 
Sbjct: 118 SQFGPVEKAVVVVDDRGRATGK 139

>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 = 97.8 bits (244), Expect = 1e-23
 Identities = 34/174 (19%), Positives = 62/174 (35%), Gaps = 27/174 (15%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
              VKNL+  + N  L Q FS+FG ++ + VVV   G++ G GFV+++    A  A+E+ 
Sbjct: 98  ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERC 157

Query: 76  QGATV----ERMELYVGPFIRRADR---IQEGSSFNNLYVKNLDDDMTEEILVEKFSEFG 128
                        + V P  +  D     ++       Y K  +          +F++ G
Sbjct: 158 GDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKERE-------QPPRFAQPG 210

Query: 129 KITSLVISKDANGTSKGFG--------SKVLYVARAQKKAERKAILRAQFERMR 174
                  S+      K                +  A++K E +        ++ 
Sbjct: 211 TFEFEYASR-----WKALDEMEKQQREQVDRNIREAKEKLEAEMEAARHEHQLM 259

>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 =  123 bits (312), Expect = 1e-33
 Identities = 49/227 (21%), Positives = 87/227 (38%), Gaps = 42/227 (18%)

Query: 3   STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQ 61
            + N  A    + + +V +L   +    L++ FS  G I S +V       +S GY +V 
Sbjct: 4   GSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 63

Query: 62  YSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILV 121
           +  P  A  A++ +    ++   + +     + D     S   N+++KNLD  +  + L 
Sbjct: 64  FQQPADAERALDTMNFDVIKGKPVRIMW--SQRDPSLRKSGVGNIFIKNLDKSIDNKALY 121

Query: 122 EKFSEFGKITSLVISKDANGTSKGFG-----------------------SKVLYVARAQK 158
           + FS FG I S  +  D NG SKG+G                        + ++V R + 
Sbjct: 122 DTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 180

Query: 159 KAERKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISS 205
           + ER+A L A+ +                     +  Y    G I +
Sbjct: 181 RKEREAELGARAKEFYPYD---------------VPDYAGSSGRIVT 212

>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 =  122 bits (309), Expect = 3e-33
 Identities = 52/133 (39%), Positives = 71/133 (53%), Gaps = 11/133 (8%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
           MWS  +   R SG+GN F+KNL  +IDN  L+  FS FG+I S KVV   E  SKGYGFV
Sbjct: 90  MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSKGYGFV 148

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQE-GSSFNNLYVKNLDDDMTEEI 119
            + T E+A  AIEK+ G  +   +++VG F  R +R  E G+     Y  ++ D      
Sbjct: 149 HFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPD------ 202

Query: 120 LVEKFSEFGKITS 132
                   G+I +
Sbjct: 203 ---YAGSSGRIVT 212

>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 = 83.5 bits (207), Expect = 7e-19
 Identities = 37/145 (25%), Positives = 59/145 (40%), Gaps = 24/145 (16%)

Query: 94  ADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-NGTSKGFGSKVLY 152
            +         +LYV +L  D+TE +L EKFS  G I S+ + +D     S G+     Y
Sbjct: 6   MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYA----Y 61

Query: 153 VARAQKKAERKAILRAQFERM-----------------RKERAELY-KNINDEVDEIELK 194
           V   Q     +A+    F+ +                 +     ++ KN++  +D   L 
Sbjct: 62  VNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALY 121

Query: 195 QYFSQCGTISSVKIMRTDRGISKGH 219
             FS  G I S K++  D   SKG+
Sbjct: 122 DTFSAFGNILSCKVVC-DENGSKGY 145

>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 = 40.7 bits (96), Expect = 3e-04
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 4/50 (8%)

Query: 174 RKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKGHC 220
               A LY  +++ +V E  L + FS  G I S+++ R D     S G+ 
Sbjct: 12  SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCR-DMITRRSLGYA 60

>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 =  120 bits (303), Expect = 6e-33
 Identities = 43/134 (32%), Positives = 63/134 (47%), Gaps = 6/134 (4%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
           N  V  L   +   +   +F   G+I+S K+V  +  G+S GYGFV Y  P+ A  AI  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 75  LQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLV 134
           L G  ++   + V      A          NLYV  L   MT++ L + FS++G+I +  
Sbjct: 64  LNGLRLQTKTIKV----SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSR 119

Query: 135 ISKD-ANGTSKGFG 147
           I  D   G S+G G
Sbjct: 120 ILVDQVTGVSRGVG 133

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 94.2 bits (235), Expect = 3e-23
 Identities = 34/131 (25%), Positives = 52/131 (39%), Gaps = 14/131 (10%)

Query: 102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG----SKVLYVARA 156
           S  NL V  L  +MT+E     F   G+I S  + +D   G S G+G           +A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 157 QKKAERKAIL-------RAQFERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKI 208
                   +         A+        A LY   +   + + EL+Q FSQ G I + +I
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120

Query: 209 MR-TDRGISKG 218
           +     G+S+G
Sbjct: 121 LVDQVTGVSRG 131

>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 = 93.0 bits (232), Expect = 1e-22
 Identities = 25/82 (30%), Positives = 45/82 (54%), Gaps = 3/82 (3%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGF 59
            ++ P+S +      N +V  L  T+   +L Q+FS++G I +S+++V Q  G S+G GF
Sbjct: 77  SYARPSSAS--IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGF 134

Query: 60  VQYSTPESALDAIEKLQGATVE 81
           +++     A +AI+ L G    
Sbjct: 135 IRFDKRIEAEEAIKGLNGQKPS 156

>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 =  116 bits (292), Expect = 3e-31
 Identities = 37/149 (24%), Positives = 71/149 (47%), Gaps = 7/149 (4%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           +V NL   I    L Q F   G I + K+++ +  K+  Y FV+Y     A  A++ L G
Sbjct: 4   YVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNG 63

Query: 78  ATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISK 137
             +E   + +  +  ++ +     +F NL+V +L+ ++ +E L   F +F    S  +  
Sbjct: 64  KQIENNIVKIN-WAFQSQQSSSDDTF-NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121

Query: 138 DAN-GTSKGFGSKVLYVARAQKKAERKAI 165
           D   G+S+G+G    +V+   +   + A+
Sbjct: 122 DMQTGSSRGYG----FVSFTSQDDAQNAM 146

>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 =  105 bits (265), Expect = 2e-27
 Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 1/89 (1%)

Query: 1   MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGF 59
            W+  + ++      N FV +L   +D+  L   F  F    S  V+   + G S+GYGF
Sbjct: 74  NWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGF 133

Query: 60  VQYSTPESALDAIEKLQGATVERMELYVG 88
           V +++ + A +A++ +QG  +    L + 
Sbjct: 134 VSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162

>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 = 83.0 bits (206), Expect = 3e-19
 Identities = 31/133 (23%), Positives = 54/133 (40%), Gaps = 23/133 (17%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
           LYV NLD  +TE+IL + F   G I ++ I  D N  +  +     +V   Q      A+
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYA----FVEYHQSHDANIAL 58

Query: 166 ------------LR----AQFERMRKE-RAELY-KNINDEVDEIELKQYFSQCGTISSVK 207
                       ++     Q ++   +    L+  ++N  VD+  L+  F    +  S  
Sbjct: 59  QTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118

Query: 208 IMR-TDRGISKGH 219
           +M     G S+G+
Sbjct: 119 VMWDMQTGSSRGY 131

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 41.4 bits (98), Expect = 1e-04
 Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

Query: 180 LY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHC 220
           LY  N++  + E  LKQYF   G I+++KIM      +  + 
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYA 44

>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 =  114 bits (287), Expect = 3e-30
 Identities = 29/190 (15%), Positives = 58/190 (30%), Gaps = 47/190 (24%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS------QEGKSKGYGFVQYSTPESALDA 71
           +V N+   I    +   F+    +              Q  + K + F+++ + +    A
Sbjct: 8   YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 67

Query: 72  IEKLQGATVERMELYVGPFIRRADRI----------------QEGSSFNNLYVKNLDDDM 115
           +    G   +   L +                              S + L++  L + +
Sbjct: 68  MA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYL 126

Query: 116 TEEILVEKFSEFGKITSLVISKD-ANGTSKGFG-----------------------SKVL 151
            ++ + E  + FG + +  + KD A G SKG+                         K L
Sbjct: 127 NDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 186

Query: 152 YVARAQKKAE 161
            V RA   A+
Sbjct: 187 LVQRASVGAK 196

>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 = 78.5 bits (194), Expect = 3e-17
 Identities = 22/158 (13%), Positives = 53/158 (33%), Gaps = 40/158 (25%)

Query: 100 GSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSL------VISKDANGTSKGFG------ 147
           G+    LYV N+   +TEE +++ F+   ++  L       +        K F       
Sbjct: 1   GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60

Query: 148 ----------------SKVLYVARAQKKAERKAI--LRAQFERMRKERAE------LY-K 182
                            + L + R         +    + +               L+  
Sbjct: 61  VDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIG 120

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
            + + +++ ++K+  +  G + +  +++ D   G+SKG
Sbjct: 121 GLPNYLNDDQVKELLTSFGPLKAFNLVK-DSATGLSKG 157

>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 =  110 bits (277), Expect = 4e-29
 Identities = 27/141 (19%), Positives = 57/141 (40%), Gaps = 20/141 (14%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSK------VVVSQEGKSKGYGFVQYSTPESALDA 71
           +V N+   I    +   F+    +          V+  Q  + K + F+++ + +    A
Sbjct: 8   YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 67

Query: 72  IE----KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEF 127
           +       QG +++         IRR    Q     + L++  L + + ++ + E  + F
Sbjct: 68  MAFDGIIFQGQSLK---------IRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSF 118

Query: 128 GKITSLVISKD-ANGTSKGFG 147
           G + +  + KD A G SKG+ 
Sbjct: 119 GPLKAFNLVKDSATGLSKGYA 139

>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 = 81.1 bits (201), Expect = 2e-18
 Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 1/85 (1%)

Query: 5   PNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYS 63
           P+    L G    F+  L + +++ ++ ++ + FG +++  +V     G SKGY F +Y 
Sbjct: 85  PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 144

Query: 64  TPESALDAIEKLQGATVERMELYVG 88
                  AI  L G  +   +L V 
Sbjct: 145 DINVTDQAIAGLNGMQLGDKKLLVQ 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 = 73.8 bits (182), Expect = 7e-16
 Identities = 22/131 (16%), Positives = 51/131 (38%), Gaps = 18/131 (13%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSL------VISKDANGTSKGFG----SKVLYVAR 155
           LYV N+   +TEE +++ F+   ++  L       +        K F       V    +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 156 AQKKAERK------AILRAQFERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKI 208
           A              I R    +      +L+   + + +++ ++K+  +  G + +  +
Sbjct: 67  AMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNL 126

Query: 209 MR-TDRGISKG 218
           ++ +  G+SKG
Sbjct: 127 VKDSATGLSKG 137

>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 =   99 bits (250), Expect = 4e-26
 Identities = 26/93 (27%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 12  SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV--SQEGKSKGYGFVQYSTPESAL 69
           SG    F+ NL   ID   L+  FS FG I  +  ++     G SKGY F+ +++ +++ 
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62

Query: 70  DAIEKLQGATVERMELYVGPFIRRADRIQEGSS 102
            AIE + G  +    + V    ++  +    SS
Sbjct: 63  AAIEAMNGQYLCNRPITVSYAFKKDSKGSGPSS 95

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 25/89 (28%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSL--VISKDANGTSKGFG----------- 147
           S  + +++ NLD ++ E++L + FS FG I     ++     G SKG+            
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62

Query: 148 ------------SKVLYVARAQKKAERKA 164
                       ++ + V+ A KK  + +
Sbjct: 63  AAIEAMNGQYLCNRPITVSYAFKKDSKGS 91

>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 = 97.2 bits (243), Expect = 2e-24
 Identities = 32/135 (23%), Positives = 59/135 (43%), Gaps = 14/135 (10%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIE--- 73
           F+  L        L + F K+G +   K++     G+S+G+GF+ +  P S  + ++   
Sbjct: 7   FIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH 66

Query: 74  KLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSL 133
            L G  ++          +RA    E      ++V  +  D+  +   E FS++G I   
Sbjct: 67  ILDGKVID---------PKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDA 117

Query: 134 VISKDAN-GTSKGFG 147
            +  D + G S+GFG
Sbjct: 118 QLMLDKDTGQSRGFG 132

>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 = 75.6 bits (187), Expect = 2e-16
 Identities = 41/130 (31%), Positives = 67/130 (51%), Gaps = 22/130 (16%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG-------SKVLYVARAQ 157
           +++  L+ D TE+ L E F ++G +T L I KD   G S+GFG       S V  V + Q
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65

Query: 158 -----KKAE-RKAILRAQFERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMR 210
                K  + ++AI R + ++  K    ++   I  +V   E +++FSQ GTI   ++M 
Sbjct: 66  HILDGKVIDPKRAIPRDEQDKTGK----IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLM- 120

Query: 211 TDR--GISKG 218
            D+  G S+G
Sbjct: 121 LDKDTGQSRG 130

>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 = 59.5 bits (145), Expect = 7e-11
 Identities = 14/69 (20%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK-- 74
           FV  +   +   +  + FS++G I  +++++ ++ G+S+G+GFV Y + ++     +   
Sbjct: 91  FVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKF 150

Query: 75  --LQGATVE 81
              +   +E
Sbjct: 151 IDFKDRKIE 159

>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 = 91.5 bits (228), Expect = 7e-23
 Identities = 19/87 (21%), Positives = 36/87 (41%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
           N ++ NL  ++D  +L  +   FG + S++++    G S+G GF +  + E     I   
Sbjct: 27  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86

Query: 76  QGATVERMELYVGPFIRRADRIQEGSS 102
            G  ++       P      +    SS
Sbjct: 87  NGKFIKTPPGVSAPTEPLLCKFSGPSS 113

>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 = 73.4 bits (181), Expect = 3e-16
 Identities = 21/95 (22%), Positives = 35/95 (36%), Gaps = 24/95 (25%)

Query: 93  RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG----- 147
           +  + QE     NLY+ NL   M E+ L      FG++ S  I +D++GTS+G G     
Sbjct: 16  QMAKQQE-QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARME 74

Query: 148 ------------------SKVLYVARAQKKAERKA 164
                             +     A  +    + +
Sbjct: 75  STEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFS 109

>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 = 68.4 bits (168), Expect = 2e-14
 Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 7/66 (10%)

Query: 160 AERKAILRAQFERMRKERAE------LY-KNINDEVDEIELKQYFSQCGTISSVKIMRTD 212
           +   + L+A   + +  + +      LY  N+   +DE EL+      G + S +I+R  
Sbjct: 2   SSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS 61

Query: 213 RGISKG 218
            G S+G
Sbjct: 62  SGTSRG 67

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

 Score = 90.3 bits (225), Expect = 1e-22
 Identities = 28/94 (29%), Positives = 43/94 (45%), Gaps = 6/94 (6%)

Query: 9   ARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESA 68
           +  SG    FV+NL        L   F++ G +  + + + + GKSKG G V++ +PE A
Sbjct: 3   SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSKGCGVVKFESPEVA 61

Query: 69  LDAIEKLQGATVERMELYVGPFIRRADRIQEGSS 102
             A   + G  +   E+ V     R DR   G S
Sbjct: 62  ERACRMMNGMKLSGREIDV-----RIDRNASGPS 90

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

 Score = 57.2 bits (139), Expect = 9e-11
 Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 100 GSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
            S    ++V+NL  D T ++L +KF+E G +    I  + NG SKG G
Sbjct: 5   SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCG 51

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

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 1/37 (2%)

Query: 182 KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
           +N+  +     LK  F++CG +    I   + G SKG
Sbjct: 14  RNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSKG 49

>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 = 89.2 bits (222), Expect = 4e-22
 Identities = 37/87 (42%), Positives = 53/87 (60%), Gaps = 1/87 (1%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
           N +VKNL   ID+ +L + FS FG I S+KV++   G+SKG+GFV +S+PE A  A+ ++
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 76  QGATVERMELYVGPFIRRADRIQEGSS 102
            G  V    LYV    R+ +R    SS
Sbjct: 76  NGRIVATKPLYVALAQRKEERQSGPSS 102

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 78.0 bits (193), Expect = 5e-18
 Identities = 38/100 (38%), Positives = 47/100 (47%), Gaps = 25/100 (25%)

Query: 88  GPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           G      DRI       NLYVKNLDD + +E L + FS FG ITS  +  +  G SKGFG
Sbjct: 1   GSSGSSGDRI-TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFG 58

Query: 148 -----------------------SKVLYVARAQKKAERKA 164
                                  +K LYVA AQ+K ER++
Sbjct: 59  FVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQS 98

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 20/50 (40%), Positives = 33/50 (66%), Gaps = 3/50 (6%)

Query: 171 ERMRKER-AELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
           +R+ + +   LY KN++D +D+  L++ FS  GTI+S K+M  + G SKG
Sbjct: 8   DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM-EGGRSKG 56

>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 = 86.5 bits (215), Expect = 4e-21
 Identities = 33/95 (34%), Positives = 46/95 (48%), Gaps = 4/95 (4%)

Query: 12  SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK----SKGYGFVQYSTPES 67
           SG    F+KNL  +     L  +FSK G I+S  +   +       S G+GFV+Y  PE 
Sbjct: 3   SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 68  ALDAIEKLQGATVERMELYVGPFIRRADRIQEGSS 102
           A  A+++LQG TV+  +L V    R        SS
Sbjct: 63  AQKALKQLQGHTVDGHKLEVRISERATKPASGPSS 97

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 67.7 bits (166), Expect = 2e-14
 Identities = 24/91 (26%), Positives = 34/91 (37%), Gaps = 27/91 (29%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANG----TSKGFG--------- 147
           S  + L++KNL+   TEE L   FS+ G I S  ISK  N      S GFG         
Sbjct: 3   SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 148 --------------SKVLYVARAQKKAERKA 164
                            L V  +++  +  +
Sbjct: 63  AQKALKQLQGHTVDGHKLEVRISERATKPAS 93

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 7/45 (15%)

Query: 180 LY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDR-----GISKG 218
           L+ KN+N    E  LK  FS+ G I S  I    +      +S G
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIKSCTIS-KKKNKAGVLLSMG 51

>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 = 87.0 bits (216), Expect = 4e-21
 Identities = 21/81 (25%), Positives = 37/81 (45%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
            FV NL   +   KL ++FS  G +  + ++  ++GKS+G G V +     A+ AI   
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76

Query: 76 QGATVERMELYVGPFIRRADR 96
           G  +    ++V    R   +
Sbjct: 77 NGQLLFDRPMHVKMDERALPK 97

>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 = 82.0 bits (203), Expect = 2e-19
 Identities = 18/104 (17%), Positives = 37/104 (35%), Gaps = 23/104 (22%)

Query: 92  RRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG---- 147
             +  +Q G   + ++V NLD  +  + L E FS  G +    I +D +G S+G G    
Sbjct: 4   GSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTF 63

Query: 148 -------------------SKVLYVARAQKKAERKAILRAQFER 172
                               + ++V   ++   +      +  +
Sbjct: 64  EQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQ 107

>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 = 50.8 bits (122), Expect = 2e-08
 Identities = 11/42 (26%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

Query: 178 AELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
           + ++  N++ +V   +LK+ FS  G +    I+    G S+G
Sbjct: 16  STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRG 57

>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 = 89.3 bits (222), Expect = 4e-21
 Identities = 35/142 (24%), Positives = 59/142 (41%), Gaps = 21/142 (14%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE--- 73
           F+  L+    +  L   F ++G +    V+      +S+G+GFV Y+T E    A+    
Sbjct: 17  FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 76

Query: 74  -KLQGATVERMELYVGPFIRRA------DRIQEGSSFNNLYVKNLDDDMTEEILVEKFSE 126
            K+ G  VE          +RA       R     +   ++V  + +D  E  L + F +
Sbjct: 77  HKVDGRVVE---------PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 127

Query: 127 FGKITSLVISKDAN-GTSKGFG 147
           +GKI  + I  D   G  +GF 
Sbjct: 128 YGKIEVIEIMTDRGSGKKRGFA 149

>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 = 71.9 bits (177), Expect = 6e-15
 Identities = 38/149 (25%), Positives = 66/149 (44%), Gaps = 23/149 (15%)

Query: 91  IRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG-- 147
           + +++  +E      L++  L  + T+E L   F ++G +T  V+ +D N   S+GFG  
Sbjct: 1   MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60

Query: 148 --SKVLYVARAQKKAE----------RKAILRAQFERMRKERAELYK----NINDEVDEI 191
             + V  V  A               ++A+ R   +R       + K     I ++ +E 
Sbjct: 61  TYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQR-PGAHLTVKKIFVGGIKEDTEEH 119

Query: 192 ELKQYFSQCGTISSVKIMRTDR--GISKG 218
            L+ YF Q G I  ++IM TDR  G  +G
Sbjct: 120 HLRDYFEQYGKIEVIEIM-TDRGSGKKRG 147

>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 = 56.1 bits (136), Expect = 1e-09
 Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 5/69 (7%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK-- 74
           FV  +    +   L   F ++G I+  +++  +  GK +G+ FV +   +S    + +  
Sbjct: 108 FVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 167

Query: 75  --LQGATVE 81
             + G   E
Sbjct: 168 HTVNGHNCE 176

>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 = 86.2 bits (214), Expect = 6e-21
 Identities = 28/88 (31%), Positives = 43/88 (48%), Gaps = 1/88 (1%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
           N F+ +L     +  L Q+F  FG++ S+KV + ++   SK +GFV Y  P SA  AI+ 
Sbjct: 27  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86

Query: 75  LQGATVERMELYVGPFIRRADRIQEGSS 102
           + G  +    L V     + D     SS
Sbjct: 87  MNGFQIGMKRLKVQLKRSKNDSKSGPSS 114

>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 = 71.6 bits (176), Expect = 1e-15
 Identities = 20/95 (21%), Positives = 35/95 (36%), Gaps = 24/95 (25%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG--------- 147
           +EG    NL++ +L  +  ++ L++ F  FG + S  +  D     SK FG         
Sbjct: 20  KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVS 79

Query: 148 --------------SKVLYVARAQKKAERKAILRA 168
                          K L V   + K + K+   +
Sbjct: 80  AQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPSS 114

>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 = 1e-07
 Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 4/42 (9%)

Query: 180 LY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           L+  ++  E  + +L Q F   G + S K+   D+   +SK 
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFI-DKQTNLSKC 68

>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 = 84.3 bits (209), Expect = 4e-20
 Identities = 17/97 (17%), Positives = 40/97 (41%)

Query: 3   STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQY 62
           S       +       V NL   + +  + ++F++FG ++ + V   + G+S G   V +
Sbjct: 24  SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHF 83

Query: 63  STPESALDAIEKLQGATVERMELYVGPFIRRADRIQE 99
                AL A+++ +G  ++   + +     + D    
Sbjct: 84  ERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHH 120

>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 = 74.7 bits (184), Expect = 1e-16
 Identities = 15/103 (14%), Positives = 31/103 (30%), Gaps = 23/103 (22%)

Query: 90  FIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG-- 147
           F       +   +   L V NLD  +++  + E F+EFG +    +  D +G S G    
Sbjct: 22  FDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADV 81

Query: 148 ---------------------SKVLYVARAQKKAERKAILRAQ 169
                                 + + +     + + +      
Sbjct: 82  HFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 124

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 46.6 bits (111), Expect = 8e-07
 Identities = 9/40 (22%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 180 LY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
           L   N++  V + ++++ F++ GT+    +     G S G
Sbjct: 38  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG 77

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 84.0 bits (208), Expect = 4e-20
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
           N F+ +L     +  L   F  FG++ S+KV + ++   SK +GFV +  P+SA  AI+ 
Sbjct: 42  NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101

Query: 75  LQGATVERMELYV 87
           + G  V    L V
Sbjct: 102 MNGFQVGTKRLKV 114

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 61.2 bits (149), Expect = 7e-12
 Identities = 19/84 (22%), Positives = 28/84 (33%), Gaps = 24/84 (28%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG--------- 147
            EG    NL++ +L  + T+  L   F  FG + S  +  D     SK FG         
Sbjct: 35  IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94

Query: 148 --------------SKVLYVARAQ 157
                         +K L V   +
Sbjct: 95  AQVAIKAMNGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 52.0 bits (125), Expect = 1e-08
 Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 10/62 (16%)

Query: 166 LRAQFERMRKERAE------LY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDR--GIS 216
           L A       ++ E      L+  ++  E  + +L   F   G + S K+   D+   +S
Sbjct: 23  LSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFI-DKQTSLS 81

Query: 217 KG 218
           K 
Sbjct: 82  KC 83

>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 = 86.1 bits (213), Expect = 5e-20
 Identities = 26/168 (15%), Positives = 50/168 (29%), Gaps = 41/168 (24%)

Query: 14  IGNA--FVKNLA-STIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALD 70
           +GN+   V NL    +    L  +F  +GD+Q  K++       K    VQ +    A  
Sbjct: 1   MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF----NKKENALVQMADGNQAQL 56

Query: 71  AIEKLQGATVERMELYVGPFIRRADRIQEGSSF--------------------------- 103
           A+  L G  +    + +     +  ++                                 
Sbjct: 57  AMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI 116

Query: 104 ----NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
                 L++ N+   ++EE L   FS  G +         +   +   
Sbjct: 117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---RKMA 161

>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 = 58.4 bits (141), Expect = 3e-10
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 3/63 (4%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
            + N+  ++    L  +FS  G +           K +    +Q  + E A+ A+  L  
Sbjct: 124 HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHN 180

Query: 78  ATV 80
             +
Sbjct: 181 HDL 183

>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 = 87.0 bits (215), Expect = 6e-20
 Identities = 25/168 (14%), Positives = 48/168 (28%), Gaps = 39/168 (23%)

Query: 12  SGIGNAFVKNL-ASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALD 70
           +G     V NL    +    L  +F  +GD+Q  K++       K    VQ +    A  
Sbjct: 32  AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF----NKKENALVQMADGNQAQL 87

Query: 71  AIEKLQGATVERMELYVGPFIRRADRIQEGSSF--------------------------- 103
           A+  L G  +    + +     +  ++                                 
Sbjct: 88  AMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI 147

Query: 104 ----NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
                 L++ N+   ++EE L   FS  G +         +   +   
Sbjct: 148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---RKMA 192

>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 = 59.2 bits (143), Expect = 2e-10
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 3/63 (4%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
            + N+  ++    L  +FS  G +           K +    +Q  + E A+ A+  L  
Sbjct: 155 HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHN 211

Query: 78  ATV 80
             +
Sbjct: 212 HDL 214

>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 = 48.8 bits (116), Expect = 7e-07
 Identities = 29/182 (15%), Positives = 52/182 (28%), Gaps = 49/182 (26%)

Query: 88  GPFIRRADRIQEGSSFNNLYVKNLD-DDMTEEILVEKFSEFGKITSLVISKDANGTS--- 143
               R A     G+  + L V NL+ + +T + L   F  +G +  + I  +    +   
Sbjct: 19  SHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQ 78

Query: 144 ----------------KGFGSKVLYVARAQKKA-------ERKAILRAQFERMRKERAE- 179
                                K + +  ++ +        +    L   +      R + 
Sbjct: 79  MADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 138

Query: 180 ---------------LY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAI 223
                          L+  NI   V E +LK  FS  G +             K   MA+
Sbjct: 139 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF-----QKDRKMAL 193

Query: 224 AQ 225
            Q
Sbjct: 194 IQ 195

>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 = 81.4 bits (202), Expect = 1e-19
 Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALD 70
          SG    +++ L     +  L ++   +G I S+K ++ +   K KGYGFV + +P +A  
Sbjct: 3  SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62

Query: 71 AIEKLQGATVE 81
          A+  L+ + V+
Sbjct: 63 AVTALKASGVQ 73

>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 = 57.2 bits (139), Expect = 8e-11
 Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 5/66 (7%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKK 159
           S  + LY++ L    T++ LV+    +GKI S     D      KG+G    +V      
Sbjct: 3   SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYG----FVDFDSPS 58

Query: 160 AERKAI 165
           A +KA+
Sbjct: 59  AAQKAV 64

>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 = 42.9 bits (102), Expect = 8e-06
 Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 4/42 (9%)

Query: 180 LY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           LY + +     + +L +     G I S K +  D+     KG
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAI-LDKTTNKCKG 48

>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 = 81.1 bits (201), Expect = 3e-19
 Identities = 24/86 (27%), Positives = 39/86 (45%)

Query: 3  STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQY 62
          S+    A+       FV NL + +    L+++F + G +    +   +EGK K +GFV +
Sbjct: 5  SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCF 64

Query: 63 STPESALDAIEKLQGATVERMELYVG 88
            PES   AI  L G  +    + V 
Sbjct: 65 KHPESVSYAIALLNGIRLYGRPINVS 90

>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 = 68.4 bits (168), Expect = 9e-15
 Identities = 18/50 (36%), Positives = 27/50 (54%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
            +  +   ++V NL+  + EEIL E F + G +T + I KD  G  K FG
Sbjct: 11  AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFG 60

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 51.9 bits (125), Expect = 7e-09
 Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 1/52 (1%)

Query: 168 AQFERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
             F    +    ++  N+   V E  L + F Q G ++ V I +   G  K 
Sbjct: 7   GMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS 58

>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 = 80.7 bits (200), Expect = 5e-19
 Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 15  GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
              FV  +   +D  ++   F+++G ++  K++  + G SKGYGFV +         +E 
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69

Query: 75  LQGATVERMELYVGPFIRRADRIQEGSS 102
                    +L +GP IR+ +       
Sbjct: 70  --QINFHGKKLKLGPAIRKQNLSTYHVQ 95

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 73.0 bits (180), Expect = 2e-16
 Identities = 20/98 (20%), Positives = 32/98 (32%), Gaps = 22/98 (22%)

Query: 97  IQEGSS-FNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG-------- 147
           + EG    N ++V  +D  M E  +   F+ +G +  + I  D  G SKG+G        
Sbjct: 2   LPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDV 61

Query: 148 -------------SKVLYVARAQKKAERKAILRAQFER 172
                         K L +  A +K             
Sbjct: 62  DVQKIVESQINFHGKKLKLGPAIRKQNLSTYHVQPRPL 99

>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 = 50.7 bits (122), Expect = 2e-08
 Identities = 13/37 (35%), Positives = 24/37 (64%)

Query: 182 KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
             I+  +DE E++ +F++ G++  VKI+    G+SKG
Sbjct: 15  GGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKG 51

>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 = 80.8 bits (200), Expect = 5e-19
 Identities = 15/72 (20%), Positives = 35/72 (48%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
              V NL   + +  + ++F++FG ++ + V   + G+S G   V +     AL A+++ 
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 90

Query: 76  QGATVERMELYV 87
            G  ++   + +
Sbjct: 91  NGVPLDGRPMNI 102

>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 = 68.1 bits (167), Expect = 2e-14
 Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 4/76 (5%)

Query: 90  FIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSK 149
           F           +   L V NLD  +++  + E F+EFG +    +  D +G S G    
Sbjct: 16  FDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTA-- 73

Query: 150 VLYVARAQKKAERKAI 165
              V   +K    KA+
Sbjct: 74  --DVHFERKADALKAM 87

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 11/56 (19%), Positives = 23/56 (41%), Gaps = 7/56 (12%)

Query: 170 FERMRKERAE------LY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
           F+      A       L   N++  V + ++++ F++ GT+    +     G S G
Sbjct: 16  FDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG 71

>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 = 80.8 bits (200), Expect = 7e-19
 Identities = 17/82 (20%), Positives = 36/82 (43%)

Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
          G  F+  L    +   L  +F K G I    ++  +  KS+G+ F+ +  P  A +A + 
Sbjct: 8  GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67

Query: 75 LQGATVERMELYVGPFIRRADR 96
          + G ++    + V    + + +
Sbjct: 68 MNGKSLHGKAIKVEQAKKPSFQ 89

>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 = 74.3 bits (183), Expect = 1e-16
 Identities = 19/99 (19%), Positives = 36/99 (36%), Gaps = 23/99 (23%)

Query: 99  EGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG----------- 147
           E      L++  L+ +  E++L   F + G I+ +++ KD    S+GF            
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAK 62

Query: 148 ------------SKVLYVARAQKKAERKAILRAQFERMR 174
                        K + V +A+K + +    R      R
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSR 101

>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 = 45.8 bits (109), Expect = 1e-06
 Identities = 12/37 (32%), Positives = 19/37 (51%)

Query: 182 KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
             +N E +E  LK  F + G IS V +++     S+G
Sbjct: 13  GGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRG 49

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 80.4 bits (199), Expect = 7e-19
 Identities = 27/89 (30%), Positives = 47/89 (52%), Gaps = 2/89 (2%)

Query: 16  NAFVKNLASTIDNLKLHQIFSK-FGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
           + FV +L   +D+  L++ F K +   +  KVV+ Q G SKGYGFV+++       A+ +
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 75  LQGAT-VERMELYVGPFIRRADRIQEGSS 102
            QGA  +    + +   I +A R++   S
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRVKPVES 99

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 65.8 bits (161), Expect = 1e-13
 Identities = 19/90 (21%), Positives = 34/90 (37%), Gaps = 25/90 (27%)

Query: 105 NLYVKNLDDDMTEEILVEKFSE-FGKITSLVISKDANGTSKGFG---------------- 147
           +L+V +L  D+ + +L E F + +       +  D  G SKG+G                
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 148 --------SKVLYVARAQKKAERKAILRAQ 169
                   SK + ++ A  KA R   + + 
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRVKPVESG 100

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 9/38 (23%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 182 KNINDEVDEIELKQYFSQC-GTISSVKIMRTDRGISKG 218
            ++  +VD+  L ++F +   +    K++    G+SKG
Sbjct: 15  GDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKG 52

>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 = 78.1 bits (193), Expect = 4e-18
 Identities = 28/100 (28%), Positives = 41/100 (41%), Gaps = 7/100 (7%)

Query: 3  STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQY 62
           +  SE+R       FV  L        + ++F  FG I    V+   +G SKG  FV++
Sbjct: 4  GSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKF 63

Query: 63 STPESALDAIEKLQGATVERM---ELYVGPFIRRADRIQE 99
          S+   A  AI  L G+         L V    + AD  +E
Sbjct: 64 SSHTEAQAAIHALHGSQTMPGASSSLVV----KFADTDKE 99

>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 = 72.7 bits (179), Expect = 4e-16
 Identities = 19/96 (19%), Positives = 29/96 (30%), Gaps = 26/96 (27%)

Query: 93  RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG----- 147
            +     G     L+V  L+   +EE ++  F  FG I    + +  +G+SKG       
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFS 64

Query: 148 ---------------------SKVLYVARAQKKAER 162
                                S  L V  A    E 
Sbjct: 65  SHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES 100

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 52.7 bits (127), Expect = 4e-09
 Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 1/53 (1%)

Query: 167 RAQFERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
            +  E       +L+   +N +  E ++ + F   G I    ++R   G SKG
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKG 57

>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 = 77.2 bits (191), Expect = 5e-18
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          N FV +L   +D+  L   F  F    S  V+   + G S+GYGFV +++ + A +A++ 
Sbjct: 3  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 75 LQGATVERMELYV 87
          +QG  +    L +
Sbjct: 63 MQGQDLNGRPLRI 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 = 56.4 bits (137), Expect = 1e-10
 Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 5/63 (7%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAER 162
            NL+V +L+ ++ +E L   F +F    S  +  D   G+S+G+G    +V+   +   +
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYG----FVSFTSQDDAQ 57

Query: 163 KAI 165
            A+
Sbjct: 58  NAM 60

>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 = 41.3 bits (98), Expect = 2e-05
 Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           ++N  VD+  L+  F    +  S  +M  D   G S+G
Sbjct: 8   DLNVNVDDETLRNAFKDFPSYLSGHVM-WDMQTGSSRG 44

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 78.4 bits (193), Expect = 2e-17
 Identities = 16/79 (20%), Positives = 38/79 (48%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
            V NL   + +  + ++F++FG ++ + V   + G+S G   V +     AL A+++ +G
Sbjct: 92  LVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKG 151

Query: 78  ATVERMELYVGPFIRRADR 96
             ++   + +     + D 
Sbjct: 152 VPLDGRPMDIQLVASQIDL 170

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 70.6 bits (173), Expect = 1e-14
 Identities = 15/103 (14%), Positives = 31/103 (30%), Gaps = 23/103 (22%)

Query: 90  FIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG-- 147
           F       +   +   L V NLD  +++  + E F+EFG +    +  D +G S G    
Sbjct: 75  FDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADV 134

Query: 148 ---------------------SKVLYVARAQKKAERKAILRAQ 169
                                 + + +     + + +      
Sbjct: 135 HFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 177

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 56.0 bits (135), Expect = 1e-09
 Identities = 12/86 (13%), Positives = 29/86 (33%), Gaps = 7/86 (8%)

Query: 140 NGTSKGFGSKVLYVARAQKKAERKAILRAQFERMRKERAELY-------KNINDEVDEIE 192
           N  +   G +      ++ K          F+        +         N++  V + +
Sbjct: 45  NRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDAD 104

Query: 193 LKQYFSQCGTISSVKIMRTDRGISKG 218
           +++ F++ GT+    +     G S G
Sbjct: 105 IQELFAEFGTLKKAAVDYDRSGRSLG 130

>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 = 79.0 bits (194), Expect = 2e-17
 Identities = 27/167 (16%), Positives = 49/167 (29%), Gaps = 43/167 (25%)

Query: 18  FVKNL-ASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
            V  L  S ++  ++  +F  +G+++  K +        G   V+ +   +   AI  L 
Sbjct: 8   MVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMK----SKPGAAMVEMADGYAVDRAITHLN 63

Query: 77  GATVERMELYVG-----------------------------------PFIRRADRIQEGS 101
              +   ++ V                                    P     +RIQ  S
Sbjct: 64  NNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPS 123

Query: 102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
             N L+  N   ++TEE   E   E G      +   +        G
Sbjct: 124 --NVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSG 168

>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 = 61.6 bits (149), Expect = 2e-11
 Identities = 11/79 (13%), Positives = 28/79 (35%), Gaps = 2/79 (2%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEK 74
                N    +      +I  + G  + + V V S + +    G +++ +   AL+ +  
Sbjct: 125 VLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGF 184

Query: 75  LQGATVERMELYVGPFIRR 93
           L    ++       P+  +
Sbjct: 185 LNHYQMKNPNGPY-PYTLK 202

>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 = 57.8 bits (139), Expect = 5e-10
 Identities = 19/172 (11%), Positives = 43/172 (25%), Gaps = 47/172 (27%)

Query: 100 GSSFNNLYVKNLD-DDMTEEILVEKFSEFGKITSLVISKDANGTS--------------- 143
           G+    L V  LD   M  + +   F  +G +  +   K   G +               
Sbjct: 1   GADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAIT 60

Query: 144 ----KGFGSKVLYVARAQ------KKAERKAILRAQFERMRKERAELYK----------- 182
                    + + V  ++       ++         ++   + R   +            
Sbjct: 61  HLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ 120

Query: 183 ---------NINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQ 225
                    N   EV E    +   + G      + +   G S+     + +
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSV-KVFSGKSERSSSGLLE 171

>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 = 75.0 bits (185), Expect = 5e-17
 Identities = 21/98 (21%), Positives = 47/98 (47%), Gaps = 7/98 (7%)

Query: 5   PNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYST 64
            +  + ++ +   FV+NLA+T+    L + FS+FG ++  K +       K Y F+ +  
Sbjct: 2   SSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDE 54

Query: 65  PESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSS 102
            + A+ A+E++ G  +E   + +        + +E  +
Sbjct: 55  RDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKA 92

>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 = 75.0 bits (185), Expect = 6e-17
 Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 20/92 (21%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD--------------A----NGT 142
           +    L+V+NL + +TEEIL + FS+FGK+  +   KD              A    NG 
Sbjct: 9   AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNG- 67

Query: 143 SKGFGSKVLYVARAQKKAERKAILRAQFERMR 174
            K    + + +  A+   +++   +AQ +   
Sbjct: 68  -KDLEGENIEIVFAKPPDQKRKERKAQRQAAS 98

>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 = 43.0 bits (102), Expect = 1e-05
 Identities = 11/32 (34%), Positives = 20/32 (62%), Gaps = 1/32 (3%)

Query: 180 LY-KNINDEVDEIELKQYFSQCGTISSVKIMR 210
           L+ +N+ + V E  L++ FSQ G +  VK ++
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERVKKLK 45

>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 = 75.0 bits (185), Expect = 5e-17
 Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 5/85 (5%)

Query: 3  STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQY 62
           +   E  +S +   +V+NL  +     + + F+        +V      K + Y FV +
Sbjct: 4  GSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVHF 58

Query: 63 STPESALDAIEKLQGATVERMELYV 87
          S  E A++A++ L G  ++   + V
Sbjct: 59 SNREDAVEAMKALNGKVLDGSPIEV 83

>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 = 52.7 bits (127), Expect = 4e-09
 Identities = 17/84 (20%), Positives = 29/84 (34%), Gaps = 22/84 (26%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISK-------------DA-------N 140
           SS   LYV+NL    +EE++ ++F+         + K             DA       N
Sbjct: 13  SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALN 72

Query: 141 GTSKGFGSKVLYVARAQKKAERKA 164
           G         + V  A+   +  +
Sbjct: 73  GKV--LDGSPIEVTLAKPVDKDSS 94

>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 = 75.9 bits (187), Expect = 6e-17
 Identities = 30/96 (31%), Positives = 49/96 (51%), Gaps = 3/96 (3%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
           N  V  + +T+D ++L Q+F ++G I+S K+V  +E  +S+GYGFV++ +  SA  AI  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 75  LQGATVERMELYVGPFIRRADRIQEGSSF--NNLYV 108
           L G  +    L V        R     +    N Y+
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139

>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 = 53.2 bits (128), Expect = 6e-09
 Identities = 26/143 (18%), Positives = 46/143 (32%), Gaps = 25/143 (17%)

Query: 57  YGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMT 116
              V    P          Q A +++++      I       E     NL V  +   + 
Sbjct: 4   IPLVSQYDPYG--------QTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVD 55

Query: 117 EEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKKAERKAI---------- 165
           E  L + F  +G I S+ I  D     S+G+G    +V      + ++AI          
Sbjct: 56  EVQLRQLFERYGPIESVKIVCDRETRQSRGYG----FVKFQSGSSAQQAIAGLNGFNILN 111

Query: 166 --LRAQFERMRKERAELYKNIND 186
             L+        +R  +   + D
Sbjct: 112 KRLKVALAASGHQRPGIAGAVGD 134

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 8/69 (11%)

Query: 153 VARAQKKAERKAILRAQFERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRT 211
           + + Q++      +  + + +R     L    I   VDE++L+Q F + G I SVKI+  
Sbjct: 22  LQQQQQQHIPPTQMNPEPDVLRN----LMVNYIPTTVDEVQLRQLFERYGPIESVKIVC- 76

Query: 212 DR--GISKG 218
           DR    S+G
Sbjct: 77  DRETRQSRG 85

>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 = 74.2 bits (183), Expect = 9e-17
 Identities = 20/89 (22%), Positives = 35/89 (39%), Gaps = 1/89 (1%)

Query: 1  MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
          M   P   +  +   N F+ NL       +L    S+        VV  + G ++ +G+V
Sbjct: 4  MLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYV 63

Query: 61 QYSTPESALDAIEKLQGATVERMELYVGP 89
           + + E    A+E L G  V   E+ +  
Sbjct: 64 DFESAEDLEKALE-LTGLKVFGNEIKLEK 91

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 4/68 (5%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQ 157
            E ++  NL++ NL+ + +   L    SE      L +     GT++ FG    YV    
Sbjct: 12  SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFG----YVDFES 67

Query: 158 KKAERKAI 165
            +   KA+
Sbjct: 68  AEDLEKAL 75

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 7/37 (18%), Positives = 15/37 (40%)

Query: 182 KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
            N+N      ELK   S+    + + ++    G ++ 
Sbjct: 23  GNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK 59

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 73.9 bits (182), Expect = 2e-16
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 7/83 (8%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
             FV+     +   +L++IF  FG ++  K++        G+ FV++   ESA  AIE++
Sbjct: 33  RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEV 85

Query: 76  QGATVERMELYVGPFIRRADRIQ 98
            G +     L V      A R +
Sbjct: 86  HGKSFANQPLEVVYSKLPAKRYR 108

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 70.8 bits (174), Expect = 2e-15
 Identities = 20/98 (20%), Positives = 33/98 (33%), Gaps = 24/98 (24%)

Query: 88  GPFIRRADRIQEGS----SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISK------ 137
              + R   +        S   L+V+    D+ E  L E F  FG +  + I        
Sbjct: 12  SGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVE 71

Query: 138 -----DA-------NGTSKGFGSKVLYVARAQKKAERK 163
                 A       +G  K F ++ L V  ++  A+R 
Sbjct: 72  FEEAESAAKAIEEVHG--KSFANQPLEVVYSKLPAKRY 107

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 62.7 bits (153), Expect = 1e-12
 Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 7/65 (10%)

Query: 153 VARAQKKAERKAILRAQFERMRKERAE------LY-KNINDEVDEIELKQYFSQCGTISS 205
           +  +       + L  +   M   +        L+ +    +V E EL + F   G +  
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE 60

Query: 206 VKIMR 210
           VKI+ 
Sbjct: 61  VKILN 65

>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 = 73.5 bits (181), Expect = 2e-16
 Identities = 32/100 (32%), Positives = 48/100 (48%), Gaps = 2/100 (2%)

Query: 3   STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQY 62
           S+ NSE++ S      V N+     +  L Q+F +FG I   +++ ++ G SKG+GFV +
Sbjct: 5   SSGNSESK-STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTF 62

Query: 63  STPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSS 102
                A  A EKL G  VE  ++ V     R       SS
Sbjct: 63  ENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPSS 102

>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 = 56.9 bits (138), Expect = 1e-10
 Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 5/73 (6%)

Query: 93  RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLY 152
            +   +  S+   L+V N+     +  L + F +FGKI  + I  +    SKGFG    +
Sbjct: 5   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFG----F 59

Query: 153 VARAQKKAERKAI 165
           V         +A 
Sbjct: 60  VTFENSADADRAR 72

>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 = 43.8 bits (104), Expect = 6e-06
 Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 2/40 (5%)

Query: 180 LY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
           L+  NI     + +L+Q F Q G I  V+I+  +   SKG
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEII-FNERGSKG 56

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

 Score = 74.0 bits (182), Expect = 2e-16
 Identities = 10/71 (14%), Positives = 29/71 (40%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
              L   +    L  +  K+G+++  ++++     K  G   V +++   A + ++ L 
Sbjct: 10 TFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLH 69

Query: 77 GATVERMELYV 87
            +V    ++ 
Sbjct: 70 LTSVMGNIIHA 80

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

 Score = 55.1 bits (133), Expect = 7e-10
 Identities = 13/96 (13%), Positives = 34/96 (35%), Gaps = 17/96 (17%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKKAER 162
             +    L+D++ E  L +   ++G++  + I          G       V     +  +
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLA----RVLFTSTRGAK 62

Query: 163 KAI------------LRAQFERMRKERAELYKNIND 186
           + +            + AQ +   ++R + Y+ I +
Sbjct: 63  ETVKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVN 98

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

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 2/42 (4%)

Query: 179 ELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDR-GISKG 218
           E+    +ND V E  LK    + G +  V+I+   R     G
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLG 49

>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 = 73.5 bits (181), Expect = 2e-16
 Identities = 25/91 (27%), Positives = 42/91 (46%), Gaps = 1/91 (1%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
           + FV +L+  I    +   F+ FG I  ++VV     GKSKGYGFV +     A +AI++
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 75  LQGATVERMELYVGPFIRRADRIQEGSSFNN 105
           + G  +   ++      R+    +     N 
Sbjct: 77  MGGQWLGGRQIRTNWATRKPPAPKSTYESNT 107

>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 = 52.0 bits (125), Expect = 1e-08
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 96  RIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVA 154
           +    + F+ ++V +L  ++T E +   F+ FG+I+   + KD   G SKG+G    +V+
Sbjct: 9   KKDTSNHFH-VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG----FVS 63

Query: 155 RAQKKAERKAI 165
              K     AI
Sbjct: 64  FFNKWDAENAI 74

>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 = 38.5 bits (90), Expect = 6e-04
 Identities = 11/38 (28%), Positives = 22/38 (57%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           +++ E+   ++K  F+  G IS  ++++ D   G SKG
Sbjct: 22  DLSPEITTEDIKAAFAPFGRISDARVVK-DMATGKSKG 58

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 73.5 bits (181), Expect = 2e-16
 Identities = 27/86 (31%), Positives = 42/86 (48%), Gaps = 2/86 (2%)

Query: 3   STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQY 62
           S  N+E +        V N+     +  L Q+F +FG I   +++ ++ G SKG+GFV +
Sbjct: 19  SHMNTENKSQP-KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTF 76

Query: 63  STPESALDAIEKLQGATVERMELYVG 88
                A  A EKL G  VE  ++ V 
Sbjct: 77  ENSADADRAREKLHGTVVEGRKIEVN 102

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.1 bits (154), Expect = 1e-12
 Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 88  GPFIRRADRIQ--EGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKG 145
              + R   +     S    L+V N+     +  L + F +FGKI  + I  +    SKG
Sbjct: 12  SGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKG 70

Query: 146 FG 147
           FG
Sbjct: 71  FG 72

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 6/71 (8%)

Query: 153 VARAQKKAERKAILRAQFERMRKERAE----LY-KNINDEVDEIELKQYFSQCGTISSVK 207
           +  +       + L  +   M  E       L+  NI     + +L+Q F Q G I  V+
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE 60

Query: 208 IMRTDRGISKG 218
           I+  +   SKG
Sbjct: 61  II-FNERGSKG 70

>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 = 73.5 bits (181), Expect = 2e-16
 Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 1/86 (1%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEKLQ 76
           ++KNL+  +    L  +F++F + +   +      G+ +G  F+ +   E A  A+  + 
Sbjct: 29  YLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVN 88

Query: 77  GATVERMELYVGPFIRRADRIQEGSS 102
           G  +    L +     +  R    SS
Sbjct: 89  GYKLYGKILVIEFGKNKKQRSSGPSS 114

>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 = 55.0 bits (133), Expect = 8e-10
 Identities = 19/91 (20%), Positives = 29/91 (31%), Gaps = 24/91 (26%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-NGTSKGFG--------- 147
             G     LY+KNL   +TE  LV  F+ F +     I      G  +G           
Sbjct: 20  NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 79

Query: 148 --------------SKVLYVARAQKKAERKA 164
                          K+L +   + K +R +
Sbjct: 80  AWQALHLVNGYKLYGKILVIEFGKNKKQRSS 110

>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 = 38.8 bits (91), Expect = 4e-04
 Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 4/42 (9%)

Query: 180 LY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           LY KN++  V E +L   F++        I       G  +G
Sbjct: 28  LYLKNLSPRVTERDLVSLFARFQEKKGPPIQ-FRMMTGRMRG 68

>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 = 73.0 bits (180), Expect = 3e-16
 Identities = 31/92 (33%), Positives = 44/92 (47%), Gaps = 1/92 (1%)

Query: 12  SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALD 70
           SG    +V +L   I    L  IF  FG I +  ++   + G+SKGYGF+ +S  E A  
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 71  AIEKLQGATVERMELYVGPFIRRADRIQEGSS 102
           A+E+L G  +    + VG    R D     SS
Sbjct: 63  ALEQLNGFELAGRPMRVGHVTERLDGGSGPSS 94

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 50.2 bits (121), Expect = 2e-08
 Identities = 23/66 (34%), Positives = 39/66 (59%), Gaps = 5/66 (7%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKK 159
           S  + LYV +L  ++TE++L   F  FGKI ++V+ KD   G SKG+G    ++  +  +
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYG----FITFSDSE 58

Query: 160 AERKAI 165
             R+A+
Sbjct: 59  CARRAL 64

>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 = 37.5 bits (88), Expect = 6e-04
 Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           +++  + E  L+  F   G I ++ +M  D   G SKG
Sbjct: 12  SLHFNITEDMLRGIFEPFGKIDNIVLM-KDSDTGRSKG 48

>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 = 73.0 bits (180), Expect = 3e-16
 Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 1/86 (1%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           FV+NL+ T     L ++FS +G +      +     K KG+ FV +  PE A+ A  ++ 
Sbjct: 12  FVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVD 71

Query: 77  GATVERMELYVGPFIRRADRIQEGSS 102
           G   +   L+V P   + +  Q G S
Sbjct: 72  GQVFQGRMLHVLPSTIKKEASQSGPS 97

>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 = 50.3 bits (121), Expect = 3e-08
 Identities = 22/95 (23%), Positives = 36/95 (37%), Gaps = 17/95 (17%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARA 156
              S    L+V+NL    +EE L + FS +G ++ L    D+     KGF     +V   
Sbjct: 3   SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFA----FVTFM 58

Query: 157 QKKAERKAI------------LRAQFERMRKERAE 179
             +   KA             L      ++KE ++
Sbjct: 59  FPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQ 93

>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 = 73.6 bits (181), Expect = 3e-16
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +++NL   I   +++ IF K+G I+   + V    +++G  +V Y     A +A++ L G
Sbjct: 12 YIRNLPYKITAEEMYDIFGKYGPIRQ--IRVGNTPETRGTAYVVYEDIFDAKNAVDHLSG 69

Query: 78 ATVERMELYVG 88
            V    L V 
Sbjct: 70 FNVSNRYLVVL 80

>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 = 60.1 bits (146), Expect = 1e-11
 Identities = 17/107 (15%), Positives = 39/107 (36%), Gaps = 28/107 (26%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG----------------- 147
            LY++NL   +T E + + F ++G I  + +       ++G                   
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHL 67

Query: 148 ------SKVLYVA-RAQKKAERKAILRAQFERMRKERAELYKNINDE 187
                 ++ L V      +A +K   + + E+++  +      IN +
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKE--KYGINTD 112

>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 = 38.5 bits (90), Expect = 6e-04
 Identities = 9/42 (21%), Positives = 20/42 (47%), Gaps = 3/42 (7%)

Query: 180 LY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHC 220
           LY +N+  ++   E+   F + G I  +++  T    ++G  
Sbjct: 11  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTA 50

>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 = 72.3 bits (178), Expect = 4e-16
 Identities = 23/100 (23%), Positives = 37/100 (37%), Gaps = 5/100 (5%)

Query: 3   STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQY 62
            +   E   +     FV NL   I   ++ ++F K+G      +      K KG+GF++ 
Sbjct: 4   GSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-----KDKGFGFIRL 58

Query: 63  STPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSS 102
            T   A  A  +L    +   +L V      A      SS
Sbjct: 59  ETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPSS 98

>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 = 54.2 bits (131), Expect = 1e-09
 Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 5/50 (10%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           +  +  + L+V NL  D+TEE + + F ++GK   + I KD     KGFG
Sbjct: 10  KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFG 54

>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 = 42.2 bits (100), Expect = 2e-05
 Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 170 FERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRG 214
            E+   +R+ L+  N+  ++ E E+++ F + G    V I + D+G
Sbjct: 8   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-DKG 52

>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 = 71.4 bits (176), Expect = 6e-16
 Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          + FV +L+  I    +   F+ FG I  ++VV     GKSKGYGFV +     A +AI++
Sbjct: 8  HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 75 LQGATVE 81
          + G  + 
Sbjct: 68 MGGQWLG 74

>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 = 53.3 bits (129), Expect = 2e-09
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 6/68 (8%)

Query: 99  EGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQ 157
            GS F+ ++V +L  ++T   +   F+ FG+I+   + KD   G SKG+G    +V+   
Sbjct: 3   LGSHFH-VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYG----FVSFFN 57

Query: 158 KKAERKAI 165
           K     AI
Sbjct: 58  KWDAENAI 65

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 71.9 bits (177), Expect = 6e-16
 Identities = 17/64 (26%), Positives = 33/64 (51%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          F+  L  +    +L +I    G ++  ++V ++ GK KG  +V+Y     A  A+ K+ G
Sbjct: 21 FISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDG 80

Query: 78 ATVE 81
           T++
Sbjct: 81 MTIK 84

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 57.7 bits (140), Expect = 6e-11
 Identities = 15/74 (20%), Positives = 25/74 (33%), Gaps = 4/74 (5%)

Query: 92  RRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVL 151
               R       + L++  L    T+E L E     G +  L +  +  G  KG      
Sbjct: 6   SGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLA---- 61

Query: 152 YVARAQKKAERKAI 165
           YV    +    +A+
Sbjct: 62  YVEYENESQASQAV 75

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 11/45 (24%), Positives = 24/45 (53%), Gaps = 3/45 (6%)

Query: 176 ERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDR-GISKG 218
           E+ +L+   +     + EL++     GT+  ++++ T+R G  KG
Sbjct: 16  EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLV-TNRAGKPKG 59

>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 = 71.6 bits (176), Expect = 7e-16
 Identities = 27/101 (26%), Positives = 38/101 (37%), Gaps = 9/101 (8%)

Query: 3   STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQY 62
           S+    A   G    +V     T     L   FS FG+I    +        +   FV Y
Sbjct: 5   SSGERRAPRKGN-TLYVYGEDMTPT--LLRGAFSPFGNIIDLSM-----DPPRNCAFVTY 56

Query: 63  STPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSF 103
              ESA  A+ +L G  VE ++L V    R+   +  G S 
Sbjct: 57  EKMESADQAVAELNGTQVESVQLKVN-IARKQPMLDSGPSS 96

>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 = 46.5 bits (111), Expect = 5e-07
 Identities = 19/90 (21%), Positives = 26/90 (28%), Gaps = 30/90 (33%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG---------- 147
           +     N LYV   D  MT  +L   FS FG I  L +        +             
Sbjct: 10  RAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESA 62

Query: 148 -------------SKVLYVARAQKKAERKA 164
                        S  L V  A+K+    +
Sbjct: 63  DQAVAELNGTQVESVQLKVNIARKQPMLDS 92

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 72.0 bits (177), Expect = 7e-16
 Identities = 29/85 (34%), Positives = 45/85 (52%), Gaps = 1/85 (1%)

Query: 5   PNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYS 63
            N +   +G    +V +L   I    L  IF  FG I+S ++++  E G+SKGYGF+ +S
Sbjct: 17  NNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76

Query: 64  TPESALDAIEKLQGATVERMELYVG 88
             E A  A+E+L G  +    + VG
Sbjct: 77  DSECAKKALEQLNGFELAGRPMKVG 101

>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 = 53.1 bits (128), Expect = 3e-09
 Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 6/75 (8%)

Query: 93  RADRIQEGS-SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKV 150
            A+ +Q+GS     LYV +L  ++TE++L   F  FG+I S+ +  D   G SKG+G   
Sbjct: 15  MANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYG--- 71

Query: 151 LYVARAQKKAERKAI 165
            ++  +  +  +KA+
Sbjct: 72  -FITFSDSECAKKAL 85

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 4/67 (5%)

Query: 155 RAQKKAERKAILRAQFERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDR 213
                +   A +    ++       LY  +++  + E  L+  F   G I S+++M  D 
Sbjct: 4   HHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLM-MDS 62

Query: 214 --GISKG 218
             G SKG
Sbjct: 63  ETGRSKG 69

>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 = 71.1 bits (175), Expect = 9e-16
 Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          +V NL  ++ N  L++IFSK+G +    ++  ++  KSKG  F+ +   +SA +    + 
Sbjct: 20 YVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAIN 79

Query: 77 GATVE 81
             + 
Sbjct: 80 NKQLF 84

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 5/63 (7%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKKAER 162
           + +YV NL   +T   L   FS++GK+  + I KD     SKG      ++    K + +
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVA----FILFLDKDSAQ 72

Query: 163 KAI 165
              
Sbjct: 73  NCT 75

>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 = 38.0 bits (89), Expect = 5e-04
 Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           N+   +   +L + FS+ G +  V IM  D+    SKG
Sbjct: 23  NLPFSLTNNDLYRIFSKYGKVVKVTIM-KDKDTRKSKG 59

>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 = 76.1 bits (186), Expect = 9e-16
 Identities = 34/236 (14%), Positives = 65/236 (27%), Gaps = 40/236 (16%)

Query: 18  FVKNLASTID----NLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
           ++ NL   I        L+ IFS+FG I    ++VS+  K +G  FV +    SA +A+ 
Sbjct: 13  YINNLNEKIKKDELKKSLYAIFSQFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR 70

Query: 74  KLQGATVERMELYVGPFIRRADRIQEG----SSFNNLYVKNLDDDMTEEILVEKFSEFGK 129
            +QG       + +      +D I +        +    K            +     G 
Sbjct: 71  SMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGA 130

Query: 130 ITSLVISKDANGTSKGFGSKVLYVARA------------------------------QKK 159
              +   +               +                                 Q+ 
Sbjct: 131 TPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQL 190

Query: 160 AERKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGI 215
              +                   N+ +E +E+ L   F+Q      V+++     I
Sbjct: 191 MPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDI 246

>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 = 55.3 bits (132), Expect = 7e-09
 Identities = 16/101 (15%), Positives = 42/101 (41%), Gaps = 29/101 (28%)

Query: 104 NNLYVKNLDDDMTEEILVEK----FSEFGKITSLVISKDANGTSKGFG------------ 147
           + +Y+ NL++ + ++ L +     FS+FG+I  +++S+  +   +G              
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATN 67

Query: 148 -----------SKVLYVARAQKKAERKAILRAQFERMRKER 177
                       K + +  A+  ++  A ++  F    ++R
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKR 108

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 54.9 bits (131), Expect = 1e-08
 Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 4/65 (6%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
             F+ NL    + L L  +F++F   +  ++V           FV++     A  A + L
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP----GRHDIAFVEFDNEVQAGAARDAL 264

Query: 76  QGATV 80
           QG  +
Sbjct: 265 QGFKI 269

>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 = 49.9 bits (118), Expect = 5e-07
 Identities = 36/219 (16%), Positives = 62/219 (28%), Gaps = 24/219 (10%)

Query: 180 LY-KNINDEVDEIELKQ----YFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERT--- 231
           +Y  N+N+++ + ELK+     FSQ G I  + + R+ +   +G    I +     T   
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 69

Query: 232 ----------SYLRIMYAK---QGPGLASTIFPVHPTLYQRALQVYQAPDFRHGGMIPNG 278
                       +RI YAK            F       ++     Q        +   G
Sbjct: 70  RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGG 129

Query: 279 FSPPPPSPLFLMAPDSVTQYRGAMMNGHANFPMPLMLSNLQKPSYNYPISQPRAGQAAAN 338
            +P   +    +           +M+     P P M      P       Q   G     
Sbjct: 130 ATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQP-PYMPPPGMIPPPGLAPGQIPPGAMPPQ 188

Query: 339 NLTNGNHRAAASNENLSSMLVATSPDERKDILGQRLYPL 377
            L  G    A          +    +  ++     L  L
Sbjct: 189 QLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSML 227

>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 = 71.5 bits (176), Expect = 1e-15
 Identities = 28/89 (31%), Positives = 46/89 (51%), Gaps = 1/89 (1%)

Query: 15  GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE 73
           G  FV  L+   +   L Q+FSK+G I    VV  +E  +S+G+GFV +   + A DA+ 
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72

Query: 74  KLQGATVERMELYVGPFIRRADRIQEGSS 102
            + G +V+  ++ V    + +D     SS
Sbjct: 73  AMNGKSVDGRQIRVDQAGKSSDNRSGPSS 101

>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 = 48.8 bits (117), Expect = 1e-07
 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 5/63 (7%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAER 162
             L+V  L  D  E+ L + FS++G+I+ +V+ KD     S+GFG    +V        +
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFG----FVTFENIDDAK 68

Query: 163 KAI 165
            A+
Sbjct: 69  DAM 71

>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 = 40.7 bits (96), Expect = 6e-05
 Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
            ++ + +E  L+Q FS+ G IS V ++  DR    S+G
Sbjct: 19  GLSFDTNEQSLEQVFSKYGQISEVVVV-KDRETQRSRG 55

>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 = 70.7 bits (174), Expect = 1e-15
 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           V  L+       L ++FSK+G I    +V  Q+  +S+G+ FV +   + A +A E+  
Sbjct: 19 GVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN 78

Query: 77 GATVE 81
          G  ++
Sbjct: 79 GMELD 83

>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 = 9e-08
 Identities = 18/74 (24%), Positives = 26/74 (35%), Gaps = 5/74 (6%)

Query: 93  RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVL 151
            +           L V  L    TE  L E FS++G I  + I  D     S+GF     
Sbjct: 5   SSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA---- 60

Query: 152 YVARAQKKAERKAI 165
           +V        ++A 
Sbjct: 61  FVYFENVDDAKEAK 74

>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 = 38.0 bits (89), Expect = 6e-04
 Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
            ++    E +L++ FS+ G I+ V I+  D+    S+G
Sbjct: 22  GLSLYTTERDLREVFSKYGPIADVSIV-YDQQSRRSRG 58

>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 = 70.7 bits (174), Expect = 2e-15
 Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 6/84 (7%)

Query: 18 FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
          ++ NL   I  D LK  LH IFS+FG I    ++VS+  K +G  FV +    SA +A+ 
Sbjct: 12 YINNLNEKIKKDELKKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALR 69

Query: 74 KLQGATVERMELYVGPFIRRADRI 97
           +QG       + +      +D I
Sbjct: 70 SMQGFPFYDKPMRIQYAKTDSDII 93

>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 = 52.2 bits (126), Expect = 6e-09
 Identities = 15/98 (15%), Positives = 38/98 (38%), Gaps = 29/98 (29%)

Query: 97  IQEGSSFNNLYVKNLDDDMTEEILVEK----FSEFGKITSLVISKDANGTSKGFG----- 147
           + E    + +Y+ NL++ + ++ L +     FS FG+I  +++S+      +G       
Sbjct: 2   VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS--LKMRGQAFVIFK 59

Query: 148 ------------------SKVLYVARAQKKAERKAILR 167
                              K + +  A+  ++  A ++
Sbjct: 60  EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97

>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 = 41.1 bits (97), Expect = 5e-05
 Identities = 12/44 (27%), Positives = 25/44 (56%), Gaps = 7/44 (15%)

Query: 180 LY-KNINDEVDEIELKQ----YFSQCGTISSVKIMRTDRGISKG 218
           +Y  N+N+++ + ELK+     FS+ G I  + + R+ +   +G
Sbjct: 11  IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRG 52

>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 = 2e-15
 Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 1/86 (1%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           FV ++       ++ + F  +G+I++  + + +  G SKGY  V+Y T + AL A E L 
Sbjct: 76  FVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN 135

Query: 77  GATVERMELYVGPFIRRADRIQEGSS 102
           GA +    + V     +  +  + S 
Sbjct: 136 GAEIMGQTIQVDWCFVKGPKRVKKSE 161

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 53.3 bits (128), Expect = 9e-09
 Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARA 156
           Q       L+V ++ ++  E+ + EKF ++G+I ++ ++ D   G SKG+      V   
Sbjct: 67  QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYA----LVEYE 122

Query: 157 QKKAERKAI 165
             K    A 
Sbjct: 123 THKQALAAK 131

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 42.1 bits (99), Expect = 6e-05
 Identities = 27/112 (24%), Positives = 47/112 (41%), Gaps = 5/112 (4%)

Query: 111 LDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQF 170
           LD D  EE  V++  + G +     +K   G   G  S       + ++   +     + 
Sbjct: 5   LDIDNAEEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEP 64

Query: 171 ERMR-KERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
              R  E   L+  +I++E  E E+++ F   G I ++ +   DR  G SKG
Sbjct: 65  GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL-DRRTGFSKG 115

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 71.7 bits (176), Expect = 2e-15
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           +V  LA  +D+  LH  F  FGDI   ++ +  E  K +G+ FV++   E A  AI+ + 
Sbjct: 67  YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 126

Query: 77  GA 78
            +
Sbjct: 127 ES 128

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 56.3 bits (136), Expect = 6e-10
 Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 5/69 (7%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARA 156
              ++   LYV  L +++ +++L   F  FG IT + I  D      +GF     +V   
Sbjct: 58  GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA----FVEFE 113

Query: 157 QKKAERKAI 165
             +    AI
Sbjct: 114 LAEDAAAAI 122

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 39.4 bits (92), Expect = 4e-04
 Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
            + +EVD+  L   F   G I+ ++I   D      +G
Sbjct: 70  GLAEEVDDKVLHAAFIPFGDITDIQIP-LDYETEKHRG 106

>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 = 70.9 bits (174), Expect = 3e-15
 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
            V  L+       L ++FSK+G I    +V  Q+  +S+G+ FV +   + A +A E+  
Sbjct: 50  GVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN 109

Query: 77  GATVE 81
           G  ++
Sbjct: 110 GMELD 114

>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 = 47.4 bits (113), Expect = 6e-07
 Identities = 19/75 (25%), Positives = 26/75 (34%), Gaps = 5/75 (6%)

Query: 92  RRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKV 150
           R             L V  L    TE  L E FS++G I  + I  D     S+GF    
Sbjct: 35  RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA--- 91

Query: 151 LYVARAQKKAERKAI 165
            +V        ++A 
Sbjct: 92  -FVYFENVDDAKEAK 105

>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 = 71.4 bits (175), Expect = 3e-15
 Identities = 19/88 (21%), Positives = 36/88 (40%), Gaps = 6/88 (6%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSK------VVVSQEGKSKGYGFVQYSTPESALDA 71
           +VKNLA  +    L  IF ++ D  S        + + +EG+ KG  F+     ++A  A
Sbjct: 49  YVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKA 108

Query: 72  IEKLQGATVERMELYVGPFIRRADRIQE 99
           +++  G  +    + V        +   
Sbjct: 109 LKEANGYVLFGKPMVVQFARSARPKQDP 136

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 59.5 bits (144), Expect = 4e-11
 Identities = 22/138 (15%), Positives = 37/138 (26%), Gaps = 36/138 (26%)

Query: 70  DAIEKLQGATVERMELYVGPFIRRADRIQE-------GSSFNNLYVKNLDDDMTEEILVE 122
              +++    + R EL  G   R              G     +YVKNL   + E+ L  
Sbjct: 5   SDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKY 64

Query: 123 KFSEFGKITS------LVISKDANGTSKGFG-----------------------SKVLYV 153
            F  +   +S        I     G  KG                          K + V
Sbjct: 65  IFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVV 124

Query: 154 ARAQKKAERKAILRAQFE 171
             A+    ++     + +
Sbjct: 125 QFARSARPKQDPKEGKRK 142

>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 = 49.8 bits (119), Expect = 1e-07
 Identities = 17/83 (20%), Positives = 27/83 (32%), Gaps = 8/83 (9%)

Query: 144 KGFGSKVLYVARAQKKAERKAILRAQFERMRKERAELY-KNINDEVDEIELKQYFSQCGT 202
           +    + L   R  ++      +   +E        +Y KN+   V E +LK  F +   
Sbjct: 13  ECISRRELEKGRISREEMETLSVFRSYEPGEPNCR-IYVKNLAKHVQEKDLKYIFGRYVD 71

Query: 203 ISSVK------IMRTDRGISKGH 219
            SS        I     G  KG 
Sbjct: 72  FSSETQRIMFDIRLMKEGRMKGQ 94

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 69.9 bits (172), Expect = 4e-15
 Identities = 24/98 (24%), Positives = 41/98 (41%), Gaps = 1/98 (1%)

Query: 6   NSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYST 64
            S    +     +V  LA  +D+  LH  F  FGDI   ++ +  E  K +G+ FV++  
Sbjct: 4   GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 63

Query: 65  PESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSS 102
            E A  AI+ +  + +    + V        +    SS
Sbjct: 64  AEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESGPSS 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 = 54.9 bits (133), Expect = 6e-10
 Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 5/63 (7%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKKAER 162
             LYV  L +++ +++L   F  FG IT + I  D      +GF     +V     +   
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA----FVEFELAEDAA 68

Query: 163 KAI 165
            AI
Sbjct: 69  AAI 71

>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 = 40.7 bits (96), Expect = 7e-05
 Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 4/51 (7%)

Query: 171 ERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
             M   +  LY   + +EVD+  L   F   G I+ ++I   D      +G
Sbjct: 6   SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIP-LDYETEKHRG 55

>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 = 69.6 bits (171), Expect = 4e-15
 Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 4/79 (5%)

Query: 3  STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQY 62
            P +  ++        KNL+  I   +L ++F    +I     +VSQ+GKSKG  ++++
Sbjct: 5  EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI----RLVSQDGKSKGIAYIEF 60

Query: 63 STPESALDAIEKLQGATVE 81
           +   A   +E+ QGA ++
Sbjct: 61 KSEADAEKNLEEKQGAEID 79

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 46.1 bits (110), Expect = 6e-07
 Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 8/68 (11%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQ 157
           ++  +   L  KNL  ++TE+ L E F +  +    +     +G SKG      Y+    
Sbjct: 11  KKVRAARTLLAKNLSFNITEDELKEVFEDALE----IRLVSQDGKSKGIA----YIEFKS 62

Query: 158 KKAERKAI 165
           +    K +
Sbjct: 63  EADAEKNL 70

>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 = 69.1 bits (170), Expect = 4e-15
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 7/77 (9%)

Query: 3  STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQ 61
          S   ++  L      +V  LA  +D+  LH  F  FGDI   ++ +  E  K +G+ FV+
Sbjct: 2  SMATTKRVL------YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 55

Query: 62 YSTPESALDAIEKLQGA 78
          +   E A  AI+ +  +
Sbjct: 56 FELAEDAAAAIDNMNES 72

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 53.3 bits (129), Expect = 2e-09
 Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 5/66 (7%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKK 159
           ++   LYV  L +++ +++L   F  FG IT + I  D      +GF     +V     +
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA----FVEFELAE 60

Query: 160 AERKAI 165
               AI
Sbjct: 61  DAAAAI 66

>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 = 38.7 bits (91), Expect = 3e-04
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 4/49 (8%)

Query: 173 MRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           M   +  LY   + +EVD+  L   F   G I+ ++I   D      +G
Sbjct: 3   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIP-LDYETEKHRG 50

>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 = 69.1 bits (170), Expect = 4e-15
 Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 2/81 (2%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV--SQEGKSKGYGFVQYSTPESALDAIEKL 75
           +  L   +    + +IFS +G I+   + V       SKGY +V++  P+ A  A++ +
Sbjct: 8  HIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHM 67

Query: 76 QGATVERMELYVGPFIRRADR 96
           G  ++  E+     +    R
Sbjct: 68 DGGQIDGQEITATAVLAPWPR 88

>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 = 54.9 bits (133), Expect = 4e-10
 Identities = 17/90 (18%), Positives = 33/90 (36%), Gaps = 18/90 (20%)

Query: 102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD--ANGTSKGFGSKVLYVARAQKK 159
               +++  L  ++T++ ++E FS +GKI  + +  +      SKG+     YV      
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYA----YVEFENPD 58

Query: 160 AERKAI------------LRAQFERMRKER 177
              KA+            + A        R
Sbjct: 59  EAEKALKHMDGGQIDGQEITATAVLAPWPR 88

>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 = 37.5 bits (88), Expect = 7e-04
 Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 2/38 (5%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIM--RTDRGISKG 218
            +   V +  + + FS  G I  + +   R    +SKG
Sbjct: 11  RLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKG 48

>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 = 69.6 bits (171), Expect = 5e-15
 Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 1/101 (0%)

Query: 3   STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQ 61
           S+ +S   + G+    V NL        L ++F K+G +    +         +G+ FV+
Sbjct: 2   SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61

Query: 62  YSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSS 102
           +     A DA   + GA ++  EL V         +   SS
Sbjct: 62  FHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPSS 102

>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 = 49.9 bits (120), Expect = 5e-08
 Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 5/75 (6%)

Query: 92  RRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKV 150
                  +      L V NL    + + L   F ++G++  + I ++      +GF    
Sbjct: 2   SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFA--- 58

Query: 151 LYVARAQKKAERKAI 165
            +V    ++  + A 
Sbjct: 59  -FVRFHDRRDAQDAE 72

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 68.8 bits (169), Expect = 1e-14
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          FV  +        +H  F+++G+I++  + + +  G  KGY  V+Y T + A  A+E L 
Sbjct: 27 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 86

Query: 77 GATVERMELYV 87
          G  +    + V
Sbjct: 87 GQDLMGQPISV 97

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 5/63 (7%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKKAER 162
             L+V  + ++ TEE + +KF+E+G+I ++ ++ D   G  KG+      V     K  +
Sbjct: 24  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT----LVEYETYKEAQ 79

Query: 163 KAI 165
            A+
Sbjct: 80  AAM 82

>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 = 68.4 bits (168), Expect = 1e-14
 Identities = 14/64 (21%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          ++ ++       ++  + S  G + + K++   + G+SKGY F+++   ES+  A+  L 
Sbjct: 6  YLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLN 65

Query: 77 GATV 80
          G  +
Sbjct: 66 GYQL 69

>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 = 49.2 bits (118), Expect = 7e-08
 Identities = 14/62 (22%), Positives = 30/62 (48%), Gaps = 5/62 (8%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAERK 163
            +Y+ ++  D TEE +++  S  G + +L +  D   G SKG+     ++     ++   
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYA----FIEFRDLESSAS 59

Query: 164 AI 165
           A+
Sbjct: 60  AV 61

>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 = 4e-04
 Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           +I  +  E ++    S  G + ++K+M  D   G SKG
Sbjct: 9   SIPYDQTEEQILDLCSNVGPVINLKMMF-DPQTGRSKG 45

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

 Score = 68.5 bits (168), Expect = 1e-14
 Identities = 17/65 (26%), Positives = 23/65 (35%), Gaps = 5/65 (7%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
           A++ N+        L  +F  FG I   K         KG  F++Y T E A   I  L
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKH-----YPEKGCCFIKYDTHEQAAVCIVAL 83

Query: 76 QGATV 80
               
Sbjct: 84 ANFPF 88

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

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 12/54 (22%), Positives = 17/54 (31%), Gaps = 6/54 (11%)

Query: 95  DRIQEGSSFN-NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
             I+         Y+ N+    TE  L+  F  FG I       +     KG  
Sbjct: 18  HIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCC 66

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 9/32 (28%), Positives = 12/32 (37%), Gaps = 1/32 (3%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDRG 214
           NI     E +L   F   G I   K    ++G
Sbjct: 34  NIPHFATEADLIPLFQNFGFILDFKHYP-EKG 64

>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 = 68.2 bits (167), Expect = 3e-14
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          FV  +        +H  F+++G+I++  + + +  G  KGY  V+Y T + A  A+E L 
Sbjct: 26 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 85

Query: 77 GATVERMELYV 87
          G  +    + V
Sbjct: 86 GQDLMGQPISV 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 = 50.1 bits (120), Expect = 6e-08
 Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 5/63 (7%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKKAER 162
             L+V  + ++ TEE + +KF+E+G+I ++ ++ D   G  KG+      V     K  +
Sbjct: 23  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT----LVEYETYKEAQ 78

Query: 163 KAI 165
            A+
Sbjct: 79  AAM 81

>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 = 67.3 bits (165), Expect = 3e-14
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           FV ++       ++ + F  +G+I++  + + +  G SKGY  V+Y T + AL A E L 
Sbjct: 30  FVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN 89

Query: 77  GATVERMELYV 87
           GA +    + V
Sbjct: 90  GAEIMGQTIQV 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 = 48.4 bits (116), Expect = 1e-07
 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 5/70 (7%)

Query: 97  IQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVAR 155
            Q       L+V ++ ++  E+ + EKF ++G+I ++ ++ D   G SKG+      V  
Sbjct: 20  PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYA----LVEY 75

Query: 156 AQKKAERKAI 165
              K    A 
Sbjct: 76  ETHKQALAAK 85

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

 Score = 67.0 bits (164), Expect = 4e-14
 Identities = 27/85 (31%), Positives = 38/85 (44%), Gaps = 5/85 (5%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           +   +AS + +  + Q FS FG I   +V        KGY FV++ST ESA  AI  + G
Sbjct: 29  YCGGIASGLTDQLMRQTFSPFGQIMEIRVF-----PEKGYSFVRFSTHESAAHAIVSVNG 83

Query: 78  ATVERMELYVGPFIRRADRIQEGSS 102
            T+E   +         D     SS
Sbjct: 84  TTIEGHVVKCYWGKESPDMTSGPSS 108

>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 = 51.2 bits (123), Expect = 2e-08
 Identities = 13/68 (19%), Positives = 30/68 (44%), Gaps = 9/68 (13%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQ 157
           Q       +Y   +   +T++++ + FS FG+I  + +  +     KG+     +V  + 
Sbjct: 20  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYS----FVRFST 70

Query: 158 KKAERKAI 165
            ++   AI
Sbjct: 71  HESAAHAI 78

>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 = 38.9 bits (91), Expect = 3e-04
 Identities = 7/32 (21%), Positives = 16/32 (50%), Gaps = 1/32 (3%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDRG 214
            I   + +  ++Q FS  G I  +++   ++G
Sbjct: 32  GIASGLTDQLMRQTFSPFGQIMEIRVFP-EKG 62

>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 = 66.9 bits (164), Expect = 5e-14
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           V NL+       L ++F  FG I    +   +  G+SKG+ F+ +   E A  AI  + 
Sbjct: 19 RVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVS 78

Query: 77 GATVERMELYV 87
          G   + + L V
Sbjct: 79 GFGYDHLILNV 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 = 54.5 bits (132), Expect = 1e-09
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARA 156
           +       + V NL +D  E  L E F  FG I+ + ++KD   G SKGF     +++  
Sbjct: 10  RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA----FISFH 65

Query: 157 QKKAERKAI 165
           +++   +AI
Sbjct: 66  RREDAARAI 74

>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 = 38.7 bits (91), Expect = 4e-04
 Identities = 12/38 (31%), Positives = 24/38 (63%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           N++++  E +L++ F   G+IS + + + D+  G SKG
Sbjct: 22  NLSEDTRETDLQELFRPFGSISRIYLAK-DKTTGQSKG 58

>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 = 67.0 bits (164), Expect = 5e-14
 Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          F++NL+   +   L ++  +FGD++  +VV+  +   SKG  F Q+ T E+A   +    
Sbjct: 19 FIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAAS 78

Query: 77 GAT 79
             
Sbjct: 79 LEA 81

>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 = 50.4 bits (121), Expect = 3e-08
 Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 5/62 (8%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAERK 163
            ++++NL  D  EE L E   +FG +  + +    +   SKG      +     ++A +K
Sbjct: 17  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA----FAQFMTQEAAQK 72

Query: 164 AI 165
            +
Sbjct: 73  CL 74

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 9/38 (23%), Positives = 18/38 (47%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           N++ + +E  L +   Q G +  V+++        SKG
Sbjct: 22  NLSFDSEEEALGEVLQQFGDLKYVRVV-LHPDTEHSKG 58

>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 = 66.1 bits (162), Expect = 7e-14
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 3/64 (4%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           + NL+ +     L ++F K   I   KV  +Q GKSKGY F+++++ E A +A+     
Sbjct: 19 VLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNK 75

Query: 78 ATVE 81
            +E
Sbjct: 76 REIE 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 = 48.0 bits (115), Expect = 1e-07
 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 7/68 (10%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQ 157
                   L + NL    TEE L E F +   I    + ++ NG SKG+     ++  A 
Sbjct: 10  TWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYA----FIEFAS 62

Query: 158 KKAERKAI 165
            +  ++A+
Sbjct: 63  FEDAKEAL 70

>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 = 66.1 bits (162), Expect = 9e-14
 Identities = 25/67 (37%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          + FV N+       +L  IFS+ G + S ++V  +E GK KGYGF +Y   E+AL A+  
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 75 LQGATVE 81
          L G    
Sbjct: 70 LNGREFS 76

>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 = 47.3 bits (113), Expect = 3e-07
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAER 162
            +++V N+  + TEE L + FSE G + S  +  D   G  KG+G    +     ++   
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYG----FCEYQDQETAL 64

Query: 163 KAI 165
            A+
Sbjct: 65  SAM 67

>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 = 67.2 bits (164), Expect = 1e-13
 Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 7   SEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTP 65
               + G+ +  V NL        L ++F K+G +    +   +   +S+G+ FV++   
Sbjct: 63  HHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 122

Query: 66  ESALDAIEKLQGATVE 81
             A DA++ + GA ++
Sbjct: 123 RDAEDAMDAMDGAVLD 138

>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 = 51.0 bits (122), Expect = 5e-08
 Identities = 20/114 (17%), Positives = 35/114 (30%), Gaps = 11/114 (9%)

Query: 59  FVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEG------SSFNNLYVKNLD 112
            V  +T E          G   E             +               +L V NL 
Sbjct: 20  AVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT 79

Query: 113 DDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAERKAI 165
              + + L   F ++G++  + I +D     S+GF     +V    K+    A+
Sbjct: 80  YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFA----FVRFHDKRDAEDAM 129

>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 = 39.1 bits (91), Expect = 7e-04
 Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           N+        L++ F + G +  V I   DR    S+G
Sbjct: 77  NLTYRTSPDTLRRVFEKYGRVGDVYIP-RDRYTKESRG 113

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 66.3 bits (162), Expect = 2e-13
 Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 7   SEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTP 65
               + G+ +  V NL        L ++F K+G +    +   +   +S+G+ FV++   
Sbjct: 40  PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 99

Query: 66  ESALDAIEKLQGATVE 81
             A DA++ + GA ++
Sbjct: 100 RDAEDAMDAMDGAVLD 115

>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 = 6e-07
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 5/75 (6%)

Query: 92  RRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKV 150
                  +     +L V NL    + + L   F ++G++  + I +D     S+GF    
Sbjct: 36  SYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFA--- 92

Query: 151 LYVARAQKKAERKAI 165
            +V    K+    A+
Sbjct: 93  -FVRFHDKRDAEDAM 106

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 66.5 bits (162), Expect = 2e-13
 Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 3/88 (3%)

Query: 18  FVKNLASTIDNLKLHQIFSKFG--DIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
           +V + +    + +L Q+    G  D+   K   ++  G+SKGY  V  ++  S    +E 
Sbjct: 59  YVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLEL 118

Query: 75  LQGATVERMELYVGPFIRRADRIQEGSS 102
           L G  +   ++ V P  R+     E  +
Sbjct: 119 LPGKVLNGEKVDVRPATRQNLSQFEAQA 146

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 44.1 bits (104), Expect = 1e-05
 Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 7/65 (10%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFG--KITSLVISKD-ANGTSKGFGSKVLYVARAQKKA 160
             +YV +     T++ L++     G   +  L  +++ ANG SKG+      V  A + +
Sbjct: 56  AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYA----EVVVASENS 111

Query: 161 ERKAI 165
             K +
Sbjct: 112 VHKLL 116

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

 Score = 65.3 bits (159), Expect = 2e-13
 Identities = 20/93 (21%), Positives = 39/93 (41%), Gaps = 6/93 (6%)

Query: 18  FVKNLASTI--DNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
            + N+   +  + L+  L+ + S  GDI    +VV     + G  ++ ++T ESA   +E
Sbjct: 33  LITNINPEVPKEKLQALLYALASSQGDI--LDIVVDLSDDNSGKAYIVFATQESAQAFVE 90

Query: 74  KLQGATVERMELYVGPFIRRADRIQEGSSFNNL 106
             QG   +   L +        ++ E  S  + 
Sbjct: 91  AFQGYPFQGNPLVITFSETPQSQVAEDGSLEHH 123

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

 Score = 41.0 bits (96), Expect = 9e-05
 Identities = 8/47 (17%), Positives = 20/47 (42%), Gaps = 4/47 (8%)

Query: 104 NNLYVKNLDDDMTEEILVEK----FSEFGKITSLVISKDANGTSKGF 146
             + + N++ ++ +E L        S  G I  +V+    + + K +
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAY 76

>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 = 64.1 bits (157), Expect = 3e-13
 Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 3/84 (3%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFG--DIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAI 72
            ++ NL     +  L +     G  DI   K   ++  G+SKG+  V   +  S+   +
Sbjct: 3  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 73 EKLQGATVERMELYVGPFIRRADR 96
          + L    +      V P  +    
Sbjct: 63 DLLPKRELHGQNPVVTPSNKLEHH 86

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 47.2 bits (113), Expect = 3e-07
 Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 7/64 (10%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFG--KITSLVISKD-ANGTSKGFGSKVLYVARAQKKAE 161
            LY+ NL    T+E L E     G   I  +   ++ ANG SKGF      V    + + 
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFA----LVGVGSEASS 58

Query: 162 RKAI 165
           +K +
Sbjct: 59  KKLM 62

>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 = 64.7 bits (158), Expect = 3e-13
 Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          F+  +   +D   L  +F +FG I    V+  +  G  KG  F+ Y   ESAL A   L 
Sbjct: 17 FIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALH 76

Query: 77 GATV 80
              
Sbjct: 77 EQKT 80

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 51.6 bits (124), Expect = 1e-08
 Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 5/69 (7%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARA 156
            +      L++  +  ++ E+ L   F EFGKI  L + KD   G  KG      ++   
Sbjct: 8   MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCA----FLTYC 63

Query: 157 QKKAERKAI 165
           ++++  KA 
Sbjct: 64  ERESALKAQ 72

>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 = 38.5 bits (90), Expect = 4e-04
 Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 3/40 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKGHC 220
            I   +DE +LK  F + G I  + +++ DR  G+ KG  
Sbjct: 20  QIPRNLDEKDLKPLFEEFGKIYELTVLK-DRFTGMHKGCA 58

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 63.9 bits (156), Expect = 4e-13
 Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 3/63 (4%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV---SQEGKSKGYGFVQYSTPESALDAIEK 74
           ++N+A       +    S +  +  + + +    Q  +++G+ FVQ S+   A   ++ 
Sbjct: 13 ILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQI 72

Query: 75 LQG 77
          LQ 
Sbjct: 73 LQS 75

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 48.9 bits (117), Expect = 8e-08
 Identities = 6/47 (12%), Positives = 21/47 (44%), Gaps = 3/47 (6%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGK--ITSLVISKD-ANGTSKGFG 147
           + + ++N+      + ++   S +    + ++ + KD     ++GF 
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFA 56

>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 = 63.0 bits (154), Expect = 7e-13
 Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 5/60 (8%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          ++ NL+  +    L Q+F       + +V         GY FV Y     A+ AIE L G
Sbjct: 12 YIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETLSG 66

>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 = 1e-07
 Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 9/65 (13%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKA 160
           S  N LY+ NL   +T + L + F +     +  +         G+     +V    +  
Sbjct: 6   SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYA----FVDYPDQNW 56

Query: 161 ERKAI 165
             +AI
Sbjct: 57  AIRAI 61

>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 = 63.0 bits (154), Expect = 8e-13
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 5/63 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V  L        L + F +FG I++   V     K   + ++QY + ++A  A  K++G
Sbjct: 21 WVGGLGPNTSLAALAREFDRFGSIRTIDHV-----KGDSFAYIQYESLDAAQAACAKMRG 75

Query: 78 ATV 80
            +
Sbjct: 76 FPL 78

>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 = 42.2 bits (100), Expect = 2e-05
 Identities = 10/44 (22%), Positives = 16/44 (36%), Gaps = 5/44 (11%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
             L+V  L  + +   L  +F  FG I ++   K        F 
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFA 56

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 64.8 bits (158), Expect = 9e-13
 Identities = 22/101 (21%), Positives = 48/101 (47%), Gaps = 6/101 (5%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           +V NL+      +++++FSK GDI+   + + +    + G+ FV+Y +   A +A+  + 
Sbjct: 43  YVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYIN 102

Query: 77  GATVERMELYV---GPFI--RRADRIQEGSSFNNLYVKNLD 112
           G  ++   +       F   R+  R + G    + Y ++ D
Sbjct: 103 GTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYD 143

>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 = 50.6 bits (121), Expect = 6e-08
 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 92  RRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKV 150
              ++ +       LYV NL    TEE + E FS+ G I  +++  D    T+ GF    
Sbjct: 28  DNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFC--- 84

Query: 151 LYVARAQKKAERKAI 165
            +V    +     A+
Sbjct: 85  -FVEYYSRADAENAM 98

>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 = 41.7 bits (98), Expect = 8e-05
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 4/72 (5%)

Query: 152 YVARAQKKAERKAILRAQFERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMR 210
           YV  +Q + +       + E++ K+   LY  N++    E ++ + FS+ G I  + +  
Sbjct: 14  YVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGL 73

Query: 211 TDR--GISKGHC 220
            D+    + G C
Sbjct: 74  -DKMKKTACGFC 84

>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 = 65.9 bits (160), Expect = 1e-12
 Identities = 22/104 (21%), Positives = 39/104 (37%), Gaps = 4/104 (3%)

Query: 3   STPNSEARLSGIGNA-FVKNLASTIDNLKLHQIFSKFG--DIQSSKVVVSQE-GKSKGYG 58
           + PN     +G   A ++ NL     +  L +     G  DI   K   ++  G+SKG+ 
Sbjct: 56  AAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFA 115

Query: 59  FVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSS 102
            V   +  S+   ++ L    +      V P  ++     E  S
Sbjct: 116 LVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQS 159

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 50.9 bits (121), Expect = 2e-07
 Identities = 19/75 (25%), Positives = 28/75 (37%), Gaps = 7/75 (9%)

Query: 94  ADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFG--KITSLVISKD-ANGTSKGFGSKV 150
                       LY+ NL    T+E L E     G   I  +   ++ ANG SKGF    
Sbjct: 59  NVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFA--- 115

Query: 151 LYVARAQKKAERKAI 165
             V    + + +K +
Sbjct: 116 -LVGVGSEASSKKLM 129

>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 = 62.2 bits (152), Expect = 1e-12
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          N +V NL  +  + ++ ++FS+FG + + K++  +E  K KG+GFV+    ES  +AI K
Sbjct: 3  NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 75 LQGATVERMELYV 87
          L         + V
Sbjct: 62 LDNTDFMGRTIRV 74

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
           N+YV NL    T E + E FS+FGK+ ++ +  D      KGFG
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFG 46

>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 = 38.3 bits (90), Expect = 4e-04
 Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           N+       ++K+ FSQ G + +VK++  DR     KG
Sbjct: 8   NLVYSATSEQVKELFSQFGKVFNVKLI-YDRETKKPKG 44

>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 = 62.7 bits (153), Expect = 1e-12
 Identities = 15/62 (24%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          +V  L   +    L ++F + G + ++ +   +  G+ +GYGFV++ + E A  AI+ + 
Sbjct: 19 YVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMD 78

Query: 77 GA 78
            
Sbjct: 79 MI 80

>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 = 54.2 bits (131), Expect = 1e-09
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%)

Query: 97  IQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-NGTSKGFGSKVLYVAR 155
           I E +    +YV  LD+ ++E +L E F + G + +  + KD   G  +G+G    +V  
Sbjct: 9   ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG----FVEF 64

Query: 156 AQKKAERKAI 165
             ++    AI
Sbjct: 65  LSEEDADYAI 74

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 62.1 bits (151), Expect = 2e-12
 Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           ++N+   +    L  +  ++G ++S + V +          V YS+ + A  A++KL G
Sbjct: 19 QIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT--DSETAVVNVTYSSKDQARQALDKLNG 76

Query: 78 ATVERMELYV 87
            +E   L V
Sbjct: 77 FQLENFTLKV 86

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 45.9 bits (109), Expect = 9e-07
 Identities = 7/48 (14%), Positives = 18/48 (37%)

Query: 99  EGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGF 146
           +      L ++N+   +  E+L     ++G + S       + T+   
Sbjct: 11  KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVN 58

>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 = 62.3 bits (152), Expect = 2e-12
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE--GKSKGYGFVQYSTPESALDAIEKL 75
           V+N+    +  ++ ++FS FG++++ ++       G  +G+GFV + T + A  A   L
Sbjct: 19 LVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNAL 78

Query: 76 QGAT 79
            +T
Sbjct: 79 CHST 82

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 55.0 bits (133), Expect = 6e-10
 Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 6/75 (8%)

Query: 93  RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT--SKGFGSKV 150
            + ++ +  + + + V+N+     +  + E FS FG++ ++ + K   GT   +GFG   
Sbjct: 5   SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG--- 61

Query: 151 LYVARAQKKAERKAI 165
            +V    K+  +KA 
Sbjct: 62  -FVDFITKQDAKKAF 75

>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 = 38.1 bits (89), Expect = 6e-04
 Identities = 10/48 (20%), Positives = 27/48 (56%), Gaps = 3/48 (6%)

Query: 174 RKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIM--RTDRGISKG 218
           ++  +++  +NI  + ++ E+++ FS  G + +V++    T  G  +G
Sbjct: 12  KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 59

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 62.0 bits (151), Expect = 3e-12
 Identities = 24/94 (25%), Positives = 38/94 (40%), Gaps = 9/94 (9%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSS--------KVVVSQE-GKSKGYGFVQYSTPESA 68
           FV+ L   +    +   F + G I+++         +   +E GK KG   V +  P SA
Sbjct: 11  FVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSA 70

Query: 69  LDAIEKLQGATVERMELYVGPFIRRADRIQEGSS 102
             AI+   G       + V    RRAD  + G +
Sbjct: 71  KAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGN 104

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 13/77 (16%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITS--------LVISKDA-NGTSKGFGS 148
           Q+ S  N ++V+ L +++T E + + F + G I +        + +  D   G  KG   
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA- 60

Query: 149 KVLYVARAQKKAERKAI 165
               V+     + + AI
Sbjct: 61  ---TVSFDDPPSAKAAI 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 = 59.5 bits (145), Expect = 1e-11
 Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDA 71
          SG+   F+ NL       ++  +F ++G +    ++       K YGFV      +A DA
Sbjct: 6  SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDA 58

Query: 72 IEKLQGATVERMELYV 87
          I  L    +  + + V
Sbjct: 59 IRNLHHYKLHGVNINV 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 = 39.9 bits (94), Expect = 1e-04
 Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 7/47 (14%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           S    L++ NL  + TE+ +   F ++GK+    I        K +G
Sbjct: 6   SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI-------IKNYG 45

>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 = 59.6 bits (145), Expect = 1e-11
 Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 9/70 (12%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSS--------KVVVSQE-GKSKGYGFVQYSTPESA 68
          FV+ L   +    +   F + G I+++         +   +E GK KG   V +  P SA
Sbjct: 17 FVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSA 76

Query: 69 LDAIEKLQGA 78
            AI+   G 
Sbjct: 77 KAAIDWFDGK 86

>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 = 43.1 bits (102), Expect = 9e-06
 Identities = 11/53 (20%), Positives = 23/53 (43%), Gaps = 9/53 (16%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSL---------VISKDANGTSKGFG 147
           N ++V+ L +++T E + + F + G I +          + +    G  KG  
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 66

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 58.9 bits (143), Expect = 1e-11
 Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 7/66 (10%)

Query: 18 FVKNL----ASTIDNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDA 71
           V N+       ++ LK  +H+IFSKFG I +      ++GK+KGY F++Y++P  A+DA
Sbjct: 5  VVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN-DFYPEEDGKTKGYIFLEYASPAHAVDA 63

Query: 72 IEKLQG 77
          ++   G
Sbjct: 64 VKNADG 69

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 40.5 bits (95), Expect = 6e-05
 Identities = 12/50 (24%), Positives = 27/50 (54%), Gaps = 7/50 (14%)

Query: 104 NNLYVKNL------DDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           + + V N+        +  + ++ + FS+FGKIT+    ++ +G +KG+ 
Sbjct: 2   SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYI 50

>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 = 58.8 bits (143), Expect = 2e-11
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V  L  TI    L   F +FG+I++  VV     + +   F+Q++T ++A  A EK   
Sbjct: 16 YVGGLGDTITETDLRNHFYQFGEIRTITVV-----QRQQCAFIQFATRQAAEVAAEKSFN 70

Query: 78 ATV 80
            +
Sbjct: 71 KLI 73

>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 = 49.2 bits (118), Expect = 5e-08
 Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 9/72 (12%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQ 157
            E  +   LYV  L D +TE  L   F +FG+I ++ + +      +     + +  R  
Sbjct: 7   GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAF-IQFATRQA 60

Query: 158 KKAERKAILRAQ 169
             AE  A  ++ 
Sbjct: 61  --AEV-AAEKSF 69

>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 = 38.4 bits (90), Expect = 3e-04
 Identities = 7/32 (21%), Positives = 18/32 (56%), Gaps = 1/32 (3%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDRG 214
            + D + E +L+ +F Q G I ++ +++  + 
Sbjct: 19  GLGDTITETDLRNHFYQFGEIRTITVVQ-RQQ 49

>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 = 59.2 bits (144), Expect = 2e-11
 Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 4/65 (6%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          FVK L+       L + F        +++V  +E G SKG+GFV +++ E A  A E ++
Sbjct: 19 FVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75

Query: 77 GATVE 81
             ++
Sbjct: 76 DGEID 80

>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 = 42.6 bits (101), Expect = 1e-05
 Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 6/68 (8%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQ 157
                   L+VK L +D TEE L E F    +    +++    G+SKGFG    +V    
Sbjct: 10  ARSQPSKTLFVKGLSEDTTEETLKESFDGSVRAR--IVTDRETGSSKGFG----FVDFNS 63

Query: 158 KKAERKAI 165
           ++  + A 
Sbjct: 64  EEDAKAAK 71

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 59.0 bits (143), Expect = 2e-11
 Identities = 11/72 (15%), Positives = 28/72 (38%), Gaps = 4/72 (5%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE-- 73
          + ++K   +      + +     G + + ++  +     KG  FV + + ESA   +E  
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 72

Query: 74 --KLQGATVERM 83
            K +   +  +
Sbjct: 73 GQKYKETDLLIL 84

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 57.8 bits (140), Expect = 7e-11
 Identities = 8/50 (16%), Positives = 22/50 (44%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           +      ++Y+K    D T + + E   + G++ ++ + +  +   KG  
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSI 55

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 11/53 (20%), Positives = 23/53 (43%), Gaps = 2/53 (3%)

Query: 167 RAQFERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKG 218
           R   +   K R  +Y K    +    ++K++    G + ++++ RT     KG
Sbjct: 2   RWILKNDVKNR-SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG 53

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 58.4 bits (142), Expect = 3e-11
 Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 7/64 (10%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          FV N+++   + +L  +F + G +    VV       K Y FV       A  AI +L G
Sbjct: 13 FVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLNG 65

Query: 78 ATVE 81
            V+
Sbjct: 66 KEVK 69

>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 = 38.7 bits (91), Expect = 3e-04
 Identities = 8/33 (24%), Positives = 15/33 (45%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD 138
           ++V N+    T + L   F   G++    + KD
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVKD 44

>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 = 58.8 bits (143), Expect = 3e-11
 Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V NL+  +  + + Q+FS+ G  +S K++         Y FV++     A  A+  + G
Sbjct: 19 YVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAMNG 77

Query: 78 ATVE 81
            + 
Sbjct: 78 RKIL 81

>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 = 54.2 bits (131), Expect = 1e-09
 Identities = 14/72 (19%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 94  ADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYV 153
           +  +++      LYV NL  D+TE ++++ FS+ G   S  +  +   ++  +     +V
Sbjct: 6   SGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT-SNDPYC----FV 60

Query: 154 ARAQKKAERKAI 165
              + +    A+
Sbjct: 61  EFYEHRDAAAAL 72

>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 = 40.3 bits (95), Expect = 1e-04
 Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHC 220
           N++ +V E+ + Q FSQ G   S K++  +   +  +C
Sbjct: 22  NLSRDVTEVLILQLFSQIGPCKSCKMIT-EHTSNDPYC 58

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 58.6 bits (142), Expect = 4e-11
 Identities = 16/80 (20%), Positives = 36/80 (45%), Gaps = 3/80 (3%)

Query: 14 IGNA-FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDA 71
          +  A  + +    +    L  +FSK G + + +  + +  GK+KG+ FV+  +   A   
Sbjct: 11 VNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKI 70

Query: 72 IEKLQGATVE-RMELYVGPF 90
          I+   G  ++ +  L++   
Sbjct: 71 IKSFHGKRLDLKHRLFLYTM 90

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
               + +    + ++ L   FS+ GK+ ++    D A G +KGF 
Sbjct: 13  GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFL 57

>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 = 58.8 bits (143), Expect = 4e-11
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 3  STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQ 61
          S  +   + +     FV  L     +  L + F  FGDI+ + V+  ++ GKS+GYGFV 
Sbjct: 6  SGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 65

Query: 62 YSTPESALDAIE 73
           +   +A  A +
Sbjct: 66 MADRAAAERACK 77

>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 = 46.9 bits (112), Expect = 6e-07
 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
           Q+ ++F  ++V  L    T+  L + F  FG I   V+  D   G S+G+G
Sbjct: 12  QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYG 62

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 58.6 bits (142), Expect = 4e-11
 Identities = 26/80 (32%), Positives = 45/80 (56%), Gaps = 8/80 (10%)

Query: 18 FVKNL----ASTIDNLK--LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDA 71
           V N+       ++ LK  +H+IFSKFG I +      ++GK+KGY F++Y++P  A+DA
Sbjct: 19 VVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN-DFYPEEDGKTKGYIFLEYASPAHAVDA 77

Query: 72 IEKLQGATVE-RMELYVGPF 90
          ++   G  ++ +    V  F
Sbjct: 78 VKNADGYKLDKQHTFRVNLF 97

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 45.9 bits (109), Expect = 1e-06
 Identities = 14/66 (21%), Positives = 33/66 (50%), Gaps = 8/66 (12%)

Query: 88  GPFIRRADRIQEGSSFNNLYVKNL------DDDMTEEILVEKFSEFGKITSLVISKDANG 141
           G  ++   +  +G   + + V N+        +  + ++ + FS+FGKIT+    ++ +G
Sbjct: 1   GDVLKDRPQEADGID-SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DG 58

Query: 142 TSKGFG 147
            +KG+ 
Sbjct: 59  KTKGYI 64

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 58.0 bits (141), Expect = 5e-11
 Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 7/70 (10%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           V N++ T  N +L   F ++G +    +V       K Y FV     E A++AI  L  
Sbjct: 14 HVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRGLDN 66

Query: 78 ATVERMELYV 87
             +   ++V
Sbjct: 67 TEFQGKRMHV 76

>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 = 38.4 bits (90), Expect = 3e-04
 Identities = 12/35 (34%), Positives = 17/35 (48%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD 138
             L+V N+    T + L  KF E+G +    I KD
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45

>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 = 58.1 bits (141), Expect = 5e-11
 Identities = 14/65 (21%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 18 FVKNLASTIDNLKLHQIFSKFG-DIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKL 75
          ++ +L   +D   + + F+  G  + S K++ ++  G   GY FV+++   +A   + K+
Sbjct: 13 WMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKI 72

Query: 76 QGATV 80
           G  +
Sbjct: 73 NGKPL 77

>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 = 46.5 bits (111), Expect = 5e-07
 Identities = 13/63 (20%), Positives = 27/63 (42%), Gaps = 6/63 (9%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFG-KITSLVISKD-ANGTSKGFGSKVLYVARAQKKAER 162
           +L++ +L+  M E  +   F+  G  + S+ I ++   G   G+     +V  A      
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYC----FVEFADLATAE 66

Query: 163 KAI 165
           K +
Sbjct: 67  KCL 69

>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 = 38.8 bits (91), Expect = 3e-04
 Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 4/41 (9%)

Query: 183 NINDEVDEIELKQYFSQCG-TISSVKIMRTDR--GISKGHC 220
           ++   +DE  + + F+  G T+ SVKI+R +R  GI  G+C
Sbjct: 16  DLEPYMDENFISRAFATMGETVMSVKIIR-NRLTGIPAGYC 55

>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 = 58.2 bits (141), Expect = 6e-11
 Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 9/94 (9%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSS--------KVVVSQE-GKSKGYGFVQYSTPESA 68
           +V+ L  ++    L   F + G ++ +         + + +E GK KG   V Y  P +A
Sbjct: 19  YVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTA 78

Query: 69  LDAIEKLQGATVERMELYVGPFIRRADRIQEGSS 102
             A+E   G   +  +L V    ++       SS
Sbjct: 79  KAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSS 112

>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 = 46.2 bits (110), Expect = 1e-06
 Identities = 15/77 (19%), Positives = 28/77 (36%), Gaps = 13/77 (16%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSL---------VISKDANGTSKGFGS 148
            E S  + +YV+ L+D +T + L + F + G +            +      G  KG   
Sbjct: 10  DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA- 68

Query: 149 KVLYVARAQKKAERKAI 165
               V+       + A+
Sbjct: 69  ---TVSYEDPPTAKAAV 82

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 58.1 bits (141), Expect = 7e-11
 Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V NL   I    +  +F K+G I+   + +        + FV++  P  A DA+    G
Sbjct: 26 YVGNLPPDIRTKDIEDVFYKYGAIRD--IDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 83

Query: 78 ATVERMELYV 87
             +   L V
Sbjct: 84 YDYDGYRLRV 93

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 2/42 (4%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           +YV NL  D+  + + + F ++G I  + +          F 
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFA 64

>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 = 56.0 bits (136), Expect = 2e-10
 Identities = 11/59 (18%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE 73
          + +V N+       +L   F   G +    ++  +  G  KG+ ++++S  ES   ++ 
Sbjct: 8  SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 50.2 bits (121), Expect = 3e-08
 Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 5/62 (8%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAERK 163
           ++YV N+D   T E L   F   G +  + I  D   G  KGF     Y+  + K++ R 
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFA----YIEFSDKESVRT 63

Query: 164 AI 165
           ++
Sbjct: 64  SL 65

>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 = 42.9 bits (102), Expect = 9e-06
 Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           N++      EL+ +F  CG+++ V I+  D+  G  KG
Sbjct: 13  NVDYGATAEELEAHFHGCGSVNRVTIL-CDKFSGHPKG 49

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 56.2 bits (136), Expect = 3e-10
 Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 8/64 (12%)

Query: 18 FVKNL-ASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
          F+ NL  + +    +  IFSK+G +    V        KGY FVQYS    A  A+    
Sbjct: 31 FIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGEN 83

Query: 77 GATV 80
          G  +
Sbjct: 84 GRVL 87

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 55.8 bits (135), Expect = 3e-10
 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 4/70 (5%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V NL +     +L + FS +G +++  +         G+ FV++  P  A DA+  L G
Sbjct: 4  YVGNLGTGAGKGELERAFSYYGPLRTVWIA----RNPPGFAFVEFEDPRDAEDAVRGLDG 59

Query: 78 ATVERMELYV 87
            +    + V
Sbjct: 60 KVICGSRVRV 69

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 4/43 (9%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
            +YV NL     +  L   FS +G + ++ I+++      GF 
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFA 40

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 55.6 bits (134), Expect = 6e-10
 Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 5/70 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
            KNL +     ++ + FS+FG +    +      +      V++  P  A  A   L  
Sbjct: 14 LAKNLPAGTLAAEIQETFSRFGSLGRVLL-----PEGGITAIVEFLEPLEARKAFRHLAY 68

Query: 78 ATVERMELYV 87
          +    + LY+
Sbjct: 69 SKFHHVPLYL 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 = 41.0 bits (96), Expect = 7e-05
 Identities = 8/44 (18%), Positives = 15/44 (34%), Gaps = 5/44 (11%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
             +  KNL        + E FS FG +  +++ +          
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITA 49

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 54.6 bits (132), Expect = 6e-10
 Identities = 12/64 (18%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSS-KVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
           V+N+  T+   ++   F  +  I  S  +  +++G   G   V + + + A  A+  L 
Sbjct: 19 KVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLN 78

Query: 77 GATV 80
             +
Sbjct: 79 DRPI 82

>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 = 39.2 bits (92), Expect = 2e-04
 Identities = 7/51 (13%), Positives = 19/51 (37%), Gaps = 1/51 (1%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLV-ISKDANGTSKGFG 147
                   + V+N+   ++ + +++ F  +  I   V +  +  G   G  
Sbjct: 10  SGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

>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 = 55.0 bits (133), Expect = 6e-10
 Identities = 13/78 (16%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 4  TPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSS-KVVVSQEGKSKGYGFVQY 62
          +  + +   G     V+N+  T+   ++   F  +  I  S  +  +++G   G   V +
Sbjct: 5  SSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64

Query: 63 STPESALDAIEKLQGATV 80
           + + A  A+  L    +
Sbjct: 65 ESRDEATAAVIDLNDRPI 82

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 7/49 (14%), Positives = 19/49 (38%), Gaps = 1/49 (2%)

Query: 100 GSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLV-ISKDANGTSKGFG 147
                 + V+N+   ++ + +++ F  +  I   V +  +  G   G  
Sbjct: 12  KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

>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 = 54.3 bits (131), Expect = 7e-10
 Identities = 14/70 (20%), Positives = 26/70 (37%), Gaps = 6/70 (8%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           VKNL    +  ++H +   +       +      ++K   FV     E A +AI+    
Sbjct: 9  LVKNLPQDSNCQEVHDLLKDYD------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQ 62

Query: 78 ATVERMELYV 87
           +    +L V
Sbjct: 63 YSFRGKDLIV 72

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 54.0 bits (131), Expect = 7e-10
 Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 5/69 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE--- 73
          F+  L+       L + F +FG+++   V+      +S+G+GFV +         +    
Sbjct: 4  FIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR 63

Query: 74 -KLQGATVE 81
           +L   T++
Sbjct: 64 HELDSKTID 72

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 42.5 bits (101), Expect = 7e-06
 Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
           +++  L    T+E L E F +FG++   ++ +D     S+GFG
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFG 45

>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 = 54.4 bits (131), Expect = 1e-09
 Identities = 15/79 (18%), Positives = 23/79 (29%), Gaps = 6/79 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           V  L  +     L     + GD+  + V         G G V++   E    A+ KL  
Sbjct: 19 VVSGLPPSGSWQDLKDHMREAGDVCYADVY------RDGTGVVEFVRKEDMTYAVRKLDN 72

Query: 78 ATVERMELYVGPFIRRADR 96
                E        + D 
Sbjct: 73 TKFRSHEGETAYIRVKVDG 91

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 55.1 bits (133), Expect = 1e-09
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 2/76 (2%)

Query: 15  GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE 73
            + +V N+        L   FS  G I    ++  +  G  KGY +++++   S   A+ 
Sbjct: 37  RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96

Query: 74  KLQGATVERMELYVGP 89
            +         + V P
Sbjct: 97  -MDETVFRGRTIKVLP 111

>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 = 49.7 bits (119), Expect = 7e-08
 Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 5/69 (7%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARA 156
           ++     ++YV N+D   T + L   FS  G I  + I  D   G  KG+     Y+  A
Sbjct: 31  KKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYA----YIEFA 86

Query: 157 QKKAERKAI 165
           ++ +   A+
Sbjct: 87  ERNSVDAAV 95

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 41.6 bits (98), Expect = 6e-05
 Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           N++      +L+ +FS CG+I+ + I+  D+  G  KG
Sbjct: 43  NVDYGSTAQDLEAHFSSCGSINRITIL-CDKFSGHPKG 79

>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 = 54.6 bits (132), Expect = 1e-09
 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE 73
          F   LA+ I    L   FS  G ++  +++  +   +SKG  +V++   +S   AI 
Sbjct: 29 FCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 85

>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 = 46.5 bits (111), Expect = 7e-07
 Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 5/61 (8%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARAQKKAERKA 164
           ++   L   +    L + FS  GK+  + I  D N   SKG      YV   + ++   A
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIA----YVEFCEIQSVPLA 83

Query: 165 I 165
           I
Sbjct: 84  I 84

>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 = 42.3 bits (100), Expect = 3e-05
 Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
            +   +   +L+ +FS  G +  V+I+ +DR    SKG
Sbjct: 32  QLAARIRPRDLEDFFSAVGKVRDVRII-SDRNSRRSKG 68

>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 = 53.7 bits (130), Expect = 2e-09
 Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 8/84 (9%)

Query: 3  STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQ 61
          S+ +S ++ + I   FV  +       +L + F KFG +    ++   E  + +G+GF+ 
Sbjct: 2  SSGSSGSKSNKI---FVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFIT 58

Query: 62 YSTPESALDAIE----KLQGATVE 81
          +   +S   A+      + G  VE
Sbjct: 59 FEDEQSVDQAVNMHFHDIMGKKVE 82

>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 = 45.6 bits (109), Expect = 1e-06
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 99  EGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
            GS  N ++V  +  +  E  L E F +FG +T +V+  DA     +GFG
Sbjct: 6   SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFG 55

>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 = 38.7 bits (91), Expect = 3e-04
 Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
            I     E EL++YF + G ++ V ++  D      +G
Sbjct: 17  GIPHNCGETELREYFKKFGVVTEVVMIY-DAEKQRPRG 53

>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 = 53.8 bits (130), Expect = 2e-09
 Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 4/68 (5%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK-- 74
           V  L        L + FS FG++   +V    + G SKG+GFV+++  E+ +  + +  
Sbjct: 19 IVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH 78

Query: 75 -LQGATVE 81
           + G   +
Sbjct: 79 MIDGRWCD 86

>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 = 45.7 bits (109), Expect = 1e-06
 Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 93  RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
            +   +     ++L V  L    TE+ L E FS FG++  + + KD   G SKGFG
Sbjct: 5   SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 3/38 (7%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
            +  +  E +LK+YFS  G +  V++ + D   G SKG
Sbjct: 22  GLPWKTTEQDLKEYFSTFGEVLMVQVKK-DLKTGHSKG 58

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 58.3 bits (140), Expect = 2e-09
 Identities = 50/348 (14%), Positives = 94/348 (27%), Gaps = 99/348 (28%)

Query: 19  VKNLASTIDNLKLHQIFSKFGDIQSSK-----VVVSQEGKSKGYGF-V------QYSTPE 66
              L   +  L+  +     G + S K      V           F +        ++PE
Sbjct: 137 YLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPE 196

Query: 67  SALDAIEKL----QGATVERMELYVGPFIR------RADRIQEGSSFNN-LYVKNLDDDM 115
           + L+ ++KL          R +      +R         R+ +   + N L V  L +  
Sbjct: 197 TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV--LLNVQ 254

Query: 116 TEEILVEKFSEFG-KITSLVISKDANGT----------------SKGFG--------SKV 150
             +     F     KI  L+ ++    T                S             K 
Sbjct: 255 NAKA-WNAF-NLSCKI--LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKY 310

Query: 151 LYVARAQKKAERKAI------LRAQFERMRKERAELYKNIN-DEVDEI-----------E 192
           L         E          + A+  R      + +K++N D++  I           E
Sbjct: 311 LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAE 370

Query: 193 LKQYFSQCGTI--SSVKIMRTDRGI-----SKGHCMAIAQTKRERTSYLRIMYAKQGPGL 245
            ++ F +   +   S  I      +      K   M +   K  + S +     KQ    
Sbjct: 371 YRKMFDRLS-VFPPSAHIPTILLSLIWFDVIKSDVMVVVN-KLHKYSLV----EKQPKES 424

Query: 246 ASTIFPVH----------PTLYQRALQVYQAPDFRHGGMIPNGFSPPP 283
             +I  ++            L++  +  Y  P         +   PP 
Sbjct: 425 TISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFD----SDDLIPPY 468

>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 = 54.9 bits (132), Expect = 2e-09
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           +V NL +  +  +L + F  +G ++S  V         G+ FV++  P  A DA+ +L G
Sbjct: 77  YVGNLGNNGNKTELERAFGYYGPLRSVWVA----RNPPGFAFVEFEDPRDAADAVRELDG 132

Query: 78  ATVERMELYV 87
            T+    + V
Sbjct: 133 RTLCGCRVRV 142

>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 = 42.2 bits (99), Expect = 5e-05
 Identities = 19/114 (16%), Positives = 40/114 (35%), Gaps = 19/114 (16%)

Query: 48  VSQEGKS-KGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFN-- 104
           +   GK+ KG    +     +A    ++         E +      +   + EGS  +  
Sbjct: 5   LILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGE-WTYDDATKTFTVTEGSHHHHH 63

Query: 105 -----------NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
                       +YV NL ++  +  L   F  +G + S+ ++++      GF 
Sbjct: 64  HMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFA 113

>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 = 2e-09
 Identities = 12/67 (17%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV---SQEGKSKGYGFVQYSTPESALDAIEK 74
          F+  +       ++ +  +K  +     +V    + + K++G+ FV+Y +  +A  A  K
Sbjct: 12 FIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRK 71

Query: 75 LQGATVE 81
          L    ++
Sbjct: 72 LMPGRIQ 78

>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 = 41.7 bits (98), Expect = 4e-05
 Identities = 8/50 (16%), Positives = 21/50 (42%), Gaps = 3/50 (6%)

Query: 101 SSFNN--LYVKNLDDDMTEEILVEKFSEFGK-ITSLVISKDANGTSKGFG 147
            S  N  L++  +      E ++E+ ++  + +  +++   A    K  G
Sbjct: 4   GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRG 53

>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 = 53.3 bits (128), Expect = 3e-09
 Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 7/71 (9%)

Query: 18 FVKNLASTI---DNLKLHQIFSKFGDIQSSKVVVSQEGK----SKGYGFVQYSTPESALD 70
          FV  L+  +   + LK  + F KFG I    +  S             +V Y   E AL 
Sbjct: 19 FVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALR 78

Query: 71 AIEKLQGATVE 81
          AI+ +    V+
Sbjct: 79 AIQCVNNVVVD 89

>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 = 38.3 bits (89), Expect = 5e-04
 Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 3/65 (4%)

Query: 104 NNLYVKNLDDDMTEEILV---EKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKA 160
           N ++V  L   + +  ++   E F +FGKI  +VI+   +       S   YV   + + 
Sbjct: 16  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 161 ERKAI 165
             +AI
Sbjct: 76  ALRAI 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 = 53.4 bits (128), Expect = 3e-09
 Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 8/64 (12%)

Query: 14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
          + N     L + +   +L  +  K G + +  +       +K Y F +Y T E +  A  
Sbjct: 30 VANG---GLGNGVSRNQLLPVLEKCGLVDALLMP-----PNKPYSFARYRTTEESKRAYV 81

Query: 74 KLQG 77
           L G
Sbjct: 82 TLNG 85

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 52.1 bits (126), Expect = 3e-09
 Identities = 13/69 (18%), Positives = 29/69 (42%), Gaps = 5/69 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE--- 73
          FV  L+       +   F +FG +  + ++  +   + +G+GFV + + +      E   
Sbjct: 3  FVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHF 62

Query: 74 -KLQGATVE 81
           ++    VE
Sbjct: 63 HEINNKMVE 71

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 43.2 bits (103), Expect = 5e-06
 Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
           ++V  L  + T E +   F +FGK+   ++  D      +GFG
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFG 44

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 37.1 bits (87), Expect = 8e-04
 Identities = 8/37 (21%), Positives = 16/37 (43%), Gaps = 3/37 (8%)

Query: 184 INDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           ++      ++K YF Q G +    +M  D+     +G
Sbjct: 7   LSVNTTVEDVKHYFEQFGKVDDAMLMF-DKTTNRHRG 42

>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 = 52.7 bits (127), Expect = 3e-09
 Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 8/71 (11%)

Query: 18 FVKNL-ASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
          F+ NL    +    L +IFS +G I    +          +GF+Q+  P+S  DAIE   
Sbjct: 26 FIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEXES 78

Query: 77 GATVERMELYV 87
                 +L +
Sbjct: 79 QEMNFGKKLIL 89

>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 = 4e-09
 Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE--- 73
          FV  L+       L   F+KFG++    + +    G+S+G+GF+ +    S    ++   
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKE 74

Query: 74 -KLQGATVE 81
           +L G  ++
Sbjct: 75 HRLDGRVID 83

>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 = 43.3 bits (103), Expect = 6e-06
 Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 95  DRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
           +  +       ++V  L  D +++ L + F++FG++    I  D N G S+GFG
Sbjct: 3   NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFG 56

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

 Score = 52.6 bits (127), Expect = 4e-09
 Identities = 20/80 (25%), Positives = 31/80 (38%), Gaps = 14/80 (17%)

Query: 2  WSTPNSEARLSGIGNAFVKNL-ASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFV 60
                ++RL      F+ NL    +    L +IFS +G I    +          +GF+
Sbjct: 4  MHNIPPKSRL------FIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFI 50

Query: 61 QYSTPESALDAIEKLQGATV 80
          Q+  P+S  DAIE       
Sbjct: 51 QFDNPQSVRDAIECESQEMN 70

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 52.3 bits (126), Expect = 6e-09
 Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 3/66 (4%)

Query: 17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKL 75
          A+V NL        +  IF     I+S ++V  ++  K KG+ +V++   +S  +A+   
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-Y 75

Query: 76 QGATVE 81
           GA + 
Sbjct: 76 DGALLG 81

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 6/61 (9%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKKAERKA 164
            YV NL  +  +  +   F +   I S+ + +D      KGF     YV   +  + ++A
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFC----YVEFDEVDSLKEA 72

Query: 165 I 165
           +
Sbjct: 73  L 73

>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 = 52.5 bits (126), Expect = 6e-09
 Identities = 14/70 (20%), Positives = 21/70 (30%), Gaps = 6/70 (8%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           V  L  +     L     + GD+  + V         G G V++   E    A+ KL  
Sbjct: 20 VVSGLPPSGSWQDLKDHMREAGDVCYADVY------RDGTGVVEFVRKEDMTYAVRKLDN 73

Query: 78 ATVERMELYV 87
                E   
Sbjct: 74 TKFRSHEGET 83

>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 = 52.2 bits (126), Expect = 6e-09
 Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 5/69 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE--- 73
          FV  L  +     L   FS++G++    ++  +   +S+G+GFV++  P      +    
Sbjct: 20 FVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRP 79

Query: 74 -KLQGATVE 81
            L G  ++
Sbjct: 80 HTLDGRNID 88

>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 = 41.8 bits (99), Expect = 3e-05
 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 99  EGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
                  L+V  LD   T+E L   FS++G++   VI KD     S+GFG
Sbjct: 12  GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61

>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 = 52.2 bits (126), Expect = 6e-09
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 4/73 (5%)

Query: 17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE--GKSKGYGFVQYSTPESALDAIEK 74
          AF+ NL   +    + + F     I + ++        + KG+G+ ++   +S L A+  
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 79

Query: 75 LQGATVERMELYV 87
          L   ++    + V
Sbjct: 80 LNEESLGNRRIRV 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 = 39.9 bits (94), Expect = 1e-04
 Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 7/62 (11%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN--GTSKGFGSKVLYVARAQKKAERK 163
            ++ NL  D+TEE + E F     I+++ + ++ +     KGFG    Y       +   
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFG----YAEFEDLDSLLS 76

Query: 164 AI 165
           A+
Sbjct: 77  AL 78

>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 = 51.9 bits (125), Expect = 9e-09
 Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 4/73 (5%)

Query: 17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE--GKSKGYGFVQYSTPESALDAIEK 74
          AF+ NL   +    + + F     I + ++        + KG+G+ ++   +S L A+  
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 75 LQGATVERMELYV 87
          L   ++    + V
Sbjct: 76 LNEESLGNKRIRV 88

>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 = 40.3 bits (95), Expect = 8e-05
 Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 3/44 (6%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT--SKGFG 147
            ++ NL  D+TEE + E F     I+++ + ++ +     KGFG
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFG 60

>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 = 51.5 bits (124), Expect = 1e-08
 Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 5/69 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE--- 73
          F+  L+       L + F +FG+++   V+      +S+G+GFV +         +    
Sbjct: 29 FIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR 88

Query: 74 -KLQGATVE 81
           +L   T++
Sbjct: 89 HELDSKTID 97

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 41.5 bits (98), Expect = 4e-05
 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
             GSS   +++  L    T+E L E F +FG++   ++ +D     S+GFG
Sbjct: 20  HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFG 70

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 50.2 bits (121), Expect = 2e-08
 Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK-- 74
          FV  L+      K+ + F  FG+++S ++ +  +  K +G+ F+ +   E     +EK  
Sbjct: 3  FVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKY 62

Query: 75 --LQGATVE 81
            +  +  E
Sbjct: 63 HNVGLSKCE 71

>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 = 43.3 bits (103), Expect = 5e-06
 Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
           ++V  L  D  EE + E F  FG++ S+ +  D      +GF 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFC 44

>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 = 37.9 bits (89), Expect = 3e-04
 Identities = 7/37 (18%), Positives = 19/37 (51%), Gaps = 3/37 (8%)

Query: 184 INDEVDEIELKQYFSQCGTISSVKIMRTDR--GISKG 218
           ++ +  E ++++YF   G + S+++   D      +G
Sbjct: 7   LSPDTPEEKIREYFGGFGEVESIELPM-DNKTNKRRG 42

>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 = 51.5 bits (124), Expect = 2e-08
 Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 5/69 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE--- 73
          F+  L+       L   + ++G +    V+      +S+G+GFV +S+      A+    
Sbjct: 31 FIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARP 90

Query: 74 -KLQGATVE 81
            + G  VE
Sbjct: 91 HSIDGRVVE 99

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 91  IRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFG 147
           +    + +E   F  L++  L  + TEE L   + ++GK+T  V+ +D     S+GFG
Sbjct: 15  VPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 72

>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 = 53.7 bits (128), Expect = 4e-08
 Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           FV  +       KL + F  +G I+   +V S+  GK +GY F++Y        A +   
Sbjct: 106 FVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHAD 165

Query: 77  GATV 80
           G  +
Sbjct: 166 GKKI 169

>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 = 44.5 bits (104), Expect = 4e-05
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 5/83 (6%)

Query: 66  ESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFS 125
               + IE+ Q      ++++  P     D   +G +F  L+V  ++ D TE  L  +F 
Sbjct: 69  RKRREKIERRQQEVETELKMW-DPH---NDPNAQGDAFKTLFVARVNYDTTESKLRREFE 124

Query: 126 EFGKITSLVISKDA-NGTSKGFG 147
            +G I  + +     +G  +G+ 
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYA 147

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 49.4 bits (118), Expect = 5e-08
 Identities = 12/60 (20%), Positives = 20/60 (33%), Gaps = 4/60 (6%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V NL        L +   + G +             +   F+ Y    +A  A+  LQG
Sbjct: 23 YVGNLPRDARVSDLKRALRELGSVPLRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQG 78

>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 = 50.1 bits (119), Expect = 1e-07
 Identities = 28/96 (29%), Positives = 38/96 (39%), Gaps = 12/96 (12%)

Query: 19  VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
           V+NL   +    LHQIFSKFG +            ++    +QY+ P SA  A   L G 
Sbjct: 51  VENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDG- 106

Query: 79  TVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDD 114
                 +Y      R D     S   +L VK  +D 
Sbjct: 107 ----QNIYNACCTLRIDF----SKLTSLNVKYNNDK 134

>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 = 39.7 bits (92), Expect = 5e-04
 Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 1/83 (1%)

Query: 61  QYSTPESALDAIEKLQGATVERMELYVGP-FIRRADRIQEGSSFNNLYVKNLDDDMTEEI 119
            +    SA  A++ +       + L      +     +   S    + V+NL   +T ++
Sbjct: 3   HHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDV 62

Query: 120 LVEKFSEFGKITSLVISKDANGT 142
           L + FS+FG +  ++     N  
Sbjct: 63  LHQIFSKFGTVLKIITFTKNNQF 85

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 48.3 bits (115), Expect = 2e-07
 Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 5/60 (8%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           V+ L  ++    L +   KFG I    ++       K    V++   +SA + +     
Sbjct: 19 HVRGLCESVVEADLVEALEKFGTICYVMMM-----PFKRQALVEFENIDSAKECVTFAAD 73

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 9/35 (25%), Positives = 18/35 (51%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD 138
             ++V+ L + + E  LVE   +FG I  +++   
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF 50

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

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 10/60 (16%), Positives = 20/60 (33%), Gaps = 5/60 (8%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           ++ L   +    L +   +FG I    V+       K    V++     A +A+     
Sbjct: 25 HIRGLIDGVVEADLVEALQEFGPISYVVVM-----PKKRQALVEFEDVLGACNAVNYAAD 79

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

 Score = 40.9 bits (96), Expect = 6e-05
 Identities = 11/35 (31%), Positives = 19/35 (54%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD 138
             ++++ L D + E  LVE   EFG I+ +V+   
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK 56

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

 Score = 50.6 bits (120), Expect = 2e-07
 Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 14/72 (19%)

Query: 18  FVKNLASTIDNLK---------LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESA 68
           +V  +   +++           +  +FS+ GDI   + V     +SK  GFV++    +A
Sbjct: 138 YVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-----ESKNCGFVKFKYQANA 192

Query: 69  LDAIEKLQGATV 80
             A E +   T+
Sbjct: 193 EFAKEAMSNQTL 204

>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 = 48.2 bits (115), Expect = 2e-07
 Identities = 10/58 (17%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSS-KVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
           + N+  +I  + + Q        +++  V+V   G+  G   VQ+   + A  +   
Sbjct: 19 HITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL 76

>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 = 38.6 bits (90), Expect = 5e-04
 Identities = 16/96 (16%), Positives = 37/96 (38%), Gaps = 6/96 (6%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLV-ISKDANGTSKGFGSKVLYVARA 156
              S+    ++ N+   +T+  +++         + V +  D NG   G       V   
Sbjct: 10  DVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA----LVQFK 65

Query: 157 QKKAERKAILRAQFERMRKERAELYKNINDEVDEIE 192
            +   RK+  R   +++    A ++    +++ EIE
Sbjct: 66  NEDDARKS-ERLHRKKLNGREAFVHVVTLEDMREIE 100

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 47.9 bits (114), Expect = 3e-07
 Identities = 17/95 (17%), Positives = 32/95 (33%), Gaps = 13/95 (13%)

Query: 5   PNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYST 64
           P    R+       +KNL        L  +  +     +            G G +++ +
Sbjct: 25  PAKRYRI------TMKNLPEGCSWQDLKDLARENSLETT--FSSVNTRDFDGTGALEFPS 76

Query: 65  PESALDAIEKLQGATVERMELYV-----GPFIRRA 94
            E  ++A+E+L         + V      P IRR+
Sbjct: 77  EEILVEALERLNNIEFRGSVITVERDDNPPPIRRS 111

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 48.1 bits (114), Expect = 3e-07
 Identities = 28/96 (29%), Positives = 38/96 (39%), Gaps = 12/96 (12%)

Query: 19  VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
           V+NL   +    LHQIFSKFG +            ++    +QY+ P SA  A   L G 
Sbjct: 33  VENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDG- 88

Query: 79  TVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDD 114
                 +Y      R D     S   +L VK  +D 
Sbjct: 89  ----QNIYNACCTLRIDF----SKLTSLNVKYNNDK 116

>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 = 46.4 bits (111), Expect = 4e-07
 Identities = 12/67 (17%), Positives = 28/67 (41%), Gaps = 7/67 (10%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK--- 74
          FV      +   +L + FS++GD+    +        + + FV ++  + A     +   
Sbjct: 9  FVGRCTGDMTEDELREFFSQYGDVMDVFIP----KPFRAFAFVTFADDQIAQSLCGEDLI 64

Query: 75 LQGATVE 81
          ++G +V 
Sbjct: 65 IKGISVH 71

>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 = 43.7 bits (104), Expect = 4e-06
 Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 4/42 (9%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           ++V     DMTE+ L E FS++G +  + I K      + F 
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFA 45

>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 = 39.1 bits (92), Expect = 2e-04
 Identities = 10/32 (31%), Positives = 17/32 (53%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDRG 214
               ++ E EL+++FSQ G +  V I +  R 
Sbjct: 12  RCTGDMTEDELREFFSQYGDVMDVFIPKPFRA 43

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 46.8 bits (111), Expect = 5e-07
 Identities = 10/64 (15%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           ++ L   +   ++  +   FG + +  ++     K K   F++ +T E+A   +     
Sbjct: 20 HIRKLPIDVTEGEVISLGLPFGKVTNLLML-----KGKNQAFIEMNTEEAANTMVNYYTS 74

Query: 78 ATVE 81
           T  
Sbjct: 75 VTPV 78

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 11/35 (31%), Positives = 22/35 (62%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN 140
           ++++ L  D+TE  ++     FGK+T+L++ K  N
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKN 53

>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 = 46.8 bits (111), Expect = 6e-07
 Identities = 9/60 (15%), Positives = 24/60 (40%), Gaps = 5/60 (8%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           ++ L   +   ++  +   FG + +  ++     K K   F++ +T E+A   +     
Sbjct: 35 HIRKLPIDVTEGEVISLGLPFGKVTNLLML-----KGKNQAFIEMNTEEAANTMVNYYTS 89

>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 = 41.4 bits (97), Expect = 6e-05
 Identities = 11/37 (29%), Positives = 22/37 (59%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN 140
             ++++ L  D+TE  ++     FGK+T+L++ K  N
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKN 68

>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 = 46.0 bits (109), Expect = 8e-07
 Identities = 10/64 (15%), Positives = 26/64 (40%), Gaps = 5/64 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           ++ L   +   ++  +   FG + +  ++     K K   F++ +T E+A+  +     
Sbjct: 19 HIRKLPGEVTETEVIALGLPFGKVTNILML-----KGKNQAFLELATEEAAITMVNYYSA 73

Query: 78 ATVE 81
           T  
Sbjct: 74 VTPH 77

>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 = 42.1 bits (99), Expect = 2e-05
 Identities = 10/35 (28%), Positives = 22/35 (62%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN 140
           L+++ L  ++TE  ++     FGK+T++++ K  N
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN 52

>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 = 47.5 bits (112), Expect = 1e-06
 Identities = 12/72 (16%), Positives = 29/72 (40%), Gaps = 1/72 (1%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
           + ++K   +      + +     G + + ++  +     KG  FV + + ESA   +E  
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 170

Query: 76  QGATVERMELYV 87
            G   +  +L +
Sbjct: 171 -GQKYKETDLLI 181

>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 = 41.0 bits (95), Expect = 2e-04
 Identities = 8/45 (17%), Positives = 21/45 (46%)

Query: 103 FNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
             ++Y+K    D T + + E   + G++ ++ + +  +   KG  
Sbjct: 109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSI 153

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 12/67 (17%), Positives = 29/67 (43%), Gaps = 7/67 (10%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK--- 74
          FV      +   +L Q F ++G++    V + +    + + FV ++  + A     +   
Sbjct: 15 FVGRCTEDMTAEELQQFFCQYGEVVD--VFIPK--PFRAFAFVTFADDKVAQSLCGEDLI 70

Query: 75 LQGATVE 81
          ++G +V 
Sbjct: 71 IKGISVH 77

>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 = 43.8 bits (104), Expect = 4e-06
 Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 4/42 (9%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           ++V    +DMT E L + F ++G++  + I K      + F 
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFA 51

>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 = 38.0 bits (89), Expect = 5e-04
 Identities = 9/32 (28%), Positives = 16/32 (50%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDRG 214
              +++   EL+Q+F Q G +  V I +  R 
Sbjct: 18  RCTEDMTAEELQQFFCQYGEVVDVFIPKPFRA 49

>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 = 44.7 bits (106), Expect = 3e-06
 Identities = 8/57 (14%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
           V  +  +     +   F     + +  ++    G++ G G V++ +P+   +A+++
Sbjct: 20 SVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKR 75

>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1 Length = 85

 Score = 44.1 bits (104), Expect = 3e-06
 Identities = 12/35 (34%), Positives = 25/35 (71%)

Query: 347 AAASNENLSSMLVATSPDERKDILGQRLYPLVKKL 381
            A+  +NLS++L   +P+++K++LG+RLY  +  +
Sbjct: 4   LASQGQNLSTVLANLTPEQQKNVLGERLYNHIVAI 38

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 5/85 (5%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           FV      +D+ +L + F  FG + S  VV+ ++     +  V+     +  +A+     
Sbjct: 12  FVSGFPRGVDSAQLSEYFLAFGPVAS--VVMDKD--KGVFAIVEMGDVGAR-EAVLSQSQ 66

Query: 78  ATVERMELYVGPFIRRADRIQEGSS 102
            ++    L V P  ++  +     S
Sbjct: 67  HSLGGHRLRVRPREQKEFQSPASKS 91

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 40.8 bits (96), Expect = 5e-05
 Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 4/43 (9%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           +++V      +    L E F  FG + S+V+ KD       F 
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD----KGVFA 48

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 1/32 (3%)

Query: 183 NINDEVDEIELKQYFSQCGTISSVKIMRTDRG 214
                VD  +L +YF   G ++SV + + D+G
Sbjct: 15  GFPRGVDSAQLSEYFLAFGPVASVVMDK-DKG 45

>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 = 43.9 bits (104), Expect = 5e-06
 Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
           ++ L        ++  FS         + +  +G+  G   V+++T E A+ A+ K
Sbjct: 19 HMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK 74

>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 = 44.0 bits (104), Expect = 5e-06
 Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSS-KVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
           ++ L       ++ Q FS    + +   + V  +G+S G  FVQ+++ E A  A++K
Sbjct: 19 RLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK 76

>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 = 44.1 bits (104), Expect = 7e-06
 Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSS-KVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
          ++K L    +N  +   F K   ++ S  +     GK+ G GFV++        A+ +
Sbjct: 29 YLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR 86

>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 = 42.8 bits (101), Expect = 8e-06
 Identities = 9/62 (14%), Positives = 23/62 (37%), Gaps = 6/62 (9%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSK------VVVSQEGKSKGYGFVQYSTPESALDA 71
          +V N+   I    +   F+    +          V+  Q  + K + F+++ + +    A
Sbjct: 10 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 69

Query: 72 IE 73
          + 
Sbjct: 70 MA 71

>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 = 42.7 bits (101), Expect = 1e-05
 Identities = 9/57 (15%), Positives = 22/57 (38%), Gaps = 1/57 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
           ++     +    + +  +      + ++V +  G   GY FV +S  E    A++ 
Sbjct: 14 KLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKC 69

>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 = 43.3 bits (102), Expect = 2e-05
 Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 17  AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
             ++ L        ++  FS         + +  +G+  G   V+++T E A+ A+ K
Sbjct: 49  VHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSK 105

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 3   STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSS-KVVVSQEGKSKGYGFVQ 61
              ++ A  +  G   ++ L       ++ Q FS    + +   + V  EGK  G  FVQ
Sbjct: 31  GRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQ 90

Query: 62  YSTPESALDAIEK 74
           +++ E A  A+ K
Sbjct: 91  FASQELAEKALGK 103

>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 = 38.7 bits (90), Expect = 5e-04
 Identities = 20/99 (20%), Positives = 44/99 (44%), Gaps = 6/99 (6%)

Query: 93  RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLV-ISKDANGTSKGFGSKVL 151
           R     + ++   + ++ L    T+E +V+ FS    + + + +  D  G   G      
Sbjct: 32  RGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEA---- 87

Query: 152 YVARAQKKAERKAILRAQFERMRKERAELYKNINDEVDE 190
           +V  A ++   KA+ + + ER+     E++K+  +EV  
Sbjct: 88  FVQFASQELAEKALGKHK-ERIGHRYIEVFKSSQEEVRS 125

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 3/60 (5%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE---GKSKGYGFVQYSTPESALDAIEK 74
          FV  L   ID  ++   F +FG +       ++       KGY F+ +    S    I+ 
Sbjct: 12 FVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDA 71

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 42.0 bits (98), Expect = 4e-05
 Identities = 16/96 (16%), Positives = 34/96 (35%), Gaps = 13/96 (13%)

Query: 19  VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
           ++N    I    L+ + +  G +Q   +      ++     V++ +   A  A   L G 
Sbjct: 30  IQNPLYPITVDVLYTVCNPVGKVQRIVIF----KRNGIQAMVEFESVLCAQKAKAALNG- 84

Query: 79  TVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDD 114
                ++Y G    + +     +    L V   D+D
Sbjct: 85  ----ADIYAGCCTLKIEY----ARPTRLNVIRNDND 112

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 40.8 bits (95), Expect = 6e-05
 Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 5/62 (8%)

Query: 19 VKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA 78
          +KNL + ID   L  +  + G + S    ++Q     G    +Y+T E A  A   L   
Sbjct: 12 LKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ-----GIALCKYTTREEANKAQMALNNC 66

Query: 79 TV 80
           +
Sbjct: 67 VL 68

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 41.0 bits (96), Expect = 6e-05
 Identities = 9/45 (20%), Positives = 20/45 (44%)

Query: 33 QIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          ++  K+G+++   V  +      G  +V++   E A  A+  L  
Sbjct: 46 EMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNN 90

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 40.1 bits (93), Expect = 9e-05
 Identities = 12/48 (25%), Positives = 27/48 (56%), Gaps = 4/48 (8%)

Query: 30 KLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           L ++  K+G++ +  +V+S   K  G   V+++T ++A  A++   G
Sbjct: 33 VLLRLLQKYGEVLN--LVLS--SKKPGTAVVEFATVKAAELAVQNEVG 76

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 4/61 (6%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV----SQEGKSKGYGFVQYSTPESALDAIE 73
           ++ L  T    ++   F +   I   K  +      +G+  G  FV ++  E A +A+ 
Sbjct: 27 RMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALR 86

Query: 74 K 74
          K
Sbjct: 87 K 87

>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 = 38.7 bits (90), Expect = 5e-04
 Identities = 9/60 (15%), Positives = 23/60 (38%), Gaps = 3/60 (5%)

Query: 18 FVKNLASTIDNLKLHQIFSKF---GDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
           ++ L  +     +    S       +     + ++EG+  G  FV+  + +    A++K
Sbjct: 21 KLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKK 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	398
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	99.97
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.96
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.96
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.96
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.96
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.96
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.96
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.95
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.94
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.94
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.94
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.93
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.93
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.92
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.92
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.92
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.92
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.9
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.9
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.86
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.83
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.82
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.81
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.81
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.81
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.81
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.81
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.81
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.81
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.8
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.8
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.8
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.8
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.8
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.8
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.8
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.8
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.8
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.8
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.79
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.79
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.79
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.79
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.79
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.79
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.79
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.79
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.79
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.79
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.79
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.79
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.79
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.79
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.78
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.78
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.78
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.78
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.78
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.78
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.78
2div_A	99	TRNA selenocysteine associated protein; structural	99.78
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.78
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.78
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.78
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.78
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.78
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.78
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.77
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.77
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.77
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.77
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.77
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.77
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.77
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.77
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.77
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.77
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.77
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.77
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.77
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.76
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.76
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.76
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.76
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.76
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.76
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.76
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.76
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.76
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.76
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.76
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.76
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.75
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.75
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.75
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.75
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.75
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.75
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.75
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.75
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.74
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.74
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.74
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.74
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.74
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.74
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.74
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.74
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.74
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.74
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.74
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.74
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.74
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.73
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.73
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.73
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.73
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.73
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.73
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.73
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.73
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.73
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.73
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.72
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.72
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.72
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.72
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.72
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.72
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.72
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.72
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.72
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.71
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.71
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.71
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.71
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.71
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.71
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.71
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.71
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.71
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.7
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.7
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.7
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.7
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.7
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.7
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.7
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.7
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.7
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.52
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.69
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.69
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.69
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.69
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.68
1x5p_A	97	Negative elongation factor E; structure genomics,	99.68
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.67
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.67
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.67
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.67
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.66
2dyd_A	85	Poly(A)-binding protein; alpha helical protein, RN	99.66
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.66
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.66
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.66
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.65
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.65
1nmr_A	85	Poly(A)-binding protein; all helical domain, pepti	99.65
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.65
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.64
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.64
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.64
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.64
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.64
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.64
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.63
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.63
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.63
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.62
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.62
1ifw_A	92	Polyadenylate-binding protein, cytoplasmic and nuc	99.62
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.62
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.62
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.61
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.61
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.61
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.6
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.59
3kuj_A	88	Polyadenylate-binding protein 1; protein-protein c	99.59
1g9l_A	144	Polyadenylate-binding protein 1; all-helical domai	99.56
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.56
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.53
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.53
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.53
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.51
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.49
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.49
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.49
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.47
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.44
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.43
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.41
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.39
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.36
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.36
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.34
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.34
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.31
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.31
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.28
1i2t_A	61	HYD protein; four alpha-helical domain, ligase; 1.	99.28
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.26
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.26
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.26
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.24
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.24
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.24
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.24
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.23
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.23
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.22
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.22
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.22
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.22
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.22
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.22
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.21
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.21
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.21
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.2
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.2
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.19
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.19
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.19
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.19
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.19
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.19
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.19
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.19
2div_A	99	TRNA selenocysteine associated protein; structural	99.19
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.19
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.18
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.18
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.18
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.18
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.18
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.18
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.18
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.18
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.17
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.17
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.17
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.17
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.17
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.17
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.16
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.16
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.16
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.16
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.16
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.16
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.16
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.16
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.16
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.15
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.15
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.15
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.15
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.15
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.15
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.15
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.15
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.15
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.14
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.14
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.14
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.14
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.14
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.14
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.13
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.13
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.13
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.13
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.12
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.12
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.12
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.12
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.11
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.11
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.11
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.11
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.11
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.1
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.1
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.09
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.09
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.09
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.08
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.07
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.07
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.07
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.06
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.06
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.03
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.03
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.02
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.01
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.01
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	98.99
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	98.99
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.99
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	98.98
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	98.98
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	98.98
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.97
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	98.97
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	98.97
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	98.97
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.96
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.51
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	98.95
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.94
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.94
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.94
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.93
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	98.93
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	98.93
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	98.92
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.92
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	98.91
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.91
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	98.9
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	98.9
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	98.88
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	98.88
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	98.87
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	98.86
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.86
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.85
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.84
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	98.84
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	98.83
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.83
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	98.83
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	98.82
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	98.82
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.81
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.81
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.79
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.78
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.77
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.76
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	98.75
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.75
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.74
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	98.73
1x5p_A	97	Negative elongation factor E; structure genomics,	98.73
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.71
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	98.69
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.64
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.63
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.63
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.57
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	98.53
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.48
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.27
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.21
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.12
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.11
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	97.7
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.5
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.42
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.41
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.32
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.02
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.94
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	96.85
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.78
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	96.22
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.82
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.71
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	92.99
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	90.96
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	90.83
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	90.82
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	89.8
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	86.67
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	84.67
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	84.56

>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=1.1e-36  Score=289.73  Aligned_cols=218  Identities=17%  Similarity=0.221  Sum_probs=170.6

Q ss_pred             ccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806            9 ARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus         9 ~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .+..+.++|||+|||.++|+++|+++|+.||.|.+|+|..+..+ ++|||||+|.+.++|.+|++ +|+..+.|+.|.|.
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            34567899999999999999999999999999999999999865 58999999999999999996 99999999999998


Q ss_pred             cccccccccccCCCCceEEeeCCCccccHHHHHHHHccCC-CEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHH--
Q 039806           89 PFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFG-KITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI--  165 (398)
Q Consensus        89 ~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG-~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~--  165 (398)
                      ++           ..++|||+|||.++|+++|+++|+.|| .|.++.++++..|.++||+...+.-.....++.....  
T Consensus       114 ~~-----------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~  182 (292)
T 2ghp_A          114 HL-----------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL  182 (292)
T ss_dssp             EC-----------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTC
T ss_pred             EC-----------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            75           468999999999999999999999999 9999999999888899985333322222222111000  


Q ss_pred             -----------------HHHHHHHhhhhhhccccCCCcc-cCHHHHHHHhhcCCCeEEEEEeeCCC--CCccce-EEEec
Q 039806          166 -----------------LRAQFERMRKERAELYKNINDE-VDEIELKQYFSQCGTISSVKIMRTDR--GISKGH-CMAIA  224 (398)
Q Consensus       166 -----------------~~~~~~~~~~~~~~~v~nL~~~-vtee~L~~~F~~fG~I~svki~~d~~--g~skGf-fV~f~  224 (398)
                                       ...........++++|+|||.+ +|+++|+++|++||.|++|+|++|..  |.++|| ||.|.
T Consensus       183 ~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~  262 (292)
T 2ghp_A          183 KIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFE  262 (292)
T ss_dssp             EETTEECEEEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEES
T ss_pred             EeCCcEEEEEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeC
Confidence                             0000012234567889999999 99999999999999999999999886  999999 99999


Q ss_pred             ccHHHHHHHHHHhccc
Q 039806          225 QTKRERTSYLRIMYAK  240 (398)
Q Consensus       225 ~~~ea~~A~l~~q~~q  240 (398)
                      +.++|.+|+ .++...
T Consensus       263 ~~~~A~~A~-~l~g~~  277 (292)
T 2ghp_A          263 NKDSAERAL-QMNRSL  277 (292)
T ss_dssp             SHHHHHHHG-GGTTEE
T ss_pred             CHHHHHHHH-HhcCCE
Confidence            999999999 776544

>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=4e-36  Score=284.65  Aligned_cols=211  Identities=18%  Similarity=0.223  Sum_probs=177.7

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..+++|||+|||.++|+++|+++|+.|| |.+|++     ++++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~-----~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~   93 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP   93 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE-----ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC
Confidence            4568999999999999999999999999 999998     5588999999999999999999999999999999998743


Q ss_pred             ccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCC-CCCccccCCchhhhHHHHHHHHHHHHHHHH-
Q 039806           92 RRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA-NGTSKGFGSKVLYVARAQKKAERKAILRAQ-  169 (398)
Q Consensus        92 ~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~-~g~s~Gf~~~~l~v~~a~~k~~~~~~~~~~-  169 (398)
                                ..++|||+|||.++|+++|+++|+.||.|.++.+++|. +|.++||+...+.-.....++...  +... 
T Consensus        94 ----------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--l~~~~  161 (284)
T 3smz_A           94 ----------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD--LLGKP  161 (284)
T ss_dssp             ----------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH--HTTCE
T ss_pred             ----------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHH--hCCCE
Confidence                      45799999999999999999999999999999999987 589999864443332222222111  1000 


Q ss_pred             ----------------HHHhhhhhhccccCCCccc-CHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHH
Q 039806          170 ----------------FERMRKERAELYKNINDEV-DEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERT  231 (398)
Q Consensus       170 ----------------~~~~~~~~~~~v~nL~~~v-tee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~  231 (398)
                                      .......++++|+|||.++ |+++|+++|++||.|++|+|++|.+|+++|| ||.|.+.++|.+
T Consensus       162 ~~g~~i~v~~a~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~  241 (284)
T 3smz_A          162 LGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEE  241 (284)
T ss_dssp             ETTEECEEEECCGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHH
T ss_pred             eCCcEEEEEECCCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHH
Confidence                            0111234568889999996 9999999999999999999999999999999 999999999999


Q ss_pred             HHHHHhccc
Q 039806          232 SYLRIMYAK  240 (398)
Q Consensus       232 A~l~~q~~q  240 (398)
                      |+..++...
T Consensus       242 A~~~l~g~~  250 (284)
T 3smz_A          242 AQQQADGLS  250 (284)
T ss_dssp             HHHHHTTCE
T ss_pred             HHHHhCCCc
Confidence            999887654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.97  E-value=1.9e-29  Score=229.05  Aligned_cols=131  Identities=24%  Similarity=0.375  Sum_probs=99.8

Q ss_pred             CccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceE
Q 039806            6 NSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERME   84 (398)
Q Consensus         6 d~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~   84 (398)
                      +|+......++|||+|||.++|+++|+++|+.||.|.+|+|++|. +|+++|||||+|.+.++|++||+.+|+..+.|+.
T Consensus         7 ~p~~p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~   86 (213)
T 4f02_A            7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP   86 (213)
T ss_dssp             --------CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcc
Confidence            344444567899999999999999999999999999999999998 8999999999999999999999999999999999


Q ss_pred             eeeecccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeC
Q 039806           85 LYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD  138 (398)
Q Consensus        85 i~V~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d  138 (398)
                      |.+.++.........  ..++|||+||++++|+++|+++|+.||.|++++|++|
T Consensus        87 i~~~~~~~~~~~~~~--~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d  138 (213)
T 4f02_A           87 VRIMWSQRDPSLRKS--GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD  138 (213)
T ss_dssp             CEEEECCCCTHHHHH--CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE
T ss_pred             ccccccccccccccc--ccccceECCcccccHHHHHHHHHhhcCCeEEEEeecc
Confidence            999887654332211  2445666666666666666666665555555555544

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.96  E-value=1.9e-28  Score=218.59  Aligned_cols=152  Identities=20%  Similarity=0.382  Sum_probs=121.8

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|.+||+. ++..+.|+.|.|.
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            34567899999999999999999999999999999999998 899999999999999999999985 9999999999999


Q ss_pred             cccccccccccC--CCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHHH
Q 039806           89 PFIRRADRIQEG--SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAIL  166 (398)
Q Consensus        89 ~~~~~~~~~~~~--~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~~  166 (398)
                      ++..+.......  ...                                                               
T Consensus        88 ~~~~~~~~~~~~~~~~~---------------------------------------------------------------  104 (196)
T 1l3k_A           88 RAVSREDSQRPGAHLTV---------------------------------------------------------------  104 (196)
T ss_dssp             ECCC-----------CC---------------------------------------------------------------
T ss_pred             cccCcccccccccCCCc---------------------------------------------------------------
Confidence            886544321110  012                                                               


Q ss_pred             HHHHHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHH
Q 039806          167 RAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       167 ~~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                                ++++|+|||.++|+++|+++|++||.|++|+|++|. +|.++|| ||+|.+.++|.+|+..
T Consensus       105 ----------~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~  165 (196)
T 1l3k_A          105 ----------KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ  165 (196)
T ss_dssp             ----------SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC
T ss_pred             ----------ceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh
Confidence                      445666666666666667777777777777777765 7788888 9999999999999864

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.96  E-value=1.4e-28  Score=213.82  Aligned_cols=151  Identities=21%  Similarity=0.331  Sum_probs=132.7

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      .+++|||+|||.++|+++|+++|+.||.|.+|++..+. +|.++|||||+|.+.++|++|++.+||..+.|+.|.|.++.
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            46899999999999999999999999999999999997 89999999999999999999999999999999999999875


Q ss_pred             ccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHHHHHHHH
Q 039806           92 RRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFE  171 (398)
Q Consensus        92 ~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~~~~~~~  171 (398)
                      ++...                                                                           
T Consensus        82 ~~~~~---------------------------------------------------------------------------   86 (168)
T 1b7f_A           82 PGGES---------------------------------------------------------------------------   86 (168)
T ss_dssp             CCSST---------------------------------------------------------------------------
T ss_pred             CCccc---------------------------------------------------------------------------
Confidence            43210                                                                           


Q ss_pred             HhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          172 RMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       172 ~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                        ...++++++|||.++++++|+++|++||.|++|+++++. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        87 --~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  155 (168)
T 1b7f_A           87 --IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI  155 (168)
T ss_dssp             --TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             --CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCE
Confidence              113457778888888888888888888888888888887 8999999 999999999999999887654

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.96  E-value=7.6e-28  Score=208.62  Aligned_cols=150  Identities=26%  Similarity=0.404  Sum_probs=124.2

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      +++|||+|||.++|+++|+++|+.||.|.+|++..+. +|.++|||||+|.+.++|++|++.|||..+.|+.|.|.++.+
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            5799999999999999999999999999999999999 999999999999999999999999999999999999998765


Q ss_pred             cccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHHHHHHHHH
Q 039806           93 RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFER  172 (398)
Q Consensus        93 ~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~~~~~~~~  172 (398)
                      .....    ..++                                                                   
T Consensus        82 ~~~~~----~~~~-------------------------------------------------------------------   90 (167)
T 1fxl_A           82 SSASI----RDAN-------------------------------------------------------------------   90 (167)
T ss_dssp             CCGGG----TTCE-------------------------------------------------------------------
T ss_pred             CcccC----CCCc-------------------------------------------------------------------
Confidence            43221    2233                                                                   


Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                            ++++|||.++++++|+++|++||.|.+|++.+|. +|.++|| ||+|.+.++|.+|+..++...
T Consensus        91 ------l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~  154 (167)
T 1fxl_A           91 ------LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK  154 (167)
T ss_dssp             ------EEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             ------EEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCc
Confidence                  5555556666666666666666666666666665 7778888 999999999999998887654

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.96  E-value=3.9e-28  Score=210.25  Aligned_cols=151  Identities=22%  Similarity=0.319  Sum_probs=119.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRA   94 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~~   94 (398)
                      ++|||+|||.++|+++|+++|+.||.|.+|++..+++++++|||||+|.+.++|.+|++.+||..+.|+.|.|.++....
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            58999999999999999999999999999999999999999999999999999999999999999999999999886544


Q ss_pred             cccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHHHHHHHHHhh
Q 039806           95 DRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFERMR  174 (398)
Q Consensus        95 ~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~~~~~~~~~~  174 (398)
                      ...  ....++|||+|||.++|+++|+++|++||                                              
T Consensus        81 ~~~--~~~~~~l~v~nl~~~~t~~~l~~~f~~~G----------------------------------------------  112 (166)
T 3md3_A           81 QSS--SDDTFNLFVGDLNVNVDDETLRNAFKDFP----------------------------------------------  112 (166)
T ss_dssp             CCC--CTTCEEEEEESCCTTCCHHHHHHHHTTST----------------------------------------------
T ss_pred             CCC--CCCCceEEECCCCCCCCHHHHHHHHhccC----------------------------------------------
Confidence            321  11344555555555555555555555555                                              


Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                                                 .|.+|++++|. +|.++|| ||+|.+.++|.+|+..++...
T Consensus       113 ---------------------------~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  153 (166)
T 3md3_A          113 ---------------------------SYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD  153 (166)
T ss_dssp             ---------------------------TEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCE
T ss_pred             ---------------------------CeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc
Confidence                                       55555555543 6677777 999999999999998776543

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.96  E-value=5.7e-28  Score=211.24  Aligned_cols=129  Identities=24%  Similarity=0.374  Sum_probs=107.6

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CC--CceeEEEEEecCHHHHHHHHHHhcCCeec---ceEe
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EG--KSKGYGFVQYSTPESALDAIEKLQGATVE---RMEL   85 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g--~skg~aFV~F~~~e~A~~Ai~~lng~~l~---gk~i   85 (398)
                      +++++|||+|||.++|+++|+++|+.||.|.+|+|+.+. +|  +++|||||+|.+.++|++|++.||+..+.   ++.+
T Consensus         1 s~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~   80 (175)
T 3nmr_A            1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPI   80 (175)
T ss_dssp             CCCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccce
Confidence            467899999999999999999999999999999999999 44  89999999999999999999999998776   5777


Q ss_pred             eeecccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCc
Q 039806           86 YVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTS  143 (398)
Q Consensus        86 ~V~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s  143 (398)
                      .+.++......   ....++|||+|||.++|+++|+++|++||.|.++.+.++.+|.+
T Consensus        81 ~~~~~~~~~~~---~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~  135 (175)
T 3nmr_A           81 QMKPADSEKNN---AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLS  135 (175)
T ss_dssp             EEEECGGGCCS---CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCE
T ss_pred             EEccccccccc---cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCE
Confidence            77776544332   12568899999999999988888888887777776666644333

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

Probab=99.96  E-value=4.9e-28  Score=219.18  Aligned_cols=162  Identities=20%  Similarity=0.316  Sum_probs=136.0

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+|+.+. +|+++|||||+|.+.++|.+|++.||+..|.|+.|.|.++.
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            35789999999999999999999999999999999998 99999999999999999999999999999999999997654


Q ss_pred             ccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHHHHHHHH
Q 039806           92 RRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFE  171 (398)
Q Consensus        92 ~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~~~~~~~  171 (398)
                      .+....                    ..                                              ......
T Consensus       107 ~~~~~~--------------------~~----------------------------------------------~~~~~~  120 (216)
T 2qfj_A          107 NIGQAQ--------------------PI----------------------------------------------IDQLAE  120 (216)
T ss_dssp             CCGGGH--------------------HH----------------------------------------------HHHHHH
T ss_pred             Cccccc--------------------hh----------------------------------------------hhhhhc
Confidence            322110                    00                                              000111


Q ss_pred             HhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          172 RMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       172 ~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .....++++|+||+.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus       121 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~  191 (216)
T 2qfj_A          121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFD  191 (216)
T ss_dssp             HHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCB
T ss_pred             ccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCE
Confidence            23456789999999999999999999999999999999996 8999999 999999999999999887544

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.95  E-value=1.6e-27  Score=207.09  Aligned_cols=143  Identities=20%  Similarity=0.359  Sum_probs=117.5

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ++++|||+|||.++|+++|+++|+.||.|.+|+++.+. +|.++|||||+|.+.++|++|++  ++..++|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            46899999999999999999999999999999999997 89999999999999999999998  4789999999998775


Q ss_pred             ccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHHHHHHHH
Q 039806           92 RRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFE  171 (398)
Q Consensus        92 ~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~~~~~~~  171 (398)
                      ++....    ..                                                                    
T Consensus        80 ~~~~~~----~~--------------------------------------------------------------------   87 (167)
T 2cjk_A           80 PRDEQD----KT--------------------------------------------------------------------   87 (167)
T ss_dssp             CHHHHH----HC--------------------------------------------------------------------
T ss_pred             chhhcc----CC--------------------------------------------------------------------
Confidence            433211    12                                                                    


Q ss_pred             HhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHH
Q 039806          172 RMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       172 ~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                           ++++++|||.++++++|+++|++||.|++|+|++|. +|.++|| ||+|.+.++|.+|+.
T Consensus        88 -----~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~  147 (167)
T 2cjk_A           88 -----GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ  147 (167)
T ss_dssp             -----EEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH
T ss_pred             -----CeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh
Confidence                 245556666666666666666667777777776664 6788888 999999999999975

>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=5e-27  Score=211.90  Aligned_cols=76  Identities=17%  Similarity=0.206  Sum_probs=71.4

Q ss_pred             CcceEEEcCCC-CCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLA-STIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp-~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ++++|||+||| .++|+++|+++|+.||.|.+|+|+++    ++|||||+|.+.++|++||+.|||..|.|+.|+|.++.
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 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK   78 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            56899999999 89999999999999999999999875    47999999999999999999999999999999999886


Q ss_pred             c
Q 039806           92 R   92 (398)
Q Consensus        92 ~   92 (398)
                      .
T Consensus        79 ~   79 (205)
T 3tyt_A           79 Q   79 (205)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.94  E-value=3.9e-26  Score=199.26  Aligned_cols=145  Identities=11%  Similarity=0.240  Sum_probs=122.6

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhcc----C-------CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKF----G-------DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE   81 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~----G-------~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~   81 (398)
                      +.++|||+|||.++|+++|+++|+.|    |       .|.++++.     .++|||||+|.+.++|++|+ .+||..+.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~-----~~~g~afV~f~~~~~A~~A~-~~~~~~~~   76 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-----QDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE-----TTTTEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec-----CCCCEEEEEeCCHHHHHHHH-HhCCcEec
Confidence            46899999999999999999999999    6       77888774     46899999999999999999 79999999


Q ss_pred             ceEeeeecccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHH
Q 039806           82 RMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAE  161 (398)
Q Consensus        82 gk~i~V~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~  161 (398)
                      |+.|.|.++.......    .                                                           
T Consensus        77 g~~i~v~~~~~~~~~~----~-----------------------------------------------------------   93 (172)
T 2g4b_A           77 GQSLKIRRPHDYQPLP----G-----------------------------------------------------------   93 (172)
T ss_dssp             TEECEEECCSSCCCCT----T-----------------------------------------------------------
T ss_pred             CceeeecCCcccCCCC----C-----------------------------------------------------------
Confidence            9999998764322110    1                                                           


Q ss_pred             HHHHHHHHHHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          162 RKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                                    .++++++|||.++++++|+++|++||.|.+|+|.+|. +|+++|| ||+|.+.++|.+|+..++..
T Consensus        94 --------------~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~  159 (172)
T 2g4b_A           94 --------------AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM  159 (172)
T ss_dssp             --------------TTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTC
T ss_pred             --------------CCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCC
Confidence                          4567778888888888888888888888888888886 8999999 99999999999999887754


Q ss_pred             c
Q 039806          240 K  240 (398)
Q Consensus       240 q  240 (398)
                      .
T Consensus       160 ~  160 (172)
T 2g4b_A          160 Q  160 (172)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=99.94  E-value=4.8e-26  Score=213.08  Aligned_cols=141  Identities=23%  Similarity=0.312  Sum_probs=121.9

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ..+..++|||+|||.++|+++|+++|+.||.|.+|++.+     ++|||||+|.+.++|.+|++.+||..|.|+.|.|.+
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~-----~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-----DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            346678999999999999999999999999999999954     579999999999999999999999999999999988


Q ss_pred             ccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHHHHHH
Q 039806           90 FIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQ  169 (398)
Q Consensus        90 ~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~~~~~  169 (398)
                      +..          .                                                                  
T Consensus        93 a~~----------~------------------------------------------------------------------   96 (261)
T 3sde_A           93 ATH----------G------------------------------------------------------------------   96 (261)
T ss_dssp             CCC----------S------------------------------------------------------------------
T ss_pred             ccc----------C------------------------------------------------------------------
Confidence            641          1                                                                  


Q ss_pred             HHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          170 FERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       170 ~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                             ++++|+||+.++|+++|+++|++||.|++|+|++|.+|+++|| ||+|.+.++|.+|+..++.
T Consensus        97 -------~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~  159 (261)
T 3sde_A           97 -------AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGD  159 (261)
T ss_dssp             -------SEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHH
T ss_pred             -------CcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcC
Confidence                   2456666777777777777777777888888888888999999 9999999999999988854

>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=99.93  E-value=6e-25  Score=207.49  Aligned_cols=188  Identities=18%  Similarity=0.215  Sum_probs=132.7

Q ss_pred             CCcceEEEcCCCCCCcHHHHH----HHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           12 SGIGNAFVKNLASTIDNLKLH----QIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~----~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      ..+++|||+|||.++|+++|+    ++|+.||.|.+|+|.+  +|++||||||+|.+.++|++||+.|||..|.|+.|+|
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   84 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   84 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEE
Confidence            457899999999999999966    8999999999999886  7889999999999999999999999999999999999


Q ss_pred             ecccccccccccCC-CC--ceEEeeCCCccccHHHHHHHHc---------------------------------------
Q 039806           88 GPFIRRADRIQEGS-SF--NNLYVKNLDDDMTEEILVEKFS---------------------------------------  125 (398)
Q Consensus        88 ~~~~~~~~~~~~~~-~~--~~lfV~nLp~~~tee~L~~~F~---------------------------------------  125 (398)
                      .++..+........ ..  +...... .....++.......                                       
T Consensus        85 ~~a~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  163 (282)
T 3pgw_A           85 QYAKTDSDIIAKMKGTFVERDRKREK-RKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPY  163 (282)
T ss_pred             EEeccCcchhhhhcCCcccchhhhhh-hhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCC
Confidence            99865543211000 00  0000000 00000000000000                                       


Q ss_pred             ---------------------------cCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHHHHHHHHHhhhhhh
Q 039806          126 ---------------------------EFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFERMRKERA  178 (398)
Q Consensus       126 ---------------------------~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~~~~~~~~~~~~~~  178 (398)
                                                 .-+.+.......+.                                  ...++
T Consensus       164 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------------------------~~~~~  209 (282)
T 3pgw_A          164 MPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSEN----------------------------------PPNHI  209 (282)
T ss_pred             CCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCC----------------------------------CCCCE
Confidence                                       00000111111121                                  01367


Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ++|+||+.++++++|+++|++||.|++|+|+++.    +|| ||+|.+.++|.+|+..++...
T Consensus       210 l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~  268 (282)
T 3pgw_A          210 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGAARDALQGFK  268 (282)
T ss_pred             EEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC----CcEEEEEeCCHHHHHHHHHHcCCcE
Confidence            8999999999999999999999999999999654    567 999999999999998887644

>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=99.93  E-value=5.9e-26  Score=198.94  Aligned_cols=127  Identities=23%  Similarity=0.250  Sum_probs=101.5

Q ss_pred             CCCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecce
Q 039806            4 TPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERM   83 (398)
Q Consensus         4 ~rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk   83 (398)
                      +-.........++|||+|||.++|+++|+++|+.||.|..+.+....+|.++|||||+|.+.++|++|++ |||..+.|+
T Consensus         3 h~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~   81 (175)
T 1fje_B            3 HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGN   81 (175)
T ss_dssp             CCCSSSSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTE
T ss_pred             ccccCCCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCe
Confidence            3344445667889999999999999999999999998776444333488999999999999999999995 999999999


Q ss_pred             EeeeecccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEE
Q 039806           84 ELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSL  133 (398)
Q Consensus        84 ~i~V~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~  133 (398)
                      .|.|.++..+.....  ...++|||+|||.++|+++|+++|++||.|..+
T Consensus        82 ~l~v~~~~~~~~~~~--~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~  129 (175)
T 1fje_B           82 EIKLEKPKGRDSKKV--RAARTLLAKNLSFNITEDELKEVFEDALEIRLV  129 (175)
T ss_dssp             EEEEECCCCSSCSTT--GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE
T ss_pred             EEEEecCCCcccccc--ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe
Confidence            999999876543321  246778888888888888777777777755544

>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=9.6e-25  Score=194.77  Aligned_cols=165  Identities=10%  Similarity=0.204  Sum_probs=124.2

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhcc----C-------CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKF----G-------DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE   81 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~----G-------~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~   81 (398)
                      .+++|||+|||.++|+++|+++|+.|    |       .|.++++     +.++|||||+|.+.++|++|+ .|||..|.
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 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-----NQDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE-----ETTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe-----cCCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            46899999999999999999999999    5       6666666     457899999999999999999 79999999


Q ss_pred             ceEeeeecccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHH
Q 039806           82 RMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAE  161 (398)
Q Consensus        82 gk~i~V~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~  161 (398)
                      |+.|.|.++..+.......... ..   ..+..               ...    ....                     
T Consensus        77 g~~i~v~~~~~~~~~~~~~~~~-~~---~~~~~---------------~~~----~~~~---------------------  112 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGMSENP-SV---YVPGV---------------VST----VVPD---------------------  112 (198)
T ss_dssp             TEEEEEECCCCCCCCCCSSSCS-SC---CCTTS---------------SCC----CSSC---------------------
T ss_pred             CceEEEeCCCCCCCCCCCcCCC-cC---CCCCC---------------ccC----CCCC---------------------
Confidence            9999999887653322111000 00   00000               000    0000                     


Q ss_pred             HHHHHHHHHHHhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          162 RKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                                   ..++++|+|||.++++++|+++|++||.|.+|+|.+|. +|.++|| ||+|.+.++|.+|+..++..
T Consensus       113 -------------~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~  179 (198)
T 2yh0_A          113 -------------SAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM  179 (198)
T ss_dssp             -------------CCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTC
T ss_pred             -------------CCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCC
Confidence                         12467778888888888888888888888888888886 8889999 99999999999999887654


Q ss_pred             c
Q 039806          240 K  240 (398)
Q Consensus       240 q  240 (398)
                      .
T Consensus       180 ~  180 (198)
T 2yh0_A          180 Q  180 (198)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=99.92  E-value=3.9e-25  Score=209.01  Aligned_cols=137  Identities=24%  Similarity=0.286  Sum_probs=125.1

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+++.+. +|.++|||||+|.+.++|.+|++.|||..++|+.|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            45799999999999999999999999999999999998 99999999999999999999999999999999999999998


Q ss_pred             ccccccccCCCCceEEeeCCCccc-cHHHHHHHHccCCCEEEEEEeeCCCCCccccCCch
Q 039806           92 RRADRIQEGSSFNNLYVKNLDDDM-TEEILVEKFSEFGKITSLVISKDANGTSKGFGSKV  150 (398)
Q Consensus        92 ~~~~~~~~~~~~~~lfV~nLp~~~-tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~  150 (398)
                      ++...... ...++|||+|||.++ |+++|+++|+.||.|.++.+++|.+|.++||+...
T Consensus       174 ~~~~~~~~-~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~  232 (284)
T 3smz_A          174 AGQLTPAL-LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLE  232 (284)
T ss_dssp             GGGCCTTT-TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEE
T ss_pred             CCCCCccc-CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEE
Confidence            76544322 367899999999995 99999999999999999999999999999996433

>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=99.92  E-value=3.5e-24  Score=196.45  Aligned_cols=181  Identities=17%  Similarity=0.243  Sum_probs=130.5

Q ss_pred             ccccCCCcceEEEcCCCC-CCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEe
Q 039806            7 SEARLSGIGNAFVKNLAS-TIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMEL   85 (398)
Q Consensus         7 ~~~~~~~~~~lfV~nLp~-~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i   85 (398)
                      |.....++++|||+|||. ++|+++|+++|+.||.|.+|+|..+.    +|||||+|.+.++|++|++.|||..+.|+.|
T Consensus        27 p~~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l  102 (229)
T 2adc_A           27 PGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPI  102 (229)
T ss_dssp             GGGGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBC
T ss_pred             CCCCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            444556789999999999 99999999999999999999998875    7899999999999999999999999999999


Q ss_pred             eeeccccccccccc----CCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHH
Q 039806           86 YVGPFIRRADRIQE----GSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAE  161 (398)
Q Consensus        86 ~V~~~~~~~~~~~~----~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~  161 (398)
                      .|.++..+......    ......-| .+-+..        -+...+...    ..+...                    
T Consensus       103 ~v~~a~~~~~~~~~~~~~~~~~~~~~-~~~~~~--------~~~~~~~~~----~~~~~~--------------------  149 (229)
T 2adc_A          103 RITLSKHQNVQLPREGQEDQGLTKDY-GNSPLH--------RFKKPGSKN----FQNIFP--------------------  149 (229)
T ss_dssp             EEECCSCCCCCCCCSSSSTTTTEEEC-TTCSSC--------CCCSTTSGG----GTTCCC--------------------
T ss_pred             EEEEecCccccCcccccccccccccc-ccCccc--------ccCCccccc----cccCCC--------------------
Confidence            99998754321100    00000000 000000        000000000    000010                    


Q ss_pred             HHHHHHHHHHHhhhhhhccccCCCcccCHHHHHHHhhcCC-CeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          162 RKAILRAQFERMRKERAELYKNINDEVDEIELKQYFSQCG-TISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG-~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                                   ..++++|+||+.++++++|+++|++|| .|++|+|+.+    ++|| ||+|.+.++|.+|+..++..
T Consensus       150 -------------~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~l~g~  212 (229)
T 2adc_A          150 -------------PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNH  212 (229)
T ss_dssp             -------------SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTC
T ss_pred             -------------CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC----CCcEEEEEECCHHHHHHHHHHHCCC
Confidence                         015678889999999999999999999 8999998653    3567 99999999999999988765


Q ss_pred             cc
Q 039806          240 KQ  241 (398)
Q Consensus       240 q~  241 (398)
                      ..
T Consensus       213 ~~  214 (229)
T 2adc_A          213 DL  214 (229)
T ss_dssp             BS
T ss_pred             cc
Confidence            43

>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=99.92  E-value=4.8e-25  Score=180.48  Aligned_cols=106  Identities=44%  Similarity=0.707  Sum_probs=76.8

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ++++|||+|||.++|+++|+++|+.||.|.+|+|+.|. +.+||||||+|.+.++|++||+.|||..|+|+.|.|.++.+
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~-~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC-CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            56799999999999999999999999999999999997 44899999999999999999999999999999999999987


Q ss_pred             cccccccC----CCCceEEeeCCCccccHHH
Q 039806           93 RADRIQEG----SSFNNLYVKNLDDDMTEEI  119 (398)
Q Consensus        93 ~~~~~~~~----~~~~~lfV~nLp~~~tee~  119 (398)
                      +..+....    ...++|||+||++++|++.
T Consensus        83 ~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           83 RKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CCC----------------------------
T ss_pred             ccccccccccccCCCCceEeCCCCCCccccc
Confidence            76654332    2667899999999999874

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

Probab=99.90  E-value=7.9e-24  Score=189.27  Aligned_cols=175  Identities=19%  Similarity=0.265  Sum_probs=121.2

Q ss_pred             CcceEEEcCCCC-CCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLAS-TIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~-~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ++++|||+|||. ++|+++|+++|+.||.|.+|++..+.    +|||||+|.+.++|++|++.|||..+.|+.|.|.++.
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            357999999999 99999999999999999999998864    7899999999999999999999999999999999887


Q ss_pred             ccccccccCC----CCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHHHH
Q 039806           92 RRADRIQEGS----SFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILR  167 (398)
Q Consensus        92 ~~~~~~~~~~----~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~~~  167 (398)
                      .+........    ....-|- +-+.        .-|...+......+.  ....                         
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~-~~~~--------~r~~~~~~~~~~~~~--~~~~-------------------------  121 (198)
T 1qm9_A           78 HQNVQLPREGQEDQGLTKDYG-NSPL--------HRFKKPGSKNFQNIF--PPSA-------------------------  121 (198)
T ss_dssp             CCSCCCSSSSSSSSSCEEESS-CCCT--------TSSSSCCCCCCSCCC--CCCC-------------------------
T ss_pred             CCCcCCCCcCCcccccccccc-CCch--------hhccCccccccccCC--CCcc-------------------------
Confidence            5432111000    0000000 0000        000000000000000  0000                         


Q ss_pred             HHHHHhhhhhhccccCCCcccCHHHHHHHhhcCC-CeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          168 AQFERMRKERAELYKNINDEVDEIELKQYFSQCG-TISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       168 ~~~~~~~~~~~~~v~nL~~~vtee~L~~~F~~fG-~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                                +++|+||+.++++++|+++|++|| .|.+|+|+.+.    +|| ||+|.+.++|.+|+..++....
T Consensus       122 ----------~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~  183 (198)
T 1qm9_A          122 ----------TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDLHNHDL  183 (198)
T ss_dssp             ----------EEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT----SSCEEEECSSHHHHHHHHHHHTSSCC
T ss_pred             ----------EEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC----CcEEEEEeCCHHHHHHHHHHhcCCcc
Confidence                      355677777777777888888888 78888776542    566 9999999999999988876543

>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=99.90  E-value=1.2e-23  Score=199.55  Aligned_cols=141  Identities=16%  Similarity=0.238  Sum_probs=117.6

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccC-CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFG-DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G-~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      .+..++|||+|||.++|+++|+++|+.|| .|.+|++..+..|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.+
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            45678999999999999999999999999 99999999999899999999999999999999999999999999999999


Q ss_pred             cccccccccc---CCCCceEEeeCCCcc-ccHHHHHHHHccCCCEEEEEEeeCCC--CCccccCCchh
Q 039806           90 FIRRADRIQE---GSSFNNLYVKNLDDD-MTEEILVEKFSEFGKITSLVISKDAN--GTSKGFGSKVL  151 (398)
Q Consensus        90 ~~~~~~~~~~---~~~~~~lfV~nLp~~-~tee~L~~~F~~fG~I~~~~i~~d~~--g~s~Gf~~~~l  151 (398)
                      +.++......   ....++|||+|||.+ +|+++|+++|+.||.|.++.+.+|.+  |.++||+...+
T Consensus       194 a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F  261 (292)
T 2ghp_A          194 SNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVF  261 (292)
T ss_dssp             CCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEE
T ss_pred             CCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEe
Confidence            8766544322   236789999999999 99999999999999999999999987  99999964333

>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=99.86  E-value=2.6e-21  Score=153.85  Aligned_cols=81  Identities=30%  Similarity=0.457  Sum_probs=77.0

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+|++|+ +|.++|||||+|.+.++|++||+.|||..|+|+.|+|.++
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            345789999999999999999999999999999999998 8999999999999999999999999999999999999998


Q ss_pred             cc
Q 039806           91 IR   92 (398)
Q Consensus        91 ~~   92 (398)
                      .+
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            54

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

Probab=99.83  E-value=1.5e-20  Score=152.33  Aligned_cols=84  Identities=14%  Similarity=0.257  Sum_probs=79.2

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..++|||+||+.++|+++|+++|++||.|.+|+|+.|. +|+++|||||+|++.++|++||+.|||..|.|+.|.|.++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            46799999999999999999999999999999999999 79999999999999999999999999999999999999987


Q ss_pred             ccccc
Q 039806           92 RRADR   96 (398)
Q Consensus        92 ~~~~~   96 (398)
                      ....+
T Consensus        85 ~~~~~   89 (110)
T 3s8s_A           85 KGQQR   89 (110)
T ss_dssp             TTHHH
T ss_pred             CCcHH
Confidence            65544

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.82  E-value=4.8e-21  Score=149.92  Aligned_cols=83  Identities=12%  Similarity=0.216  Sum_probs=76.4

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccC-CeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHh-cCCeecceEeeeecc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFG-DIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKL-QGATVERMELYVGPF   90 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G-~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~l-ng~~l~gk~i~V~~~   90 (398)
                      +.+|||+|||.++|+++|+++|+.|| .|.+|+|++|+ +|.+||||||+|.+.++|++||+.+ |+..++|++|.|.++
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            46899999999999999999999999 89999999998 8999999999999999999999977 456899999999999


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      .++...
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            876544

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=9.1e-20  Score=145.74  Aligned_cols=91  Identities=23%  Similarity=0.361  Sum_probs=84.3

Q ss_pred             CccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceE
Q 039806            6 NSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERME   84 (398)
Q Consensus         6 d~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~   84 (398)
                      ++..+....++|||+|||.++|+++|+++|+.||.|.+|+|..++ ++.++|||||+|.+.++|++||+.||+..|+|+.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   86 (103)
T 2cq0_A            7 GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLI   86 (103)
T ss_dssp             CSCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcE
Confidence            445556778999999999999999999999999999999999997 9999999999999999999999999999999999


Q ss_pred             eeeecccccccc
Q 039806           85 LYVGPFIRRADR   96 (398)
Q Consensus        85 i~V~~~~~~~~~   96 (398)
                      |.|.++.++..+
T Consensus        87 l~v~~a~~~~~~   98 (103)
T 2cq0_A           87 LNVEWAKPSTNS   98 (103)
T ss_dssp             CEEEESSCCCCS
T ss_pred             EEEEECCCCCCC
Confidence            999999876554

>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=99.81  E-value=5.4e-20  Score=150.10  Aligned_cols=103  Identities=23%  Similarity=0.310  Sum_probs=93.6

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      .+++|||+|||.++|+++|+++|+.||.|.+|++..+  +.++|||||+|.+.++|.+|++.|||..++|+.|.|.++.+
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   84 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNA   84 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecC
Confidence            4679999999999999999999999999999999875  55689999999999999999999999999999999999876


Q ss_pred             cccccccCCCCceEEeeCCCccccHHHHHHHHccCCC
Q 039806           93 RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGK  129 (398)
Q Consensus        93 ~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~  129 (398)
                      +...            ++++...++++|.++|++||.
T Consensus        85 ~~~~------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           85 NRAF------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHHT------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             Chhh------------hhhhHhHhHHHHHHHHHHhCC
Confidence            5533            567888999999999999984

>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=99.81  E-value=1.5e-19  Score=139.68  Aligned_cols=82  Identities=29%  Similarity=0.454  Sum_probs=75.9

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|++..+. +|.++|||||+|.+.++|++|++.|||..++|+.|.|.++
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            356799999999999999999999999999999999997 9999999999999999999999999999999999999998


Q ss_pred             ccc
Q 039806           91 IRR   93 (398)
Q Consensus        91 ~~~   93 (398)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            754

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.81  E-value=3.9e-20  Score=145.74  Aligned_cols=81  Identities=15%  Similarity=0.266  Sum_probs=75.1

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCC--eeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCC----eecceE
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGD--IQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGA----TVERME   84 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~--I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~----~l~gk~   84 (398)
                      ..-.+|||+|||+++|+++|+++|++||.  |.+|++++|+ +|++||||||+|.+.++|++||+.|||.    .|+|++
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            45678999999999999999999999995  6799999998 8999999999999999999999999997    589999


Q ss_pred             eeeecccc
Q 039806           85 LYVGPFIR   92 (398)
Q Consensus        85 i~V~~~~~   92 (398)
                      |.|+++.+
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999763

>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=99.81  E-value=1.9e-19  Score=137.88  Aligned_cols=81  Identities=27%  Similarity=0.470  Sum_probs=76.9

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      +.+|||+|||.++|+++|+++|+.||.|.+|++..+. +|.++|||||+|.+.++|++|++.|||..++|+.|.|.++.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            3689999999999999999999999999999999997 899999999999999999999999999999999999999876


Q ss_pred             cc
Q 039806           93 RA   94 (398)
Q Consensus        93 ~~   94 (398)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.81  E-value=1.5e-19  Score=145.94  Aligned_cols=89  Identities=33%  Similarity=0.527  Sum_probs=82.0

Q ss_pred             CccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceE
Q 039806            6 NSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERME   84 (398)
Q Consensus         6 d~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~   84 (398)
                      .......+.++|||+|||.++|+++|+++|+.||.|.+|+|..+. +|.++|||||+|.+.++|++|++.|||..|+|+.
T Consensus        18 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~   97 (108)
T 2jrs_A           18 NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRP   97 (108)
T ss_dssp             SSCCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSC
T ss_pred             ccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            334445677899999999999999999999999999999999997 8999999999999999999999999999999999


Q ss_pred             eeeecccccc
Q 039806           85 LYVGPFIRRA   94 (398)
Q Consensus        85 i~V~~~~~~~   94 (398)
                      |.|.++.++.
T Consensus        98 l~V~~a~~k~  107 (108)
T 2jrs_A           98 MKVGHVTERT  107 (108)
T ss_dssp             CEEECSCSSC
T ss_pred             EEEEEcccCC
Confidence            9999987664

>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=99.81  E-value=2.4e-19  Score=143.76  Aligned_cols=90  Identities=27%  Similarity=0.323  Sum_probs=83.0

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecc---eE
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVER---ME   84 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g---k~   84 (398)
                      ..+....++|||+|||.++|+++|+++|+.||.|.+|+|..+.+|.++|||||+|.+.++|++||+.|||..+.|   +.
T Consensus         9 ~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~   88 (105)
T 2dnh_A            9 ESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSS   88 (105)
T ss_dssp             CCSCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSC
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCcc
Confidence            334556899999999999999999999999999999999999999999999999999999999999999999998   99


Q ss_pred             eeeeccccccccc
Q 039806           85 LYVGPFIRRADRI   97 (398)
Q Consensus        85 i~V~~~~~~~~~~   97 (398)
                      |.|.++..+.++.
T Consensus        89 l~V~~a~~~~~~~  101 (105)
T 2dnh_A           89 LVVKFADTDKESG  101 (105)
T ss_dssp             CEEEESCSSCCCS
T ss_pred             EEEEECccCcccC
Confidence            9999998776553

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.8e-19  Score=144.67  Aligned_cols=85  Identities=25%  Similarity=0.361  Sum_probs=79.7

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      +....++|||+|||.++|+++|+++|+.||.|.+|+|..|. +|.++|||||+|.+.++|++|++.|||..|+|+.|.|.
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            34567889999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             cccccc
Q 039806           89 PFIRRA   94 (398)
Q Consensus        89 ~~~~~~   94 (398)
                      ++.++.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            987654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=1.9e-19  Score=143.88  Aligned_cols=90  Identities=39%  Similarity=0.638  Sum_probs=83.3

Q ss_pred             ccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806            7 SEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus         7 ~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      ........++|||+|||.++|+++|+++|+.||.|.+|+|..+ +|.++|||||+|.+.++|++||+.||+..|.|+.|.
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2d9p_A            8 DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLY   86 (103)
T ss_dssp             CCCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            3444567889999999999999999999999999999999999 899999999999999999999999999999999999


Q ss_pred             eeccccccccc
Q 039806           87 VGPFIRRADRI   97 (398)
Q Consensus        87 V~~~~~~~~~~   97 (398)
                      |.++.++..+.
T Consensus        87 V~~a~~~~~~~   97 (103)
T 2d9p_A           87 VALAQRKEERQ   97 (103)
T ss_dssp             EEECSSCCCCC
T ss_pred             EEEecccccCC
Confidence            99998876654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.80  E-value=2.4e-19  Score=142.22  Aligned_cols=89  Identities=21%  Similarity=0.281  Sum_probs=82.1

Q ss_pred             CCCCCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeE--------EEEEEcC-CCCceeEEEEEecCHHHHHHHH
Q 039806            2 WSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQS--------SKVVVSQ-EGKSKGYGFVQYSTPESALDAI   72 (398)
Q Consensus         2 ~s~rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~--------vki~~d~-~g~skg~aFV~F~~~e~A~~Ai   72 (398)
                      |++..+.......++|||+|||.++|+++|+++|+.||.|.+        |+|..|+ +|+++|||||+|.+.++|++|+
T Consensus         1 ~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai   80 (99)
T 2la6_A            1 MGHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAI   80 (99)
T ss_dssp             CCSSCSCCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHH
Confidence            455555666677899999999999999999999999999999        9999997 8999999999999999999999


Q ss_pred             HHhcCCeecceEeeeecc
Q 039806           73 EKLQGATVERMELYVGPF   90 (398)
Q Consensus        73 ~~lng~~l~gk~i~V~~~   90 (398)
                      +.|||..|.|+.|.|.++
T Consensus        81 ~~l~g~~~~g~~l~V~~A   98 (99)
T 2la6_A           81 DWFDGKEFSGNPIKVSFA   98 (99)
T ss_dssp             HHHTTCBSSSSBCEEEEC
T ss_pred             HHhCCCEeCCcEEEEEec
Confidence            999999999999999876

>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=99.80  E-value=2.7e-19  Score=145.99  Aligned_cols=88  Identities=30%  Similarity=0.427  Sum_probs=81.8

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|..+. ++.++|||||+|.+.++|++||+.||+..|+|+.|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456899999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             ccccccccc
Q 039806           89 PFIRRADRI   97 (398)
Q Consensus        89 ~~~~~~~~~   97 (398)
                      ++.++..+.
T Consensus       101 ~a~~~~~~~  109 (115)
T 2cpz_A          101 LKRSKNDSK  109 (115)
T ss_dssp             CCCCSCCCC
T ss_pred             EcCCCCcCC
Confidence            998776543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=3.4e-19  Score=141.57  Aligned_cols=84  Identities=21%  Similarity=0.353  Sum_probs=79.5

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+|..+.+|+++|||||+|.+.++|++|++.||+..|+|+.|.|.++.
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            45689999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cccc
Q 039806           92 RRAD   95 (398)
Q Consensus        92 ~~~~   95 (398)
                      ++..
T Consensus        95 ~~~~   98 (100)
T 2do4_A           95 SGPS   98 (100)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            6653

>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=99.80  E-value=5.6e-20  Score=143.37  Aligned_cols=81  Identities=20%  Similarity=0.267  Sum_probs=71.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccC--CeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFG--DIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G--~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      .+|||+|||.++|+++|+++|+.||  .|.+|+|+.|+ +|+++|||||+|.+.++|++||+.|||..|+|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999998 99999999999999999999999999999999999999987


Q ss_pred             cccc
Q 039806           92 RRAD   95 (398)
Q Consensus        92 ~~~~   95 (398)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3.7e-19  Score=139.84  Aligned_cols=84  Identities=24%  Similarity=0.324  Sum_probs=78.5

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      .......++|||+|||.++|+++|+++|+.||.|.+|++..+. ++.++|||||+|.+.++|++|++.|||..|+|+.|.
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (95)
T 2cqc_A            9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   88 (95)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3345567899999999999999999999999999999999998 799999999999999999999999999999999999


Q ss_pred             eeccc
Q 039806           87 VGPFI   91 (398)
Q Consensus        87 V~~~~   91 (398)
                      |.++.
T Consensus        89 v~~a~   93 (95)
T 2cqc_A           89 VSGPS   93 (95)
T ss_dssp             EECCS
T ss_pred             EEecC
Confidence            99875

>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=99.80  E-value=1.7e-19  Score=142.97  Aligned_cols=86  Identities=29%  Similarity=0.478  Sum_probs=81.3

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ..+.++|||+|||.++|+++|+++|+.||.|.+|+|..+. ++.++|||||+|.+.++|++||+.|||..|.|+.|.|.+
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            3567899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      +.++..+
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9877655

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.80  E-value=4.7e-19  Score=144.48  Aligned_cols=87  Identities=29%  Similarity=0.428  Sum_probs=81.9

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|..+. ++.++|||||+|.+.++|++||+.|||..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45677899999999999999999999999999999999997 99999999999999999999999999999999999999


Q ss_pred             cccccccc
Q 039806           89 PFIRRADR   96 (398)
Q Consensus        89 ~~~~~~~~   96 (398)
                      ++.++..+
T Consensus        91 ~a~~~~~~   98 (115)
T 2dgo_A           91 WATRKPPA   98 (115)
T ss_dssp             ESSCCCCC
T ss_pred             EccCCCCC
Confidence            99877654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=1.6e-19  Score=144.31  Aligned_cols=89  Identities=21%  Similarity=0.318  Sum_probs=82.0

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      .....+.++|||+|||.++|+++|+++|+.||.|.+|+|..+. ++.++|||||+|.+.++|++||+.|||..|+|+.|.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A            7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             SSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            3445667899999999999999999999999999999999998 799999999999999999999999999999999999


Q ss_pred             eecccccccc
Q 039806           87 VGPFIRRADR   96 (398)
Q Consensus        87 V~~~~~~~~~   96 (398)
                      |.++..+..+
T Consensus        87 V~~a~~~~~~   96 (103)
T 2dnm_A           87 VQVARYGRRD   96 (103)
T ss_dssp             EEECSSCCSC
T ss_pred             EEECCcCCCC
Confidence            9999865544

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=2.4e-19  Score=140.95  Aligned_cols=85  Identities=34%  Similarity=0.550  Sum_probs=80.4

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      +..++|||+|||.++|+++|+++|+.||.|.+|++..+. +++++|||||+|.+.++|++|++.||+..|+|+.|+|.++
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            457899999999999999999999999999999999998 8999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      ..+..+
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            877655

>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=99.79  E-value=4.5e-19  Score=139.39  Aligned_cols=81  Identities=27%  Similarity=0.377  Sum_probs=77.0

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+|..+.+|.++|||||+|.+.++|++|++.||+..|+|+.|.|.++
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             c
Q 039806           91 I   91 (398)
Q Consensus        91 ~   91 (398)
                      .
T Consensus        93 ~   93 (95)
T 2ywk_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.79  E-value=2.7e-19  Score=143.44  Aligned_cols=89  Identities=18%  Similarity=0.286  Sum_probs=82.5

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      .......++|||+|||.++|+++|+++|+.||.|.+|+|..+. ++.++|||||+|.+.++|++||+.||+..|+|+.|.
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            3445667899999999999999999999999999999999998 999999999999999999999999999999999999


Q ss_pred             eecccccccc
Q 039806           87 VGPFIRRADR   96 (398)
Q Consensus        87 V~~~~~~~~~   96 (398)
                      |.++.++..+
T Consensus        89 v~~a~~~~~~   98 (105)
T 1x5u_A           89 VNKASAHNKN   98 (105)
T ss_dssp             EEETTTTSCC
T ss_pred             EEECCCCCcC
Confidence            9999876554

>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=99.79  E-value=3.4e-19  Score=144.16  Aligned_cols=86  Identities=26%  Similarity=0.381  Sum_probs=80.5

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      +....++|||+|||.++|+++|+++|+.||.|.+|+|..+. +|.++|||||+|.+.++|.+||+.|||..|+|+.|.|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999997 89999999999999999999999999999999999999


Q ss_pred             ccccccc
Q 039806           89 PFIRRAD   95 (398)
Q Consensus        89 ~~~~~~~   95 (398)
                      ++.++..
T Consensus       102 ~a~~~~~  108 (110)
T 1oo0_B          102 WCFVKGP  108 (110)
T ss_dssp             ESEESSC
T ss_pred             EcccCCC
Confidence            9887654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=2.1e-19  Score=143.25  Aligned_cols=91  Identities=23%  Similarity=0.333  Sum_probs=83.1

Q ss_pred             ccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEe
Q 039806            7 SEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMEL   85 (398)
Q Consensus         7 ~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i   85 (398)
                      ++......++|||+|||.++|+++|+++|+.||.|.+|+|+.|. ++.++|||||+|.+.++|++||+.||+..|+|+.|
T Consensus         5 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   84 (102)
T 2cqb_A            5 SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI   84 (102)
T ss_dssp             SSCSCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEE
T ss_pred             cCCcCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            34445677899999999999999999999999999999999997 89999999999999999999999999999999999


Q ss_pred             eeeccccccccc
Q 039806           86 YVGPFIRRADRI   97 (398)
Q Consensus        86 ~V~~~~~~~~~~   97 (398)
                      .|.++.++..+.
T Consensus        85 ~V~~a~~~~~~~   96 (102)
T 2cqb_A           85 RVNLAKPMRIKE   96 (102)
T ss_dssp             EEEECCCCCCCC
T ss_pred             EEEeCCCCCCCC
Confidence            999998766543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=1.8e-19  Score=142.04  Aligned_cols=85  Identities=29%  Similarity=0.499  Sum_probs=80.4

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEE-EEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSS-KVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~v-ki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ++.++|||+|||.++|+++|+++|+.||.|.+| +|+.|+ +|.++|||||+|.+.++|++|++.||+..|+|+.|.|.+
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            567899999999999999999999999999999 999996 999999999999999999999999999999999999999


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      +.++..+
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9876654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=3.6e-19  Score=141.20  Aligned_cols=85  Identities=18%  Similarity=0.338  Sum_probs=79.6

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+|+.|. ++.++|||||+|.+.++|++||+ +|+..|+|+.|.|.+
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            3456899999999999999999999999999999999998 89999999999999999999998 999999999999999


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      +.++..+
T Consensus        86 a~~~~~~   92 (99)
T 2dgs_A           86 AEPRDSK   92 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCCccc
Confidence            9876654

>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=99.79  E-value=3.6e-19  Score=136.91  Aligned_cols=79  Identities=25%  Similarity=0.422  Sum_probs=75.7

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|++..|. ++.++|||||+|.+.++|++|++.|||..++|+.|.|.++
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            467899999999999999999999999999999999996 9999999999999999999999999999999999999876

>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=99.79  E-value=4.9e-19  Score=143.31  Aligned_cols=90  Identities=23%  Similarity=0.412  Sum_probs=82.8

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhc------CCee
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQ------GATV   80 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~ln------g~~l   80 (398)
                      .......++|||+|||.++|+++|+++|+.||.|.+|+|..|. +|.++|||||+|.+.++|++||+.+|      +..|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~   88 (111)
T 1x4h_A            9 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL   88 (111)
T ss_dssp             CCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES
T ss_pred             CCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEE
Confidence            3345567899999999999999999999999999999999998 89999999999999999999999999      9999


Q ss_pred             cceEeeeeccccccccc
Q 039806           81 ERMELYVGPFIRRADRI   97 (398)
Q Consensus        81 ~gk~i~V~~~~~~~~~~   97 (398)
                      +|+.|.|.++.++..+.
T Consensus        89 ~g~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           89 DGRQLKVDLAVTRDEAA  105 (111)
T ss_dssp             SSCEEEEECCCCCCCCC
T ss_pred             cCEEEEEEECCCCccCC
Confidence            99999999998776553

>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=99.79  E-value=4e-19  Score=140.13  Aligned_cols=83  Identities=19%  Similarity=0.315  Sum_probs=78.4

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      +++|||+|||.++|+++|+++|+.||.|.+|+|..+. +|.++|||||+|.+.++|++|++.|||..++|+.|.|.++.+
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            5799999999999999999999999999999999998 899999999999999999999999999999999999999887


Q ss_pred             cccc
Q 039806           93 RADR   96 (398)
Q Consensus        93 ~~~~   96 (398)
                      +...
T Consensus        82 ~~~~   85 (96)
T 2x1f_A           82 SDIS   85 (96)
T ss_dssp             SSGG
T ss_pred             CCCC
Confidence            6543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.79  E-value=1.5e-19  Score=143.92  Aligned_cols=94  Identities=21%  Similarity=0.349  Sum_probs=83.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRA   94 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~~   94 (398)
                      ++|||+|||.++|+++|+++|+.||.|.+|++..+    ++|||||+|.+.++|++|++.|||..++|+.|.|.++.++.
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            48999999999999999999999999999999887    78999999999999999999999999999999999998766


Q ss_pred             cccccCC------CCceEEeeCCC
Q 039806           95 DRIQEGS------SFNNLYVKNLD  112 (398)
Q Consensus        95 ~~~~~~~------~~~~lfV~nLp  112 (398)
                      .+.....      ...+|||+||+
T Consensus        77 ~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           77 RRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             CcccCCCCCccccCCCceecCCCC
Confidence            4422211      36789999986

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.79  E-value=8.1e-20  Score=145.46  Aligned_cols=83  Identities=19%  Similarity=0.313  Sum_probs=78.3

Q ss_pred             CcceEEEcCCCC------CCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecc-eE
Q 039806           13 GIGNAFVKNLAS------TIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVER-ME   84 (398)
Q Consensus        13 ~~~~lfV~nLp~------~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g-k~   84 (398)
                      .+++|||+|||.      ++++++|+++|+.||.|.+|+|+.|+ +|++||||||+|.+.++|++||+.|||..|.| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            467999999999      99999999999999999999999999 79999999999999999999999999999999 99


Q ss_pred             eeeeccccccc
Q 039806           85 LYVGPFIRRAD   95 (398)
Q Consensus        85 i~V~~~~~~~~   95 (398)
                      |.|.++.++..
T Consensus        85 l~V~~a~~~~~   95 (100)
T 3ns6_A           85 LFLYTMKDVER   95 (100)
T ss_dssp             CEEEESHHHHH
T ss_pred             EEEEECchhhh
Confidence            99999876543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=4.2e-19  Score=139.31  Aligned_cols=82  Identities=21%  Similarity=0.324  Sum_probs=77.1

Q ss_pred             ccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806            9 ARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus         9 ~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      ......++|||+|||.++|+++|+++|+.||.|.+|++..+. ++.++|||||+|.+.++|++|++.||+..|+|+.|.|
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            344567899999999999999999999999999999999998 7999999999999999999999999999999999999


Q ss_pred             ecc
Q 039806           88 GPF   90 (398)
Q Consensus        88 ~~~   90 (398)
                      .++
T Consensus        91 ~~a   93 (94)
T 2e5h_A           91 SIA   93 (94)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            886

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3.1e-19  Score=142.29  Aligned_cols=87  Identities=30%  Similarity=0.504  Sum_probs=81.3

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|..+. ++.++|||||+|.+.++|++||+.||+..|+|+.|+|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             cccccccc
Q 039806           89 PFIRRADR   96 (398)
Q Consensus        89 ~~~~~~~~   96 (398)
                      ++.++...
T Consensus        88 ~a~~~~~~   95 (102)
T 1x5s_A           88 QAGKSSDN   95 (102)
T ss_dssp             EEECCCCC
T ss_pred             ECCCCCCC
Confidence            99876654

>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=99.79  E-value=1.2e-18  Score=139.18  Aligned_cols=88  Identities=30%  Similarity=0.453  Sum_probs=80.5

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      .......++|||+|||.++|+++|+++|+.||.|.+|+|..+..+ ++|||||+|.+.++|++||+.||+..|+|+.|.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            334566789999999999999999999999999999999998754 8999999999999999999999999999999999


Q ss_pred             ecccccccc
Q 039806           88 GPFIRRADR   96 (398)
Q Consensus        88 ~~~~~~~~~   96 (398)
                      .++.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cq3_A           88 NNATARVMT   96 (103)
T ss_dssp             EECCSSCCC
T ss_pred             EEcccCCCC
Confidence            999876654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=1.1e-18  Score=141.91  Aligned_cols=86  Identities=24%  Similarity=0.298  Sum_probs=79.9

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+|..+.+|+++|||||+|.+.++|++||+.||+..|+|+.|.|.++
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            44578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      .....+
T Consensus        92 ~~~~~~   97 (114)
T 2do0_A           92 ERALPK   97 (114)
T ss_dssp             SCCCCC
T ss_pred             ccCCCC
Confidence            754433

>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=99.78  E-value=3.9e-19  Score=142.73  Aligned_cols=91  Identities=24%  Similarity=0.344  Sum_probs=82.7

Q ss_pred             ccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCee---cc
Q 039806            7 SEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATV---ER   82 (398)
Q Consensus         7 ~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l---~g   82 (398)
                      +.......++|||+|||.++|+++|+++|+.||.|.+|+|+.|. +|+++|||||+|.+.++|++||+.||+..+   .|
T Consensus         6 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g   85 (106)
T 2dgp_A            6 SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMN   85 (106)
T ss_dssp             CSCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCS
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCC
Confidence            33445677899999999999999999999999999999999998 899999999999999999999999999987   89


Q ss_pred             eEeeeeccccccccc
Q 039806           83 MELYVGPFIRRADRI   97 (398)
Q Consensus        83 k~i~V~~~~~~~~~~   97 (398)
                      +.|.|.++..+..+.
T Consensus        86 ~~l~v~~a~~~~~~~  100 (106)
T 2dgp_A           86 RPIQVKPADSESRGG  100 (106)
T ss_dssp             SCCEEEECCCCSCCC
T ss_pred             ceEEEEECCcccccC
Confidence            999999998766543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=9.1e-19  Score=140.38  Aligned_cols=86  Identities=21%  Similarity=0.432  Sum_probs=80.5

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      ...+.++|||+|||.++|+++|+++|+.||.|.+|+|..++ ++.++|||||+|.+.++|++||+. |+..|+|+.|.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            34567899999999999999999999999999999999997 899999999999999999999998 9999999999999


Q ss_pred             cccccccc
Q 039806           89 PFIRRADR   96 (398)
Q Consensus        89 ~~~~~~~~   96 (398)
                      ++.++...
T Consensus        91 ~a~~~~~~   98 (105)
T 2dh8_A           91 PCTPRGMQ   98 (105)
T ss_dssp             CSCCSSCC
T ss_pred             EccCCCCC
Confidence            99877654

>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=99.78  E-value=8.9e-19  Score=135.42  Aligned_cols=82  Identities=18%  Similarity=0.394  Sum_probs=74.8

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      +......++|||+|||.++|+++|+++|+.||.|.+|+++.+. +|+++|||||+|.+.++|++|++ +++..|+|+.|.
T Consensus         5 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~   83 (87)
T 3s7r_A            5 SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVID   83 (87)
T ss_dssp             --CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEE
Confidence            3445677899999999999999999999999999999999998 89999999999999999999996 588999999999


Q ss_pred             eecc
Q 039806           87 VGPF   90 (398)
Q Consensus        87 V~~~   90 (398)
                      |.++
T Consensus        84 v~~A   87 (87)
T 3s7r_A           84 PKKA   87 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9864

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=6.9e-19  Score=141.46  Aligned_cols=87  Identities=18%  Similarity=0.370  Sum_probs=81.2

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEc-C-CCCceeEEEEEecCHHHHHHHHHHh-cCCeecceEee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS-Q-EGKSKGYGFVQYSTPESALDAIEKL-QGATVERMELY   86 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d-~-~g~skg~aFV~F~~~e~A~~Ai~~l-ng~~l~gk~i~   86 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|..+ . ++.++|||||+|.+.++|++||+.| |+..|.|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            4556789999999999999999999999999999999999 4 9999999999999999999999999 99999999999


Q ss_pred             eecccccccc
Q 039806           87 VGPFIRRADR   96 (398)
Q Consensus        87 V~~~~~~~~~   96 (398)
                      |.++.++...
T Consensus        91 v~~a~~~~~~  100 (107)
T 2cph_A           91 LEWADSEVTV  100 (107)
T ss_dssp             EEECCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999876654

>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=99.78  E-value=1.3e-18  Score=139.00  Aligned_cols=87  Identities=20%  Similarity=0.307  Sum_probs=79.7

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|..|..+ ++|||||+|.+.++|++||+.||+..|.|+.|.|.+
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            4556789999999999999999999999999999999998743 789999999999999999999999999999999999


Q ss_pred             cccccccc
Q 039806           90 FIRRADRI   97 (398)
Q Consensus        90 ~~~~~~~~   97 (398)
                      +..+..+.
T Consensus        90 a~~~~~~~   97 (103)
T 2cqi_A           90 ATTPSSQK   97 (103)
T ss_dssp             CCCTTCCC
T ss_pred             CCCCcccc
Confidence            98766553

>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=99.78  E-value=4.6e-19  Score=147.76  Aligned_cols=85  Identities=24%  Similarity=0.334  Sum_probs=79.8

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|+.|. +|+++|||||+|.+.++|++||+.|||..|+|+.|.|.
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            34567899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             cccccc
Q 039806           89 PFIRRA   94 (398)
Q Consensus        89 ~~~~~~   94 (398)
                      ++.++.
T Consensus       122 ~a~~~~  127 (129)
T 2kxn_B          122 FSITKR  127 (129)
T ss_dssp             CCSSSS
T ss_pred             EecCCC
Confidence            987654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=6.1e-19  Score=139.79  Aligned_cols=85  Identities=16%  Similarity=0.319  Sum_probs=79.2

Q ss_pred             ccCCCcceEEEcCCCCCCcHHHHHHHHhccCCee-EEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceE--
Q 039806            9 ARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQ-SSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERME--   84 (398)
Q Consensus         9 ~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~-~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~--   84 (398)
                      ......++|||+|||.++|+++|+++|+.||.|. +|+|+.|+ +|.++|||||+|.+.++|++|++.|||..|.|+.  
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~   83 (99)
T 2div_A            4 GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPA   83 (99)
T ss_dssp             CCCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSC
T ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcc
Confidence            3445678999999999999999999999999999 99999998 9999999999999999999999999999999999  


Q ss_pred             --eeeeccccc
Q 039806           85 --LYVGPFIRR   93 (398)
Q Consensus        85 --i~V~~~~~~   93 (398)
                        |+|.++...
T Consensus        84 ~~l~v~~a~~~   94 (99)
T 2div_A           84 KRFKLNYATYS   94 (99)
T ss_dssp             EECCEEETTCC
T ss_pred             eeEEEeecCCC
Confidence              999888654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.78  E-value=8.4e-19  Score=147.91  Aligned_cols=88  Identities=31%  Similarity=0.516  Sum_probs=81.9

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|+.++ +|+++|||||+|.+.++|++||+.|||..|+|+.|+|.
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            34556899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             ccccccccc
Q 039806           89 PFIRRADRI   97 (398)
Q Consensus        89 ~~~~~~~~~   97 (398)
                      ++..+..+.
T Consensus       118 ~a~~~~~~~  126 (139)
T 1u6f_A          118 LAASGHQRP  126 (139)
T ss_dssp             ESSCCCCCC
T ss_pred             ECCCCCCCC
Confidence            998776553

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=7.9e-19  Score=140.44  Aligned_cols=86  Identities=30%  Similarity=0.468  Sum_probs=80.6

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhc-cCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCe-ecceEeeeec
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSK-FGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGAT-VERMELYVGP   89 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~-~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~-l~gk~i~V~~   89 (398)
                      ...++|||+|||.++|+++|+++|+. ||.|.+|+|+.|.+|.++|||||+|.+.++|++||+.||+.. |+|+.|.|.+
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~   86 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSV   86 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCB
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEE
Confidence            45679999999999999999999999 999999999999999999999999999999999999999999 9999999999


Q ss_pred             cccccccc
Q 039806           90 FIRRADRI   97 (398)
Q Consensus        90 ~~~~~~~~   97 (398)
                      +.++..+.
T Consensus        87 a~~~~~~~   94 (104)
T 2dhg_A           87 AIPKASRV   94 (104)
T ss_dssp             CCCCCSCC
T ss_pred             ccCCCcCC
Confidence            98766553

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=1.3e-18  Score=138.99  Aligned_cols=85  Identities=24%  Similarity=0.305  Sum_probs=79.0

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .....++|||+|||.++|+++|+++|+.|| |.+|+|+.|. +|+++|||||+|.+.++|++|| .||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            345678999999999999999999999997 9999999998 8999999999999999999999 799999999999999


Q ss_pred             cccccccc
Q 039806           89 PFIRRADR   96 (398)
Q Consensus        89 ~~~~~~~~   96 (398)
                      ++..+..+
T Consensus        89 ~a~~~~~~   96 (103)
T 2dng_A           89 IAEGRKQD   96 (103)
T ss_dssp             ECCCCCCC
T ss_pred             EecCCCCC
Confidence            99876554

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=1e-18  Score=138.20  Aligned_cols=85  Identities=38%  Similarity=0.566  Sum_probs=78.7

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCC--C--CceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE--G--KSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~--g--~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      .+.++|||+|||.++|+++|+++|+.||.|.+|+|..+.+  |  .++|||||+|.+.++|++||+.|||..|+|+.|.|
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            4568999999999999999999999999999999999873  4  89999999999999999999999999999999999


Q ss_pred             ecccccccc
Q 039806           88 GPFIRRADR   96 (398)
Q Consensus        88 ~~~~~~~~~   96 (398)
                      .++.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876654

>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=99.78  E-value=6.6e-19  Score=144.05  Aligned_cols=85  Identities=20%  Similarity=0.413  Sum_probs=80.1

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+|..+.+|.++|||||+|.+.++|++||+.|||..|+|+.|.|.++.
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            45679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccccc
Q 039806           92 RRADR   96 (398)
Q Consensus        92 ~~~~~   96 (398)
                      ++...
T Consensus        85 ~~~~~   89 (116)
T 2fy1_A           85 KPSFQ   89 (116)
T ss_dssp             CSSCS
T ss_pred             CCCCC
Confidence            76544

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

Probab=99.78  E-value=1.2e-18  Score=136.16  Aligned_cols=84  Identities=27%  Similarity=0.381  Sum_probs=78.2

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      .++.++|||+|||.++|+++|+++|+.||.|.+|+|..+ +|.++|||||+|.+.++|++|++.||+..|+|+.|.|.++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            356789999999999999999999999999999999985 7899999999999999999999999999999999999998


Q ss_pred             ccccc
Q 039806           91 IRRAD   95 (398)
Q Consensus        91 ~~~~~   95 (398)
                      .+...
T Consensus        84 ~~~~~   88 (92)
T 2dgv_A           84 RNASG   88 (92)
T ss_dssp             SCCSS
T ss_pred             CCCCC
Confidence            76554

>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=99.78  E-value=1.5e-18  Score=139.57  Aligned_cols=81  Identities=20%  Similarity=0.411  Sum_probs=77.1

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+|..+.+|+++|||||+|.+.++|++||+.|||..|.|+.|.|.++
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999886


Q ss_pred             c
Q 039806           91 I   91 (398)
Q Consensus        91 ~   91 (398)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.77  E-value=5.9e-19  Score=136.54  Aligned_cols=82  Identities=21%  Similarity=0.447  Sum_probs=76.2

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCC-ceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGK-SKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~-skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++..+. ++. ++|||||+|.+.++|++|++.|||..++|+.|.|.++
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            45799999999999999999999999999999999988 444 8999999999999999999999999999999999998


Q ss_pred             cccc
Q 039806           91 IRRA   94 (398)
Q Consensus        91 ~~~~   94 (398)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.77  E-value=8.3e-19  Score=140.43  Aligned_cols=87  Identities=18%  Similarity=0.321  Sum_probs=80.1

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-C-CCceeEEEEEecCHHHHHHHHHHhcCCeecceEe
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-E-GKSKGYGFVQYSTPESALDAIEKLQGATVERMEL   85 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~-g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i   85 (398)
                      .......++|||+|||.++|+++|+++|+.|| |.+|+|+.+. + |+++|||||+|.+.++|++|| .||+..|.|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   86 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRI   86 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEE
Confidence            34455678999999999999999999999999 9999999998 5 999999999999999999999 899999999999


Q ss_pred             eeecccccccc
Q 039806           86 YVGPFIRRADR   96 (398)
Q Consensus        86 ~V~~~~~~~~~   96 (398)
                      .|.++..+..+
T Consensus        87 ~V~~a~~~~~~   97 (104)
T 1wi8_A           87 RVDVADQAQDK   97 (104)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99999877654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=4.7e-19  Score=141.77  Aligned_cols=81  Identities=15%  Similarity=0.138  Sum_probs=76.0

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ..++|||+|||.++|+++|.++|+.||.|.+|+|+.|.+|.++|||||+|.+.++|.+||+ +|+..|+|+.|.|.+...
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            4578999999999999999999999999999999999999999999999999999999999 899999999999988765


Q ss_pred             cc
Q 039806           93 RA   94 (398)
Q Consensus        93 ~~   94 (398)
                      ..
T Consensus        89 ~~   90 (103)
T 1s79_A           89 YF   90 (103)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.77  E-value=8.7e-19  Score=150.90  Aligned_cols=83  Identities=23%  Similarity=0.321  Sum_probs=77.5

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccC--CeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFG--DIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G--~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      +.++|||+|||.++|+++|+++|+.||  .|.+|+|+.|+ +|+++|||||+|.+.++|++||+.|||..|+|+.|.|.+
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  99999999998 999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 039806           90 FIRRAD   95 (398)
Q Consensus        90 ~~~~~~   95 (398)
                      +.++..
T Consensus       134 a~~~~~  139 (156)
T 3n9u_C          134 ATRQNL  139 (156)
T ss_dssp             CCHHHH
T ss_pred             cCCCcc
Confidence            876543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=9.9e-19  Score=139.54  Aligned_cols=81  Identities=11%  Similarity=0.148  Sum_probs=73.4

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcC--CeecceEeeee
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG--ATVERMELYVG   88 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng--~~l~gk~i~V~   88 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+|+++     ||||||+|++.++|++||+.+++  ..|.|+.|+|.
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            456789999999999999999999999999999999874     69999999999999999998864  78999999999


Q ss_pred             cccccccc
Q 039806           89 PFIRRADR   96 (398)
Q Consensus        89 ~~~~~~~~   96 (398)
                      ++..+...
T Consensus        88 ~A~~~~~~   95 (105)
T 1sjq_A           88 FSNHKELK   95 (105)
T ss_dssp             CCSSSSCC
T ss_pred             EcCCCCCC
Confidence            99876544

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.2e-18  Score=142.33  Aligned_cols=88  Identities=25%  Similarity=0.378  Sum_probs=80.2

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      .......++|||+|||.++|+++|+++|+.||.|.+|+|+.++ +++++|||||+|.+.++|++||+.+|+ .|.|+.|.
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~   89 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   89 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEE
Confidence            3345567899999999999999999999999999999999998 899999999999999999999999998 89999999


Q ss_pred             eecccccccc
Q 039806           87 VGPFIRRADR   96 (398)
Q Consensus        87 V~~~~~~~~~   96 (398)
                      |.++..+...
T Consensus        90 V~~a~~~~~~   99 (116)
T 2cqd_A           90 VNLAYLGAKP   99 (116)
T ss_dssp             EEESTTTCCC
T ss_pred             EEEcccCCCc
Confidence            9998765433

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.77  E-value=8.8e-19  Score=143.52  Aligned_cols=81  Identities=30%  Similarity=0.422  Sum_probs=76.6

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|..|+ +|+++|||||+|.+.++|++||+.|||..|+|+.|+|.
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            34567899999999999999999999999999999999997 89999999999999999999999999999999999998


Q ss_pred             cc
Q 039806           89 PF   90 (398)
Q Consensus        89 ~~   90 (398)
                      ++
T Consensus       116 ~a  117 (118)
T 2khc_A          116 LK  117 (118)
T ss_dssp             EC
T ss_pred             ec
Confidence            75

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=8e-19  Score=141.93  Aligned_cols=86  Identities=29%  Similarity=0.450  Sum_probs=78.5

Q ss_pred             ccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806            7 SEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus         7 ~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      +.......++|||+|||.++|+++|+++|+.||.|.+|++..|.. .++|||||+|.+.++|++|++.|||..|+|+.|.
T Consensus        22 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  100 (109)
T 2err_A           22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEGRKIE  100 (109)
T ss_dssp             CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECE
T ss_pred             CccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            344456788999999999999999999999999999999999864 4899999999999999999999999999999999


Q ss_pred             eeccccc
Q 039806           87 VGPFIRR   93 (398)
Q Consensus        87 V~~~~~~   93 (398)
                      |.++.++
T Consensus       101 V~~a~~~  107 (109)
T 2err_A          101 VNNATAR  107 (109)
T ss_dssp             EEECCCS
T ss_pred             EEECCCC
Confidence            9998754

>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=99.77  E-value=4.2e-19  Score=142.02  Aligned_cols=84  Identities=31%  Similarity=0.538  Sum_probs=79.3

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++..+. +|.++|||||+|.+.++|++|++.|||..|.|+.|.|.++.
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            35799999999999999999999999999999999997 89999999999999999999999999999999999999988


Q ss_pred             ccccc
Q 039806           92 RRADR   96 (398)
Q Consensus        92 ~~~~~   96 (398)
                      ++..+
T Consensus        87 ~~~~~   91 (104)
T 1p1t_A           87 SEKNK   91 (104)
T ss_dssp             CTTHH
T ss_pred             Cccch
Confidence            76554

>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=99.77  E-value=1.5e-18  Score=134.58  Aligned_cols=80  Identities=18%  Similarity=0.339  Sum_probs=75.8

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      +.++|||+|||.++|+++|+++|+.||.|.+|++..+. +|+++|||||+|.+.++|++|+ .+||..+.|+.|.|.++.
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            35799999999999999999999999999999999998 9999999999999999999999 899999999999999886


Q ss_pred             cc
Q 039806           92 RR   93 (398)
Q Consensus        92 ~~   93 (398)
                      ++
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>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=99.77  E-value=1.2e-18  Score=137.41  Aligned_cols=85  Identities=14%  Similarity=0.207  Sum_probs=77.5

Q ss_pred             ccCCCcceEEEcCCCCCCcHHHHH----HHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceE
Q 039806            9 ARLSGIGNAFVKNLASTIDNLKLH----QIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERME   84 (398)
Q Consensus         9 ~~~~~~~~lfV~nLp~~vte~~L~----~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~   84 (398)
                      ...++.++|||+|||.++|+++|+    ++|+.||.|.+|+|..|..+  +|||||+|.+.++|++||+.|||..|+|+.
T Consensus         4 ~~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~   81 (96)
T 2dgx_A            4 GSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKK   81 (96)
T ss_dssp             CCCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            334567899999999999999999    99999999999999998855  899999999999999999999999999999


Q ss_pred             eeeeccccccc
Q 039806           85 LYVGPFIRRAD   95 (398)
Q Consensus        85 i~V~~~~~~~~   95 (398)
                      |+|.++.++..
T Consensus        82 l~V~~a~~~~~   92 (96)
T 2dgx_A           82 ILVSLATGASG   92 (96)
T ss_dssp             EEEEECCCSSC
T ss_pred             EEEEEcCCCCC
Confidence            99999876543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.3e-18  Score=141.47  Aligned_cols=87  Identities=22%  Similarity=0.328  Sum_probs=81.2

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCee--------EEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQ--------SSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATV   80 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~--------~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l   80 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.        .|+|..|. +|+++|||||+|.+.++|++||+.||+..|
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            455678999999999999999999999999999        69999996 899999999999999999999999999999


Q ss_pred             cceEeeeecccccccc
Q 039806           81 ERMELYVGPFIRRADR   96 (398)
Q Consensus        81 ~gk~i~V~~~~~~~~~   96 (398)
                      .|+.|.|.++.++..+
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999999877654

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.77  E-value=1e-18  Score=133.52  Aligned_cols=73  Identities=22%  Similarity=0.332  Sum_probs=69.7

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ++..|||+||+..+|+++|+++|++||+|.+|++..     +||||||+|.++++|++|++.||+..+.|++|+|..+
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            467899999999999999999999999999999965     7899999999999999999999999999999999886

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=4.7e-19  Score=136.39  Aligned_cols=80  Identities=25%  Similarity=0.470  Sum_probs=75.6

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ++.++|||+|||.++|+++|+++|+.||.|.+|+|..++ +|.++|||||+|.+.++|++|++.|||..|.|+.|++.+.
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            467899999999999999999999999999999999997 8999999999999999999999999999999999998765


Q ss_pred             c
Q 039806           91 I   91 (398)
Q Consensus        91 ~   91 (398)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.76  E-value=8.6e-19  Score=141.75  Aligned_cols=86  Identities=16%  Similarity=0.279  Sum_probs=75.9

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      ...+.++|||+|||.++|+++|+++|+.||.|.+|+|..|. +|.++|||||+|.+.++|++||+.+ +..|+|+.|.|.
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            44567899999999999999999999999999999999998 8999999999999999999999975 699999999999


Q ss_pred             cccccccc
Q 039806           89 PFIRRADR   96 (398)
Q Consensus        89 ~~~~~~~~   96 (398)
                      ++.++..+
T Consensus       100 ~a~~~~~~  107 (109)
T 2rs2_A          100 VAFPRRAQ  107 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            98876543

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

Probab=99.76  E-value=1.6e-18  Score=136.97  Aligned_cols=83  Identities=13%  Similarity=0.181  Sum_probs=72.4

Q ss_pred             ccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCe--ecceE
Q 039806            7 SEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGAT--VERME   84 (398)
Q Consensus         7 ~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~--l~gk~   84 (398)
                      +......+++|||+|||.++|+++|+++|+.||.|.+|++++     +||||||+|++.++|.+|++.||+..  |.|++
T Consensus        14 ~~~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~   88 (100)
T 3r27_A           14 DPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAADNQIYIAGHP   88 (100)
T ss_dssp             ---CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEE
T ss_pred             ccccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc-----CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcE
Confidence            334445678999999999999999999999999999999975     57999999999999999999999874  78999


Q ss_pred             eeeecccccc
Q 039806           85 LYVGPFIRRA   94 (398)
Q Consensus        85 i~V~~~~~~~   94 (398)
                      |+|.++.++.
T Consensus        89 i~V~~S~~k~   98 (100)
T 3r27_A           89 AFVNYSTSQK   98 (100)
T ss_dssp             EEEEECSCSC
T ss_pred             EEEEeccccc
Confidence            9999987643

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2.5e-18  Score=134.13  Aligned_cols=82  Identities=12%  Similarity=0.141  Sum_probs=77.1

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ....++|||+|||.++|+++|+++|+.| .|.+|+|+.+.+|+++|||||+|.+.++|++||+ +|+..|+|+.|.|.++
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            3456899999999999999999999999 9999999999999999999999999999999999 9999999999999998


Q ss_pred             cccc
Q 039806           91 IRRA   94 (398)
Q Consensus        91 ~~~~   94 (398)
                      .++.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7653

>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=99.76  E-value=1.2e-18  Score=137.79  Aligned_cols=83  Identities=16%  Similarity=0.152  Sum_probs=77.3

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+++.+. +|+++|||||+|.+.++|++||+.|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            4456899999999999999999999999999999888887 999999999999999999999999999999999999998


Q ss_pred             cccc
Q 039806           90 FIRR   93 (398)
Q Consensus        90 ~~~~   93 (398)
                      +..+
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            7643

>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=99.76  E-value=7.1e-19  Score=143.25  Aligned_cols=84  Identities=23%  Similarity=0.389  Sum_probs=78.6

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+|+.|. +|.++|||||+|.+.++|++|| .||+..|+|+.|.|.++.
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            35799999999999999999999999999999999998 7999999999999999999999 899999999999999988


Q ss_pred             cccccc
Q 039806           92 RRADRI   97 (398)
Q Consensus        92 ~~~~~~   97 (398)
                      .+..+.
T Consensus       103 ~~~~~~  108 (114)
T 2cq4_A          103 AEKNRL  108 (114)
T ss_dssp             HHHHHH
T ss_pred             CCccCC
Confidence            766553

>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=99.76  E-value=8.6e-19  Score=137.77  Aligned_cols=81  Identities=16%  Similarity=0.190  Sum_probs=74.9

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+++.+. +|+++|||||+|.+.++|++||+.||+..|.|+.|.|.+
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            4456899999999999999999999999999999999987 899999999999999999999999999999999999998


Q ss_pred             cc
Q 039806           90 FI   91 (398)
Q Consensus        90 ~~   91 (398)
                      +.
T Consensus        92 a~   93 (95)
T 2ek1_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            65

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.76  E-value=2.4e-18  Score=142.27  Aligned_cols=84  Identities=18%  Similarity=0.366  Sum_probs=79.1

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+|..+.+|+++|||||+|.+.++|++|++.|||..|+|+.|+|.++
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            35568999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccc
Q 039806           91 IRRA   94 (398)
Q Consensus        91 ~~~~   94 (398)
                      ....
T Consensus       112 ~~~~  115 (124)
T 2kt5_A          112 ASQI  115 (124)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            7644

>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=99.76  E-value=4.4e-19  Score=141.12  Aligned_cols=87  Identities=18%  Similarity=0.296  Sum_probs=74.4

Q ss_pred             CccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC--CCCceeEEEEEecCHHHHHHHHHHhcCCeecce
Q 039806            6 NSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ--EGKSKGYGFVQYSTPESALDAIEKLQGATVERM   83 (398)
Q Consensus         6 d~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~--~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk   83 (398)
                      .+.......++|||+|||.++|+++|+++|+.|| |.+|+|..+.  +|+++|||||+|.+.++|.+|| .|||..|+|+
T Consensus        11 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~   88 (100)
T 2j76_E           11 RSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNR   88 (100)
T ss_dssp             ---------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTB
T ss_pred             CCcCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCe
Confidence            3344556788999999999999999999999999 9999999996  8999999999999999999999 8999999999


Q ss_pred             Eeeeecccccc
Q 039806           84 ELYVGPFIRRA   94 (398)
Q Consensus        84 ~i~V~~~~~~~   94 (398)
                      .|.|.++.++.
T Consensus        89 ~l~V~~a~~~~   99 (100)
T 2j76_E           89 RIRVDVADQAQ   99 (100)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEeccCCC
Confidence            99999987653

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.76  E-value=1.3e-18  Score=142.84  Aligned_cols=83  Identities=12%  Similarity=0.093  Sum_probs=77.7

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCC---eeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGD---IQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~---I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      ....++|||+|||.++|+++|+++|+.||.   |.+|+|+.|.+|+++|||||+|.+.++|++||+ +|+..|+|+.|.|
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            456789999999999999999999999999   899999999999999999999999999999999 9999999999999


Q ss_pred             ecccccc
Q 039806           88 GPFIRRA   94 (398)
Q Consensus        88 ~~~~~~~   94 (398)
                      .++..+.
T Consensus        93 ~~a~~~~   99 (118)
T 2db1_A           93 FKSHRTE   99 (118)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9886544

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.76  E-value=7.1e-19  Score=146.98  Aligned_cols=85  Identities=16%  Similarity=0.218  Sum_probs=79.2

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeE--EEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCC----eecce
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQS--SKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGA----TVERM   83 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~--vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~----~l~gk   83 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+  |+|++|+ +|++||||||+|.+. +|.+||+.|||.    .|+|+
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            456789999999999999999999999999977  9999999 999999999999999 999999999999    99999


Q ss_pred             Eeeeecccccccc
Q 039806           84 ELYVGPFIRRADR   96 (398)
Q Consensus        84 ~i~V~~~~~~~~~   96 (398)
                      .|.|.++.++..+
T Consensus        99 ~l~V~~a~~~~~~  111 (131)
T 2m2b_A           99 TINVEFAKGSKRD  111 (131)
T ss_dssp             CCCCEECCCSCCC
T ss_pred             EEEEEECCCCCCC
Confidence            9999999876544

>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=99.76  E-value=4.2e-18  Score=146.57  Aligned_cols=85  Identities=19%  Similarity=0.258  Sum_probs=80.0

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|++||+.||+..|+|+.|.|.++
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            467899999999999999999999999999999999998 8999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      ..+..+
T Consensus       117 ~~~~~~  122 (156)
T 1h2v_Z          117 AGFKEG  122 (156)
T ss_dssp             SCCCTT
T ss_pred             CCCCCc
Confidence            865543

>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=99.75  E-value=8.2e-18  Score=134.30  Aligned_cols=84  Identities=20%  Similarity=0.321  Sum_probs=77.7

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+|+.+. +|+++|||||+|.+.++|++||+  ++..|+|+.|.|.+
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            3456899999999999999999999999999999999998 89999999999999999999998  57899999999999


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      +.++.+.
T Consensus        90 a~~~~~~   96 (103)
T 2cqg_A           90 PNSKQSQ   96 (103)
T ss_dssp             CCTTCCC
T ss_pred             cCCCCcC
Confidence            9876654

>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=99.75  E-value=7.5e-18  Score=135.98  Aligned_cols=85  Identities=20%  Similarity=0.271  Sum_probs=77.0

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|..  ++.++|||||+|++.++|++||+.||+..|+|+.|.|.+
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC--SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE--CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            345678999999999999999999999999999999955  456899999999999999999999999999999999999


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      +..+..+
T Consensus        96 a~~~~~~  102 (109)
T 1x4a_A           96 PRSGRGT  102 (109)
T ss_dssp             CCCCCCC
T ss_pred             cccCCCC
Confidence            9876544

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.75  E-value=8.1e-19  Score=131.75  Aligned_cols=74  Identities=15%  Similarity=0.363  Sum_probs=71.2

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      +|||+|||.++|+++|+++|+.||.|.+|++..++ +|+++|||||+|.+.++|++|++ +|+..|+|+.|.|.++
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            59999999999999999999999999999999998 89999999999999999999998 9999999999999874

>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=99.75  E-value=2.4e-18  Score=142.58  Aligned_cols=87  Identities=24%  Similarity=0.347  Sum_probs=80.9

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      ...+.++|||+|||.++|+++|+++|+.||.|.+|+|+.+. ++.++|||||+|.+.++|++||+.|||..|+|+.|.|.
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            34567899999999999999999999999999999999998 99999999999999999999999999999999999999


Q ss_pred             cccccccc
Q 039806           89 PFIRRADR   96 (398)
Q Consensus        89 ~~~~~~~~   96 (398)
                      ++..+...
T Consensus        98 ~a~~~~~~  105 (126)
T 3ex7_B           98 WCFVRGPP  105 (126)
T ss_dssp             ESEESSSC
T ss_pred             EecCCCCC
Confidence            99866544

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.75  E-value=2.6e-18  Score=137.89  Aligned_cols=85  Identities=28%  Similarity=0.444  Sum_probs=76.7

Q ss_pred             cccCCCcceEEEcCCCCCC------cHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec
Q 039806            8 EARLSGIGNAFVKNLASTI------DNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE   81 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~v------te~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~   81 (398)
                      .......++|||+|||.++      |+++|+++|+.||.|.+|+|. ..+|+++|||||+|.+.++|.+||+.|||..|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~   87 (105)
T 2nlw_A            9 QEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD   87 (105)
T ss_dssp             CSCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECS
T ss_pred             CCCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccC
Confidence            3344457899999999999      789999999999999999998 458999999999999999999999999999999


Q ss_pred             ce-Eeeeeccccc
Q 039806           82 RM-ELYVGPFIRR   93 (398)
Q Consensus        82 gk-~i~V~~~~~~   93 (398)
                      |+ .|.|.++...
T Consensus        88 g~~~l~V~~a~~~  100 (105)
T 2nlw_A           88 KQHTFRVNLFTDF  100 (105)
T ss_dssp             TTCEEEEECSCCC
T ss_pred             CCceEEEEEcchH
Confidence            98 9999998643

>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=99.75  E-value=2.6e-18  Score=139.36  Aligned_cols=88  Identities=22%  Similarity=0.288  Sum_probs=79.8

Q ss_pred             ccccCCCcceEEEcCCCCCCcHHHHH---HHHhccCCeeEEEEEEcC-CC---CceeEEEEEecCHHHHHHHHHHhcCCe
Q 039806            7 SEARLSGIGNAFVKNLASTIDNLKLH---QIFSKFGDIQSSKVVVSQ-EG---KSKGYGFVQYSTPESALDAIEKLQGAT   79 (398)
Q Consensus         7 ~~~~~~~~~~lfV~nLp~~vte~~L~---~~F~~~G~I~~vki~~d~-~g---~skg~aFV~F~~~e~A~~Ai~~lng~~   79 (398)
                      +..|....++|||+|||.++|+++|+   ++|+.||.|.+|+|..+. ++   .++|||||+|++.++|++||+.|||..
T Consensus         8 ~~~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~   87 (111)
T 2cpi_A            8 ASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVV   87 (111)
T ss_dssp             SCCCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             ccccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCE
Confidence            34566678899999999999999999   999999999999999887 43   566999999999999999999999999


Q ss_pred             ecceEeeeecccccc
Q 039806           80 VERMELYVGPFIRRA   94 (398)
Q Consensus        80 l~gk~i~V~~~~~~~   94 (398)
                      |+|+.|.|.++.++.
T Consensus        88 ~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           88 VDGRTLKASLGTTKY  102 (111)
T ss_dssp             ETTEEEEEESCCCCS
T ss_pred             ECCEEEEEEeccccc
Confidence            999999999998765

>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=99.75  E-value=2e-18  Score=137.89  Aligned_cols=84  Identities=13%  Similarity=0.140  Sum_probs=76.0

Q ss_pred             ccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806            9 ARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus         9 ~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      ......++|||+|||.++|+++|+++|+.||. .+|+|+.|++|++||||||+|++.++|++||+ +|+..|+|+.|.|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (102)
T 1wez_A           10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            34456789999999999999999999999995 59999999999999999999999999999995 79999999999998


Q ss_pred             cccccc
Q 039806           89 PFIRRA   94 (398)
Q Consensus        89 ~~~~~~   94 (398)
                      .+....
T Consensus        88 ~~~~~~   93 (102)
T 1wez_A           88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            876543

>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=99.75  E-value=4.1e-18  Score=146.79  Aligned_cols=85  Identities=24%  Similarity=0.386  Sum_probs=80.0

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+|..|. +|.++|||||+|.+.++|++||+.|||..|.|+.|.|.++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            446899999999999999999999999999999999997 9999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      .++..+
T Consensus       148 ~~~~~~  153 (158)
T 2kn4_A          148 RYGRPP  153 (158)
T ss_dssp             CCSSCC
T ss_pred             CCCCCC
Confidence            876544

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.9e-18  Score=139.51  Aligned_cols=81  Identities=15%  Similarity=0.273  Sum_probs=74.9

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ..+..+|||+|||.++|+++|+++|+.| .|.+|+|+.|++|+++|||||+|.+.++|++|| .+|+..|+|+.|.|..+
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            3446799999999999999999999999 899999999999999999999999999999999 59999999999999887


Q ss_pred             ccc
Q 039806           91 IRR   93 (398)
Q Consensus        91 ~~~   93 (398)
                      ..+
T Consensus        91 ~~~   93 (109)
T 2dnn_A           91 TER   93 (109)
T ss_dssp             CHH
T ss_pred             Ccc
Confidence            644

>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=99.74  E-value=3.3e-18  Score=137.08  Aligned_cols=84  Identities=20%  Similarity=0.237  Sum_probs=77.2

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeE-EEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQS-SKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~-vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+ |+|+.|.+|+++|||||+|++.++|++||+. |+..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            3456789999999999999999999999999998 8899988999999999999999999999997 9999999999998


Q ss_pred             cccccc
Q 039806           89 PFIRRA   94 (398)
Q Consensus        89 ~~~~~~   94 (398)
                      ++.++.
T Consensus        90 ~~~~~~   95 (104)
T 1wg5_A           90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            876543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=6.4e-18  Score=134.62  Aligned_cols=90  Identities=22%  Similarity=0.352  Sum_probs=81.0

Q ss_pred             CCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecce
Q 039806            5 PNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERM   83 (398)
Q Consensus         5 rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk   83 (398)
                      .++..+....++|||+|||.++|+++|+++|+.|   .+|+++.+. ++.++|||||+|.+.++|++||+.||+..|.|+
T Consensus         6 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   82 (102)
T 2fc8_A            6 SGPNARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGN   82 (102)
T ss_dssp             CTTSSSSCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            4555667788999999999999999999999977   378888887 999999999999999999999999999999999


Q ss_pred             Eeeeeccccccccc
Q 039806           84 ELYVGPFIRRADRI   97 (398)
Q Consensus        84 ~i~V~~~~~~~~~~   97 (398)
                      .|.|.++.++.++.
T Consensus        83 ~l~V~~a~~~~~~~   96 (102)
T 2fc8_A           83 KVTLDWAKPKGEGG   96 (102)
T ss_dssp             ECEEEECCCCCSSS
T ss_pred             EEEEEEecCCCCCC
Confidence            99999998876653

>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=99.74  E-value=1.4e-18  Score=141.54  Aligned_cols=86  Identities=17%  Similarity=0.202  Sum_probs=79.4

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCe-eEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDI-QSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I-~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .....++|||+|||.++|+++|+++|+.||.| .+|+|+.|.+|+++|||||+|.+.++|++||+. |+..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            34567899999999999999999999999999 899999999999999999999999999999996 9999999999999


Q ss_pred             cccccccc
Q 039806           89 PFIRRADR   96 (398)
Q Consensus        89 ~~~~~~~~   96 (398)
                      ++..+..+
T Consensus        90 ~a~~~~~~   97 (114)
T 2cpy_A           90 VVTLEDMR   97 (114)
T ss_dssp             EECHHHHH
T ss_pred             ECCHHHHH
Confidence            98866543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.74  E-value=4.7e-19  Score=141.06  Aligned_cols=93  Identities=22%  Similarity=0.264  Sum_probs=79.9

Q ss_pred             CCCCCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCee
Q 039806            2 WSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATV   80 (398)
Q Consensus         2 ~s~rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l   80 (398)
                      |............++|||+|||.++|+++|+++|+.||.|.+ +++.+. +|+++|||||+|.+.++|++||+ |||..|
T Consensus         5 ~~~p~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~   82 (101)
T 1fj7_A            5 LEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKV   82 (101)
T ss_dssp             CCCSCCSTTCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCB
T ss_pred             CCCCCCcccCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEE
Confidence            333333334456789999999999999999999999999988 666665 89999999999999999999998 999999


Q ss_pred             cceEeeeecccccccc
Q 039806           81 ERMELYVGPFIRRADR   96 (398)
Q Consensus        81 ~gk~i~V~~~~~~~~~   96 (398)
                      .|+.|.|.++.++..+
T Consensus        83 ~g~~l~V~~a~~~~~~   98 (101)
T 1fj7_A           83 FGNEIKLEKPKGRDGT   98 (101)
T ss_dssp             TTBCCEEECCSCCCCS
T ss_pred             CCcEEEEEEcCCCCCC
Confidence            9999999999876554

>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=99.74  E-value=8.9e-18  Score=136.64  Aligned_cols=82  Identities=21%  Similarity=0.372  Sum_probs=75.7

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCee--------cc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATV--------ER   82 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l--------~g   82 (398)
                      ..+.++|||+|||.++|+++|+++|+.||.|.+|+|..+.+|.++|||||+|.+.++|++||+.|||..|        .+
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            3567899999999999999999999999999999999999999999999999999999999999999999        56


Q ss_pred             eEeeeecccc
Q 039806           83 MELYVGPFIR   92 (398)
Q Consensus        83 k~i~V~~~~~   92 (398)
                      +.|.|.++.+
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            7788877764

>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=99.74  E-value=2e-18  Score=145.00  Aligned_cols=83  Identities=12%  Similarity=0.080  Sum_probs=77.2

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCC---eeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGD---IQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~---I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      ....++|||+|||.++|+++|+++|+.||.   |.+|+|+.|++|+++|||||+|++.++|++||+ +|+..|+|+.|.|
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            345689999999999999999999999999   899999999999999999999999999999999 9999999999999


Q ss_pred             ecccccc
Q 039806           88 GPFIRRA   94 (398)
Q Consensus        88 ~~~~~~~   94 (398)
                      .++..+.
T Consensus       120 ~~a~~~e  126 (136)
T 2hgl_A          120 FKSHRTE  126 (136)
T ss_dssp             EECCHHH
T ss_pred             EECChHH
Confidence            9876543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=2.4e-18  Score=140.51  Aligned_cols=84  Identities=15%  Similarity=0.308  Sum_probs=78.8

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|++||+. |+..|+|+.|.|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            45899999999999999999999999999999999997 899999999999999999999997 9999999999999998


Q ss_pred             cccccc
Q 039806           92 RRADRI   97 (398)
Q Consensus        92 ~~~~~~   97 (398)
                      ++..+.
T Consensus       105 ~~~~~~  110 (116)
T 1x4b_A          105 AREESG  110 (116)
T ss_dssp             SCCCCC
T ss_pred             CCccCC
Confidence            876553

>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=1.3e-18  Score=146.22  Aligned_cols=89  Identities=22%  Similarity=0.373  Sum_probs=81.6

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      .....+.++|||+|||.++|+++|+++|+.||.|.+|+|..+. +++++|||||+|.+.++|++||+.|||..|.|+.|.
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            3344557899999999999999999999999999999999998 899999999999999999999999999999999999


Q ss_pred             eecccccccc
Q 039806           87 VGPFIRRADR   96 (398)
Q Consensus        87 V~~~~~~~~~   96 (398)
                      |.++..+..+
T Consensus       121 V~~a~~~~~~  130 (135)
T 2lea_A          121 VQMARYGRPP  130 (135)
T ss_dssp             EEECCCCCCC
T ss_pred             EEECCCCCCC
Confidence            9998866544

>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=99.74  E-value=6.1e-18  Score=138.22  Aligned_cols=83  Identities=11%  Similarity=0.134  Sum_probs=74.4

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhc--CCeecceEeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ--GATVERMELYV   87 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~ln--g~~l~gk~i~V   87 (398)
                      ....+++|||+|||.++|+++|+++|+.||.|.+|+|+.+     ||||||+|++.++|.+|++.+|  +..|.|+.|+|
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            3456789999999999999999999999999999999874     7999999999999999999887  46899999999


Q ss_pred             eccccccccc
Q 039806           88 GPFIRRADRI   97 (398)
Q Consensus        88 ~~~~~~~~~~   97 (398)
                      .++..+....
T Consensus       102 ~~a~~k~~~~  111 (119)
T 2ad9_A          102 QFSNHKELKT  111 (119)
T ss_dssp             EECSSSSCCC
T ss_pred             EEccCCCCCc
Confidence            9998765543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.74  E-value=2e-18  Score=131.76  Aligned_cols=74  Identities=31%  Similarity=0.538  Sum_probs=68.8

Q ss_pred             cceEEEcCCCCCC------cHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecce-Eee
Q 039806           14 IGNAFVKNLASTI------DNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERM-ELY   86 (398)
Q Consensus        14 ~~~lfV~nLp~~v------te~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk-~i~   86 (398)
                      +++|||+|||.++      |+++|+++|+.||.|.+|++. +.+|+++|||||+|.+.++|++|++.|||..|+|+ .|+
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            3689999999999      789999999999999999988 45899999999999999999999999999999999 888


Q ss_pred             ee
Q 039806           87 VG   88 (398)
Q Consensus        87 V~   88 (398)
                      |.
T Consensus        80 V~   81 (81)
T 2krb_A           80 VN   81 (81)
T ss_dssp             CC
T ss_pred             eC
Confidence            73

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=1.5e-18  Score=130.84  Aligned_cols=75  Identities=16%  Similarity=0.342  Sum_probs=71.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ++|||+|||.++|+++|+++|+.||.|.+|++..++ +|+++|||||+|.+.++|++|++.+| ..++|+.|.|.++
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            479999999999999999999999999999999998 89999999999999999999999988 9999999999875

>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=99.74  E-value=3.8e-18  Score=137.65  Aligned_cols=85  Identities=19%  Similarity=0.215  Sum_probs=78.0

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCC-eeEEEEE-EcC-CCCceeEEEEEecCHHHHHHHHHHhc--CCeecceEee
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGD-IQSSKVV-VSQ-EGKSKGYGFVQYSTPESALDAIEKLQ--GATVERMELY   86 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~-I~~vki~-~d~-~g~skg~aFV~F~~~e~A~~Ai~~ln--g~~l~gk~i~   86 (398)
                      ...++|||+|||.++|+++|+++|+.||. |.+|+++ .+. +|.++|||||+|.+.++|.+|++.||  +..++|+.|.
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            45689999999999999999999999998 9999998 666 78999999999999999999999996  5899999999


Q ss_pred             eecccccccc
Q 039806           87 VGPFIRRADR   96 (398)
Q Consensus        87 V~~~~~~~~~   96 (398)
                      |.++.++...
T Consensus        86 V~~a~~~~~~   95 (109)
T 2dis_A           86 VDWAEPEIDV   95 (109)
T ss_dssp             EEESCSSCST
T ss_pred             EEEcCCCCCc
Confidence            9999876654

>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=99.73  E-value=8.9e-19  Score=136.34  Aligned_cols=80  Identities=25%  Similarity=0.432  Sum_probs=73.0

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRR   93 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~   93 (398)
                      ++|||+|||.++|+++|+++|+.||.|.+|++..+. +|.++|||||+|.+.+ |.+|++.|||..++|+.|.|.++..+
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            589999999999999999999999999999999998 7999999999999999 99999999999999999999998765


Q ss_pred             cc
Q 039806           94 AD   95 (398)
Q Consensus        94 ~~   95 (398)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.73  E-value=8.1e-18  Score=141.75  Aligned_cols=81  Identities=25%  Similarity=0.406  Sum_probs=75.8

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|..++ +|+++|||||+|.+.++|++|++.|||..|+|+.|+|.
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            34567899999999999999999999999999999999997 89999999999999999999999999999999999998


Q ss_pred             cc
Q 039806           89 PF   90 (398)
Q Consensus        89 ~~   90 (398)
                      ++
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            74

>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=99.73  E-value=1.3e-17  Score=132.74  Aligned_cols=81  Identities=11%  Similarity=0.198  Sum_probs=72.7

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhc--CCeecceEeeee
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ--GATVERMELYVG   88 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~ln--g~~l~gk~i~V~   88 (398)
                      ...+++|||+|||.++|+++|+++|+.||.|.+|+++++     ||||||+|++.++|.+|++.++  +..|.|+.|+|.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   86 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   86 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEE
Confidence            346789999999999999999999999999999998764     7999999999999999999774  678999999999


Q ss_pred             cccccccc
Q 039806           89 PFIRRADR   96 (398)
Q Consensus        89 ~~~~~~~~   96 (398)
                      ++..+...
T Consensus        87 ~a~~~~~~   94 (101)
T 2cq1_A           87 YSNHKELK   94 (101)
T ss_dssp             ECSCSSCC
T ss_pred             EcCcccCc
Confidence            99866544

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.73  E-value=3.4e-18  Score=154.71  Aligned_cols=110  Identities=42%  Similarity=0.687  Sum_probs=85.4

Q ss_pred             CCCCCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec
Q 039806            2 WSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE   81 (398)
Q Consensus         2 ~s~rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~   81 (398)
                      |+...........++|||+|||.++|+++|+++|+.||.|.+|+|+.|. +.++|||||+|.+.++|++||+.|||..|+
T Consensus        91 ~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~-~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~  169 (213)
T 4f02_A           91 WSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLN  169 (213)
T ss_dssp             ECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             cccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC-CCCceEEEEEeCCHHHHHHHHHHhCCCEEC
Confidence            3444444455567899999999999999999999999999999999986 448999999999999999999999999999


Q ss_pred             ceEeeeecccccccccccCC-CCceEEeeCCC
Q 039806           82 RMELYVGPFIRRADRIQEGS-SFNNLYVKNLD  112 (398)
Q Consensus        82 gk~i~V~~~~~~~~~~~~~~-~~~~lfV~nLp  112 (398)
                      |+.|.|.++.++.++..... .....+..++|
T Consensus       170 g~~i~V~~a~~~~~~~~~~~~~~~~~~p~~~P  201 (213)
T 4f02_A          170 DRKVFVGRFKSRKEREAELGARAKEFYPYDVP  201 (213)
T ss_dssp             TEECEEEECCCHHHHHHHHC------------
T ss_pred             CEEEEEEEcCCCcccchhhhcccCCCCCCCCC
Confidence            99999999988776543322 33444444444

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.73  E-value=4.1e-18  Score=134.20  Aligned_cols=91  Identities=23%  Similarity=0.369  Sum_probs=77.9

Q ss_pred             CCCCCCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCee
Q 039806            1 MWSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATV   80 (398)
Q Consensus         1 m~s~rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l   80 (398)
                      ||-...........++|||+|||.++|+++|+++|+.||.|..|    +.++.++|||||+|.+.++|.+|++.|||..|
T Consensus         3 ~~~~p~~~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   78 (96)
T 1fjc_A            3 MLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI   78 (96)
T ss_dssp             CSSCTTTTSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEE
T ss_pred             cccCccccccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            34444444445567899999999999999999999999988766    44789999999999999999999999999999


Q ss_pred             cceEeeeeccccccc
Q 039806           81 ERMELYVGPFIRRAD   95 (398)
Q Consensus        81 ~gk~i~V~~~~~~~~   95 (398)
                      +|+.|.|.++..+..
T Consensus        79 ~g~~l~v~~a~~~~~   93 (96)
T 1fjc_A           79 DGRSVSLYYTGEKGG   93 (96)
T ss_dssp             TTEEEEEEECSSSCC
T ss_pred             CCeEEEEEEcCCCCC
Confidence            999999999876543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.73  E-value=8.9e-18  Score=138.73  Aligned_cols=81  Identities=19%  Similarity=0.327  Sum_probs=76.5

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      +.++|||+|||.++|+++|+++|+.||.|.+|+|..|+ +|.++|||||+|.+.++|++|| .|||..|+|+.|.|.++.
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            46799999999999999999999999999999999997 9999999999999999999999 799999999999999987


Q ss_pred             ccc
Q 039806           92 RRA   94 (398)
Q Consensus        92 ~~~   94 (398)
                      ...
T Consensus       114 ~~~  116 (124)
T 2jwn_A          114 TNM  116 (124)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            544

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.5e-17  Score=129.48  Aligned_cols=79  Identities=23%  Similarity=0.457  Sum_probs=73.5

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|++.       +|||||+|.+.++|++|++.||+..|+|+.|.|.++
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            3567899999999999999999999999999999996       689999999999999999999999999999999999


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      .++..+
T Consensus        78 ~~~~~~   83 (90)
T 2dnq_A           78 KNKSKA   83 (90)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            876654

>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=99.73  E-value=6.2e-18  Score=134.64  Aligned_cols=81  Identities=17%  Similarity=0.159  Sum_probs=72.3

Q ss_pred             cCCCcceEEEcCCCC-CCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcC--CeecceEee
Q 039806           10 RLSGIGNAFVKNLAS-TIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG--ATVERMELY   86 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~-~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng--~~l~gk~i~   86 (398)
                      +...+++|||+|||. ++|+++|+++|+.||.|.+|+|+++     +|||||+|++.++|.+||+.||+  ..|.|+.|+
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            344678999999999 9999999999999999999999864     58999999999999999999986  469999999


Q ss_pred             eeccccccc
Q 039806           87 VGPFIRRAD   95 (398)
Q Consensus        87 V~~~~~~~~   95 (398)
                      |.++.++..
T Consensus        86 V~~a~~~~~   94 (102)
T 1x4d_A           86 VHLSQKYKR   94 (102)
T ss_dssp             EEEECCCTT
T ss_pred             EEECCCCCC
Confidence            999886543

>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=1.6e-17  Score=144.30  Aligned_cols=86  Identities=24%  Similarity=0.374  Sum_probs=78.9

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+|..+. +|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.+
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      +.++..+
T Consensus       149 a~~~~~~  155 (165)
T 1rk8_A          149 CFVKGPK  155 (165)
T ss_dssp             SEECC--
T ss_pred             ecCCCCC
Confidence            9876554

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.73  E-value=6.2e-18  Score=134.74  Aligned_cols=82  Identities=24%  Similarity=0.529  Sum_probs=76.3

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+|..|.+|.++|||||+|.+.++|++|++  |+..++|+.|.|.++.+
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            4679999999999999999999999999999999999999999999999999999999999  99999999999999886


Q ss_pred             cccc
Q 039806           93 RADR   96 (398)
Q Consensus        93 ~~~~   96 (398)
                      +...
T Consensus        86 ~~~~   89 (102)
T 2xs2_A           86 KQNL   89 (102)
T ss_dssp             CC--
T ss_pred             Ccch
Confidence            6543

>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=99.72  E-value=2.1e-17  Score=130.64  Aligned_cols=79  Identities=24%  Similarity=0.357  Sum_probs=71.5

Q ss_pred             cccCCCcceEEEcCCCC-CCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806            8 EARLSGIGNAFVKNLAS-TIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~-~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      ......+++|||+|||. ++|+++|+++|+.||.|.+|++       ++|||||+|.+.++|++|++.|||..++|+.|.
T Consensus        16 ~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   88 (97)
T 2xnq_A           16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLI   88 (97)
T ss_dssp             ---CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE-------CSSEEEEEESSHHHHHHHHHHHTTSEETTEECE
T ss_pred             cCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            33456788999999998 9999999999999999999999       479999999999999999999999999999999


Q ss_pred             eeccccc
Q 039806           87 VGPFIRR   93 (398)
Q Consensus        87 V~~~~~~   93 (398)
                      |.++..+
T Consensus        89 V~~a~~~   95 (97)
T 2xnq_A           89 LEVSSSN   95 (97)
T ss_dssp             EEECCCC
T ss_pred             EEecCCC
Confidence            9998654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=1.1e-17  Score=132.05  Aligned_cols=81  Identities=17%  Similarity=0.255  Sum_probs=73.3

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      .....++|||+|||.++|+++|+++|+.||.|. |+++.+   .++|||||+|.+.++|++|++.|||..|+|+.|.|.+
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            344578999999999999999999999999997 777764   5899999999999999999999999999999999999


Q ss_pred             ccccc
Q 039806           90 FIRRA   94 (398)
Q Consensus        90 ~~~~~   94 (398)
                      +.++.
T Consensus        91 a~~~~   95 (97)
T 2e5j_A           91 ARQQR   95 (97)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87654

>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=99.72  E-value=2.6e-18  Score=142.12  Aligned_cols=83  Identities=18%  Similarity=0.259  Sum_probs=75.1

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|.++.+. +|+++|||||+|.+.++|++||+ +|+..|+|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3456899999999999999999999999999986666555 99999999999999999999999 999999999999999


Q ss_pred             ccccc
Q 039806           90 FIRRA   94 (398)
Q Consensus        90 ~~~~~   94 (398)
                      +.++.
T Consensus       101 a~~~~  105 (124)
T 1wel_A          101 ITKKG  105 (124)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            87654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.4e-17  Score=132.52  Aligned_cols=84  Identities=25%  Similarity=0.325  Sum_probs=76.2

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      .....++|||+|||.++|+++|+++|+.||.|   +++.+.+++++|||||+|.+.++|++||+.||+..|.|+.|.|.+
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            34567899999999999999999999999977   677777899999999999999999999999999999999999999


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      +.++..+
T Consensus        88 a~~~~~~   94 (101)
T 2fc9_A           88 QGPRGSP   94 (101)
T ss_dssp             CSSCCCC
T ss_pred             cCCCCCC
Confidence            9876544

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

Probab=99.72  E-value=9.6e-18  Score=139.16  Aligned_cols=84  Identities=20%  Similarity=0.251  Sum_probs=75.4

Q ss_pred             CCcceEEEcCCCCCCcHHHHH----HHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           12 SGIGNAFVKNLASTIDNLKLH----QIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~----~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      ..+++|||+|||.++++++|+    ++|+.||.|.+|.+.  .++++||||||+|.+.++|.+||+.|||..|.|+.|.|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~--~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V  104 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD--LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI  104 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC--CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec--cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEE
Confidence            456799999999999999876    699999999998874  36889999999999999999999999999999999999


Q ss_pred             eccccccccc
Q 039806           88 GPFIRRADRI   97 (398)
Q Consensus        88 ~~~~~~~~~~   97 (398)
                      .++..+....
T Consensus       105 ~~a~~~~~~~  114 (127)
T 2a3j_A          105 TFSETPQSQV  114 (127)
T ss_dssp             EECCCCCHHH
T ss_pred             EEccCcchhc
Confidence            9998776553

>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=99.72  E-value=2.3e-18  Score=138.67  Aligned_cols=84  Identities=11%  Similarity=0.116  Sum_probs=77.9

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCC---eeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGD---IQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~---I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      .....++|||+|||.++|+++|+++|+.||.   |.+|+|+.|.+|+++|||||+|.+.++|++||+ +|+..|+|+.|.
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            3456789999999999999999999999998   899999999999999999999999999999999 999999999999


Q ss_pred             eecccccc
Q 039806           87 VGPFIRRA   94 (398)
Q Consensus        87 V~~~~~~~   94 (398)
                      |.++.++.
T Consensus        86 V~~a~~~~   93 (107)
T 2lmi_A           86 VYEINNED   93 (107)
T ss_dssp             CEECCHHH
T ss_pred             EEECCHHH
Confidence            99887544

>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=99.72  E-value=7.3e-18  Score=154.31  Aligned_cols=81  Identities=20%  Similarity=0.278  Sum_probs=76.0

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccC--CeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFG--DIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G--~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ..++|||+||+.++|+++|+++|+.||  .|.+|+|++|+ +|++||||||+|.+.++|++||+.||+..|.|+.|+|.+
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            457899999999999999999999999  99999999998 999999999999999999999999999999999999998


Q ss_pred             cccc
Q 039806           90 FIRR   93 (398)
Q Consensus        90 ~~~~   93 (398)
                      +.+.
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8654

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

Probab=99.72  E-value=1.8e-17  Score=131.84  Aligned_cols=76  Identities=25%  Similarity=0.301  Sum_probs=71.1

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|++.     +++|||||+|.+.++|.+|++.|||..|+|+.|.|.++.
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-----~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-----PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-----TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-----cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            346799999999999999999999999999999997     378999999999999999999999999999999999986


Q ss_pred             c
Q 039806           92 R   92 (398)
Q Consensus        92 ~   92 (398)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.72  E-value=3.1e-17  Score=132.25  Aligned_cols=80  Identities=19%  Similarity=0.174  Sum_probs=74.0

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecc-----eEe
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVER-----MEL   85 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g-----k~i   85 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+|..|      |||||+|.+.++|++||+.||+..|.|     +.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            345789999999999999999999999999999999876      899999999999999999999999999     999


Q ss_pred             eeecccccccc
Q 039806           86 YVGPFIRRADR   96 (398)
Q Consensus        86 ~V~~~~~~~~~   96 (398)
                      .|.++.++...
T Consensus        86 ~V~~a~~~~~~   96 (108)
T 1x4c_A           86 RVKVDGPRSPS   96 (108)
T ss_dssp             EEEESSCCSCC
T ss_pred             EEEeCCCCCCC
Confidence            99999876544

>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=99.72  E-value=1.9e-17  Score=132.56  Aligned_cols=80  Identities=15%  Similarity=0.165  Sum_probs=71.8

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCC--eecceEeeeec
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA--TVERMELYVGP   89 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~--~l~gk~i~V~~   89 (398)
                      ..+++|||+|||.++|+++|+++|+.||.|.+|+|++     .||||||+|++.++|.+|++.||+.  .|.|+.|+|.+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~-----~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~   87 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-----FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEC-----CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            4578999999999999999999999999999999876     3799999999999999999988764  59999999999


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      +..+...
T Consensus        88 a~~~~~~   94 (104)
T 1wex_A           88 STSKRIT   94 (104)
T ss_dssp             CSSSSCC
T ss_pred             ccCcccc
Confidence            9876544

>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=99.71  E-value=1.6e-17  Score=131.63  Aligned_cols=83  Identities=24%  Similarity=0.335  Sum_probs=75.3

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      .......++|||+|||.++|+++|+++|+.||.|.+|++.+     ++|||||+|.+.++|++|++.|||..|+|+.|.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~-----~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v   83 (99)
T 2cpj_A            9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-----DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV   83 (99)
T ss_dssp             SCCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET-----TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEE
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEec-----CCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEE
Confidence            34456778999999999999999999999999999999975     4799999999999999999999999999999999


Q ss_pred             eccccccc
Q 039806           88 GPFIRRAD   95 (398)
Q Consensus        88 ~~~~~~~~   95 (398)
                      .++.++..
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpj_A           84 RFACHSAS   91 (99)
T ss_dssp             EESSCCSC
T ss_pred             EEcCCCCC
Confidence            99876543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=6.9e-18  Score=139.16  Aligned_cols=82  Identities=16%  Similarity=0.152  Sum_probs=75.3

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCe----eEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDI----QSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I----~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      ..+..+|||+|||+++|+++|+++|+.||.|    .+|+|+.|.+|+++|||||+|.+.++|++||+. |+..|.|+.|.
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            4567899999999999999999999999975    689999999999999999999999999999996 99999999999


Q ss_pred             eeccccc
Q 039806           87 VGPFIRR   93 (398)
Q Consensus        87 V~~~~~~   93 (398)
                      |..+..+
T Consensus        99 V~~a~~~  105 (123)
T 2dha_A           99 LFRSTAA  105 (123)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9887644

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=3.9e-17  Score=127.60  Aligned_cols=80  Identities=24%  Similarity=0.350  Sum_probs=73.3

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|++.       ++||||+|.+.++|++|++.||+..|.|+.|.|.+
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 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC-------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            44567899999999999999999999999999999995       45999999999999999999999999999999999


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      +.++...
T Consensus        79 a~~~~~~   85 (92)
T 2dgt_A           79 STSRLRT   85 (92)
T ss_dssp             SSCCCSC
T ss_pred             ccCCCCC
Confidence            9876544

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.71  E-value=1.1e-17  Score=135.30  Aligned_cols=78  Identities=17%  Similarity=0.136  Sum_probs=71.3

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccC-CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFG-DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G-~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...+|||+|||.++|+++|+++|+.|| .|..|+|..+   .++|||||+|++.++|++||+.|||..|+|+.|.|.++.
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~  103 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDD  103 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            457999999999999999999999999 8999998643   489999999999999999999999999999999999886


Q ss_pred             cc
Q 039806           92 RR   93 (398)
Q Consensus        92 ~~   93 (398)
                      ..
T Consensus       104 ~~  105 (111)
T 2jvr_A          104 NP  105 (111)
T ss_dssp             C-
T ss_pred             CC
Confidence            44

>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=99.71  E-value=4e-18  Score=127.82  Aligned_cols=74  Identities=19%  Similarity=0.355  Sum_probs=70.2

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      +|||+|||.++|+++|+++|+.||.|.+|++..+. +|.++|||||+|.+.++|++|++ +++..++|+.|.|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            59999999999999999999999999999999998 89999999999999999999999 4899999999999764

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=4e-17  Score=126.99  Aligned_cols=80  Identities=24%  Similarity=0.368  Sum_probs=73.0

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      +....++|||+|||.++|+++|+++|+.||.|.+|++.       ++||||+|.+.++|++|++.|||..|+|+.|.|.+
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 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34567899999999999999999999999999999995       45999999999999999999999999999999999


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      +.++..+
T Consensus        78 a~~~~~~   84 (90)
T 2dnp_A           78 STKGQKK   84 (90)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            9876544

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.71  E-value=5.5e-17  Score=139.75  Aligned_cols=90  Identities=26%  Similarity=0.477  Sum_probs=82.0

Q ss_pred             CCCCCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCee
Q 039806            2 WSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATV   80 (398)
Q Consensus         2 ~s~rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l   80 (398)
                      |+...........++|||+|||.++|+++|+++|+.||.|.+|++..+. +|.++|||||+|.+.++|.+|++.|||..+
T Consensus        75 ~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  154 (166)
T 3md3_A           75 WAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL  154 (166)
T ss_dssp             ECCCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             EcCCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Confidence            3444444556678899999999999999999999999999999999997 899999999999999999999999999999


Q ss_pred             cceEeeeeccc
Q 039806           81 ERMELYVGPFI   91 (398)
Q Consensus        81 ~gk~i~V~~~~   91 (398)
                      +|+.|.|.++.
T Consensus       155 ~g~~i~v~~a~  165 (166)
T 3md3_A          155 NGRPLRINWAA  165 (166)
T ss_dssp             TTEECEEEESC
T ss_pred             CCcEEEEEecC
Confidence            99999999875

>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=99.71  E-value=2.3e-17  Score=130.21  Aligned_cols=80  Identities=20%  Similarity=0.306  Sum_probs=73.2

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec--ceEeeee
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE--RMELYVG   88 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~--gk~i~V~   88 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|++..+     +|||||+|.+.++|++|++.||+..|.  |+.|.|.
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            345689999999999999999999999999999999753     789999999999999999999999999  9999999


Q ss_pred             ccccccc
Q 039806           89 PFIRRAD   95 (398)
Q Consensus        89 ~~~~~~~   95 (398)
                      ++.++..
T Consensus        89 ~a~~~~~   95 (97)
T 1why_A           89 FAKSGPS   95 (97)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCCC
Confidence            9887643

>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=99.71  E-value=6.2e-18  Score=137.74  Aligned_cols=85  Identities=18%  Similarity=0.315  Sum_probs=74.3

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|.+..+. +|+++|||||+|.+.++|++||+.|||..|+|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            356899999999999999999999999999443333332 7889999999999999999999999999999999999999


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      .++..+
T Consensus       103 ~~~~~~  108 (115)
T 2cpx_A          103 KNKKQR  108 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCC
Confidence            877655

>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=99.71  E-value=4.3e-17  Score=131.55  Aligned_cols=81  Identities=31%  Similarity=0.379  Sum_probs=74.9

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|+|..+     +|||||+|.+.++|.+|++.|||..|+|+.|.|.++
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            345789999999999999999999999999999999875     799999999999999999999999999999999999


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      .++...
T Consensus        97 ~~~~~~  102 (109)
T 1x4g_A           97 KESPDM  102 (109)
T ss_dssp             CCCCSS
T ss_pred             CCCCCC
Confidence            876544

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

Probab=99.70  E-value=1.9e-17  Score=130.52  Aligned_cols=80  Identities=25%  Similarity=0.390  Sum_probs=71.6

Q ss_pred             cCCCcceEEEcCCCC-CCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLAS-TIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~-~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      +....++|||+|||. ++|+++|+++|+.||.|.+|+|       ++|||||+|.+.++|++|++.|||..+.|+.|.|.
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE-------ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            345678999999998 9999999999999999999999       47999999999999999999999999999999999


Q ss_pred             cccccccc
Q 039806           89 PFIRRADR   96 (398)
Q Consensus        89 ~~~~~~~~   96 (398)
                      ++..+...
T Consensus        79 ~a~~~~~~   86 (96)
T 2kvi_A           79 VSSSNARP   86 (96)
T ss_dssp             EEECCCC-
T ss_pred             EcCcCCCC
Confidence            98766544

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1e-16  Score=127.00  Aligned_cols=80  Identities=21%  Similarity=0.378  Sum_probs=73.2

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhcc--CCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKF--GDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~--G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      .....++|||+|||.++|+++|+++|+.|  |.|.+|++       .+|||||+|.+.++|++||+.|||..|.|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE-------eCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            34567899999999999999999999999  99999987       5789999999999999999999999999999999


Q ss_pred             ecccccccc
Q 039806           88 GPFIRRADR   96 (398)
Q Consensus        88 ~~~~~~~~~   96 (398)
                      .++.++..+
T Consensus        84 ~~a~~~~~~   92 (99)
T 2cpd_A           84 TLAKPVDKD   92 (99)
T ss_dssp             ECCCCCCCC
T ss_pred             EECCCCCCC
Confidence            999876543

>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=99.70  E-value=1.3e-17  Score=131.53  Aligned_cols=83  Identities=25%  Similarity=0.321  Sum_probs=76.0

Q ss_pred             CCcceEEEcCCCCCCcHHHHH----HHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           12 SGIGNAFVKNLASTIDNLKLH----QIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~----~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      ..+++|||+|||.++|+++|+    ++|+.||.|.+|++..  +|.++|||||+|.+.++|.+|++.|||..++|+.|.|
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   83 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEE
Confidence            456899999999999999999    9999999999999874  5778999999999999999999999999999999999


Q ss_pred             ecccccccc
Q 039806           88 GPFIRRADR   96 (398)
Q Consensus        88 ~~~~~~~~~   96 (398)
                      .++.++...
T Consensus        84 ~~a~~~~~~   92 (97)
T 1nu4_A           84 QYAKTDSDI   92 (97)
T ss_dssp             EECSSCCTH
T ss_pred             EEccCCCcc
Confidence            998876543

>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=99.70  E-value=4.9e-17  Score=124.92  Aligned_cols=75  Identities=29%  Similarity=0.332  Sum_probs=70.2

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHh-cCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL-QGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~l-ng~~l~gk~i~V~~   89 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|++..     ++|||||+|.+.++|++|++.| |+..++|+.|.|.+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~-----~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-----RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC-----CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            34578999999999999999999999999999999986     5799999999999999999999 99999999999988


Q ss_pred             c
Q 039806           90 F   90 (398)
Q Consensus        90 ~   90 (398)
                      +
T Consensus        84 a   84 (85)
T 2ytc_A           84 G   84 (85)
T ss_dssp             C
T ss_pred             c
Confidence            6

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.70  E-value=4.5e-17  Score=131.35  Aligned_cols=79  Identities=28%  Similarity=0.447  Sum_probs=72.4

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|++.       +|||||+|.+.++|++|++.|||..++|+.|.|.++
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  100 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS  100 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            4567899999999999999999999999999999996       699999999999999999999999999999999998


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      ..+..+
T Consensus       101 ~~~~~r  106 (108)
T 2jvo_A          101 KLPAKR  106 (108)
T ss_dssp             SCCC--
T ss_pred             cCCCCC
Confidence            876543

>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=99.70  E-value=5.6e-17  Score=129.48  Aligned_cols=80  Identities=25%  Similarity=0.470  Sum_probs=73.3

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      .+..++|||+|||.++|+++|+++|+.||.|.+|+|.       ++||||+|.+.++|++||+.||+..|.|+.|.|.++
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 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            3457899999999999999999999999999999985       579999999999999999999999999999999999


Q ss_pred             ccccccc
Q 039806           91 IRRADRI   97 (398)
Q Consensus        91 ~~~~~~~   97 (398)
                      .++..+.
T Consensus        81 ~~~~~~~   87 (103)
T 2dgu_A           81 KPPDQKR   87 (103)
T ss_dssp             CCCCCCC
T ss_pred             CCCcccc
Confidence            8766543

>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=99.70  E-value=3.8e-18  Score=143.69  Aligned_cols=83  Identities=13%  Similarity=0.147  Sum_probs=74.7

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      .....++|||+|||.++|+++|+++|+.|| |.+|+|+.|++|+++|||||+|++.++|++|| .+|+..|+|+.|.|..
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            345567999999999999999999999999 77999999999999999999999999999999 6899999999999988


Q ss_pred             ccccc
Q 039806           90 FIRRA   94 (398)
Q Consensus        90 ~~~~~   94 (398)
                      +..+.
T Consensus       120 a~~~~  124 (139)
T 2hgn_A          120 NSTTG  124 (139)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            76544

>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=99.70  E-value=1.4e-17  Score=137.71  Aligned_cols=80  Identities=23%  Similarity=0.242  Sum_probs=73.6

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCee--EEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQ--SSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~--~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ...++|||+|||+++|+++|+++|+.| .|.  +|+|+.|++|+++|||||+|++.++|++||+ +++..|+|+.|.|..
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEE
Confidence            456889999999999999999999999 677  9999999999999999999999999999998 478999999999988


Q ss_pred             cccc
Q 039806           90 FIRR   93 (398)
Q Consensus        90 ~~~~   93 (398)
                      +.++
T Consensus       118 a~~~  121 (126)
T 2hgm_A          118 SSQE  121 (126)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            7654

>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=99.70  E-value=1.6e-17  Score=134.23  Aligned_cols=81  Identities=12%  Similarity=0.103  Sum_probs=72.2

Q ss_pred             CCCcceEEEcCCCCC-CcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcC--CeecceEeee
Q 039806           11 LSGIGNAFVKNLAST-IDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG--ATVERMELYV   87 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~-vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng--~~l~gk~i~V   87 (398)
                      ...+++|||+|||.+ +|+++|+++|+.||.|.+|+|.+     +||||||+|++.++|++||+.||+  ..|.|+.|+|
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            445789999999998 99999999999999999999974     679999999999999999998864  5699999999


Q ss_pred             ecccccccc
Q 039806           88 GPFIRRADR   96 (398)
Q Consensus        88 ~~~~~~~~~   96 (398)
                      .++.++...
T Consensus        97 ~~a~~~~~~  105 (112)
T 1x4f_A           97 DLSEKYKKL  105 (112)
T ss_dssp             EEECSCSSS
T ss_pred             EECcccccc
Confidence            998766543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.52  E-value=1.4e-18  Score=141.97  Aligned_cols=87  Identities=26%  Similarity=0.327  Sum_probs=80.8

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeE--------EEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQS--------SKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVE   81 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~--------vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~   81 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+        |+|..|+ +|.++|||||+|.+.++|++||+.|||..|.
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            346789999999999999999999999999999        9999997 8999999999999999999999999999999


Q ss_pred             ceEeeeeccccccccc
Q 039806           82 RMELYVGPFIRRADRI   97 (398)
Q Consensus        82 gk~i~V~~~~~~~~~~   97 (398)
                      |+.|.|.++.++..+.
T Consensus        84 g~~l~V~~a~~~~~~~   99 (116)
T 2lcw_A           84 GNPIKVSFATRRADFN   99 (116)
Confidence            9999999998776553

>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=99.69  E-value=3.3e-17  Score=128.21  Aligned_cols=80  Identities=25%  Similarity=0.413  Sum_probs=71.7

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCC-eeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcC-CeecceEeeee
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGD-IQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG-ATVERMELYVG   88 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~-I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng-~~l~gk~i~V~   88 (398)
                      ....++|||+|||.++|+++|+++|+.||. |..+.+.      ++|||||+|.+.++|++|++.||| ..|+|+.|.|.
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            345689999999999999999999999999 6666662      679999999999999999999999 99999999999


Q ss_pred             cccccccc
Q 039806           89 PFIRRADR   96 (398)
Q Consensus        89 ~~~~~~~~   96 (398)
                      ++.++..+
T Consensus        79 ~a~~~~~~   86 (93)
T 2cqh_A           79 YSVSKKLR   86 (93)
T ss_dssp             ECCCCCCC
T ss_pred             EccCcccc
Confidence            99876655

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.69  E-value=5.3e-17  Score=142.68  Aligned_cols=83  Identities=18%  Similarity=0.363  Sum_probs=78.3

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+|..+.+|.++|||||+|.+.++|++||+.|||..|+|+.|.|.++.
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ccc
Q 039806           92 RRA   94 (398)
Q Consensus        92 ~~~   94 (398)
                      ...
T Consensus       166 ~~~  168 (177)
T 2f3j_A          166 SQI  168 (177)
T ss_dssp             SGG
T ss_pred             CCC
Confidence            543

>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=99.69  E-value=2.9e-17  Score=133.17  Aligned_cols=77  Identities=18%  Similarity=0.184  Sum_probs=71.4

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      +...++|||+|||.++|+++|+++|+.||.|.+|+|..     ++|||||+|.+.++|++||+.|||..|.|+.|+|.++
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   81 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34568999999999999999999999999999999864     6799999999999999999999999999999999998


Q ss_pred             cc
Q 039806           91 IR   92 (398)
Q Consensus        91 ~~   92 (398)
                      ..
T Consensus        82 ~~   83 (111)
T 1whx_A           82 PI   83 (111)
T ss_dssp             ET
T ss_pred             CC
Confidence            64

>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=99.69  E-value=1.1e-16  Score=129.47  Aligned_cols=77  Identities=29%  Similarity=0.409  Sum_probs=71.4

Q ss_pred             CCcceEEEcCCCCC-CcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLAST-IDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~-vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++|||+|||.+ +|+++|+++|+.||.|.+|+|       ++|||||+|++.++|++|++.||+..|+|+.|.|.++
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            34589999999999 999999999999999999999       6799999999999999999999999999999999998


Q ss_pred             ccccc
Q 039806           91 IRRAD   95 (398)
Q Consensus        91 ~~~~~   95 (398)
                      .....
T Consensus        98 ~~~~~  102 (110)
T 1wf1_A           98 GEPKP  102 (110)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            75443

>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=99.68  E-value=7.4e-17  Score=137.79  Aligned_cols=80  Identities=24%  Similarity=0.361  Sum_probs=74.6

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+|..+    ++|||||+|.+.++|.+||+.|||..|+|+.|.|.+
T Consensus        69 ~~~~~~~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           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL  144 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3456789999999999999999999999999999999876    689999999999999999999999999999999999


Q ss_pred             cccc
Q 039806           90 FIRR   93 (398)
Q Consensus        90 ~~~~   93 (398)
                      +.++
T Consensus       145 a~~~  148 (150)
T 2i2y_A          145 SNGE  148 (150)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8764

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

Probab=99.68  E-value=2e-16  Score=124.84  Aligned_cols=79  Identities=25%  Similarity=0.300  Sum_probs=72.1

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ....++|||+||  ++|+++|+++|+.||.|.+|+|.     .++|||||+|.+.++|++||+.||+..|.|+.|.|.++
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            346789999997  89999999999999999999994     47899999999999999999999999999999999999


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      .++..+
T Consensus        85 ~~~~~~   90 (97)
T 1x5p_A           85 RKQPML   90 (97)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            876554

>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=99.67  E-value=2.8e-16  Score=135.19  Aligned_cols=124  Identities=15%  Similarity=0.137  Sum_probs=79.2

Q ss_pred             EEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccccccc---------cccCCCCceEEeeCCCc
Q 039806           43 SSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADR---------IQEGSSFNNLYVKNLDD  113 (398)
Q Consensus        43 ~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~~~~---------~~~~~~~~~lfV~nLp~  113 (398)
                      +++|..+.. +++|||||+|.+.++|++|++.+++....+..+.+.........         .......++|||+|||+
T Consensus         2 ~~kl~ln~~-~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~   80 (158)
T 2kn4_A            2 QYKLILNGK-TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTY   80 (158)
T ss_dssp             EEEEEEECS-SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCT
T ss_pred             cEEEEecCc-cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCC
Confidence            678888764 69999999999999999999988764333333333221111100         00111345555555555


Q ss_pred             cccHHHHHHHHccCCCEEEEEEeeCCCCCccccCCchhhhHHHHHHHHHHHHHHHHHHHhhhhhhccccCCCcccCHHHH
Q 039806          114 DMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAILRAQFERMRKERAELYKNINDEVDEIEL  193 (398)
Q Consensus       114 ~~tee~L~~~F~~fG~I~~~~i~~d~~g~s~Gf~~~~l~v~~a~~k~~~~~~~~~~~~~~~~~~~~~v~nL~~~vtee~L  193 (398)
                      ++|+++|+++|+.||                                                                 
T Consensus        81 ~~~~~~l~~~F~~~G-----------------------------------------------------------------   95 (158)
T 2kn4_A           81 RTSPDTLRRVFEKYG-----------------------------------------------------------------   95 (158)
T ss_dssp             TCCHHHHHHHHHHHS-----------------------------------------------------------------
T ss_pred             CCCHHHHHHHHHhcC-----------------------------------------------------------------
Confidence            555555555555555                                                                 


Q ss_pred             HHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          194 KQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       194 ~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                              .|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        96 --------~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~  136 (158)
T 2kn4_A           96 --------RVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAV  136 (158)
T ss_dssp             --------CEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEE
T ss_pred             --------CeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCE
Confidence                    55555555553 6777787 999999999999998776544

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=2.4e-16  Score=123.62  Aligned_cols=79  Identities=20%  Similarity=0.352  Sum_probs=70.2

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ..+.++|||+|||.++|+++|+++|+.||.|.+|  +.+. +|+   ||||+|.+.++|++||+ |||..|+|+.|.|.+
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~   78 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRP   78 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEE
Confidence            3456799999999999999999999999999987  4554 555   99999999999999999 999999999999998


Q ss_pred             cccccc
Q 039806           90 FIRRAD   95 (398)
Q Consensus        90 ~~~~~~   95 (398)
                      +..+..
T Consensus        79 a~~~~~   84 (94)
T 2e5g_A           79 REQKEF   84 (94)
T ss_dssp             SCCSCC
T ss_pred             CCcCCC
Confidence            875543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.67  E-value=2.9e-16  Score=129.91  Aligned_cols=80  Identities=28%  Similarity=0.311  Sum_probs=72.3

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeE-EEEEecCHHHHHHHHHHhcCCeecc--eEeeee
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGY-GFVQYSTPESALDAIEKLQGATVER--MELYVG   88 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~-aFV~F~~~e~A~~Ai~~lng~~l~g--k~i~V~   88 (398)
                      +..-+|||+||++.+|+++|+++|++||.|.+|+|..+    ++|| |||+|++.++|++|++.|||..|.|  +.|+|.
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            45677889999999999999999999999999999874    3677 9999999999999999999999988  899999


Q ss_pred             ccccccc
Q 039806           89 PFIRRAD   95 (398)
Q Consensus        89 ~~~~~~~   95 (398)
                      ++..+..
T Consensus       102 ~ak~~~l  108 (130)
T 3zzy_A          102 FSKLTSL  108 (130)
T ss_dssp             ECSCSSC
T ss_pred             ecCCCce
Confidence            9876543

>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=99.67  E-value=2.3e-16  Score=135.47  Aligned_cols=82  Identities=27%  Similarity=0.258  Sum_probs=74.1

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecc--eEeeee
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVER--MELYVG   88 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g--k~i~V~   88 (398)
                      .+...+|||+||++++|+++|+++|++||.|.+|+|..+.   ++|||||+|++.++|++|++.|||..|.|  +.|+|+
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~---~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS---SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            4556789999999999999999999999999999997654   67999999999999999999999999966  999999


Q ss_pred             ccccccc
Q 039806           89 PFIRRAD   95 (398)
Q Consensus        89 ~~~~~~~   95 (398)
                      ++..+..
T Consensus       120 ~Ak~~~l  126 (164)
T 1sjr_A          120 FSKLTSL  126 (164)
T ss_dssp             ECSSSSC
T ss_pred             EecCCcc
Confidence            9987643

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=1.5e-16  Score=125.12  Aligned_cols=81  Identities=21%  Similarity=0.320  Sum_probs=72.6

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEE-EEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSS-KVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~v-ki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .....++|||+|||.++|+++|+++|+.||.|.+| .|+.++   ..|.|||+|.+.++|++||+.|||..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~---~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   87 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---ETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVA   87 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSS---SSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34457899999999999999999999999999999 488776   22349999999999999999999999999999999


Q ss_pred             ccccc
Q 039806           89 PFIRR   93 (398)
Q Consensus        89 ~~~~~   93 (398)
                      ++.++
T Consensus        88 ~a~~~   92 (96)
T 2e44_A           88 YIPDE   92 (96)
T ss_dssp             ECCCC
T ss_pred             EcCcc
Confidence            98766

>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding protein; NMR {Triticum aestivum}

Probab=99.66  E-value=4.2e-18  Score=127.52  Aligned_cols=42  Identities=33%  Similarity=0.573  Sum_probs=40.3

Q ss_pred             hhHHhhhhcCChHHHhhhhhcccchhhhccccceeceeeeee
Q 039806          352 ENLSSMLVATSPDERKDILGQRLYPLVKKLKVITHIFVKGQF  393 (398)
Q Consensus       352 ~~~~s~la~a~p~~qk~mLGe~Lyplv~~~~~~~~~~~~~~~  393 (398)
                      ..++++||+++|++||+||||+|||||++++|++|+|||||+
T Consensus         8 ~~~as~La~~~p~~Qkq~LGE~LyplV~~~~p~~AgKITGML   49 (85)
T 2dyd_A            8 GALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGML   49 (85)
T ss_dssp             TTSCHHHHCCCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHH
T ss_pred             hhhHHHHHcCCHHHHHHHHHHHHHHHHHHhCccccchhhhhh
Confidence            358999999999999999999999999999999999999997

>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=99.66  E-value=1.6e-16  Score=123.16  Aligned_cols=75  Identities=24%  Similarity=0.323  Sum_probs=69.8

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...++|||+|||.++|+++|+++|+.| .|.+|++.     +++|||||+|.+.++|++|++.|||..++|+.|.|.++.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            356789999999999999999999999 99999994     589999999999999999999999999999999999875


Q ss_pred             c
Q 039806           92 R   92 (398)
Q Consensus        92 ~   92 (398)
                      .
T Consensus        77 ~   77 (88)
T 1wg1_A           77 T   77 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.66  E-value=4e-16  Score=135.42  Aligned_cols=79  Identities=24%  Similarity=0.454  Sum_probs=75.9

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|++..+. +|.++|||||+|.+.++|.+|++.|||..++|+.|.|.++
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            446899999999999999999999999999999999997 9999999999999999999999999999999999999886

>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=99.66  E-value=1e-16  Score=135.74  Aligned_cols=85  Identities=22%  Similarity=0.334  Sum_probs=74.0

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEE------EEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEe
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSK------VVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMEL   85 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vk------i~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i   85 (398)
                      ..+++|||+|||.++|+++|+++|+.||.|.+|.      +....+|+++|||||+|.+.++|.+||+.|||..|.|+.|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            4568999999999999999999999999998751      2222478999999999999999999999999999999999


Q ss_pred             eeecccccccc
Q 039806           86 YVGPFIRRADR   96 (398)
Q Consensus        86 ~V~~~~~~~~~   96 (398)
                      .|.++.....+
T Consensus       123 ~V~~a~~~~~~  133 (143)
T 3egn_A          123 VVQFARSARPK  133 (143)
T ss_dssp             EEEECCCSCC-
T ss_pred             EEEECCCCCCc
Confidence            99999765544

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.65  E-value=1.8e-16  Score=129.18  Aligned_cols=76  Identities=14%  Similarity=0.246  Sum_probs=69.4

Q ss_pred             ceEEEcCC----CCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecC----HHH----HHHHHH--HhcCCe
Q 039806           15 GNAFVKNL----ASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYST----PES----ALDAIE--KLQGAT   79 (398)
Q Consensus        15 ~~lfV~nL----p~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~----~e~----A~~Ai~--~lng~~   79 (398)
                      .+|||+||    |+++++++|+++|+.||.|.+|+++.|+ +|.++|||||+|.+    +++    |.+||+  .+||..
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    9999999999999999999999999999 99999999999996    433    899988  789999


Q ss_pred             ecceEeeeecc
Q 039806           80 VERMELYVGPF   90 (398)
Q Consensus        80 l~gk~i~V~~~   90 (398)
                      |+|+.|+|..-
T Consensus        83 I~Gr~irV~ln   93 (136)
T 2j8a_A           83 IMGFKFEVILN   93 (136)
T ss_dssp             ETTEEEEEEEC
T ss_pred             ecCcEEEEEEC
Confidence            99999999863

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=1.3e-16  Score=129.80  Aligned_cols=77  Identities=21%  Similarity=0.261  Sum_probs=68.2

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-C---CCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-E---GKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~---g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      +..++|||+|||.++|+++|+++|+.||.|. ++++.+. +   |+++|||||+|++.++|++||+.++  .++|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4578999999999999999999999999999 8888877 5   7999999999999999999999885  378888877


Q ss_pred             eccc
Q 039806           88 GPFI   91 (398)
Q Consensus        88 ~~~~   91 (398)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            6544

>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1

Probab=99.65  E-value=5.7e-18  Score=126.78  Aligned_cols=43  Identities=30%  Similarity=0.570  Sum_probs=41.0

Q ss_pred             hhHHhhhhcCChHHHhhhhhcccchhhhccccceeceeeeeee
Q 039806          352 ENLSSMLVATSPDERKDILGQRLYPLVKKLKVITHIFVKGQFR  394 (398)
Q Consensus       352 ~~~~s~la~a~p~~qk~mLGe~Lyplv~~~~~~~~~~~~~~~~  394 (398)
                      +.++++||+|+|++||+||||+|||||++++|++|+|||||+-
T Consensus         9 ~l~~s~La~a~p~~Qkq~LGE~LyplV~~~~p~~AgKITGMLL   51 (85)
T 1nmr_A            9 QNLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLL   51 (85)
T ss_dssp             CTTHHHHTTCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHCS
T ss_pred             ccCHHHHHcCChHHHHHHHHHHHHHHHHHhCccccchhhHhHh
Confidence            4789999999999999999999999999999999999999973

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

Probab=99.65  E-value=5e-16  Score=139.90  Aligned_cols=85  Identities=24%  Similarity=0.466  Sum_probs=79.6

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+|..+. +|+++|||||+|.+.++|.+|++.|||..|+|+.|.|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            455799999999999999999999999999999999997 9999999999999999999999999999999999999998


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      ..+...
T Consensus       203 ~~~~~~  208 (216)
T 2qfj_A          203 VTPPMP  208 (216)
T ss_dssp             SSCSST
T ss_pred             cCCCCC
Confidence            876443

>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=99.64  E-value=3.1e-16  Score=126.85  Aligned_cols=77  Identities=22%  Similarity=0.341  Sum_probs=68.9

Q ss_pred             CCCcceEEE--cCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCee-----cce
Q 039806           11 LSGIGNAFV--KNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATV-----ERM   83 (398)
Q Consensus        11 ~~~~~~lfV--~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l-----~gk   83 (398)
                      ...+++|||  +||+.++|+++|+++|++||.|.+|.|..     +||||||+|++.++|++|++.|||..|     .|+
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~-----~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-----TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            345678999  67999999999999999999999998864     479999999999999999999999988     689


Q ss_pred             Eeeeecccc
Q 039806           84 ELYVGPFIR   92 (398)
Q Consensus        84 ~i~V~~~~~   92 (398)
                      .|+|.++..
T Consensus        97 ~l~v~~a~~  105 (114)
T 2cq2_A           97 TLYLNFVEK  105 (114)
T ss_dssp             ECEEEEESC
T ss_pred             EEEEEeccc
Confidence            999988753

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.64  E-value=7.4e-16  Score=136.89  Aligned_cols=83  Identities=23%  Similarity=0.398  Sum_probs=79.1

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|++..+. +|.++|||||+|.+.++|.+|++.|||..|+|+.|.|.++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            567899999999999999999999999999999999998 9999999999999999999999999999999999999998


Q ss_pred             cccc
Q 039806           91 IRRA   94 (398)
Q Consensus        91 ~~~~   94 (398)
                      .++.
T Consensus       192 ~~~~  195 (198)
T 2yh0_A          192 SVGA  195 (198)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.64  E-value=4.5e-16  Score=155.37  Aligned_cols=88  Identities=23%  Similarity=0.396  Sum_probs=81.0

Q ss_pred             ccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEe
Q 039806            7 SEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMEL   85 (398)
Q Consensus         7 ~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i   85 (398)
                      +.......++|||+|||.+||+++|.++|+.||.|.+|+|+.+. +|.++|||||+|.+.++|.+||+.|||..|.|+.|
T Consensus        95 ~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i  174 (437)
T 3pgw_S           95 PNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV  174 (437)
T ss_pred             ccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEE
Confidence            33444556899999999999999999999999999999999997 99999999999999999999999999999999999


Q ss_pred             eeecccccc
Q 039806           86 YVGPFIRRA   94 (398)
Q Consensus        86 ~V~~~~~~~   94 (398)
                      .|.++..+.
T Consensus       175 ~V~~a~~~~  183 (437)
T 3pgw_S          175 LVDVERGRT  183 (437)
T ss_pred             EEEEeCCCC
Confidence            999987654

>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=99.64  E-value=4.8e-16  Score=120.79  Aligned_cols=77  Identities=14%  Similarity=0.301  Sum_probs=63.3

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCee--cceEeeee
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATV--ERMELYVG   88 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l--~gk~i~V~   88 (398)
                      .....+|||+|||.++|+++|+++|++||.|.+|+|+++    +||||||+|++.++|++    +++..+  .|+.|.|.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            345679999999999999999999999999999999875    89999999999999983    566654  59999999


Q ss_pred             ccccccc
Q 039806           89 PFIRRAD   95 (398)
Q Consensus        89 ~~~~~~~   95 (398)
                      ++.++.+
T Consensus        80 ~a~~k~~   86 (89)
T 3d2w_A           80 NAEPKHN   86 (89)
T ss_dssp             ECC----
T ss_pred             EcCCCCc
Confidence            9887654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=5.4e-16  Score=119.62  Aligned_cols=75  Identities=19%  Similarity=0.257  Sum_probs=66.8

Q ss_pred             Ccce-EEEcCCCCCCcHHH----HHHHHhcc-CCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806           13 GIGN-AFVKNLASTIDNLK----LHQIFSKF-GDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus        13 ~~~~-lfV~nLp~~vte~~----L~~~F~~~-G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      ++.+ |||+|||.++++++    |+++|+.| |+|++|      +|   |+|||.|.+.++|++|++.|||..+.||+|+
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            3445 99999999999888    66899999 599988      23   9999999999999999999999999999999


Q ss_pred             eecccccccc
Q 039806           87 VGPFIRRADR   96 (398)
Q Consensus        87 V~~~~~~~~~   96 (398)
                      |.++..+++-
T Consensus        78 v~~A~~~sd~   87 (96)
T 2diu_A           78 VSFTPKNREL   87 (96)
T ss_dssp             EESSCCSCCC
T ss_pred             EEecCCCcce
Confidence            9999877654

>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=99.64  E-value=2e-16  Score=129.06  Aligned_cols=75  Identities=20%  Similarity=0.199  Sum_probs=65.7

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceE-----ee
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERME-----LY   86 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~-----i~   86 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+|+.+      |||||+|++.++|++||+.|||..|+|+.     |.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            35689999999999999999999999999999999765      89999999999999999999999999998     55


Q ss_pred             eecccc
Q 039806           87 VGPFIR   92 (398)
Q Consensus        87 V~~~~~   92 (398)
                      |....+
T Consensus        88 v~~~~~   93 (115)
T 3beg_B           88 VKVDGP   93 (115)
T ss_dssp             EEECC-
T ss_pred             eccCCC
Confidence            555443

>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=99.63  E-value=8.9e-16  Score=136.11  Aligned_cols=84  Identities=18%  Similarity=0.385  Sum_probs=74.9

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+|..|. +|.++|||||+|.+.++|.+||+. ++..|+|+.|.|.++.
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecC
Confidence            45799999999999999999999999999999999998 899999999999999999999986 8999999999999998


Q ss_pred             cccccc
Q 039806           92 RRADRI   97 (398)
Q Consensus        92 ~~~~~~   97 (398)
                      ++.+..
T Consensus       182 ~k~~~~  187 (196)
T 1l3k_A          182 SKQEMA  187 (196)
T ss_dssp             ------
T ss_pred             ChhHhc
Confidence            877653

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.63  E-value=1.8e-15  Score=121.20  Aligned_cols=83  Identities=12%  Similarity=0.129  Sum_probs=74.0

Q ss_pred             cCCCcceEEEcCCCC-----CCcHHHHHHHHhccCCeeEEEEEEcC--CCCceeEEEEEecCHHHHHHHHHHhcCCeecc
Q 039806           10 RLSGIGNAFVKNLAS-----TIDNLKLHQIFSKFGDIQSSKVVVSQ--EGKSKGYGFVQYSTPESALDAIEKLQGATVER   82 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~-----~vte~~L~~~F~~~G~I~~vki~~d~--~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g   82 (398)
                      ....+++|+|+||-.     +-++++|++.|++||.|.+|+|.+++  ++.++|||||+|.+.++|.+|++.|||..++|
T Consensus         4 ~~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~G   83 (105)
T 2pe8_A            4 GKCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGG   83 (105)
T ss_dssp             GGSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            345678999999973     23789999999999999999999986  36899999999999999999999999999999


Q ss_pred             eEeeeecccc
Q 039806           83 MELYVGPFIR   92 (398)
Q Consensus        83 k~i~V~~~~~   92 (398)
                      +.|.|.++..
T Consensus        84 r~i~v~~a~~   93 (105)
T 2pe8_A           84 RVVKACFYNL   93 (105)
T ss_dssp             EECEEEECCH
T ss_pred             cEEEEEEcCH
Confidence            9999998864

>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=99.63  E-value=9.1e-16  Score=133.32  Aligned_cols=78  Identities=22%  Similarity=0.366  Sum_probs=73.7

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec---ceEeeeec
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE---RMELYVGP   89 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~---gk~i~V~~   89 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++..+.+|.++|||||+|.+.++|.+|++.|||..+.   +++|.|.+
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~  173 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKF  173 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEe
Confidence            567999999999999999999999999999999999999999999999999999999999999998776   49999987


Q ss_pred             c
Q 039806           90 F   90 (398)
Q Consensus        90 ~   90 (398)
                      +
T Consensus       174 a  174 (175)
T 3nmr_A          174 A  174 (175)
T ss_dssp             C
T ss_pred             c
Confidence            6

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.62  E-value=2.4e-15  Score=123.76  Aligned_cols=78  Identities=17%  Similarity=0.132  Sum_probs=69.6

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeE-EEEEecCHHHHHHHHHHhcCCeecc--eEeeee
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGY-GFVQYSTPESALDAIEKLQGATVER--MELYVG   88 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~-aFV~F~~~e~A~~Ai~~lng~~l~g--k~i~V~   88 (398)
                      +....|||+||+..+|+++|+++|+.||.|.+|+|...     .|| |||+|++.++|.+|++.|||..|.|  +.|+|.
T Consensus        23 s~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~   97 (124)
T 2e5i_A           23 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIE   97 (124)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEE
T ss_pred             CcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEE
Confidence            44556789999999999999999999999999999763     286 9999999999999999999999987  689999


Q ss_pred             cccccc
Q 039806           89 PFIRRA   94 (398)
Q Consensus        89 ~~~~~~   94 (398)
                      ++..+.
T Consensus        98 ~Ak~~~  103 (124)
T 2e5i_A           98 YARPTR  103 (124)
T ss_dssp             CCSCSC
T ss_pred             EecCCc
Confidence            987664

>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=99.62  E-value=3e-16  Score=135.58  Aligned_cols=80  Identities=19%  Similarity=0.429  Sum_probs=75.9

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|++..|. +|.++|||||+|.+.++|.+|++ +|+..++|+.|.|.++.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            35689999999999999999999999999999999997 89999999999999999999998 89999999999999987


Q ss_pred             cc
Q 039806           92 RR   93 (398)
Q Consensus        92 ~~   93 (398)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear; all-helical domain, RNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.144.1.1

Probab=99.62  E-value=1.2e-17  Score=126.87  Aligned_cols=42  Identities=14%  Similarity=0.116  Sum_probs=40.3

Q ss_pred             hhHHhhhhcCChHHHhhhhhcccchhhhc--cccceeceeeeee
Q 039806          352 ENLSSMLVATSPDERKDILGQRLYPLVKK--LKVITHIFVKGQF  393 (398)
Q Consensus       352 ~~~~s~la~a~p~~qk~mLGe~Lyplv~~--~~~~~~~~~~~~~  393 (398)
                      +.+||+||+|+|++||+||||+|||||++  ++|++|+|||||+
T Consensus         6 p~~a~~la~~~p~~Qkq~LGE~LyplV~~~~~~pelAgKITGML   49 (92)
T 1ifw_A            6 PRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMI   49 (92)
T ss_dssp             SSCCSSCCSCSCHHHHHHHHHHHHHHHGGGCCCHHHHHHHHHHH
T ss_pred             ccchHHHhcCChHHHHHHHHHHHHHHHHHhhcCccccchhhHhH
Confidence            46889999999999999999999999999  9999999999997

>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=99.62  E-value=1.8e-15  Score=130.64  Aligned_cols=80  Identities=31%  Similarity=0.461  Sum_probs=75.2

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecc--eEeee
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVER--MELYV   87 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g--k~i~V   87 (398)
                      ....++|||+|||.++|+++|+++|+.||.|.+|++..+. +|.++|||||+|.+.++|.+|++.|||..+.|  ++|.|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEE
Confidence            3456799999999999999999999999999999999998 99999999999999999999999999999988  99999


Q ss_pred             ecc
Q 039806           88 GPF   90 (398)
Q Consensus        88 ~~~   90 (398)
                      .++
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            764

>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=99.62  E-value=8.2e-16  Score=118.47  Aligned_cols=71  Identities=14%  Similarity=0.331  Sum_probs=66.3

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhcc----C-------CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKF----G-------DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE   81 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~----G-------~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~   81 (398)
                      ..++|||+|||.++|+++|+++|+.|    |       .|.+|++.+     ++|||||+|.+.++|++|+ .|||..|+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~-----~kg~afV~f~~~~~a~~A~-~l~g~~~~   78 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ-----DKNFAFLEFRSVDETTQAM-AFDGIIFQ   78 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECS-----SSSEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecC-----CCcEEEEEcCCHHHHHHHH-hcCCCEEC
Confidence            46799999999999999999999999    8       999999965     4799999999999999999 89999999


Q ss_pred             ceEeeeec
Q 039806           82 RMELYVGP   89 (398)
Q Consensus        82 gk~i~V~~   89 (398)
                      |+.|.|+.
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            99999974

>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=99.61  E-value=2e-15  Score=130.02  Aligned_cols=79  Identities=30%  Similarity=0.491  Sum_probs=73.3

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceE--eeee
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERME--LYVG   88 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~--i~V~   88 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|++..+. +|.++|||||+|.+.++|.+|++.|||..+.|+.  |.|.
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~  165 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK  165 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEE
Confidence            456789999999999999999999999999999999998 9999999999999999999999999999999975  7776


Q ss_pred             cc
Q 039806           89 PF   90 (398)
Q Consensus        89 ~~   90 (398)
                      ++
T Consensus       166 ~A  167 (167)
T 1fxl_A          166 FA  167 (167)
T ss_dssp             EC
T ss_pred             eC
Confidence            53

>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=99.61  E-value=3.5e-16  Score=121.07  Aligned_cols=79  Identities=15%  Similarity=0.322  Sum_probs=67.9

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..+++|||+|||.++|+++|+++|+.||.|.+|+|..+    ++|||||+|.+.++|++|+..  ...+.|+.|.|.++.
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            35689999999999999999999999999999999865    789999999999999865331  345689999999988


Q ss_pred             ccccc
Q 039806           92 RRADR   96 (398)
Q Consensus        92 ~~~~~   96 (398)
                      ++...
T Consensus        77 ~~~~~   81 (88)
T 1wf0_A           77 PKHNS   81 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76654

>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=99.61  E-value=1.3e-15  Score=132.78  Aligned_cols=88  Identities=22%  Similarity=0.323  Sum_probs=76.7

Q ss_pred             CCCCCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec
Q 039806            2 WSTPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE   81 (398)
Q Consensus         2 ~s~rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~   81 (398)
                      |+...........++|||+|||.++|+++|+++|+.||.|..+    +.+|.++|||||+|.+.++|.+|++.|||..|+
T Consensus        87 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~  162 (175)
T 1fje_B           87 KPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEID  162 (175)
T ss_dssp             CCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEET
T ss_pred             cCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            3444444444567899999999999999999999999988765    558999999999999999999999999999999


Q ss_pred             ceEeeeeccccc
Q 039806           82 RMELYVGPFIRR   93 (398)
Q Consensus        82 gk~i~V~~~~~~   93 (398)
                      |+.|.|.++.++
T Consensus       163 g~~i~v~~a~~k  174 (175)
T 1fje_B          163 GRSVSLYYTGEK  174 (175)
T ss_dssp             TEEEEEEECSSC
T ss_pred             CeEEEEEecCCC
Confidence            999999998765

>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=99.60  E-value=2.4e-15  Score=133.91  Aligned_cols=79  Identities=15%  Similarity=0.153  Sum_probs=73.3

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRR   93 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~   93 (398)
                      .++|||+|||.++|+++|+++|+.||.|.+|+|.++.+|.++|||||+|++.++|++|++.+ +..++|+.|.|.+....
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 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDY  187 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHH
Confidence            57999999999999999999999999999999999999999999999999999999999855 56999999999876543

>3kuj_A Polyadenylate-binding protein 1; protein-protein complex, methylation, mRNA processing, mRNA nucleus, phosphoprotein, RNA-binding, spliceosome; 1.40A {Homo sapiens} PDB: 3ktr_A 3kui_A 3ktp_A 3kus_A* 3kut_A 3pkn_A 2rqg_B 2rqh_B 3kur_A 3pth_A 2x04_A

Probab=99.59  E-value=7.4e-17  Score=121.92  Aligned_cols=42  Identities=31%  Similarity=0.580  Sum_probs=40.3

Q ss_pred             hhHHhhhhcCChHHHhhhhhcccchhhhccccceeceeeeee
Q 039806          352 ENLSSMLVATSPDERKDILGQRLYPLVKKLKVITHIFVKGQF  393 (398)
Q Consensus       352 ~~~~s~la~a~p~~qk~mLGe~Lyplv~~~~~~~~~~~~~~~  393 (398)
                      ..++|+||+|+|++||+||||+|||||++++|++|+|||||+
T Consensus         6 ~l~~s~la~a~p~~Qkq~LGE~Lyp~V~~~~p~~A~KITGML   47 (88)
T 3kuj_A            6 PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGML   47 (88)
T ss_dssp             CCCHHHHHTSCHHHHHHHHHHHHHHHHHHHCTTTHHHHHHHH
T ss_pred             cchHHHHHcCCHHHHHHHHHHHhHHHHHhhCCCccchhhhHh
Confidence            368999999999999999999999999999999999999996

>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A 1jh4_A

Probab=99.56  E-value=1.4e-15  Score=125.23  Aligned_cols=42  Identities=31%  Similarity=0.566  Sum_probs=40.4

Q ss_pred             hHHhhhhcCChHHHhhhhhcccchhhhccccceeceeeeeee
Q 039806          353 NLSSMLVATSPDERKDILGQRLYPLVKKLKVITHIFVKGQFR  394 (398)
Q Consensus       353 ~~~s~la~a~p~~qk~mLGe~Lyplv~~~~~~~~~~~~~~~~  394 (398)
                      .++++||+|+|++||+||||+|||||++++|++|+||||||-
T Consensus        53 l~as~La~a~p~eQkq~LGE~LyplV~~~~p~~A~KITGMLL   94 (144)
T 1g9l_A           53 LTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLL   94 (144)
T ss_dssp             CSHHHHTTCTTTTTTTTTTSSSHHHHHHHTTSCCSSHHHHTT
T ss_pred             hhHHHHHcCCHHHHHHHHHHHHHHHHHHhCccccchhhhhhc
Confidence            589999999999999999999999999999999999999973

>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=99.56  E-value=1.7e-14  Score=116.88  Aligned_cols=84  Identities=23%  Similarity=0.315  Sum_probs=72.4

Q ss_pred             ccCCCcceEEEcCCCCCCc-----------HHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcC
Q 039806            9 ARLSGIGNAFVKNLASTID-----------NLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG   77 (398)
Q Consensus         9 ~~~~~~~~lfV~nLp~~vt-----------e~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng   77 (398)
                      .+...+++|+|+||-...+           +++|+++|++||.|.+|.| .|.  .++|||||+|.+.++|.+|++.|||
T Consensus        10 ~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            3566789999999954433           6899999999999999966 544  3899999999999999999999999


Q ss_pred             CeecceEeeeeccccccc
Q 039806           78 ATVERMELYVGPFIRRAD   95 (398)
Q Consensus        78 ~~l~gk~i~V~~~~~~~~   95 (398)
                      ..|+|+.|.|.++..+..
T Consensus        87 ~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             CEETTEECEEEECCSCCC
T ss_pred             CEECCcEEEEEEeCCCCC
Confidence            999999999999876544

>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=99.53  E-value=2.5e-14  Score=121.93  Aligned_cols=93  Identities=15%  Similarity=0.195  Sum_probs=67.9

Q ss_pred             EEEEEcCCCCceeEEEEEecCHHHHHHHHHHh-cCCeecceEeeeeccccccccc------------ccCCCCceEEeeC
Q 039806           44 SKVVVSQEGKSKGYGFVQYSTPESALDAIEKL-QGATVERMELYVGPFIRRADRI------------QEGSSFNNLYVKN  110 (398)
Q Consensus        44 vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~l-ng~~l~gk~i~V~~~~~~~~~~------------~~~~~~~~lfV~n  110 (398)
                      ..+..+. ...+|+++|+|.+.++|++|++.+ ||..++| .|.+.++..+....            ......++|||+|
T Consensus         3 ~al~l~g-~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~n   80 (150)
T 2i2y_A            3 YKLILNG-KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGN   80 (150)
T ss_dssp             EEEEECC-SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEES
T ss_pred             eEeeecc-ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeC
Confidence            3444432 356899999999999999999999 9999999 99999887643221            1112567788888


Q ss_pred             CCccccHHHHHHHHccCCCEEEEEEeeC
Q 039806          111 LDDDMTEEILVEKFSEFGKITSLVISKD  138 (398)
Q Consensus       111 Lp~~~tee~L~~~F~~fG~I~~~~i~~d  138 (398)
                      ||+++|+++|+++|+.||.|.++.+++|
T Consensus        81 l~~~~t~~~l~~~F~~~G~i~~v~i~~~  108 (150)
T 2i2y_A           81 LGNNGNKTELERAFGYYGPLRSVWVARN  108 (150)
T ss_dssp             CCSCCSCHHHHHHHHHHSCEEEEEECSS
T ss_pred             CCCCCCHHHHHHHHHhhCCEEEEEEeeC
Confidence            7777777777777777776666665543

>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=99.53  E-value=4e-15  Score=119.02  Aligned_cols=72  Identities=15%  Similarity=0.282  Sum_probs=64.5

Q ss_pred             EcCCCCCCcHHHHHHHH------------hccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806           19 VKNLASTIDNLKLHQIF------------SKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus        19 V~nLp~~vte~~L~~~F------------~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      +.||+..+|+++|.+.|            ++||.|.+|+|.++.+++++|||||+|.+.++|.+|++.|||..++|+.|+
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            56677777887777666            999999999999988889999999999999999999999999999999999


Q ss_pred             eecc
Q 039806           87 VGPF   90 (398)
Q Consensus        87 V~~~   90 (398)
                      |.++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9875

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

Probab=99.53  E-value=1.1e-14  Score=133.14  Aligned_cols=79  Identities=25%  Similarity=0.329  Sum_probs=70.8

Q ss_pred             CCcceEEEcCCCCCC---------cHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCee--
Q 039806           12 SGIGNAFVKNLASTI---------DNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATV--   80 (398)
Q Consensus        12 ~~~~~lfV~nLp~~v---------te~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l--   80 (398)
                      ...++|||+||+.++         ++++|+++|+.||.|.+|+|+.     +||||||+|.+.++|+.|++.|||..|  
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-----~kG~AFV~F~~~~~Ae~A~~am~g~~l~~  206 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQANAEFAKEAMSNQTLLL  206 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHHHTTCCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-----CCCEEEEEeCCHHHHHHHHHHhCCCEEec
Confidence            457899999999998         7999999999999999999985     689999999999999999999999999  


Q ss_pred             ----------cceEeeeeccccccc
Q 039806           81 ----------ERMELYVGPFIRRAD   95 (398)
Q Consensus        81 ----------~gk~i~V~~~~~~~~   95 (398)
                                .|+.|.|.++.....
T Consensus       207 ~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          207 PSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             TTSTTGGGGGGSCCCEEEECC----
T ss_pred             cccccccccCCCCEEEEEEccCCCC
Confidence                      899999999976543

>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=99.51  E-value=4.7e-14  Score=131.42  Aligned_cols=84  Identities=32%  Similarity=0.481  Sum_probs=76.1

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhc-CCeec---ceEeeee
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ-GATVE---RMELYVG   88 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~ln-g~~l~---gk~i~V~   88 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+|+.|.+|+++|||||+|.+.++|.+||+.|| +..+.   ++.|.|.
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~  174 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE  174 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEe
Confidence            4679999999999999999999999999999999999999999999999999999999999994 55555   8999999


Q ss_pred             cccccccc
Q 039806           89 PFIRRADR   96 (398)
Q Consensus        89 ~~~~~~~~   96 (398)
                      ++......
T Consensus       175 ~~~~~~~~  182 (261)
T 3sde_A          175 PMEQFDDE  182 (261)
T ss_dssp             ECCCEESS
T ss_pred             eccccCcc
Confidence            98765443

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.49  E-value=7.2e-14  Score=131.32  Aligned_cols=76  Identities=20%  Similarity=0.298  Sum_probs=70.8

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec-ceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE-RMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~-gk~i~V~~~   90 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+|..++    +|||||+|.+.++|.+|++.|||..|. |+.|+|.++
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a  280 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFA  280 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEe
Confidence            356789999999999999999999999999999999654    589999999999999999999999999 999999987


Q ss_pred             c
Q 039806           91 I   91 (398)
Q Consensus        91 ~   91 (398)
                      .
T Consensus       281 k  281 (282)
T 3pgw_A          281 K  281 (282)
T ss_pred             c
Confidence            5

>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=99.49  E-value=3.7e-14  Score=113.52  Aligned_cols=81  Identities=14%  Similarity=0.107  Sum_probs=70.6

Q ss_pred             CcceEEEcCCC--CCCc--------HHHHHHHHhccCCeeEEEEEEcCC---CCceeEEEEEecCHHHHHHHHHHhcCCe
Q 039806           13 GIGNAFVKNLA--STID--------NLKLHQIFSKFGDIQSSKVVVSQE---GKSKGYGFVQYSTPESALDAIEKLQGAT   79 (398)
Q Consensus        13 ~~~~lfV~nLp--~~vt--------e~~L~~~F~~~G~I~~vki~~d~~---g~skg~aFV~F~~~e~A~~Ai~~lng~~   79 (398)
                      .++.|.|+|+=  .++.        ++||++.|++||.|.+|+|.++..   +.++|||||+|.+.++|.+|++.|||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            57789999983  3442        368999999999999999999873   3689999999999999999999999999


Q ss_pred             ecceEeeeeccccc
Q 039806           80 VERMELYVGPFIRR   93 (398)
Q Consensus        80 l~gk~i~V~~~~~~   93 (398)
                      ++||.|.|.++...
T Consensus        84 f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           84 FANRVVVTKYCDPD   97 (105)
T ss_dssp             ETTEECEEEEECHH
T ss_pred             eCCCEEEEEEeCHH
Confidence            99999999987543

>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=99.49  E-value=3.4e-14  Score=127.70  Aligned_cols=76  Identities=13%  Similarity=0.170  Sum_probs=67.4

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCe--eEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecce----Eee
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDI--QSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERM----ELY   86 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I--~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk----~i~   86 (398)
                      .+++|||+|||.++|+++|+++|+.||.|  .+|++..+. +.++|||||+|++.++|.+||+.|||..|.|+    ++.
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~  200 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYT  200 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEE
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceE
Confidence            35689999999999999999999999999  899998876 55679999999999999999999999999886    455


Q ss_pred             eec
Q 039806           87 VGP   89 (398)
Q Consensus        87 V~~   89 (398)
                      |++
T Consensus       201 vk~  203 (205)
T 3tyt_A          201 LKL  203 (205)
T ss_dssp             CEE
T ss_pred             EEe
Confidence            543

>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=99.47  E-value=9e-14  Score=113.52  Aligned_cols=82  Identities=15%  Similarity=0.181  Sum_probs=71.7

Q ss_pred             CCCcceEEEcCCCC--CC---cHHHHHHHHhccCCeeEEEEEEcC-----CCCceeEEEEEecCHHHHHHHHHHhcCCee
Q 039806           11 LSGIGNAFVKNLAS--TI---DNLKLHQIFSKFGDIQSSKVVVSQ-----EGKSKGYGFVQYSTPESALDAIEKLQGATV   80 (398)
Q Consensus        11 ~~~~~~lfV~nLp~--~v---te~~L~~~F~~~G~I~~vki~~d~-----~g~skg~aFV~F~~~e~A~~Ai~~lng~~l   80 (398)
                      ...++.|+|+|+-.  ++   .++||++.|++||.|.+|+|.++.     ++.++||+||+|.+.++|.+|++.|||..+
T Consensus        17 ~~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f   96 (118)
T 3ue2_A           17 KQESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWF   96 (118)
T ss_dssp             HHSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEE
Confidence            34678999999942  22   468999999999999999999986     257889999999999999999999999999


Q ss_pred             cceEeeeecccc
Q 039806           81 ERMELYVGPFIR   92 (398)
Q Consensus        81 ~gk~i~V~~~~~   92 (398)
                      +|+.|.|.++..
T Consensus        97 ~GR~i~v~~~~~  108 (118)
T 3ue2_A           97 AGRKVVAEVYDQ  108 (118)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCcEEEEEEcCh
Confidence            999999998753

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

Probab=99.44  E-value=1.4e-13  Score=122.42  Aligned_cols=76  Identities=17%  Similarity=0.236  Sum_probs=70.6

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccC-CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec-ceEeeeecc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFG-DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE-RMELYVGPF   90 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G-~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~-gk~i~V~~~   90 (398)
                      .+++|||+|||.++|+++|+++|+.|| .|.+|++..+    ++|||||+|.+.++|.+|++.|||..++ |+.|.|.++
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a  194 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS  194 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEee
Confidence            378899999999999999999999999 9999999664    4789999999999999999999999999 999999997


Q ss_pred             cc
Q 039806           91 IR   92 (398)
Q Consensus        91 ~~   92 (398)
                      .+
T Consensus       195 ~~  196 (198)
T 1qm9_A          195 KS  196 (198)
T ss_dssp             CC
T ss_pred             cc
Confidence            65

>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=99.43  E-value=2e-13  Score=124.66  Aligned_cols=76  Identities=17%  Similarity=0.243  Sum_probs=70.5

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccC-CeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec-ceEeeeeccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFG-DIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE-RMELYVGPFI   91 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G-~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~-gk~i~V~~~~   91 (398)
                      +++|||+|||.++|+++|+++|+.|| .|.+|++..+    ++|||||+|.+.++|.+|++.|||..+. |+.|.|.++.
T Consensus       151 ~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~  226 (229)
T 2adc_A          151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK  226 (229)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEec
Confidence            68899999999999999999999999 9999999653    4789999999999999999999999999 9999999986


Q ss_pred             cc
Q 039806           92 RR   93 (398)
Q Consensus        92 ~~   93 (398)
                      ++
T Consensus       227 ~~  228 (229)
T 2adc_A          227 ST  228 (229)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.41  E-value=9.5e-13  Score=104.14  Aligned_cols=79  Identities=15%  Similarity=0.151  Sum_probs=66.4

Q ss_pred             CCCcceEEEcCCC-------CCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecce
Q 039806           11 LSGIGNAFVKNLA-------STIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERM   83 (398)
Q Consensus        11 ~~~~~~lfV~nLp-------~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk   83 (398)
                      .+...+|.|+-..       .++|+++|+++|++||.|.+|+|+    ++++|||||+|++.++|++||+.++  .+.|+
T Consensus         7 ~~~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~   80 (100)
T 2d9o_A            7 GQGTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQNEV--GLVDN   80 (100)
T ss_dssp             CCSSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHTCC--BCSSS
T ss_pred             CCccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHhcC--CCCCC
Confidence            3446678887665       458999999999999999999998    4689999999999999999999744  46799


Q ss_pred             Eeeeeccccccc
Q 039806           84 ELYVGPFIRRAD   95 (398)
Q Consensus        84 ~i~V~~~~~~~~   95 (398)
                      .|.|.++..+..
T Consensus        81 ~l~V~~a~~~~~   92 (100)
T 2d9o_A           81 PLKISWLEGQPQ   92 (100)
T ss_dssp             BCEEECSSCCCC
T ss_pred             eEEEEEccCCCC
Confidence            999999876543

>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=99.39  E-value=4.5e-13  Score=105.99  Aligned_cols=65  Identities=18%  Similarity=0.268  Sum_probs=59.8

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .++++|+|||.++|+++|+++|++||.|++|+|++|+ +|+++|| ||+|.+.++|.+|+..++...
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~   85 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLR   85 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCE
Confidence            4568999999999999999999999999999999997 8999999 999999999999998876543

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

Probab=99.36  E-value=8.3e-13  Score=106.56  Aligned_cols=67  Identities=16%  Similarity=0.235  Sum_probs=61.6

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ..++++|+||++++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++....
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~   73 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSV   73 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEE
Confidence            35688999999999999999999999999999999998 7999999 9999999999999998876543

>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=99.36  E-value=1.1e-12  Score=125.98  Aligned_cols=76  Identities=24%  Similarity=0.304  Sum_probs=65.8

Q ss_pred             CCCcceEEEcC--CCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec---ce--
Q 039806           11 LSGIGNAFVKN--LASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE---RM--   83 (398)
Q Consensus        11 ~~~~~~lfV~n--Lp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~---gk--   83 (398)
                      ...+.+|||+|  |+.++|+++|+++|++||.|.+|++..     +||||||+|++.++|++||+.|||..+.   |+  
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~   89 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCce
Confidence            45678999999  578999999999999999999987743     6799999999999999999999999873   34  


Q ss_pred             Eeeeeccc
Q 039806           84 ELYVGPFI   91 (398)
Q Consensus        84 ~i~V~~~~   91 (398)
                      .++|.+..
T Consensus        90 ~ly~~~~~   97 (345)
T 3tht_A           90 TLYLNFVE   97 (345)
T ss_dssp             ECEEEECS
T ss_pred             EEEEEEee
Confidence            67777764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.34  E-value=5.2e-13  Score=104.76  Aligned_cols=63  Identities=6%  Similarity=0.154  Sum_probs=58.2

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCC--eEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGT--ISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~--I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      .+++|+|||+++|+++|+++|++||.  |.+|+|++|+ +|++||| ||+|.+.++|.+|+..++..
T Consensus        10 ~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~   76 (95)
T 2lkz_A           10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSL   76 (95)
T ss_dssp             CEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSS
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCC
Confidence            57899999999999999999999995  6799999997 8999999 99999999999999888754

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.34  E-value=2.2e-13  Score=106.07  Aligned_cols=61  Identities=13%  Similarity=0.240  Sum_probs=56.7

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCC-CeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHh
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCG-TISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG-~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ++++|+|||.++||++|+++|++|| .|++|+|++|+ +|++||| ||+|.+.++|.+|+..+.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~   65 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQ   65 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcC
Confidence            5788999999999999999999999 89999999997 8999999 999999999999987653

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.31  E-value=3e-12  Score=102.00  Aligned_cols=61  Identities=15%  Similarity=0.225  Sum_probs=57.6

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHH
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      ...++++|+|||.++|+++|+++|++||.|++|+|++|..|+++|| ||+|.+.++|.+|+.
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~   70 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE   70 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH
Confidence            3468899999999999999999999999999999999988999999 999999999999986

>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=99.31  E-value=5e-12  Score=102.46  Aligned_cols=78  Identities=13%  Similarity=0.074  Sum_probs=66.6

Q ss_pred             CCcceEEEcCCCCCC----------cHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec
Q 039806           12 SGIGNAFVKNLASTI----------DNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE   81 (398)
Q Consensus        12 ~~~~~lfV~nLp~~v----------te~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~   81 (398)
                      ..++.|.|+|+=..-          .++||++.|++||.|.+|+|.++.   ++|||||+|.+.++|.+|++.|||..++
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            356789999886432          245789999999999999996653   6899999999999999999999999999


Q ss_pred             ceEeeeecccc
Q 039806           82 RMELYVGPFIR   92 (398)
Q Consensus        82 gk~i~V~~~~~   92 (398)
                      |+.|.|.++..
T Consensus        82 GR~i~v~~~~~   92 (114)
T 3s6e_A           82 GKMITAAYVPL   92 (114)
T ss_dssp             TEECEEEEECH
T ss_pred             CEEEEEEEEcH
Confidence            99999998753

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.28  E-value=2.6e-12  Score=101.66  Aligned_cols=67  Identities=12%  Similarity=0.163  Sum_probs=61.6

Q ss_pred             hhhhhccccCCCc------ccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNIND------EVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~------~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..+++++|+|||.      ++++++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~   78 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKR   78 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCB
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcc
Confidence            3467899999999      99999999999999999999999998 6999999 999999999999998877554

>1i2t_A HYD protein; four alpha-helical domain, ligase; 1.04A {Homo sapiens} SCOP: a.144.1.1 PDB: 3ntw_A

Probab=99.28  E-value=1.4e-13  Score=96.83  Aligned_cols=28  Identities=29%  Similarity=0.554  Sum_probs=27.4

Q ss_pred             Hhhhhhcccchhhhccccceeceeeeee
Q 039806          366 RKDILGQRLYPLVKKLKVITHIFVKGQF  393 (398)
Q Consensus       366 qk~mLGe~Lyplv~~~~~~~~~~~~~~~  393 (398)
                      ||+||||+|||+|++++|++|+|||||+
T Consensus         1 qkq~LGe~Lyp~V~~~~p~~A~KITGML   28 (61)
T 1i2t_A            1 HRQALGERLYPRVQAMQPAFASKITGML   28 (61)
T ss_dssp             CHHHHHHHHHHHHHHHCGGGHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhCcccccchhhhh
Confidence            7999999999999999999999999997

>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=99.26  E-value=9.1e-12  Score=97.24  Aligned_cols=68  Identities=18%  Similarity=0.242  Sum_probs=62.1

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ....++++|+|||.++++++|+++|++||.|++|+|++|.+|+++|| ||+|.+.++|.+|+..++...
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~   81 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIR   81 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCE
Confidence            34567899999999999999999999999999999999999999999 999999999999998776543

>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=99.26  E-value=4.9e-12  Score=102.74  Aligned_cols=64  Identities=20%  Similarity=0.245  Sum_probs=57.7

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..+++|+|||.++|+++|+++|++||.|++|+|++|. +.+||| ||+|.+.++|.+|+.+++...
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~-~~~kg~afV~f~~~~~A~~Ai~~l~~~~   69 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGML   69 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESCHHHHHHHHHHHTTCE
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC-CCCCceEEEEECCHHHHHHHHHHcCCCE
Confidence            3568999999999999999999999999999999985 458999 999999999999998877544

>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=99.26  E-value=4.7e-12  Score=98.11  Aligned_cols=64  Identities=16%  Similarity=0.159  Sum_probs=57.3

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCC--CeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCG--TISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG--~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .+++|+||+.++|+++|+++|++||  .|.+|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~   69 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRE   69 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCe
Confidence            3678899999999999999999999  99999999997 9999999 999999999999998877654

>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=99.24  E-value=1.1e-11  Score=95.15  Aligned_cols=65  Identities=14%  Similarity=0.210  Sum_probs=59.7

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ..++++|+|||.++++++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+..++..
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   71 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQ   71 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC
Confidence            45788999999999999999999999999999999996 8999999 99999999999999877654

>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=99.24  E-value=9.4e-12  Score=99.09  Aligned_cols=66  Identities=17%  Similarity=0.313  Sum_probs=61.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+||+.++++++|+++|++||.|++|+|++|.+|+++|| ||+|.+.++|.+|+..++...
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   80 (105)
T 2dnh_A           14 RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQ   80 (105)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCc
Confidence            457899999999999999999999999999999999999999999 999999999999998877654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.24  E-value=7.6e-12  Score=95.64  Aligned_cols=66  Identities=11%  Similarity=0.142  Sum_probs=60.5

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   71 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASG   71 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCe
Confidence            45788999999999999999999999999999999986 8999999 999999999999998777543

>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=99.24  E-value=9.2e-12  Score=95.59  Aligned_cols=63  Identities=14%  Similarity=0.246  Sum_probs=57.8

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHH
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                      ....++++|+|||.++++++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+..
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~   72 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ   72 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh
Confidence            3456789999999999999999999999999999999997 7999999 9999999999999843

>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=99.23  E-value=1.7e-11  Score=94.42  Aligned_cols=65  Identities=23%  Similarity=0.378  Sum_probs=59.4

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ...++++|+|||.++++++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+ .++..
T Consensus         4 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~   70 (89)
T 3ucg_A            4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDES   70 (89)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTC
T ss_pred             CcCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCC
Confidence            346789999999999999999999999999999999997 8999999 99999999999998 66543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.23  E-value=1.4e-11  Score=97.21  Aligned_cols=66  Identities=11%  Similarity=0.214  Sum_probs=60.9

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|++|+|++|.+|+++|| ||+|.+.++|.+|+..++...
T Consensus        16 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~   82 (100)
T 2do4_A           16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMT   82 (100)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCE
Confidence            457789999999999999999999999999999999999999999 999999999999998877543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.22  E-value=2.1e-11  Score=95.05  Aligned_cols=67  Identities=16%  Similarity=0.158  Sum_probs=60.9

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~   81 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME   81 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCE
Confidence            456789999999999999999999999999999999987 7899999 999999999999998876543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.22  E-value=1.5e-11  Score=99.47  Aligned_cols=67  Identities=19%  Similarity=0.228  Sum_probs=61.7

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+||+.++++++|+++|++||.|++|+|++|.+|+++|| ||+|.+.++|.+|+..++...
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~   80 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQL   80 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            3467899999999999999999999999999999999999999999 999999999999998877544

>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=99.22  E-value=1.4e-11  Score=96.58  Aligned_cols=65  Identities=17%  Similarity=0.202  Sum_probs=59.8

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +++++|+||+.++++++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   68 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ   68 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCe
Confidence            4678999999999999999999999999999999986 7999999 999999999999998776543

>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=99.22  E-value=7.6e-12  Score=99.44  Aligned_cols=58  Identities=14%  Similarity=0.170  Sum_probs=54.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHH
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSY  233 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~  233 (398)
                      ..++++|+|||+++|+++|+++|++||. ++|+|++|++|+++|| ||+|.+.++|.+|+
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al   72 (102)
T 1wez_A           14 TGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAM   72 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHHHHHHH
Confidence            4567899999999999999999999994 5999999999999999 99999999999998

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.22  E-value=1.1e-11  Score=99.62  Aligned_cols=65  Identities=14%  Similarity=0.193  Sum_probs=57.1

Q ss_pred             HhhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHH
Q 039806          172 RMRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRI  236 (398)
Q Consensus       172 ~~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~  236 (398)
                      .....++++|+||+.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..+
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~   87 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS   87 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC
Confidence            34556889999999999999999999999999999999987 7999999 99999999999998765

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.22  E-value=1.3e-11  Score=98.05  Aligned_cols=67  Identities=16%  Similarity=0.238  Sum_probs=61.5

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhc-CCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQ-CGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~-fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+||+.++|+++|+++|++ ||.|++|+|++|.+|+++|| ||+|.+.++|.+|+..++...
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~   75 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAV   75 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCc
Confidence            34578999999999999999999999 99999999999999999999 999999999999998777543

>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=99.21  E-value=1.9e-11  Score=92.77  Aligned_cols=64  Identities=16%  Similarity=0.181  Sum_probs=58.5

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .+++|+|||.++++++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~   67 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQD   67 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCe
Confidence            367889999999999999999999999999999995 8999999 999999999999998776543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.21  E-value=2e-11  Score=95.26  Aligned_cols=66  Identities=17%  Similarity=0.259  Sum_probs=60.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   71 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFE   71 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCe
Confidence            35688999999999999999999999999999999987 7999999 999999999999998877543

>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=99.21  E-value=1.4e-11  Score=96.91  Aligned_cols=66  Identities=15%  Similarity=0.197  Sum_probs=60.9

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   74 (99)
T 1whw_A            7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQV   74 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCE
Confidence            45789999999999999999999999999999999998 9999999 999999999999998776544

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.20  E-value=1.3e-11  Score=98.18  Aligned_cols=61  Identities=11%  Similarity=0.089  Sum_probs=55.0

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ....++++|+|||+++||++|+++|++||.|++|+|+++     ||| ||+|++.++|.+|+..++.
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~   74 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTS   74 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhcc
Confidence            345678999999999999999999999999999999965     788 9999999999999987653

>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=99.20  E-value=2.1e-11  Score=97.35  Aligned_cols=68  Identities=13%  Similarity=0.194  Sum_probs=62.1

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ....++++|+||+.++++++|+++|++||.|++|+|+++.+|+++|| ||+|.+.++|.+|+..++...
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~   94 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVP   94 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            34567899999999999999999999999999999999999999999 999999999999998876543

>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=99.19  E-value=1.5e-11  Score=93.78  Aligned_cols=67  Identities=15%  Similarity=0.207  Sum_probs=60.5

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   73 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE   73 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCE
Confidence            346788999999999999999999999999999999985 8999999 999999999999998776543

>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=99.19  E-value=1.3e-11  Score=100.40  Aligned_cols=67  Identities=18%  Similarity=0.260  Sum_probs=61.1

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++|.+|+++|| ||+|.+.++|.+|+..+....
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~   72 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKS   72 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCE
Confidence            3457889999999999999999999999999999999999999999 999999999999998766443

>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=99.19  E-value=1e-11  Score=99.04  Aligned_cols=67  Identities=18%  Similarity=0.318  Sum_probs=61.3

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        11 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~   79 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQK   79 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCc
Confidence            345778999999999999999999999999999999987 7999999 999999999999998887654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.19  E-value=2.3e-11  Score=95.73  Aligned_cols=63  Identities=16%  Similarity=0.329  Sum_probs=57.9

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHh
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+. ++
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~   72 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MH   72 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hC
Confidence            345789999999999999999999999999999999987 7999999 999999999999986 54

>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=99.19  E-value=2e-11  Score=98.12  Aligned_cols=63  Identities=14%  Similarity=0.220  Sum_probs=59.2

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHh
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ..++++|+|||.++++++|+++|++||.|.+|+|++|. +|.++|| ||+|.+.++|.+|+..++
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~   78 (111)
T 1x4h_A           14 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAAS   78 (111)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhc
Confidence            45789999999999999999999999999999999997 7899999 999999999999998876

>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=99.19  E-value=1.8e-11  Score=99.16  Aligned_cols=66  Identities=14%  Similarity=0.184  Sum_probs=60.8

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+||+.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~   91 (115)
T 2cpz_A           24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQ   91 (115)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCE
Confidence            35789999999999999999999999999999999998 8999999 999999999999998876543

>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=99.19  E-value=1.5e-11  Score=97.91  Aligned_cols=61  Identities=13%  Similarity=0.181  Sum_probs=57.0

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEE-EEEeeCCCCCccce-EEEecccHHHHHHHHH
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISS-VKIMRTDRGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~s-vki~~d~~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                      ...+++|+|||.++++++|+++|++||.|.+ |+|++|.+|+++|| ||+|.+.++|.+|+..
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~   76 (104)
T 1wg5_A           14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK   76 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh
Confidence            3567889999999999999999999999998 99999999999999 9999999999999876

>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=99.19  E-value=2.1e-11  Score=98.67  Aligned_cols=66  Identities=17%  Similarity=0.326  Sum_probs=59.8

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+||+.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+ .++...
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~   90 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQR   90 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCE
Confidence            345789999999999999999999999999999999988 6899999 99999999999999 776543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.19  E-value=1.7e-11  Score=96.48  Aligned_cols=66  Identities=21%  Similarity=0.256  Sum_probs=60.5

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeE-EEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTIS-SVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~-svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ...++++|+|||.++++++|+++|++||.|. +|+|++|. +|+++|| ||+|.+.++|.+|+..++..
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   75 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGK   75 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTS
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCC
Confidence            3467899999999999999999999999999 99999997 8999999 99999999999999876654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.19  E-value=2.7e-11  Score=94.31  Aligned_cols=65  Identities=18%  Similarity=0.234  Sum_probs=59.5

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ..++++|+|||.++++++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+..++..
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   81 (94)
T 2e5h_A           15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNK   81 (94)
T ss_dssp             CTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCC
Confidence            45788999999999999999999999999999999987 6899999 99999999999999876644

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.18  E-value=1.7e-11  Score=97.21  Aligned_cols=67  Identities=16%  Similarity=0.301  Sum_probs=60.9

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~   81 (103)
T 2cq0_A           13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFG   81 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCe
Confidence            345788999999999999999999999999999999996 8999999 999999999999998776543

>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=99.18  E-value=2e-11  Score=97.14  Aligned_cols=67  Identities=13%  Similarity=0.211  Sum_probs=61.0

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   81 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIK   81 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCe
Confidence            346789999999999999999999999999999999987 8999999 999999999999998766543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.18  E-value=2.6e-11  Score=96.15  Aligned_cols=65  Identities=26%  Similarity=0.362  Sum_probs=60.2

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++|+++|+++|++||.|++|+|++| +|.++|| ||+|.+.++|.+|+..++...
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~   79 (103)
T 2d9p_A           14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRI   79 (103)
T ss_dssp             SCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCB
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4578899999999999999999999999999999999 9999999 999999999999998877544

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.18  E-value=2.9e-11  Score=96.28  Aligned_cols=62  Identities=18%  Similarity=0.247  Sum_probs=57.8

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHH
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~   77 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS   77 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh
Confidence            345789999999999999999999999999999999996 8999999 9999999999999876

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.18  E-value=1.1e-11  Score=92.83  Aligned_cols=60  Identities=15%  Similarity=0.246  Sum_probs=56.6

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHh
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      +++|+|||.++++++|+++|++||.|.+|++++|. +|+++|| ||.|.+.++|.+|+..+.
T Consensus         2 ~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~   63 (77)
T 1uaw_A            2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR   63 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC
Confidence            57889999999999999999999999999999987 7999999 999999999999998776

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.18  E-value=3.1e-11  Score=96.24  Aligned_cols=66  Identities=14%  Similarity=0.225  Sum_probs=60.3

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+||+.++++++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        22 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   89 (106)
T 1p27_B           22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD   89 (106)
T ss_dssp             TBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCB
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCE
Confidence            45678999999999999999999999999999999987 7999999 999999999999998776543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.18  E-value=2.2e-11  Score=97.90  Aligned_cols=60  Identities=8%  Similarity=0.183  Sum_probs=56.0

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHh
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ..+++|+|||+++|+++|+++|+.| .|++|+|++|.+|+++|| ||+|.+.++|.+|+ ++.
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~   76 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRN   76 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcC
Confidence            4678999999999999999999999 899999999999999999 99999999999998 444

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.18  E-value=3e-11  Score=97.88  Aligned_cols=67  Identities=15%  Similarity=0.210  Sum_probs=60.9

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+||+.++++++|+++|++||.|++|+|++|. +|.++|| ||+|.+.++|.+|+..++...
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   81 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW   81 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            345789999999999999999999999999999999996 8999999 999999999999998776543

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.17  E-value=2.6e-11  Score=103.94  Aligned_cols=65  Identities=15%  Similarity=0.116  Sum_probs=59.2

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCC--CeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCG--TISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG--~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ..++++|+||+.++|+++|+++|++||  .|++|+|++|. +|+++|| ||+|.+.++|.+|+..+...
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~  122 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGK  122 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC
Confidence            457899999999999999999999999  99999999996 9999999 99999999999999886644

>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=99.17  E-value=3.9e-11  Score=99.53  Aligned_cols=67  Identities=16%  Similarity=0.158  Sum_probs=61.0

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..+....
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~  112 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME  112 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCE
Confidence            346789999999999999999999999999999999986 7899999 999999999999998877543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.17  E-value=1.4e-11  Score=101.19  Aligned_cols=62  Identities=11%  Similarity=0.160  Sum_probs=57.1

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCe----EEEEEeeCCCCCccce-EEEecccHHHHHHHHH
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTI----SSVKIMRTDRGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I----~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                      ....+++|+|||+++|+++|+++|++||.|    .+|+|++|.+|+++|| ||+|.+.++|.+|+..
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~   87 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK   87 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh
Confidence            445789999999999999999999999976    6999999999999999 9999999999999865

>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=99.17  E-value=3.5e-11  Score=95.46  Aligned_cols=61  Identities=21%  Similarity=0.304  Sum_probs=57.1

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHH
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                      ..++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~   76 (103)
T 2cqg_A           14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ   76 (103)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc
Confidence            45678999999999999999999999999999999996 7999999 9999999999999874

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.17  E-value=2.3e-11  Score=96.55  Aligned_cols=66  Identities=14%  Similarity=0.161  Sum_probs=60.5

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~   79 (103)
T 2dnm_A           12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAE   79 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCC
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCE
Confidence            45789999999999999999999999999999999987 6999999 999999999999998877544

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.17  E-value=2.6e-11  Score=98.66  Aligned_cols=65  Identities=12%  Similarity=0.169  Sum_probs=59.5

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ..++++|+||+.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++..
T Consensus        39 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~  105 (118)
T 2khc_A           39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGF  105 (118)
T ss_dssp             CSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCC
Confidence            35778999999999999999999999999999999986 8999999 99999999999999876543

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

Probab=99.16  E-value=3.9e-11  Score=92.98  Aligned_cols=65  Identities=18%  Similarity=0.206  Sum_probs=59.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|++|+|+++ +|+++|| ||+|.+.++|.+|+..++...
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~   72 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMK   72 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            4578899999999999999999999999999999985 8899999 999999999999998877544

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.16  E-value=2.3e-11  Score=101.67  Aligned_cols=79  Identities=14%  Similarity=0.125  Sum_probs=35.6

Q ss_pred             eEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccccccccccCCCCceEEeeCCCccccHHHHHHHHccCCCEEEEEE
Q 039806           56 GYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVI  135 (398)
Q Consensus        56 g~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i  135 (398)
                      -++|++|++...|..|++.++|....|+.- +....+    .......++|||+|||.++|+++|+++|+.||.|.++.+
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~~~----~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i   79 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYGRP----PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYI   79 (135)
T ss_dssp             -------------------------------CCSCCS----CSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEEC
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCCC-CCcCCC----CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE
Confidence            367888999999999999998876666432 222211    111225789999999999999999999999888888877


Q ss_pred             eeCC
Q 039806          136 SKDA  139 (398)
Q Consensus       136 ~~d~  139 (398)
                      ++|.
T Consensus        80 ~~~~   83 (135)
T 2lea_A           80 PRDR   83 (135)
T ss_dssp             CCCS
T ss_pred             EecC
Confidence            7664

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.16  E-value=1.7e-11  Score=92.91  Aligned_cols=63  Identities=16%  Similarity=0.108  Sum_probs=56.3

Q ss_pred             hhccccCCCccc------CHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          177 RAELYKNINDEV------DEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       177 ~~~~v~nL~~~v------tee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ++++|+|||..+      ++++|+++|++||.|.+|+|. ..+|+++|| ||+|.+.++|.+|+..++...
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~   71 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYK   71 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcc
Confidence            578899999999      779999999999999999988 468999999 999999999999987765443

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.16  E-value=2.4e-11  Score=96.19  Aligned_cols=66  Identities=18%  Similarity=0.290  Sum_probs=60.5

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|++|+|++|. +++++|| ||+|.+.++|.+|+..++...
T Consensus        11 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~   78 (102)
T 1x5s_A           11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKS   78 (102)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCE
Confidence            45789999999999999999999999999999999987 8899999 999999999999998877543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.16  E-value=1.9e-11  Score=99.25  Aligned_cols=64  Identities=14%  Similarity=0.229  Sum_probs=58.9

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHh
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++|. +++++|| ||+|.+.++|.+|+..+.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~   80 (116)
T 2cqd_A           15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN   80 (116)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCC
Confidence            345789999999999999999999999999999999986 7999999 999999999999987655

>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=99.16  E-value=3.9e-11  Score=96.97  Aligned_cols=66  Identities=20%  Similarity=0.240  Sum_probs=61.0

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|++|+|++|.+|.++|| ||+|.+.++|.+|+..++...
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~   90 (114)
T 1x5o_A           24 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKF   90 (114)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            356789999999999999999999999999999999999999999 999999999999998877554

>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=99.16  E-value=2.5e-11  Score=96.37  Aligned_cols=67  Identities=22%  Similarity=0.288  Sum_probs=61.0

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|.+|+|+++. +|.++|| ||+|.+.++|.+|+..++...
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~   74 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGRE   74 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBS
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCe
Confidence            456889999999999999999999999999999999986 8999999 999999999999998766543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.16  E-value=1.9e-11  Score=96.72  Aligned_cols=66  Identities=15%  Similarity=0.211  Sum_probs=60.3

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        11 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~   78 (102)
T 2cqb_A           11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE   78 (102)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            45788999999999999999999999999999999985 8999999 999999999999998776543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.16  E-value=4e-11  Score=94.40  Aligned_cols=66  Identities=14%  Similarity=0.265  Sum_probs=60.1

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEE--------EEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISS--------VKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~s--------vki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+||+.++++++|+++|++||.|.+        |+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A           12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            3567889999999999999999999999999        9999996 8999999 999999999999998776543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.15  E-value=4.2e-11  Score=95.54  Aligned_cols=66  Identities=15%  Similarity=0.345  Sum_probs=60.1

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC--CCCccce-EEEecccHHHHHHHHHH-hcc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD--RGISKGH-CMAIAQTKRERTSYLRI-MYA  239 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~--~g~skGf-fV~f~~~~ea~~A~l~~-q~~  239 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|+++.  +|+++|| ||+|.+.++|.+|+..+ +..
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~   82 (107)
T 2cph_A           13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHST   82 (107)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCC
Confidence            345789999999999999999999999999999999983  9999999 99999999999999888 443

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.15  E-value=4.3e-11  Score=97.13  Aligned_cols=62  Identities=18%  Similarity=0.301  Sum_probs=57.4

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHH
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                      ...++++|+||+.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~   88 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA   88 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh
Confidence            345789999999999999999999999999999999996 7999999 9999999999999865

>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=99.15  E-value=1.4e-11  Score=99.78  Aligned_cols=62  Identities=13%  Similarity=0.192  Sum_probs=57.4

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCe-EEEEEeeCCCCCccce-EEEecccHHHHHHHHH
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTI-SSVKIMRTDRGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I-~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                      ...++++|+|||.++|+++|+++|++||.| .+|+|++|.+|+++|| ||+|.+.++|.+|+..
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~   76 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL   76 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh
Confidence            345788999999999999999999999999 9999999999999999 9999999999999654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.15  E-value=1.2e-11  Score=102.76  Aligned_cols=64  Identities=9%  Similarity=0.201  Sum_probs=59.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEE--EEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISS--VKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~s--vki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ..++++|+||+.++|+++|+++|++||.|.+  |+|++|. +|++||| ||+|.+. +|.+|+..++..
T Consensus        22 ~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~   89 (131)
T 2m2b_A           22 ANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQAL   89 (131)
T ss_dssp             CCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCC
Confidence            4567999999999999999999999999977  9999998 9999999 9999999 999999988754

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.15  E-value=1.7e-11  Score=95.93  Aligned_cols=66  Identities=27%  Similarity=0.284  Sum_probs=60.0

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEE-EEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSV-KIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~sv-ki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|.+| +|++|. +|.++|| ||+|.+.++|.+|+..++...
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~   72 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQY   72 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCE
Confidence            45788999999999999999999999999999 999994 9999999 999999999999998766543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.15  E-value=2.5e-11  Score=90.42  Aligned_cols=56  Identities=13%  Similarity=0.216  Sum_probs=52.7

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHH
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      ++|+|||.++++++|+++|++||.|.+|+++++. +|+++|| ||+|.+.++|.+|+.
T Consensus         2 l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~   59 (75)
T 2mss_A            2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE   59 (75)
T ss_dssp             EEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS
T ss_pred             EEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH
Confidence            6789999999999999999999999999999987 8999999 999999999988864

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

Probab=99.15  E-value=5.3e-11  Score=93.74  Aligned_cols=61  Identities=16%  Similarity=0.122  Sum_probs=55.0

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      .++++++|+|||+++|+++|+++|++||.|++|++++     +||| ||+|.+.++|.+|+..++..
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~AFVef~~~~~A~~Av~~ln~~   80 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAADN   80 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHHS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc-----CCCEEEEEECCHHHHHHHHHHhcCC
Confidence            4567899999999999999999999999999999984     4788 99999999999999887643

>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=99.15  E-value=1.5e-11  Score=103.24  Aligned_cols=59  Identities=14%  Similarity=0.161  Sum_probs=55.0

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHH
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSY  233 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~  233 (398)
                      ...++++|+|||+++|+++|+++|++|| |++|+|++|++|+++|| ||+|++.++|.+|+
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al  103 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM  103 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH
Confidence            4457899999999999999999999999 77999999999999999 99999999999998

>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=99.15  E-value=6.8e-11  Score=93.75  Aligned_cols=66  Identities=23%  Similarity=0.315  Sum_probs=59.0

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++|..+ ++|| ||+|.+.++|.+|+..++...
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~   79 (103)
T 2cq3_A           13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTV   79 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            34578899999999999999999999999999999998755 8999 999999999999998776543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.14  E-value=4e-11  Score=98.53  Aligned_cols=67  Identities=13%  Similarity=0.185  Sum_probs=61.7

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+||+.++++++|+++|++||.|++|+|++|.+|+++|| ||+|.+.++|.+|+..++...
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~  100 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVP  100 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCE
Confidence            3457899999999999999999999999999999999999999999 999999999999998877654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.14  E-value=3.3e-11  Score=101.03  Aligned_cols=67  Identities=24%  Similarity=0.295  Sum_probs=60.7

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+||+.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        40 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~  108 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFN  108 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            345789999999999999999999999999999999987 7899999 999999999999998776543

>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=99.14  E-value=5.2e-11  Score=95.61  Aligned_cols=67  Identities=19%  Similarity=0.255  Sum_probs=60.7

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~   92 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAE   92 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCE
Confidence            345679999999999999999999999999999999986 8999999 999999999999998776543

>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=99.14  E-value=2.2e-11  Score=90.66  Aligned_cols=58  Identities=10%  Similarity=0.304  Sum_probs=54.0

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHH
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                      +++++|||.++++++|+++|++||.|.+|++++|. +|+++|| ||+|.+.++|.+|+..
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~   60 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK   60 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh
Confidence            36789999999999999999999999999999986 7999999 9999999999999863

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.14  E-value=5.2e-11  Score=97.75  Aligned_cols=64  Identities=20%  Similarity=0.358  Sum_probs=58.6

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ..++++|+||+.++++++|+++|++||.|++|+|++|. +|.++|| ||+|.+.++|.+|+ +++..
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~  100 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDET  100 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCC
Confidence            45789999999999999999999999999999999985 8999999 99999999999998 65543

>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=99.14  E-value=2.2e-11  Score=101.87  Aligned_cols=63  Identities=10%  Similarity=0.177  Sum_probs=58.0

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCC---eEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGT---ISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~---I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ...+++|+|||+++|+++|+++|++||.   |++|+|++|..|+++|| ||+|++.++|.+|+. +..
T Consensus        43 ~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g  109 (136)
T 2hgl_A           43 EGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDR  109 (136)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCC
Confidence            3567899999999999999999999999   89999999999999999 999999999999987 544

>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=99.13  E-value=3.7e-11  Score=99.07  Aligned_cols=61  Identities=13%  Similarity=0.168  Sum_probs=55.9

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeE--EEEEeeCCCCCccce-EEEecccHHHHHHHHH
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTIS--SVKIMRTDRGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~--svki~~d~~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                      ...++++|+|||+++|+++|+++|++| .|+  +|+|++|++|+++|| ||+|.+.++|.+|+..
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~  103 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK  103 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH
Confidence            345678999999999999999999999 677  999999999999999 9999999999999864

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.13  E-value=2.7e-11  Score=95.91  Aligned_cols=60  Identities=22%  Similarity=0.393  Sum_probs=56.9

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHH
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      ..++++|+|||.++++++|+++|++||.|.+|+|++|.+|+++|| ||+|.+.++|.+|+.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~   68 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE   68 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh
Confidence            457889999999999999999999999999999999999999999 999999999999986

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.13  E-value=3.7e-11  Score=94.35  Aligned_cols=66  Identities=23%  Similarity=0.322  Sum_probs=58.9

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCC--C--Cccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDR--G--ISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~--g--~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|++|+|++|..  |  +++|| ||+|.+.++|.+|+..++...
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~   74 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHT   74 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCe
Confidence            457889999999999999999999999999999998763  4  88999 999999999999998776543

>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=99.13  E-value=5.6e-11  Score=95.35  Aligned_cols=66  Identities=17%  Similarity=0.232  Sum_probs=60.1

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+||+.++++++|+++|++||.|.+|+|+++. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        25 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~   92 (108)
T 2jrs_A           25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFE   92 (108)
T ss_dssp             SCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCE
Confidence            45678999999999999999999999999999999986 8999999 999999999999998776543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.12  E-value=6e-11  Score=94.13  Aligned_cols=62  Identities=13%  Similarity=0.148  Sum_probs=57.0

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ..++++|+|||.++++++|+++|++|| |++|+|++|. +|+++|| ||+|.+.++|.+|+ +++.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g   77 (103)
T 2dng_A           14 PPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDG   77 (103)
T ss_dssp             SCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTT
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCC
Confidence            457889999999999999999999997 9999999997 7999999 99999999999998 6654

>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=99.12  E-value=2.9e-11  Score=95.50  Aligned_cols=65  Identities=17%  Similarity=0.211  Sum_probs=56.9

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC--CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD--RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~--~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ....++++|+||+.++++++|+++|++|| |++|+|++|.  +|+++|| ||+|.+.++|.+|+ .++..
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~   83 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEE   83 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCC
Confidence            34567899999999999999999999999 9999999986  8999999 99999999999999 66544

>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=99.12  E-value=5.5e-11  Score=94.53  Aligned_cols=63  Identities=17%  Similarity=0.232  Sum_probs=57.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-C-CCccce-EEEecccHHHHHHHHHHhcc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-R-GISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~-g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ..++++|+|||.++++++|+++|++|| |++|+|++|. + |+++|| ||+|.+.++|.+|+ .++..
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~   79 (104)
T 1wi8_A           14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEE   79 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCC
Confidence            457889999999999999999999999 9999999987 4 899999 99999999999999 76644

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.12  E-value=5.2e-11  Score=90.86  Aligned_cols=59  Identities=15%  Similarity=0.177  Sum_probs=53.6

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++|+||+..+||++|+++|.+||+|.++++..     +||| ||+|.+.+||.+|+..+....
T Consensus         8 ~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~   67 (89)
T 2wbr_A            8 SWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCV   67 (89)
T ss_dssp             CEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             ceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCE
Confidence            4577899999999999999999999999999974     7999 999999999999999887543

>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=99.11  E-value=6.7e-11  Score=93.77  Aligned_cols=66  Identities=18%  Similarity=0.241  Sum_probs=58.8

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++|..+ ++|| ||+|.+.++|.+|+..++...
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~   79 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRK   79 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCC
Confidence            34578999999999999999999999999999999998543 7899 999999999999998777554

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.11  E-value=2.9e-11  Score=98.63  Aligned_cols=63  Identities=10%  Similarity=0.194  Sum_probs=57.7

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCC---eEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGT---ISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~---I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ..++++|+|||.++|+++|+++|+.||.   |++|+|++|.+|+++|| ||+|.+.++|.+|+. ++.
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g   82 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDR   82 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCC
Confidence            3467889999999999999999999999   89999999999999999 999999999999987 543

>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=99.11  E-value=5.3e-11  Score=96.96  Aligned_cols=59  Identities=12%  Similarity=0.123  Sum_probs=53.7

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ..++++|+|||+++||++|+++|++||.|++|+|+++     ||| ||+|++.++|.+|+..+..
T Consensus        30 ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~   89 (119)
T 2ad9_A           30 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTS   89 (119)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhcc
Confidence            4578999999999999999999999999999999965     788 9999999999999987653

>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=99.11  E-value=7.1e-11  Score=93.55  Aligned_cols=58  Identities=16%  Similarity=0.189  Sum_probs=53.0

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHh
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ..++++|+|||+++++++|+++|++||.|++|+|+++     ||| ||+|++.++|.+|+..++
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~   72 (101)
T 2cq1_A           14 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYS   72 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhc
Confidence            4578999999999999999999999999999999864     788 999999999999988765

>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=99.11  E-value=7.7e-11  Score=97.03  Aligned_cols=66  Identities=14%  Similarity=0.225  Sum_probs=60.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+||+.++|+++|+++|++||.|++|+|++|. +|.++|| ||+|.+.++|.+|+..++...
T Consensus        21 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   88 (126)
T 3ex7_B           21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD   88 (126)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCB
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCe
Confidence            35679999999999999999999999999999999997 9999999 999999999999998776543

>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=99.10  E-value=3.1e-11  Score=94.13  Aligned_cols=66  Identities=12%  Similarity=0.182  Sum_probs=59.0

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|.+++++++. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~   81 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRP   81 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCe
Confidence            35789999999999999999999999999999988876 8899999 999999999999998776543

>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=99.10  E-value=5.2e-11  Score=94.44  Aligned_cols=59  Identities=15%  Similarity=0.126  Sum_probs=53.7

Q ss_pred             hhhhccccCCCc-ccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          175 KERAELYKNIND-EVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       175 ~~~~~~v~nL~~-~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ..++++|+|||+ ++|+++|+++|++||.|++|+|+++     +|| ||+|++.++|.+|+..++.
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~   74 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTT   74 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcC
Confidence            467899999999 9999999999999999999999865     577 9999999999999988764

>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=99.09  E-value=1.1e-10  Score=99.89  Aligned_cols=67  Identities=13%  Similarity=0.134  Sum_probs=61.1

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++|+++|+++|++||.|++|+|++|. +++++|| ||+|.+.++|.+|+..++...
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~  105 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTR  105 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCE
Confidence            356789999999999999999999999999999999997 7999999 999999999999998776543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.09  E-value=7e-11  Score=94.89  Aligned_cols=67  Identities=19%  Similarity=0.227  Sum_probs=59.4

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ....++++|+||+.++++++|+++|++||.|++|+|++|. +.++|| ||+|.+.++|.+|+..++...
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~~~kg~afV~f~~~~~A~~Ai~~l~g~~   93 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-RGSKGFGFVTFENSADADRAREKLHGTV   93 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT-TBCTTEEEEECCCSHHHHHHHHHHTTCE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC-CCCceEEEEEECCHHHHHHHHHHcCCCE
Confidence            3456789999999999999999999999999999999885 458999 999999999999998776543

>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=99.09  E-value=7e-11  Score=107.79  Aligned_cols=66  Identities=17%  Similarity=0.172  Sum_probs=59.3

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCC--CeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCG--TISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG--~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+||+.++|+++|+++|++||  .|++|+|++|. +|++||| ||+|.+.++|.+|+..+....
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~  136 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRE  136 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCe
Confidence            456799999999999999999999999  99999999997 9999999 999999999999988766443

>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=99.09  E-value=6.3e-11  Score=90.90  Aligned_cols=65  Identities=12%  Similarity=0.148  Sum_probs=57.9

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCC-ccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGI-SKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~-skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .++++|+|||.++++++|+++|++||.|.+|+|++|. ++. ++|| ||+|.+.++|.+|+..++...
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   71 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQ   71 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCe
Confidence            4678899999999999999999999999999999887 344 8999 999999999999998776544

>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=99.09  E-value=1.1e-10  Score=92.89  Aligned_cols=59  Identities=15%  Similarity=0.144  Sum_probs=53.5

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ..++++|+||++++++++|+++|++||.|++|+|+++     ||| ||+|.+.++|.+|+..++.
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~   73 (104)
T 1wex_A           14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAAD   73 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhcc
Confidence            4578999999999999999999999999999999853     788 9999999999999987754

>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=99.08  E-value=2.7e-11  Score=93.57  Aligned_cols=63  Identities=17%  Similarity=0.249  Sum_probs=57.3

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.+ |.+|+..++...
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~   66 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTD   66 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSC
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCE
Confidence            467889999999999999999999999999999987 7999999 99999999 999988766543

>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=99.08  E-value=9.1e-11  Score=90.69  Aligned_cols=55  Identities=18%  Similarity=0.307  Sum_probs=48.5

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHH
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERT  231 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~  231 (398)
                      .....+++|+|||.++||++|+++|++||.|++|+|+++    +||| ||+|.+.++|.+
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~   63 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS   63 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH
Confidence            345678899999999999999999999999999999975    7999 999999999884

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.08  E-value=9.7e-11  Score=90.65  Aligned_cols=63  Identities=10%  Similarity=0.155  Sum_probs=58.0

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ..++++|+|||.++++++|+++|++| .|.+|+|++|.+|+++|| ||+|.+.++|.+|+. ++..
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~   72 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNRE   72 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSE
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCc
Confidence            35678899999999999999999999 999999999999999999 999999999999987 5543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.08  E-value=8.4e-11  Score=94.87  Aligned_cols=66  Identities=20%  Similarity=0.342  Sum_probs=60.1

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeE--------EEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTIS--------SVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~--------svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|.        .|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   89 (113)
T 2cpe_A           14 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   89 (113)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCc
Confidence            457899999999999999999999999999        69999994 8999999 999999999999998776544

>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=99.07  E-value=3.9e-11  Score=94.22  Aligned_cols=64  Identities=13%  Similarity=0.191  Sum_probs=58.2

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      .++++|+|||.++++++|+++|++||.|++++++.+. +|+++|| ||+|.+.++|.+|+..++..
T Consensus        15 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~   80 (98)
T 2cqp_A           15 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDR   80 (98)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            4678899999999999999999999999998888775 8999999 99999999999999877654

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.07  E-value=1.2e-10  Score=97.53  Aligned_cols=65  Identities=15%  Similarity=0.208  Sum_probs=59.9

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ..++++|+|||.++++++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++..
T Consensus        62 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~  128 (140)
T 2ku7_A           62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES  128 (140)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEE
T ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCC
Confidence            46789999999999999999999999999999999985 8999999 99999999999999876654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.07  E-value=2.4e-10  Score=87.25  Aligned_cols=73  Identities=21%  Similarity=0.265  Sum_probs=62.2

Q ss_pred             CcceEEEcCCCC----CCcH----HHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceE
Q 039806           13 GIGNAFVKNLAS----TIDN----LKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERME   84 (398)
Q Consensus        13 ~~~~lfV~nLp~----~vte----~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~   84 (398)
                      ..+||+|.-++.    +.-.    .+|.+.|+.||+|.+++++.|.       +||+|++.++|.+||+ |||..++||.
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~-------~fVtF~d~~sAlaAi~-mnG~~v~Gr~   77 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK-------MWVTFLEGSSALNVLS-LNGKELLNRT   77 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS-------EEEEESSHHHHHHGGG-GTTCEETTEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC-------EEEEECChHHHHHHHh-cCCeEeCCeE
Confidence            456888888762    3323    5789999999999999998865       9999999999999998 9999999999


Q ss_pred             eeeeccccc
Q 039806           85 LYVGPFIRR   93 (398)
Q Consensus        85 i~V~~~~~~   93 (398)
                      |+|....+.
T Consensus        78 LkV~lkt~d   86 (91)
T 2dnr_A           78 ITIALKSPS   86 (91)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999987643

>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=99.06  E-value=4.6e-11  Score=95.64  Aligned_cols=60  Identities=8%  Similarity=0.169  Sum_probs=56.2

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCC---eEEEEEeeCCCCCccce-EEEecccHHHHHHHH
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGT---ISSVKIMRTDRGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~---I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      ...+++|+|||.++|+++|+++|+.||.   |.+|+|++|..|+++|| ||+|.+.++|.+|+.
T Consensus        10 ~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~   73 (107)
T 2lmi_A           10 DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE   73 (107)
T ss_dssp             SCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH
Confidence            4567889999999999999999999998   99999999999999999 999999999999987

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.06  E-value=9.5e-11  Score=93.44  Aligned_cols=65  Identities=15%  Similarity=0.108  Sum_probs=58.6

Q ss_pred             hhhhccccCCCccc------CHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEV------DEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~v------tee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||..+      ++++|+++|++||.|.+|+|+ ..+|+++|| ||+|.+.++|.+|+..++...
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~   85 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYK   85 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcc
Confidence            35688999999999      789999999999999999998 468999999 999999999999998876554

>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=99.06  E-value=1.5e-10  Score=90.74  Aligned_cols=63  Identities=14%  Similarity=0.149  Sum_probs=57.2

Q ss_pred             hhhccccCCCcccCHHHHH----HHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELK----QYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~----~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .++++|+|||.++++++|+    ++|++||.|++|+|++|..+  +|| ||+|.+.++|.+|+..++...
T Consensus         9 ~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~   76 (96)
T 2dgx_A            9 GADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYK   76 (96)
T ss_dssp             CEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCE
Confidence            4678899999999999999    99999999999999998866  778 999999999999999887654

>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=99.06  E-value=9.3e-11  Score=93.91  Aligned_cols=63  Identities=8%  Similarity=0.105  Sum_probs=57.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCC-eEEEEEe-eCC-CCCccce-EEEecccHHHHHHHHHHh
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGT-ISSVKIM-RTD-RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~-I~svki~-~d~-~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ..++++|+|||.++++++|+++|++||. |++|+|+ +|. +|+++|| ||+|.+.++|.+|+..++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~   73 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLM   73 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhh
Confidence            4577899999999999999999999998 9999998 665 7899999 999999999999987764

>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=99.05  E-value=4.1e-10  Score=112.29  Aligned_cols=64  Identities=16%  Similarity=0.310  Sum_probs=59.4

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ++|+|+||+..+|+++|+++|++||.|++|+|+.|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus       103 ~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~  168 (437)
T 3pgw_S          103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKK  168 (437)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCE
Confidence            578999999999999999999999999999999986 8999999 999999999999998876544

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.05  E-value=8.2e-11  Score=95.27  Aligned_cols=62  Identities=15%  Similarity=0.154  Sum_probs=56.1

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-C---CCccce-EEEecccHHHHHHHHHH
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-R---GISKGH-CMAIAQTKRERTSYLRI  236 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~---g~skGf-fV~f~~~~ea~~A~l~~  236 (398)
                      ...++++|+|||.++++++|+++|++||.|. +.++.+. +   |+++|| ||+|.+.++|.+|+..+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~   72 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC   72 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh
Confidence            3457899999999999999999999999999 8888776 4   799999 99999999999999876

>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=99.03  E-value=1.4e-10  Score=93.39  Aligned_cols=66  Identities=11%  Similarity=0.174  Sum_probs=58.4

Q ss_pred             hhhhccccCCCcccCHHHHH---HHhhcCCCeEEEEEeeCC-CC---Cccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELK---QYFSQCGTISSVKIMRTD-RG---ISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~---~~F~~fG~I~svki~~d~-~g---~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+   ++|++||.|++|+|++|. ++   +++|| ||+|.+.++|.+|+..++...
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~   87 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVV   87 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCE
Confidence            35678899999999999999   999999999999999886 33   56699 999999999999999877654

>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=99.03  E-value=1.3e-10  Score=93.70  Aligned_cols=60  Identities=12%  Similarity=0.135  Sum_probs=54.1

Q ss_pred             hhhhhccccCCCcc-cCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          174 RKERAELYKNINDE-VDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       174 ~~~~~~~v~nL~~~-vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ...++++|+||+++ +++++|+++|++||.|++|+|++     +||| ||+|++.++|.+|+..++.
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~aFVef~~~~~A~~Ai~~l~~   84 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----MKSQAFIEMETREDAMAMVDHCLK   84 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhcc
Confidence            34678999999998 99999999999999999999983     5888 9999999999999987764

>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=99.02  E-value=3.6e-10  Score=90.51  Aligned_cols=64  Identities=6%  Similarity=0.103  Sum_probs=56.8

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++|+++|+++|++||.|++|+|..+  +.++|| ||+|.+.++|.+|+..++...
T Consensus        21 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~   85 (109)
T 1x4a_A           21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYD   85 (109)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcEEEEEECCHHHHHHHHHHcCCCE
Confidence            4578999999999999999999999999999999654  568899 999999999999998877543

>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=99.01  E-value=5.7e-10  Score=98.99  Aligned_cols=63  Identities=14%  Similarity=0.203  Sum_probs=58.4

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHH
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRI  236 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~  236 (398)
                      ...++++|+|||.++++++|+++|++||.|.+|+|.++.+|+++|| ||+|.+.++|.+|+...
T Consensus       107 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~  170 (193)
T 2voo_A          107 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP  170 (193)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT
T ss_pred             cccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC
Confidence            3457899999999999999999999999999999999999999999 99999999999998543

>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=99.01  E-value=4.2e-10  Score=97.20  Aligned_cols=66  Identities=20%  Similarity=0.269  Sum_probs=60.3

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||..+++++|+++|++||.|.+|+|+++. +|.++|| ||+|.+.++|.+|+..++...
T Consensus        71 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~  138 (165)
T 1rk8_A           71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAE  138 (165)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            35679999999999999999999999999999999996 9999999 999999999999998877544

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=98.99  E-value=2.6e-10  Score=99.76  Aligned_cols=67  Identities=13%  Similarity=0.185  Sum_probs=61.2

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+||+.++++++|+++|++||.|++|+|++|.+|.++|| ||+|.+.++|.+|+..++...
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~  153 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVP  153 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCE
Confidence            3457899999999999999999999999999999999999999999 999999999999998776543

>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=98.99  E-value=5.5e-10  Score=90.29  Aligned_cols=64  Identities=13%  Similarity=0.198  Sum_probs=57.2

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|.+|+|++|  +.++|| ||+|.+.++|.+|+..++...
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~   71 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFN   71 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCB
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCE
Confidence            4578999999999999999999999999999999965  456888 999999999999998877554

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.99  E-value=7.1e-10  Score=90.09  Aligned_cols=79  Identities=14%  Similarity=0.086  Sum_probs=68.0

Q ss_pred             cccCCCcceEEEcCCCCC-CcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecC-HHHHHHHHHHhc--CCeecce
Q 039806            8 EARLSGIGNAFVKNLAST-IDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYST-PESALDAIEKLQ--GATVERM   83 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~-vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~-~e~A~~Ai~~ln--g~~l~gk   83 (398)
                      +..-...+-|+|+||+.+ ++.++|+++|+.||.|..|.+..+..     .|||.|.+ .++|..|++++|  +..|+|.
T Consensus        12 ~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~-----tgfVrf~~~~~~A~~av~~ln~~~~~i~g~   86 (121)
T 1owx_A           12 SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK-----EGIILFKEKAKEALGKAKDANNGNLQLRNK   86 (121)
T ss_dssp             CCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS-----EEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             cccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC-----EEEEEECCChHHHHHHHHHhhcCCcEEeCc
Confidence            344455678999999999 99999999999999999999988662     59999999 899999999995  6788998


Q ss_pred             Eeeeeccc
Q 039806           84 ELYVGPFI   91 (398)
Q Consensus        84 ~i~V~~~~   91 (398)
                      .+.++...
T Consensus        87 ~~~~evL~   94 (121)
T 1owx_A           87 EVTWEVLE   94 (121)
T ss_dssp             SEEEEECC
T ss_pred             EEEEEECC
Confidence            88887654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=98.98  E-value=2.4e-10  Score=93.12  Aligned_cols=49  Identities=16%  Similarity=0.285  Sum_probs=46.0

Q ss_pred             hhccccCC----CcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecc
Q 039806          177 RAELYKNI----NDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQ  225 (398)
Q Consensus       177 ~~~~v~nL----~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~  225 (398)
                      ..++|+||    ++.++|++|+++|+.||.|.+|+++.|+ +|+++|| ||.|.+
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d   57 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYAS   57 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC-
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECC
Confidence            46788999    9999999999999999999999999999 9999999 999996

>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=98.98  E-value=2.1e-10  Score=94.25  Aligned_cols=63  Identities=10%  Similarity=0.118  Sum_probs=54.9

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEE-EeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVK-IMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svk-i~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ...+++|+|||.++|+++|+++|+.||.|.++. +..+.+|+++|| ||+|.+.++|.+|+. ++.
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g   88 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHK   88 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCC
Confidence            346789999999999999999999999999954 455569999999 999999999999987 443

>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=98.98  E-value=4.9e-10  Score=89.70  Aligned_cols=60  Identities=12%  Similarity=0.188  Sum_probs=54.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...+++|+|||.++++++|+++|++||.|++|+|++|      || ||+|.+.++|.+|+..++...
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~   74 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTK   74 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCC
Confidence            3567899999999999999999999999999999976      77 999999999999998876544

>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=98.97  E-value=2.2e-10  Score=92.39  Aligned_cols=63  Identities=11%  Similarity=0.214  Sum_probs=55.0

Q ss_pred             hhhhhhccc--cCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          173 MRKERAELY--KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       173 ~~~~~~~~v--~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..+.+.++|  +||+.+++|++|+++|++||.|++|.|+.     .||| ||+|++.++|.+|+.+++...
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~-----~rgfaFV~f~~~~~A~~Ai~~lnG~~   87 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKE   87 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-----TCSCEEEEESSHHHHHHHHHHTTTCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCE
Confidence            345677999  66999999999999999999999999863     3788 999999999999999888764

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.97  E-value=3.5e-10  Score=89.26  Aligned_cols=64  Identities=17%  Similarity=0.240  Sum_probs=56.8

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|   +|+++.+|+++|| ||+|.+.++|.+|+..++...
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~   77 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKRE   77 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            346789999999999999999999999987   6777789999999 999999999999998776543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=98.97  E-value=4.4e-10  Score=88.68  Aligned_cols=59  Identities=17%  Similarity=0.201  Sum_probs=54.2

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +++|+|||.++|+++|+++|++||.|++|+|+++    ++|| ||+|.+.++|.+|+..++...
T Consensus         2 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~   61 (101)
T 2hvz_A            2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKV   61 (101)
T ss_dssp             EEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCe
Confidence            5788999999999999999999999999999977    7888 999999999999998877543

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

Probab=98.97  E-value=4.4e-10  Score=92.80  Aligned_cols=65  Identities=18%  Similarity=0.147  Sum_probs=56.5

Q ss_pred             hhhhhccccCCCcccCHHHHH----HHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELK----QYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~----~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+||++.+++++|+    ++|++||.|++|.+.  .+|+++|| ||+|.+.++|.+|+..++...
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~--~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~   96 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD--LSDDNSGKAYIVFATQESAQAFVEAFQGYP   96 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC--CCCSSCCCEEEEESSHHHHHHHHHHSTTCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec--cCCCcCCEEEEEECCHHHHHHHHHHHCCCE
Confidence            346789999999999999876    699999999999885  46889999 999999999999998777543

>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=98.96  E-value=7e-10  Score=86.84  Aligned_cols=62  Identities=6%  Similarity=0.116  Sum_probs=55.1

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|++|++.++     +|| ||+|.+.++|.+|+..++...
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~   77 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFP   77 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCE
Confidence            34578999999999999999999999999999999854     677 999999999999998877554

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.51  E-value=6.5e-11  Score=96.07  Aligned_cols=66  Identities=14%  Similarity=0.258  Sum_probs=59.7

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEE--------EEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISS--------VKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~s--------vki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ...++++|+|||.++++++|+++|++||.|.+        |+|++|. +|+++|| ||+|.+.++|.+|+..++..
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   80 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   80 (116)
Confidence            45678999999999999999999999999999        9999985 8999999 99999999999998766543

>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=98.95  E-value=2.9e-10  Score=87.39  Aligned_cols=54  Identities=19%  Similarity=0.304  Sum_probs=49.0

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHH
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTS  232 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A  232 (398)
                      .+++++|+|||.++++++|+++|++||.|++|+|+++    ++|| ||+|.+.++|.+|
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~   58 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSL   58 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHH
Confidence            4578999999999999999999999999999999865    7888 9999999999754

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

Probab=98.94  E-value=8.3e-10  Score=87.05  Aligned_cols=61  Identities=16%  Similarity=0.174  Sum_probs=54.7

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+||+.++++++|+++|++||.|++|++.     +++|| ||+|.+.++|.+|+..++...
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-----~~~g~afV~f~~~~~A~~Ai~~l~g~~   87 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-----PEKGCCFIKYDTHEQAAVCIVALANFP   87 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-----TTTTEEEEECSSHHHHHHHHHHHTTCE
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-----cCCCEEEEEECCHHHHHHHHHHhCCCe
Confidence            35789999999999999999999999999999998     56888 999999999999998776443

>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=98.94  E-value=6.2e-10  Score=90.24  Aligned_cols=62  Identities=13%  Similarity=0.193  Sum_probs=54.2

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ....+++|+||+.++++++|+++|++||.|++|+|+.|      || ||+|++.++|.+|+..++....
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~   76 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKF   76 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEE
Confidence            34578999999999999999999999999999999866      78 9999999999999988876543

>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=98.94  E-value=1.2e-09  Score=83.74  Aligned_cols=71  Identities=18%  Similarity=0.237  Sum_probs=61.2

Q ss_pred             CCcceEEEcCCCCC-----C-cH---HHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecc
Q 039806           12 SGIGNAFVKNLAST-----I-DN---LKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVER   82 (398)
Q Consensus        12 ~~~~~lfV~nLp~~-----v-te---~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g   82 (398)
                      ...+||+|.-++.+     + ++   .+|.+.|+.||+|..+++..|.       +||+|.+.++|.+||+ |||..++|
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-------~fVtF~d~~sAl~AI~-ldG~~v~G   84 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-------MLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-------EEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-------EEEEEcChHHHHHHHh-cCCeeeCC
Confidence            34679999988754     2 21   4688999999999999999875       9999999999999998 99999999


Q ss_pred             eEeeeecc
Q 039806           83 MELYVGPF   90 (398)
Q Consensus        83 k~i~V~~~   90 (398)
                      |.|+|.+-
T Consensus        85 r~L~V~~k   92 (95)
T 1ufw_A           85 RAVKISGP   92 (95)
T ss_dssp             EEEEEECC
T ss_pred             eEEEEecc
Confidence            99999763

>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=98.93  E-value=7e-10  Score=89.36  Aligned_cols=62  Identities=19%  Similarity=0.310  Sum_probs=55.3

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +..++++|+|||.++++++|+++|++||.|++|+|.+     ++|| ||+|.+.++|.+|+..++...
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~   70 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSK   70 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            3457899999999999999999999999999999973     5777 999999999999998887654

>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=98.93  E-value=9.8e-10  Score=86.34  Aligned_cols=61  Identities=15%  Similarity=0.275  Sum_probs=54.8

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|++|+|.++     +|| ||+|.+.++|.+|+..++...
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~   75 (99)
T 2cpj_A           14 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMP   75 (99)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCE
Confidence            4568899999999999999999999999999999844     788 999999999999998877544

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.93  E-value=1.2e-09  Score=84.32  Aligned_cols=59  Identities=17%  Similarity=0.216  Sum_probs=53.3

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|+       +|| ||+|.+.++|.+|+..++..
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~   65 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHY   65 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCC
Confidence            345788999999999999999999999999999998       678 99999999999999877654

>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=98.92  E-value=1e-09  Score=87.84  Aligned_cols=63  Identities=14%  Similarity=0.229  Sum_probs=56.1

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ....++++|+||+.++++++|+++|++||.|.+|+|+++     +|| ||+|.+.++|.+|+..++...
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~   85 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTT   85 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCE
Confidence            344678999999999999999999999999999999966     788 999999999999998876543

>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=98.92  E-value=1.8e-09  Score=97.70  Aligned_cols=67  Identities=15%  Similarity=0.166  Sum_probs=60.9

Q ss_pred             CcHHHHHHHHhccCCeeEEEEEEcC-----CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           26 IDNLKLHQIFSKFGDIQSSKVVVSQ-----EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        26 vte~~L~~~F~~~G~I~~vki~~d~-----~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      -.+++|++.|++||.|.+|+|.++.     ++.++|++||+|.+.++|.+|++.|||..++||.|.|.++..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            4678899999999999999999665     348999999999999999999999999999999999998753

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=98.91  E-value=6.1e-10  Score=89.69  Aligned_cols=63  Identities=11%  Similarity=0.050  Sum_probs=55.2

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCC-CeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCG-TISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG-~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ....++|+|||.++++++|+++|++|| .|++|+|..   +.++|| ||+|.+.++|.+|+..+....
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~---~~~rGfaFV~F~~~e~A~~Ai~~lng~~   91 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT---RDFDGTGALEFPSEEILVEALERLNNIE   91 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS---CSSSCCEEEEESSHHHHHHHHHHTTTEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc---CCCCCEEEEEECCHHHHHHHHHHcCCCE
Confidence            346788999999999999999999999 999999963   358899 999999999999998776543

>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=98.91  E-value=1.3e-09  Score=82.90  Aligned_cols=58  Identities=14%  Similarity=0.277  Sum_probs=52.8

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHH
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRI  236 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~  236 (398)
                      ...++++|+|||.++++++|+++|++||.|.+|++++     ++|| ||+|.+.++|.+|+..+
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~-----~kg~afV~f~~~~~A~~a~~~l   68 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-----RQQCAFIQFATRQAAEVAAEKS   68 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHTT
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC-----CCCEEEEEECCHHHHHHHHHHh
Confidence            3457889999999999999999999999999999995     4788 99999999999999866

>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=98.90  E-value=4.1e-10  Score=88.03  Aligned_cols=65  Identities=18%  Similarity=0.275  Sum_probs=57.9

Q ss_pred             hhhhhccccCCCcccCHHHHH----HHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELK----QYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~----~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+    ++|++||.|.+|+|.+  +|+++|| ||+|.+.++|.+|+..++...
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~   75 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFP   75 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCE
Confidence            456789999999999999999    9999999999999973  6788899 999999999999998877544

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=98.90  E-value=2.4e-09  Score=85.33  Aligned_cols=68  Identities=12%  Similarity=0.095  Sum_probs=56.9

Q ss_pred             hhhhhccccCCCc-----ccCHHHHHHHhhcCCCeEEEEEeeCC--CCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          174 RKERAELYKNIND-----EVDEIELKQYFSQCGTISSVKIMRTD--RGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       174 ~~~~~~~v~nL~~-----~vtee~L~~~F~~fG~I~svki~~d~--~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ..+++++++||-.     +-++++|+++|++||.|++|+|++|+  +++++|| ||.|.+.++|.+|+..++....
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~   81 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYF   81 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEE
Confidence            3456788888863     33789999999999999999999986  3689999 9999999999999998886543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.88  E-value=1.1e-10  Score=92.13  Aligned_cols=64  Identities=13%  Similarity=0.039  Sum_probs=55.7

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|.+ ++++|. +|+++|| ||+|.+.++|.+|+. ++...
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~   81 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLK   81 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcE
Confidence            4568899999999999999999999999988 666664 8999999 999999999999996 65433

>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=98.88  E-value=2.1e-09  Score=92.02  Aligned_cols=61  Identities=16%  Similarity=0.108  Sum_probs=54.3

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      .++|+||++.+|+++|+++|++||.|++|+|..+   .++|| ||+|.+.++|.+|+..++....
T Consensus        48 ~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k---~~rgfAFVeF~d~~~A~~Ai~~LnG~~i  109 (164)
T 1sjr_A           48 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNI  109 (164)
T ss_dssp             EEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES---SSCEEEEEEESCHHHHHHHHHHSTTBCS
T ss_pred             EEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCCEEEEEECCHHHHHHHHHHhCCCEe
Confidence            4567999999999999999999999999999754   35788 9999999999999999887665

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=98.87  E-value=1.8e-09  Score=86.46  Aligned_cols=61  Identities=16%  Similarity=0.258  Sum_probs=55.0

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ....++++|+||+.++++++|+++|++||.|++|+|+       +|| ||+|.+.++|.+|+..++...
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~   89 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKS   89 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCE
Confidence            4456789999999999999999999999999999998       788 999999999999998877544

>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=98.86  E-value=3.4e-09  Score=83.08  Aligned_cols=61  Identities=15%  Similarity=0.151  Sum_probs=54.3

Q ss_pred             hhhhhhccccCCCc-ccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          173 MRKERAELYKNIND-EVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       173 ~~~~~~~~v~nL~~-~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ....++++|+||+. ++++++|+++|++||.|.+|+|.       +|| ||+|.+.++|.+|+..++...
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~   81 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEM   81 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCE
Confidence            44577899999998 99999999999999999999993       788 999999999999998876543

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

Probab=98.86  E-value=2.4e-09  Score=83.64  Aligned_cols=61  Identities=15%  Similarity=0.158  Sum_probs=53.6

Q ss_pred             hhhhhhccccCCCc-ccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          173 MRKERAELYKNIND-EVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       173 ~~~~~~~~v~nL~~-~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ....++++|+|||. ++++++|+++|++||.|.+|+|.       +|| ||+|.+.++|.+|+..++...
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~   69 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEM   69 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSS
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCe
Confidence            44567899999998 99999999999999999999995       788 999999999999998876543

>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=98.85  E-value=2.3e-09  Score=84.85  Aligned_cols=59  Identities=20%  Similarity=0.250  Sum_probs=52.9

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+||+.++|+++|+++|++||.|++|+|+       +|| ||+|.+.++|.+|+..++...
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~   69 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKD   69 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCc
Confidence            45788999999999999999999999999999997       446 999999999999998877554

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.84  E-value=8.8e-10  Score=86.00  Aligned_cols=64  Identities=27%  Similarity=0.286  Sum_probs=56.0

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ....++++|+|||.++++++|+++|++||.|..+    +.+|+++|| ||+|.+.++|.+|+..++...
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   77 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAE   77 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCE
Confidence            3456789999999999999999999999988776    458899999 999999999999998777543

>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=98.84  E-value=3.1e-09  Score=85.19  Aligned_cols=59  Identities=17%  Similarity=0.277  Sum_probs=53.3

Q ss_pred             hhhhccccCCCcc-cCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDE-VDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~-vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+||+.+ +++++|+++|++||.|++|+|       ++|| ||+|.+.++|.+|+..++...
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~   86 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRV   86 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCE
Confidence            3478999999999 999999999999999999999       5788 999999999999998877544

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.83  E-value=2.3e-09  Score=83.91  Aligned_cols=62  Identities=6%  Similarity=0.115  Sum_probs=54.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|. ++++.   ++++|| ||+|.+.++|.+|+..++...
T Consensus        18 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~---~~~~g~afV~f~~~~~a~~A~~~l~g~~   80 (97)
T 2e5j_A           18 LAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW---QGPRRRAFLHYPDSAAAQQAVSCLQGLR   80 (97)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE---ETTTTEEEEECSSHHHHHHHHHHHTTCC
T ss_pred             CCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc---CCCCcEEEEEECCHHHHHHHHHHhCCCE
Confidence            356889999999999999999999999997 77774   478899 999999999999998877544

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.83  E-value=3.2e-09  Score=81.81  Aligned_cols=60  Identities=8%  Similarity=0.201  Sum_probs=53.1

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++|+++|+++|++||.|++|+|+++       | ||+|.+.++|.+|+..++...
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~-------~afV~f~~~~~a~~A~~~l~g~~   67 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLNGKE   67 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS-------CEEEEESCHHHHHHHHHHHTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC-------EEEEEECCHHHHHHHHHHhCCCE
Confidence            34678899999999999999999999999999999843       5 999999999999998877543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=98.83  E-value=5.1e-09  Score=86.37  Aligned_cols=60  Identities=17%  Similarity=0.118  Sum_probs=53.2

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce--EEEecccHHHHHHHHHHhccccC
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH--CMAIAQTKRERTSYLRIMYAKQG  242 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf--fV~f~~~~ea~~A~l~~q~~q~~  242 (398)
                      ++|+||++.+|+++|+++|++||.|.+|+|+.+    ++||  ||+|.+.++|.+|+..++.....
T Consensus        31 I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~   92 (130)
T 3zzy_A           31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIY   92 (130)
T ss_dssp             EEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEE
T ss_pred             EEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeec
Confidence            446999999999999999999999999999864    3677  99999999999999999876653

>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=98.82  E-value=1.7e-09  Score=87.33  Aligned_cols=63  Identities=16%  Similarity=0.233  Sum_probs=55.0

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCe----EEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTI----SSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I----~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++|+++|+++|++||.|    ..+++.   +|+++|| ||+|.+.++|.+|+..++...
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~---~g~~~g~afV~f~~~~~a~~Ai~~l~g~~   91 (115)
T 2cpx_A           24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYK   91 (115)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE---CSSSCSEEEEECSSHHHHHHHHHHSTTCB
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC---CCccceEEEEEECCHHHHHHHHHHhCCCE
Confidence            45789999999999999999999999999    455554   8899999 999999999999998776543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.82  E-value=3.8e-09  Score=83.27  Aligned_cols=64  Identities=16%  Similarity=0.267  Sum_probs=56.1

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+||+.++++++|+++|+.|+   +|++++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~   78 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGE   78 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCE
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCe
Confidence            3467899999999999999999999874   68888886 8999999 999999999999998877543

>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=98.81  E-value=4e-09  Score=80.52  Aligned_cols=60  Identities=15%  Similarity=0.189  Sum_probs=53.7

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcC----C-------CeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQC----G-------TISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~f----G-------~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      +..++++|+|||.++++++|+++|++|    |       .|.+|++.++     +|| ||+|.+.++|.+|+ .++..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~   75 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGI   75 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCC
Confidence            456889999999999999999999999    8       9999999854     788 99999999999998 76644

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.81  E-value=4.2e-09  Score=81.50  Aligned_cols=60  Identities=12%  Similarity=0.191  Sum_probs=53.2

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++       +| ||+|.+.++|.+|+..++...
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~   68 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGLDNTE   68 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS-------SEEEEEESCHHHHHHHHHHHTTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCe
Confidence            3457889999999999999999999999999999983       36 999999999999998877554

>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=98.79  E-value=3.1e-09  Score=81.59  Aligned_cols=60  Identities=8%  Similarity=0.099  Sum_probs=54.3

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++| .|++|+|.     +++|| ||+|.+.++|.+|+..++...
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~   64 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYS   64 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCe
Confidence            45788999999999999999999999 99999994     78899 999999999999999887654

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=98.78  E-value=3.4e-09  Score=84.25  Aligned_cols=52  Identities=6%  Similarity=0.030  Sum_probs=45.8

Q ss_pred             CHHHHHHHh-hcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          189 DEIELKQYF-SQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       189 tee~L~~~F-~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .+++|+++| ++||.|++|+|+++.+|+++|| ||.|.+.++|.+|+..++...
T Consensus        39 ~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~   92 (104)
T 1jmt_A           39 FFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRW   92 (104)
T ss_dssp             HHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCE
T ss_pred             HHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCE
Confidence            346677777 9999999999999988999999 999999999999998887654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.77  E-value=9.5e-09  Score=80.62  Aligned_cols=60  Identities=10%  Similarity=0.111  Sum_probs=53.5

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcC--CCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQC--GTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~f--G~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ..++++|+||+.++++++|+++|++|  |.|.+|++.       +|| ||+|.+.++|.+|+..++....
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~   76 (99)
T 2cpd_A           14 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVL   76 (99)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEE
T ss_pred             CcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEe
Confidence            45788999999999999999999999  999999985       668 9999999999999988876543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.76  E-value=1.4e-08  Score=83.21  Aligned_cols=58  Identities=10%  Similarity=0.034  Sum_probs=51.4

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce--EEEecccHHHHHHHHHHhcccc
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH--CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf--fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ++|+||++.+++++|+++|++||.|++|+|+..     .||  ||+|.+.++|.+|+..++....
T Consensus        28 l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i   87 (124)
T 2e5i_A           28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADI   87 (124)
T ss_dssp             EEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             EEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEe
Confidence            346999999999999999999999999999753     275  9999999999999999887654

>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=98.75  E-value=2e-09  Score=90.55  Aligned_cols=67  Identities=21%  Similarity=0.189  Sum_probs=56.5

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEE------EEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSV------KIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~sv------ki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+||+.++|+++|+++|++||.|.+|      .|....+|+++|| ||.|.+.++|.+|+..++...
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~  116 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYV  116 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCE
Confidence            345679999999999999999999999999875      1222258999999 999999999999998887654

>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=98.75  E-value=3.6e-09  Score=82.03  Aligned_cols=58  Identities=10%  Similarity=0.106  Sum_probs=51.2

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCC-eEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGT-ISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~-I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ..++++|+|||.++|+++|+++|++||. |..+.+.      ++|| ||+|.+.++|.+|+..++.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g   66 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSG   66 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccC
Confidence            4568899999999999999999999999 6666663      5888 9999999999999988775

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.74  E-value=4.9e-09  Score=81.69  Aligned_cols=63  Identities=13%  Similarity=0.151  Sum_probs=54.1

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEE-EeeCC-CCCccceEEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVK-IMRTD-RGISKGHCMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svk-i~~d~-~g~skGffV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|++|+ |++|. +|.  | ||+|.+.++|.+|+..++...
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~--a-fV~f~~~~~a~~Ai~~l~g~~   78 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV--V-NVTYSSKDQARQALDKLNGFQ   78 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE--E-EEEESSHHHHHHHHHHHTTCB
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE--E-EEEECCHHHHHHHHHHhCCCE
Confidence            356789999999999999999999999999995 88775 333  5 899999999999998777654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.73  E-value=1.5e-08  Score=78.68  Aligned_cols=58  Identities=17%  Similarity=0.302  Sum_probs=49.3

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ..++++|+|||.++++++|+++|++||.|.+|  +.|. +|+   | ||+|.+.++|.+|+. +..
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g   66 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQ   66 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCC
Confidence            34678999999999999999999999999998  4443 555   6 999999999999987 543

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

Probab=98.73  E-value=1.2e-08  Score=79.76  Aligned_cols=59  Identities=10%  Similarity=0.104  Sum_probs=52.1

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+||  ++|+++|+++|++||.|.+|+|.     +++|| ||+|.+.++|.+|+..++...
T Consensus        14 ~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~   73 (97)
T 1x5p_A           14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQ   73 (97)
T ss_dssp             CCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEE
T ss_pred             CCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCe
Confidence            4567889996  89999999999999999999995     67888 999999999999998876554

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=98.71  E-value=1.2e-08  Score=81.27  Aligned_cols=66  Identities=14%  Similarity=0.107  Sum_probs=53.3

Q ss_pred             hhhhccccCC--Cccc--------CHHHHHHHhhcCCCeEEEEEeeCCC---CCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNI--NDEV--------DEIELKQYFSQCGTISSVKIMRTDR---GISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL--~~~v--------tee~L~~~F~~fG~I~svki~~d~~---g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +++.++++|+  +.++        .+++|+++|++||.|++|+|+++..   ++++|| ||.|++.++|.+|+..++...
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            3456666776  2232        3479999999999999999998874   368999 999999999999999888654

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

Probab=98.69  E-value=1.6e-08  Score=92.19  Aligned_cols=64  Identities=14%  Similarity=0.183  Sum_probs=57.1

Q ss_pred             hhhhhhccccCCCccc---------CHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          173 MRKERAELYKNINDEV---------DEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~v---------tee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ....++|+|+||+.++         +|++|+++|++||.|++|+|+.     ++|| ||.|.+.++|.+|+.+++....
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-----~kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-----CCCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4457889999999998         7999999999999999999984     5899 9999999999999988886544

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.63  E-value=4.6e-08  Score=77.04  Aligned_cols=47  Identities=11%  Similarity=0.151  Sum_probs=43.2

Q ss_pred             CcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHH
Q 039806          185 NDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLR  235 (398)
Q Consensus       185 ~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~  235 (398)
                      +.++++++|+++|++||.|++|+|+    ++++|| ||+|.+.++|.+|+..
T Consensus        26 ~~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~   73 (100)
T 2d9o_A           26 KGGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQN   73 (100)
T ss_dssp             CCSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHh
Confidence            3578999999999999999999998    478999 9999999999999876

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.63  E-value=3.9e-08  Score=79.92  Aligned_cols=67  Identities=10%  Similarity=0.112  Sum_probs=55.7

Q ss_pred             hhhhhccccCCCc--cc---CHHHHHHHhhcCCCeEEEEEeeCC-----CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNIND--EV---DEIELKQYFSQCGTISSVKIMRTD-----RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~--~v---tee~L~~~F~~fG~I~svki~~d~-----~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..+++++++|+-.  ++   .+++|+++|++||+|++|+|++|.     +++++|| ||.|.+.++|.+|+..++...
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~   95 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRW   95 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCE
Confidence            4678888888842  22   368999999999999999999875     3568899 999999999999999887654

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=98.57  E-value=2.9e-08  Score=95.28  Aligned_cols=64  Identities=13%  Similarity=0.225  Sum_probs=55.6

Q ss_pred             hhhhhhccccC--CCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          173 MRKERAELYKN--INDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       173 ~~~~~~~~v~n--L~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ..++++++|+|  |+..+||++|+++|++||+|++|++.+     +||| ||+|.+.+||.+|+.+++....
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~   81 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEV   81 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCcc
Confidence            34567889988  688999999999999999999988753     5789 9999999999999999887665

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.53  E-value=8.8e-08  Score=73.75  Aligned_cols=56  Identities=14%  Similarity=0.229  Sum_probs=47.9

Q ss_pred             hhh-ccccCCCcccCHHH----HHHHhhcC-CCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERA-ELYKNINDEVDEIE----LKQYFSQC-GTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~-~~v~nL~~~vtee~----L~~~F~~f-G~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..+ ++|.||++++++++    |+++|++| |+|.+|      +|   || ||.|.+.++|.+|+.+++...
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------tg---G~AfV~F~~~esA~~A~~~l~G~~   70 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------TG---CSAILRFINQDSAERAQKRMENED   70 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------CT---TCEEEEESSHHHHHHHHHHHTTCC
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------ec---CEEEEEECCHHHHHHHHHHhcCCc
Confidence            344 66899999999988    55899999 599998      33   88 999999999999999988755

>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=98.48  E-value=1.3e-07  Score=76.01  Aligned_cols=64  Identities=16%  Similarity=0.152  Sum_probs=51.3

Q ss_pred             hhhhhccccCCCccc-----------CHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEV-----------DEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~v-----------tee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..+++++++||-...           ++++|+++|++||.|++|.| .|.  .++|| ||+|.+.++|.+|+..++...
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            346778889984332           26899999999999999966 454  37999 999999999999998877543

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.27  E-value=3.9e-06  Score=65.65  Aligned_cols=74  Identities=12%  Similarity=0.099  Sum_probs=66.8

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhcc-----CCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKF-----GDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~-----G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      ...++|-|-|||..++++.|+.+.+.+     |.|..+.+..|.     +=|+|+|++..+|-+|.-.|||..|.|++|+
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH-----~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF-----NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT-----TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC-----CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            346789999999999999999999999     999988888776     3499999999999999999999999999999


Q ss_pred             eecc
Q 039806           87 VGPF   90 (398)
Q Consensus        87 V~~~   90 (398)
                      ++-.
T Consensus        94 ~gTv   97 (117)
T 2l9w_A           94 SGTI   97 (117)
T ss_dssp             EECH
T ss_pred             ecCH
Confidence            9654

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.21  E-value=1.1e-06  Score=70.70  Aligned_cols=48  Identities=4%  Similarity=0.054  Sum_probs=42.3

Q ss_pred             HHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          190 EIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       190 ee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +++|+++|++||.|++|+|.++.   ++|| ||.|.+.++|.+|+..++...
T Consensus        31 ~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~   79 (114)
T 3s6e_A           31 KDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRW   79 (114)
T ss_dssp             HHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCE
T ss_pred             HHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            47899999999999999997653   5888 999999999999999888654

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.12  E-value=1.8e-06  Score=69.95  Aligned_cols=57  Identities=16%  Similarity=0.183  Sum_probs=49.2

Q ss_pred             hhhccccCCCcc-cCHHHHHHHhhcCCCeEEEEEeeCCCCCccceEEEecc-cHHHHHHHHHH
Q 039806          176 ERAELYKNINDE-VDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQ-TKRERTSYLRI  236 (398)
Q Consensus       176 ~~~~~v~nL~~~-vtee~L~~~F~~fG~I~svki~~d~~g~skGffV~f~~-~~ea~~A~l~~  236 (398)
                      ...++|+||+.+ +++++|+++|++||.|.+|.+.++.+   .| ||.|.+ ..+|..|..++
T Consensus        18 G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~---tg-fVrf~~~~~~A~~av~~l   76 (121)
T 1owx_A           18 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK---EG-IILFKEKAKEALGKAKDA   76 (121)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS---EE-EEEESSCHHHHHHHHHHT
T ss_pred             CeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC---EE-EEEECCChHHHHHHHHHh
Confidence            456778999999 99999999999999999999987653   46 899999 68888888765

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.11  E-value=1.8e-05  Score=61.32  Aligned_cols=90  Identities=18%  Similarity=0.199  Sum_probs=73.5

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhc-----cCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEe
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSK-----FGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMEL   85 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~-----~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i   85 (398)
                      .+...+|.|.|||.+++++.|.-+|+.     =|.|.+++...       +-|+|.|.+.+.|++.|++ ..+.|++..|
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            345578999999999999999999977     25788887743       4599999999999999983 3778899999


Q ss_pred             eeecccccccccccCCCCceEEeeCCCcccc
Q 039806           86 YVGPFIRRADRIQEGSSFNNLYVKNLDDDMT  116 (398)
Q Consensus        86 ~V~~~~~~~~~~~~~~~~~~lfV~nLp~~~t  116 (398)
                      .|.+...+        ...++++.+|++.++
T Consensus        77 sV~P~~~~--------~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           77 SLRPAPPR--------APARLLLQGLPPGTS   99 (104)
T ss_dssp             EEEECCCC--------CCCCCCCCSCCCCCC
T ss_pred             EEEcCCCC--------CcceEeeecCCCCCC
Confidence            99876554        356899999998775

>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=97.70  E-value=3.7e-05  Score=69.06  Aligned_cols=54  Identities=9%  Similarity=0.015  Sum_probs=46.9

Q ss_pred             ccCHHHHHHHhhcCCCeEEEEEeeCC-----CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          187 EVDEIELKQYFSQCGTISSVKIMRTD-----RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       187 ~vtee~L~~~F~~fG~I~svki~~d~-----~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +-.+++|++.|++||.|.+|+|+++.     +++++|| ||+|.+.++|.+|+..+....
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~  199 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRW  199 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCB
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCce
Confidence            34568999999999999999998654     4489999 999999999999999988654

>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=97.50  E-value=0.00023  Score=55.38  Aligned_cols=75  Identities=16%  Similarity=0.111  Sum_probs=63.2

Q ss_pred             CcceEEEcCCCCCC-c----HHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           13 GIGNAFVKNLASTI-D----NLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        13 ~~~~lfV~nLp~~v-t----e~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      .-.+|+|.||+.+| +    .+.++++|..|+++.+....+.     =+-..|.|.+.++|.+|-..|++..+.|++++|
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            34689999999877 2    2567899999999988877763     235789999999999999999999999999999


Q ss_pred             ecccc
Q 039806           88 GPFIR   92 (398)
Q Consensus        88 ~~~~~   92 (398)
                      -.+..
T Consensus        79 YFgq~   83 (104)
T 1wey_A           79 YFAQT   83 (104)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            88763

>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=97.42  E-value=0.00061  Score=52.04  Aligned_cols=68  Identities=7%  Similarity=0.179  Sum_probs=56.1

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-C-C-CceeEEEEEecCHHHHHHHHHHhcCCeecc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-E-G-KSKGYGFVQYSTPESALDAIEKLQGATVER   82 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~-g-~skg~aFV~F~~~e~A~~Ai~~lng~~l~g   82 (398)
                      .+|-|++||++.|++++.+.++.+..+.......-+ + + ..-.-|||.|.+.|++..-.+.++|..+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            479999999999999999999999887766665544 2 2 233569999999999999999999998754

>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=97.41  E-value=0.00064  Score=52.06  Aligned_cols=55  Identities=25%  Similarity=0.311  Sum_probs=46.6

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ   76 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~ln   76 (398)
                      .+-++| ++|+++...||.++|+.||.| .|+.+.|-      -|||.|.+++.|..|+..++
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT------EEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            445666 999999999999999999965 47777664      59999999999999999764

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.32  E-value=0.00027  Score=55.33  Aligned_cols=64  Identities=11%  Similarity=0.092  Sum_probs=56.5

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcC-----CCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHHhcccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQC-----GTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~f-----G~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      +..+++-+-|||+.++++.++.+.+++     |.|+.|.+..|..    |-+|+|.+...|.+|.|++.....
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~----GAivef~d~~~AgKasLaL~G~ef   87 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN----GAIIIFRDSKFAAKMLMILNGSQF   87 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT----EEEEECSCHHHHHHHHHHHSSEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC----ceEEEEccchhhHHHHhhcCCeee
Confidence            347888889999999999999999999     9999999997754    449999999999999999887653

>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=97.02  E-value=0.0025  Score=50.94  Aligned_cols=74  Identities=15%  Similarity=0.183  Sum_probs=58.8

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecc-eEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVER-MELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g-k~i~V~~   89 (398)
                      ....+-|.|-+.|.+. ...+.+.|++||+|++....  .   ...+-.|.|.+..+|++||. .||+.|+| --|-|.+
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~--~---~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS--N---TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKP   93 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC--S---SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC--C---CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEE
Confidence            3456789999999986 55688899999999988761  1   23489999999999999998 59999985 5666666


Q ss_pred             cc
Q 039806           90 FI   91 (398)
Q Consensus        90 ~~   91 (398)
                      ..
T Consensus        94 ~~   95 (119)
T 1wwh_A           94 CI   95 (119)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.94  E-value=0.00094  Score=54.15  Aligned_cols=79  Identities=25%  Similarity=0.378  Sum_probs=56.9

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEE-EEEEcC-------------CC-CceeEEEEEecCHHHHHHHHHHhc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSS-KVVVSQ-------------EG-KSKGYGFVQYSTPESALDAIEKLQ   76 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~v-ki~~d~-------------~g-~skg~aFV~F~~~e~A~~Ai~~ln   76 (398)
                      .+...|.|-+.|++.+. .+.+.|++||.|++- .+..+.             -+ ....+-.|.|++..+|.+||. .|
T Consensus         5 ~~e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~N   82 (132)
T 3p3d_A            5 NGELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-EN   82 (132)
T ss_dssp             ---CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TT
T ss_pred             cCceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hC
Confidence            45667999999887766 577899999999762 111100             00 123467899999999999998 59


Q ss_pred             CCeecceEeeeecccc
Q 039806           77 GATVERMELYVGPFIR   92 (398)
Q Consensus        77 g~~l~gk~i~V~~~~~   92 (398)
                      |+.|+|.-|-|.+..+
T Consensus        83 G~ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           83 GAVFNGVLLGVIPYTK   98 (132)
T ss_dssp             TCEETTEECEEEECCH
T ss_pred             CeEeCcEEEEEEECCH
Confidence            9999999888877653

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.85  E-value=0.00096  Score=50.71  Aligned_cols=43  Identities=12%  Similarity=0.125  Sum_probs=36.2

Q ss_pred             HHHHHHhhcCCCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHHhccc
Q 039806          191 IELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       191 e~L~~~F~~fG~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .+|.+.|++||+|++++|..|.     + ||+|.+.++|.+|+. +...+
T Consensus        30 ~~L~~~F~~~G~Vi~vr~~~d~-----~-fVtF~d~~sAlaAi~-mnG~~   72 (91)
T 2dnr_A           30 DELLQQFASFGEVILIRFVEDK-----M-WVTFLEGSSALNVLS-LNGKE   72 (91)
T ss_dssp             HHHHHHHHTTCCEEEEEECSSS-----E-EEEESSHHHHHHGGG-GTTCE
T ss_pred             HHHHHHHHhCCCeEEEEEecCC-----E-EEEECChHHHHHHHh-cCCeE
Confidence            6799999999999999999763     4 899999999988885 55443

>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=96.78  E-value=0.0025  Score=48.91  Aligned_cols=53  Identities=26%  Similarity=0.352  Sum_probs=45.3

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhc
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ   76 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~ln   76 (398)
                      -++| ++|+++...||.++|+.||.| .|+.+.|-      -|||.|.+++.|..|+..++
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            3555 999999999999999999944 57777664      59999999999999999764

>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=96.22  E-value=0.0037  Score=47.76  Aligned_cols=43  Identities=23%  Similarity=0.188  Sum_probs=36.9

Q ss_pred             HHHHHHhhcCCCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHHhccc
Q 039806          191 IELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       191 e~L~~~F~~fG~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .+|.+.|++||+|+.+++..|.     + ||+|.+.++|.+|+. +...+
T Consensus        39 ~~L~~~F~~~G~Vilvr~v~d~-----~-fVtF~d~~sAl~AI~-ldG~~   81 (95)
T 1ufw_A           39 TELMQTLGSYGTIVLVRINQGQ-----M-LVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETTE-----E-EEECSCSHHHHHHHH-GGGSE
T ss_pred             HHHHHHHHHCCCEEEEEEecCc-----E-EEEEcChHHHHHHHh-cCCee
Confidence            5699999999999999999774     5 899999999999996 55443

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.82  E-value=0.0058  Score=46.94  Aligned_cols=70  Identities=7%  Similarity=0.125  Sum_probs=50.7

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC--CC-CceeEEEEEecCHHHHHHHHHHhcCCeecc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ--EG-KSKGYGFVQYSTPESALDAIEKLQGATVER   82 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~--~g-~skg~aFV~F~~~e~A~~Ai~~lng~~l~g   82 (398)
                      .+-+|-|+.||++.||+++.+.++.+-.+.......-.  .+ ..-.-|||.|.+.|+...-.+..+|..+-+
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            35579999999999999999888776544322221111  11 112358999999999999999999987754

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.71  E-value=0.0054  Score=60.74  Aligned_cols=56  Identities=21%  Similarity=0.266  Sum_probs=42.1

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHH
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK   74 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~   74 (398)
                      .++|+|. .+..+++++|.++|++||.|.++..-.+. |   -||.|+|.+.+++.++++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-g---~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-G---LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-S---EEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-C---eEEEEEeCCHHHHHHHHhc
Confidence            4679997 79999999999999999999988876542 2   5999999999999987753

>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=92.99  E-value=0.077  Score=41.15  Aligned_cols=63  Identities=11%  Similarity=0.119  Sum_probs=48.7

Q ss_pred             hhhccccCCCccc-C----HHHHHHHhhcCCCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHHhccccC
Q 039806          176 ERAELYKNINDEV-D----EIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAKQG  242 (398)
Q Consensus       176 ~~~~~v~nL~~~v-t----ee~L~~~F~~fG~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~q~~q~~  242 (398)
                      .+++++.||+.++ +    .+.++++|..|+.+.+....+.=    |-.-|.|.+.++|.+|+++++...-+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF----RRirv~F~~~~~A~~AR~~Lh~~~f~   72 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF----KRVRINFSNPLSAADARLRLHKTEFL   72 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT----TEEEEECSSTTHHHHHHHTSTTSEET
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc----eEEEEEeCChHHHHHHHHHhccceec
Confidence            3567889998876 2    25789999999999888777321    11179999999999999999977644

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=90.96  E-value=0.49  Score=47.53  Aligned_cols=64  Identities=23%  Similarity=0.308  Sum_probs=48.7

Q ss_pred             CCCCccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhc
Q 039806            3 STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ   76 (398)
Q Consensus         3 s~rd~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~ln   76 (398)
                      +..|+...+  ..-++|+ ++..+...+|.++|+.||.| +|+.+.|      -.|||.|.+.++|..+++.++
T Consensus       431 ~g~d~~~~R--~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          431 EGPDLQPKR--DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             SSCCCCCCG--GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CCCCCCCCc--CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC------CeEEEEECCHHHHHHHHHHHH
Confidence            444554432  3456665 99999999999999999965 5665443      359999999999999999875

>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=90.83  E-value=0.45  Score=35.98  Aligned_cols=60  Identities=5%  Similarity=-0.019  Sum_probs=44.5

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce---EEEecccHHHHHHHHHHh
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH---CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf---fV~f~~~~ea~~A~l~~q  237 (398)
                      ++.|++||...||+++.+.++....+.....+..+ ..+..-+   ||.|.+.+++..-....+
T Consensus         3 KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~   66 (91)
T 1uw4_A            3 KVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFD   66 (91)
T ss_dssp             EEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHT
T ss_pred             EEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhC
Confidence            46779999999999999999999988777665443 2222222   999999887776555444

>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=90.82  E-value=0.51  Score=37.49  Aligned_cols=56  Identities=9%  Similarity=-0.006  Sum_probs=41.7

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHH
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRI  236 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~  236 (398)
                      ++.+.|.+.+.+. -+.+.++|++||+|++....   ++ .--..|.|+++.+|++|+.+.
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~---~~-~NWihI~Y~s~~~A~rAL~kN   79 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS---NT-GNWMHIRYQSKLQARKALSKD   79 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC---SS-SSEEEEEESSHHHHHHHHTTT
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC---CC-CCeEEEEeCCHHHHHHHHHhC
Confidence            4455567777774 66778899999999988862   11 122389999999999998654

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=89.80  E-value=0.46  Score=36.69  Aligned_cols=54  Identities=15%  Similarity=0.181  Sum_probs=44.6

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcC-----CCeEEEEEeeCCCCCccceEEEecccHHHHHHHHH
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQC-----GTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLR  235 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~f-----G~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~  235 (398)
                      .+++.|.|||.+++++.|.-+|++-     |.|.+++...      .+-.|+|.+.+.|.+-+.+
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~------~~AvItF~d~~va~rVL~k   66 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG------CGGVLTFREPADAERVLAQ   66 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET------TEEEEEESSHHHHHHHHTC
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC------CcEEEEEcChHHHHHHhcC
Confidence            4678889999999999999999882     7899998863      2238999999999877665

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=86.67  E-value=0.31  Score=48.17  Aligned_cols=54  Identities=20%  Similarity=0.253  Sum_probs=37.7

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce--EEEecccHHHHHHHHH
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH--CMAIAQTKRERTSYLR  235 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf--fV~f~~~~ea~~A~l~  235 (398)
                      .+.++|. .+.++++.+|.++|++||.|.++..-.     ++|.  .|+|++.+++..++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~-----~~g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYE-----SFGLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEEC-----SSSEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEc-----cCCeEEEEEeCCHHHHHHHHhc
Confidence            4666665 799999999999999999999998763     3454  7899998888866444

>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=84.67  E-value=1.1  Score=34.14  Aligned_cols=52  Identities=15%  Similarity=0.197  Sum_probs=40.5

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHH
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRI  236 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~  236 (398)
                      .+.+ +.|.++.-.||.++|+.||.| .|+-+.|     .-.||.|.+++.|..|+...
T Consensus        18 Vf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidD-----TsAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           18 VLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD-----TSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             EEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEET-----TEEEEECSCHHHHHHHHHHH
T ss_pred             EEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcC-----CeEEEEecCHHHHHHHHHhc
Confidence            4445 899999999999999999954 4666654     22399999999998877644

>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=84.56  E-value=1.1  Score=34.30  Aligned_cols=52  Identities=13%  Similarity=0.146  Sum_probs=40.7

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHH
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRI  236 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~  236 (398)
                      .+.+ +.|.++.-.||.++|+.|| =..|+-+.|     .-.||.|.+++.|..|+...
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidD-----TsAlvvf~~~~~a~~al~~i   59 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDD-----TSAFVSLSQPEQVKIAVNTS   59 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEET-----TEEEEEEEEECHHHHHHHHH
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcC-----CeEEEEecCHHHHHHHHHhc
Confidence            3444 8999999999999999999 445666655     22399999999998887654

---

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	398
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-06
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-12
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-08
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	6e-11
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-05
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-04
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-10
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-04
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-10
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-05
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-06
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-10
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-04
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-04
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-05
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-09
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-09
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-05
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-09
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-04
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-05
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	7e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	0.002
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-08
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	0.002
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-08
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	0.002
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	5e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	9e-04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 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:) 1e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 0.004
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	9e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-04
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-07
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-07
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-07
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	4e-07
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	0.003
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-07
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	4e-07
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	0.004
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	6e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	0.003
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	7e-07
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-04
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-06
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	0.002
d1nmra_	85	a.144.1.1 (A:) poly(A) binding protein {Protozoan	1e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	5e-04
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-06
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	0.004
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-06
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	0.002
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-04
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	4e-06
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-06
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	0.001
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-06
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-04
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	6e-06
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	8e-06
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	0.004
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	0.004
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-05
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	8e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	0.003
d1g9la_	144	a.144.1.1 (A:) poly(A) binding protein {Human (Hom	2e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	5e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	3e-04
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-04
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	3e-04
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	5e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	5e-04
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	7e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	0.001
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	0.001
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	0.003
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	0.004

>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 = 61.2 bits (148), Expect = 1e-12
 Identities = 43/88 (48%), Positives = 57/88 (64%), Gaps = 1/88 (1%)

Query: 9  ARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESA 68
           R SG+GN F+KNL  +IDN  L+  FS FG+I S KVV  + G SKGYGFV + T E+A
Sbjct: 3  LRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAA 61

Query: 69 LDAIEKLQGATVERMELYVGPFIRRADR 96
            AIEK+ G  +   +++VG F  R +R
Sbjct: 62 ERAIEKMNGMLLNDRKVFVGRFKSRKER 89

>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 = 42.7 bits (100), Expect = 4e-06
 Identities = 20/84 (23%), Positives = 33/84 (39%), Gaps = 22/84 (26%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKG--------------- 145
           S   N+++KNLD  +  + L + FS FG I S  +  D NG+                  
Sbjct: 6   SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 65

Query: 146 -------FGSKVLYVARAQKKAER 162
                     + ++V R + + ER
Sbjct: 66  EKMNGMLLNDRKVFVGRFKSRKER 89

>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 = 63.1 bits (152), Expect = 2e-12
 Identities = 34/172 (19%), Positives = 61/172 (35%), Gaps = 25/172 (14%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           F+  L+    +  L   F ++G +    V+      +S+G+GFV Y+T E    A+    
Sbjct: 10  FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 69

Query: 77  G-ATVERMELYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVI 135
                  +E         + R     +   ++V  + +D  E  L + F ++GKI  + I
Sbjct: 70  HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEI 129

Query: 136 SKD-ANGTSKGFG----------------------SKVLYVARAQKKAERKA 164
             D  +G  +GF                            V +A  K E  +
Sbjct: 130 MTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMAS 181

>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 = 52.3 bits (124), Expect = 1e-08
 Identities = 31/151 (20%), Positives = 52/151 (34%), Gaps = 19/151 (12%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN-GTSKGFGSKVLYVARA 156
           +E      L++  L  + T+E L   F ++G +T  V+ +D N   S+GFG         
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 157 QKKAERKAILRAQFERMRKERAELY-----------------KNINDEVDEIELKQYFSQ 199
              A      +     +  +RA                      I ++ +E  L+ YF Q
Sbjct: 61  VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 120

Query: 200 CGTISSVKIMR-TDRGISKGHCMAIAQTKRE 229
            G I  ++IM     G  +G           
Sbjct: 121 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 151

>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 = 56.1 bits (135), Expect = 6e-11
 Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 1/73 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          +V +L   +    L++ FS  G I S +V       +S GY +V +  P  A  A++ + 
Sbjct: 4  YVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMN 63

Query: 77 GATVERMELYVGP 89
             ++   + +  
Sbjct: 64 FDVIKGKPVRIMW 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 = 40.3 bits (94), Expect = 2e-05
 Identities = 18/52 (34%), Positives = 27/52 (51%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARA 156
           +LYV +L  D+TE +L EKFS  G I S+ + +D         + V +   A
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 53

>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 = 37.2 bits (86), Expect = 3e-04
 Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 1/47 (2%)

Query: 178 AELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHCMAI 223
           A LY  +++ +V E  L + FS  G I S+++ R            +
Sbjct: 1   ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 47

>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 = 55.3 bits (133), Expect = 1e-10
 Identities = 16/73 (21%), Positives = 36/73 (49%)

Query: 15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEK 74
          G   V NL   + +  + ++F++FG ++ + V   + G+S G   V +     AL A+++
Sbjct: 1  GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 75 LQGATVERMELYV 87
            G  ++   + +
Sbjct: 61 YNGVPLDGRPMNI 73

>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 = 36.8 bits (85), Expect = 3e-04
 Identities = 11/35 (31%), Positives = 19/35 (54%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDAN 140
           L V NLD  +++  + E F+EFG +    +  D +
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS 37

>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 = 1e-10
 Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          N +V NL  TI + +L  IF K+G I    ++  +  G+ +G  FV+Y+  E A +AI  
Sbjct: 8  NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 75 LQGATVE 81
          L     E
Sbjct: 68 LNNVIPE 74

>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 = 39.9 bits (93), Expect = 3e-05
 Identities = 11/27 (40%), Positives = 16/27 (59%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKIT 131
           NLYV NL   +T++ L   F ++G I 
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIV 34

>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 = 54.2 bits (130), Expect = 4e-10
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE--GKSKGYGFVQYSTPESALDAIEKL 75
           V+N+    +  ++ ++FS FG++++ ++       G  +G+GFV + T + A  A   L
Sbjct: 12 LVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNAL 71

Query: 76 QGAT 79
            +T
Sbjct: 72 CHST 75

>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 = 43.4 bits (102), Expect = 2e-06
 Identities = 11/52 (21%), Positives = 26/52 (50%)

Query: 96  RIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG 147
           ++ +  + + + V+N+     +  + E FS FG++ ++ + K   GT    G
Sbjct: 1   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 52

>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 = 54.6 bits (131), Expect = 5e-10
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +++NL   I   +++ IF K+G I+  +V      +++G  +V Y     A +A + L G
Sbjct: 11 YIRNLPYKITAEEMYDIFGKYGPIRQIRVG--NTPETRGTAYVVYEDIFDAKNACDHLSG 68

Query: 78 ATVERMELYV 87
            V    L V
Sbjct: 69 FNVCNRYLVV 78

>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 = 38.1 bits (88), Expect = 3e-04
 Identities = 16/100 (16%), Positives = 36/100 (36%), Gaps = 26/100 (26%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG---------------- 147
             LY++NL   +T E + + F ++G I    I       ++G                  
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQ--IRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 148 -------SKVLYVARAQ-KKAERKAILRAQFERMRKERAE 179
                  ++ L V      +A +K   + + E+++  + +
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEK 105

>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 = 52.8 bits (126), Expect = 1e-09
 Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 2/81 (2%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE--GKSKGYGFVQYSTPESALDAIEKL 75
          F+ NL   ID   L+  FS FG I  +  ++     G SKGY F+ +++ +++  AIE +
Sbjct: 2  FIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAM 61

Query: 76 QGATVERMELYVGPFIRRADR 96
           G  +    + V    ++  +
Sbjct: 62 NGQYLCNRPITVSYAFKKDSK 82

>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 = 37.4 bits (86), Expect = 3e-04
 Identities = 16/82 (19%), Positives = 29/82 (35%), Gaps = 25/82 (30%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFG------------------ 147
           +++ NLD ++ E++L + FS FG I           T    G                  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 148 -------SKVLYVARAQKKAER 162
                  ++ + V+ A KK  +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 52.7 bits (126), Expect = 1e-09
 Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 4/74 (5%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE----GKSKGYGFVQYSTPESALDAIE 73
          F+KNL  +     L  +FSK G I+S  +   +       S G+GFV+Y  PE A  A++
Sbjct: 2  FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 74 KLQGATVERMELYV 87
          +LQG TV+  +L V
Sbjct: 62 QLQGHTVDGHKLEV 75

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 20/60 (33%), Positives = 29/60 (48%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYVARAQKKAERKAI 165
           L++KNL+   TEE L   FS+ G I S  ISK  N           +V   + +  +KA+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

>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 = 52.7 bits (126), Expect = 1e-09
 Identities = 21/76 (27%), Positives = 31/76 (40%), Gaps = 3/76 (3%)

Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDA 71
          S +    V+NL   +    LHQIFSKFG +            ++    +QY+ P SA  A
Sbjct: 5  SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHA 61

Query: 72 IEKLQGATVERMELYV 87
             L G  +      +
Sbjct: 62 KLSLDGQNIYNACCTL 77

>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 = 51.2 bits (122), Expect = 4e-09
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          N  V  L   + + +L+ +F   G I + +++   + G S GY FV +++   +  AI+ 
Sbjct: 4  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 75 LQGATVERMELYV 87
          L G TV    L V
Sbjct: 64 LNGITVRNKRLKV 76

>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 = 40.4 bits (94), Expect = 2e-05
 Identities = 12/31 (38%), Positives = 14/31 (45%)

Query: 102 SFNNLYVKNLDDDMTEEILVEKFSEFGKITS 132
           S  NL V  L  DMT+  L   F   G I +
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINT 31

>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 = 51.0 bits (122), Expect = 5e-09
 Identities = 22/86 (25%), Positives = 32/86 (37%), Gaps = 8/86 (9%)

Query: 18  FVKNLAS-TIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
           F+ NL +  +    +  IFSK+G I    V        KG+ FVQY    +A  A+    
Sbjct: 19  FIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGED 71

Query: 77  GATVERMELYVGPFIRRADRIQEGSS 102
           G  +    L +             SS
Sbjct: 72  GRMIAGQVLDINLAAEPKVNRSGPSS 97

>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 = 36.8 bits (85), Expect = 5e-04
 Identities = 11/79 (13%), Positives = 27/79 (34%), Gaps = 21/79 (26%)

Query: 104 NNLYVKNLD-DDMTEEILVEKFSEFGKITSLVIS------------------KDANGTSK 144
           + +++ NL+   + +  +   FS++GKI    +                      +G   
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRM- 74

Query: 145 GFGSKVLYVARAQKKAERK 163
               +VL +  A +    +
Sbjct: 75  -IAGQVLDINLAAEPKVNR 92

>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 = 6e-09
 Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAIEK 74
          N +V  L  T+   +L Q+FS++G I +S+++V Q    S+G GF+++     A +AI+ 
Sbjct: 8  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 75 LQGATVE 81
          L G    
Sbjct: 68 LNGQKPS 74

>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 = 38.9 bits (90), Expect = 7e-05
 Identities = 12/28 (42%), Positives = 19/28 (67%)

Query: 105 NLYVKNLDDDMTEEILVEKFSEFGKITS 132
           NLYV  L   MT++ L + FS++G+I +
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIIT 35

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.6 bits (118), Expect = 1e-08
 Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 5/69 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE--- 73
          F+  L+       L + F +FG+++   V+      +S+G+GFV +         +    
Sbjct: 4  FIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR 63

Query: 74 -KLQGATVE 81
           +L   T++
Sbjct: 64 HELDSKTID 72

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.1 bits (83), Expect = 7e-04
 Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKKAERKA 164
           +++  L    T+E L E F +FG++   ++ +D     S+GFG    +V    +    K 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFG----FVTFMDQAGVDKV 58

Query: 165 I 165
           +
Sbjct: 59  L 59

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 28/92 (30%), Positives = 44/92 (47%), Gaps = 1/92 (1%)

Query: 12  SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALD 70
           SG G  FV+NL+ T     L ++FS +G +      +    K  KG+ FV +  PE A+ 
Sbjct: 6   SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 71  AIEKLQGATVERMELYVGPFIRRADRIQEGSS 102
           A  ++ G   +   L+V P   + +  Q G S
Sbjct: 66  AYAEVDGQVFQGRMLHVLPSTIKKEASQSGPS 97

>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 = 48.0 bits (114), Expect = 3e-08
 Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK-- 74
          FV  L+      K+ + F  FG+++S ++ +  +  K +G+ F+ +   E     +EK  
Sbjct: 3  FVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKY 62

Query: 75 --LQGATVE 81
            +  +  E
Sbjct: 63 HNVGLSKCE 71

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 9/25 (36%), Positives = 14/25 (56%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKI 130
           ++V  L  D  EE + E F  FG++
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEV 26

>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 = 48.9 bits (116), Expect = 3e-08
 Identities = 11/67 (16%), Positives = 28/67 (41%), Gaps = 3/67 (4%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK---SKGYGFVQYSTPESALDAIEK 74
          F+  +       ++ +  +K  +     +V +       ++G+ FV+Y +  +A  A  K
Sbjct: 5  FIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRK 64

Query: 75 LQGATVE 81
          L    ++
Sbjct: 65 LMPGRIQ 71

>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 = 35.4 bits (81), Expect = 0.002
 Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 3/61 (4%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGT---SKGFGSKVLYVARAQKKAER 162
           L++  +      E ++E+ ++  +    VI   +      ++GF        RA   A R
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 163 K 163
           K
Sbjct: 64  K 64

>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 = 48.4 bits (115), Expect = 3e-08
 Identities = 16/71 (22%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEKLQ 76
          +V NL+      +++++FSK GDI+   + +   +  + G+ FV+Y +   A +A+  + 
Sbjct: 11 YVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYIN 70

Query: 77 GATVERMELYV 87
          G  ++   +  
Sbjct: 71 GTRLDDRIIRT 81

>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 = 35.3 bits (81), Expect = 0.002
 Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 9/81 (11%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLY-----VARAQKKA 160
           LYV NL    TEE + E FS+ G I  +++  D    +      V Y        A +  
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 161 ERKAI----LRAQFERMRKER 177
               +    +R  ++   KE 
Sbjct: 70  NGTRLDDRIIRTDWDAGFKEG 90

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 5e-08
 Identities = 30/93 (32%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 3  STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQY 62
          S+ NSE++ S      V N+     +  L Q+F +FG I   +++   E  SKG+GFV +
Sbjct: 1  SSGNSESK-STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF-NERGSKGFGFVTF 58

Query: 63 STPESALDAIEKLQGATVERMELYVGPFIRRAD 95
               A  A EKL G  VE  ++ V     R  
Sbjct: 59 ENSADADRAREKLHGTVVEGRKIEVNNATARVM 91

>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 = 36.2 bits (83), Expect = 9e-04
 Identities = 11/41 (26%), Positives = 20/41 (48%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD 138
           +  S+   L+V N+     +  L + F +FGKI  + I  +
Sbjct: 6   ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN 46

>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 = 48.1 bits (114), Expect = 6e-08
 Identities = 13/81 (16%), Positives = 33/81 (40%), Gaps = 4/81 (4%)

Query: 85  LYVGPFIRRADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSK 144
           +Y  P           S+ +++ ++   D+  EE+  E   ++G++  + +  +      
Sbjct: 9   IYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLV 68

Query: 145 GFGSKVLYVARAQKKAERKAI 165
           G      YV   +++   KA+
Sbjct: 69  GNV----YVKFRREEDAEKAV 85

>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 = 47.7 bits (113), Expect = 1e-07
 Identities = 11/85 (12%), Positives = 32/85 (37%)

Query: 3   STPNSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQY 62
           S+ +++   S + +  ++            ++  K+G+++   V  +      G  +V++
Sbjct: 16  SSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKF 75

Query: 63  STPESALDAIEKLQGATVERMELYV 87
              E A  A+  L         ++ 
Sbjct: 76  RREEDAEKAVIDLNNRWFNGQPIHA 100

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 0.004
 Identities = 6/51 (11%), Positives = 18/51 (35%), Gaps = 1/51 (1%)

Query: 171 ERMRKERAELY-KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGHC 220
           + +R   +++  +   DE  E    +   + G +  + +         G+ 
Sbjct: 21  DGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNV 71

>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 = 47.3 bits (112), Expect = 9e-08
 Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          F+  L + +++ ++ ++ + FG +++  +V     G SKGY F +Y        AI  L 
Sbjct: 5  FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 64

Query: 77 GATVERMELYV 87
          G  +   +L V
Sbjct: 65 GMQLGDKKLLV 75

>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 = 46.5 bits (110), Expect = 2e-07
 Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 5/71 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +   +AS + +  + Q FS FG I   +V        KGY FV++ST ESA  AI  + G
Sbjct: 22 YCGGIASGLTDQLMRQTFSPFGQIMEIRVF-----PEKGYSFVRFSTHESAAHAIVSVNG 76

Query: 78 ATVERMELYVG 88
           T+E   +   
Sbjct: 77 TTIEGHVVKCY 87

>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 = 38.4 bits (89), Expect = 1e-04
 Identities = 8/40 (20%), Positives = 19/40 (47%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISK 137
           Q       +Y   +   +T++++ + FS FG+I  + +  
Sbjct: 13  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP 52

>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 = 46.2 bits (109), Expect = 2e-07
 Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 6/84 (7%)

Query: 18 FVKNLASTIDNLKLHQ----IFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE 73
          ++ NL   I   +L +    IFS+FG I    V  S   K +G  FV +    SA +A+ 
Sbjct: 7  YINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNALR 64

Query: 74 KLQGATVERMELYVGPFIRRADRI 97
           +QG       + +      +D I
Sbjct: 65 SMQGFPFYDKPMRIQYAKTDSDII 88

>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 = 46.2 bits (109), Expect = 2e-07
 Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          +V  L   +    L ++F + G + ++ +   +  G+ +GYGFV++ + E A  AI+ + 
Sbjct: 13 YVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMD 72

Query: 77 GATVERMELYV 87
             +    + V
Sbjct: 73 MIKLYGKPIRV 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 = 37.3 bits (86), Expect = 3e-04
 Identities = 11/36 (30%), Positives = 20/36 (55%)

Query: 97  IQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITS 132
           I E +    +YV  LD+ ++E +L E F + G + +
Sbjct: 3   ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVN 38

>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 = 45.8 bits (108), Expect = 3e-07
 Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 5/70 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V+NL  +     + + F+        +V      K + Y FV +S  E A++A++ L G
Sbjct: 12 YVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKALNG 66

Query: 78 ATVERMELYV 87
            ++   + V
Sbjct: 67 KVLDGSPIEV 76

>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 = 45.7 bits (108), Expect = 4e-07
 Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          +  V  L        L + FS FG++   +V    + G SKG+GFV+++  E+ +  + +
Sbjct: 10 DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 75 LQG 77
             
Sbjct: 70 RHM 72

>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 = 34.6 bits (79), Expect = 0.003
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 5/63 (7%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFGSKVLYVARAQKKAER 162
           ++L V  L    TE+ L E FS FG++  + + KD   G SKGFG    +V   + + + 
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG----FVRFTEYETQV 64

Query: 163 KAI 165
           K +
Sbjct: 65  KVM 67

>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 = 45.0 bits (106), Expect = 4e-07
 Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 5/69 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAIE--- 73
          F+  L+       L   FSKFG++    + +      S+G+GFV +   ES    ++   
Sbjct: 3  FIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKE 62

Query: 74 -KLQGATVE 81
           KL G  ++
Sbjct: 63 HKLNGKVID 71

>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 = 45.8 bits (108), Expect = 4e-07
 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
           N F+ +L     +  L Q+F  FG++ S+KV + ++   SK +GFV Y  P SA  AI+ 
Sbjct: 20  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 79

Query: 75  LQGATVERMELYVGPFIRRADR 96
           + G  +    L V     + D 
Sbjct: 80  MNGFQIGMKRLKVQLKRSKNDS 101

>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 = 34.3 bits (78), Expect = 0.004
 Identities = 18/92 (19%), Positives = 32/92 (34%), Gaps = 28/92 (30%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVIS--------------------- 136
           +EG    NL++ +L  +  ++ L++ F  FG + S  +                      
Sbjct: 13  KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVS 72

Query: 137 -----KDANGTSKGFGSKVLYVARAQKKAERK 163
                +  NG     G K L V   + K + K
Sbjct: 73  AQAAIQSMNGFQ--IGMKRLKVQLKRSKNDSK 102

>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 = 44.7 bits (105), Expect = 6e-07
 Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEK 74
          N  V  L   +   +   +F   G+I+S K+V  +  G+S GYGFV Y  P+ A  AI  
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 75 LQGATVERMELYV 87
          L G  ++   + V
Sbjct: 64 LNGLRLQTKTIKV 76

>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 = 34.3 bits (78), Expect = 0.003
 Identities = 10/28 (35%), Positives = 13/28 (46%)

Query: 102 SFNNLYVKNLDDDMTEEILVEKFSEFGK 129
           S  NL V  L  +MT+E     F   G+
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGE 28

>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 = 44.7 bits (105), Expect = 7e-07
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAIEKLQ 76
           V  L+       L ++FSK+G I    +V  Q+ + S+G+ FV +   + A +A E+  
Sbjct: 13 GVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERAN 72

Query: 77 GATVERMELYV 87
          G  ++   + V
Sbjct: 73 GMELDGRRIRV 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 = 37.4 bits (86), Expect = 2e-04
 Identities = 14/49 (28%), Positives = 19/49 (38%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLY 152
             L V  L    TE  L E FS++G I  + I  D         + V +
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 58

>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 = 44.3 bits (104), Expect = 1e-06
 Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE--- 73
          F+  L+    +  L   F ++G +    V+      +S+G+GFV Y+T E    A+    
Sbjct: 10 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 69

Query: 74 -KLQGATVE 81
           K+ G  VE
Sbjct: 70 HKVDGRVVE 78

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG 147
           +E      L++  L  + T+E L   F ++G +T  V+ +D     S+GFG
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 51

>d1nmra_ a.144.1.1 (A:) poly(A) binding protein {Protozoan (Trypanosoma cruzi) [TaxId: 5693]} Length = 85

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Protozoan (Trypanosoma cruzi) [TaxId: 5693]

 Score = 43.6 bits (103), Expect = 1e-06
 Identities = 12/35 (34%), Positives = 25/35 (71%)

Query: 347 AAASNENLSSMLVATSPDERKDILGQRLYPLVKKL 381
            A+  +NLS++L   +P+++K++LG+RLY  +  +
Sbjct: 4   LASQGQNLSTVLANLTPEQQKNVLGERLYNHIVAI 38

>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 = 43.9 bits (103), Expect = 2e-06
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAIEKLQ 76
          +V  LA  +D+  LH  F  FGDI   ++ +  E +  +G+ FV++   E A  AI+ + 
Sbjct: 9  YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 68

Query: 77 GATVERMELYV 87
           + +    + V
Sbjct: 69 ESELFGRTIRV 79

>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 = 5e-04
 Identities = 16/86 (18%), Positives = 32/86 (37%), Gaps = 9/86 (10%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLY-----VAR 155
           ++   LYV  L +++ +++L   F  FG IT + I  D         + V +      A 
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 156 AQKKAERKAI----LRAQFERMRKER 177
           A        +    +R    +  + +
Sbjct: 63  AIDNMNESELFGRTIRVNLAKPMRIK 88

>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 = 43.4 bits (102), Expect = 2e-06
 Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 5/80 (6%)

Query: 8  EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPES 67
          E   +     FV NL   I   ++ ++F K+G     K       K KG+GF++  T   
Sbjct: 2  EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYG-----KAGEVFIHKDKGFGFIRLETRTL 56

Query: 68 ALDAIEKLQGATVERMELYV 87
          A  A  +L    +   +L V
Sbjct: 57 AEIAKVELDNMPLRGKQLRV 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 = 33.8 bits (77), Expect = 0.004
 Identities = 11/31 (35%), Positives = 19/31 (61%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKIT 131
           +  + L+V NL  D+TEE + + F ++GK  
Sbjct: 6   TQRSRLFVGNLPPDITEEEMRKLFEKYGKAG 36

>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 = 43.9 bits (103), Expect = 2e-06
 Identities = 13/80 (16%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           F+  L+       L   + ++G +    V+      +S+G+GFV +S+      A+   +
Sbjct: 24  FIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-AR 82

Query: 77  GATVERMELYVGPFIRRADR 96
             +++   +     + R + 
Sbjct: 83  PHSIDGRVVEPKRAVAREES 102

>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 = 35.0 bits (80), Expect = 0.002
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 23/88 (26%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD-ANGTSKGFG--------- 147
           +E   F  L++  L  + TEE L   + ++GK+T  V+ +D A+  S+GFG         
Sbjct: 15  REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 74

Query: 148 -------------SKVLYVARAQKKAER 162
                         +V+   RA  + E 
Sbjct: 75  VDAAMAARPHSIDGRVVEPKRAVAREES 102

>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 = 42.8 bits (100), Expect = 3e-06
 Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 6/80 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          ++ NL+  +    L Q+F       + +V         GY FV Y     A+ AIE L G
Sbjct: 5  YIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETLSG 59

Query: 78 AT-VERMELYVGPFIRRADR 96
             +    + V   + +  R
Sbjct: 60 KVELHGKIMEVDYSVSKKLR 79

>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 = 38.5 bits (89), Expect = 1e-04
 Identities = 13/79 (16%), Positives = 25/79 (31%), Gaps = 21/79 (26%)

Query: 104 NNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD--------------------ANGTS 143
           N LY+ NL   +T + L + F +     +  +                        +G  
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKV 61

Query: 144 KGFGSKVLYVARAQKKAER 162
           +    K++ V  +  K  R
Sbjct: 62  E-LHGKIMEVDYSVSKKLR 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 = 43.1 bits (101), Expect = 3e-06
 Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
            KNL+  I   +L ++F    +I+    +VSQ+GKSKG  ++++ +   A   +E+ QG
Sbjct: 20 LAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 75

Query: 78 ATVERMELYV 87
          A ++   + +
Sbjct: 76 AEIDGRSVSL 85

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.2 bits (101), Expect = 4e-06
 Identities = 14/90 (15%), Positives = 24/90 (26%), Gaps = 10/90 (11%)

Query: 12 SGIGNAFVKNLASTI-----DNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPE 66
          SG            +        K   +F  +    + +       KS     + +S P 
Sbjct: 3  SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-----KSFKRVRINFSNPL 57

Query: 67 SALDAIEKLQGATVERMELYVGPFIRRADR 96
          SA DA  +L        E+ +         
Sbjct: 58 SAADARLRLHKTEFLGKEMKLYFAQTLHIG 87

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 4e-06
 Identities = 10/77 (12%), Positives = 25/77 (32%), Gaps = 7/77 (9%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVV------SQEGKSKGYGFVQYSTPESALDA 71
          +V N+   I    +   F+    +              Q  + K + F+++ + +    A
Sbjct: 5  YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 64

Query: 72 IEKLQGATVERMELYVG 88
          +    G   +   L + 
Sbjct: 65 M-AFDGIIFQGQSLKIR 80

>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 = 40.1 bits (93), Expect = 3e-05
 Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 6/61 (9%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKITSLVISK------DANGTSKGFGSKVLYVARAQKK 159
           LYV N+   +TEE +++ F+   ++  L  +             K F            +
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 160 A 160
           A
Sbjct: 64  A 64

>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 = 5e-06
 Identities = 14/91 (15%), Positives = 34/91 (37%), Gaps = 6/91 (6%)

Query: 12  SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDA 71
           SG    FV      +   +L + FS++G      + V      + + FV ++  + A   
Sbjct: 3   SGSSGVFVGRCTGDMTEDELREFFSQYG----DVMDVFIPKPFRAFAFVTFADDQIAQSL 58

Query: 72  IEKLQGATVERMELYVGPFIRRADRIQEGSS 102
               +   ++ + +++     + +     SS
Sbjct: 59  CG--EDLIIKGISVHISNAEPKHNSNSGPSS 87

>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 = 35.4 bits (81), Expect = 0.001
 Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 17/80 (21%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVIS-----------------KDANGTS 143
           S  + ++V     DMTE+ L E FS++G +  + I                  +   G  
Sbjct: 3   SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGED 62

Query: 144 KGFGSKVLYVARAQKKAERK 163
                  ++++ A+ K    
Sbjct: 63  LIIKGISVHISNAEPKHNSN 82

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (100), Expect = 5e-06
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIEKLQ 76
           F   LA+ I    L   FS  G ++  +++  +   +SKG  +V++   +S       L 
Sbjct: 22  FCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV-PLAIGLT 80

Query: 77  GATVERMELYVGPFIRRADRI 97
           G  +  + + V       +R+
Sbjct: 81  GQRLLGVPIIVQASQAEKNRL 101

>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 = 36.9 bits (85), Expect = 5e-04
 Identities = 14/88 (15%), Positives = 26/88 (29%), Gaps = 8/88 (9%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKGFGSKVLYV---- 153
            E      ++   L   +    L + FS  GK+  + I  D N       + V +     
Sbjct: 13  PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 72

Query: 154 ARAQKKAERKAI----LRAQFERMRKER 177
                    + +    +  Q  +  K R
Sbjct: 73  VPLAIGLTGQRLLGVPIIVQASQAEKNR 100

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.5 bits (99), Expect = 6e-06
 Identities = 17/74 (22%), Positives = 33/74 (44%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
          N ++ NL  ++D  +L  +   FG + S++++    G S+G GF +  + E     I   
Sbjct: 20 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 76 QGATVERMELYVGP 89
           G  ++       P
Sbjct: 80 NGKFIKTPPGVSAP 93

>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 = 41.6 bits (97), Expect = 8e-06
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           V NL+       L ++F  FG I    +   +  G+SKG+ F+ +   E A  AI  + 
Sbjct: 12 RVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVS 71

Query: 77 GATVERMELYV 87
          G   + + L V
Sbjct: 72 GFGYDHLILNV 82

>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 = 34.3 bits (78), Expect = 0.004
 Identities = 11/35 (31%), Positives = 15/35 (42%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITS 132
           +       + V NL +D  E  L E F  FG I+ 
Sbjct: 3   RRADDNATIRVTNLSEDTRETDLQELFRPFGSISR 37

>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 = 1e-05
 Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           V+N+  T+   ++   F  +  I  S  +   E G   G   V + + + A  A+  L 
Sbjct: 13 KVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLN 72

Query: 77 GATVERMELYV 87
             +   ++ +
Sbjct: 73 DRPIGSRKVKL 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 = 33.9 bits (77), Expect = 0.004
 Identities = 7/48 (14%), Positives = 20/48 (41%), Gaps = 1/48 (2%)

Query: 101 SSFNNLYVKNLDDDMTEEILVEKFSEFGKIT-SLVISKDANGTSKGFG 147
                + V+N+   ++ + +++ F  +  I  S+ +  +  G   G  
Sbjct: 7   PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 54

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 1/80 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAIEKLQ 76
          FV  L+   +   L Q+FSK+G I    VV  +E + S+G+GFV +   + A DA+  + 
Sbjct: 9  FVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMN 68

Query: 77 GATVERMELYVGPFIRRADR 96
          G +V+  ++ V    + +D 
Sbjct: 69 GKSVDGRQIRVDQAGKSSDN 88

>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 = 41.2 bits (96), Expect = 1e-05
 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 2/70 (2%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V NL   I    +  +F K+G I    + +        + FV++  P  A DA+    G
Sbjct: 18 YVGNLPPDIRTKDIEDVFYKYGAI--RDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 75

Query: 78 ATVERMELYV 87
             +   L V
Sbjct: 76 YDYDGYRLRV 85

>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 = 41.3 bits (96), Expect = 2e-05
 Identities = 19/88 (21%), Positives = 34/88 (38%), Gaps = 9/88 (10%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVS---------QEGKSKGYGFVQYSTPESA 68
          +V+ L  ++    L   F + G ++ +K             + GK KG   V Y  P +A
Sbjct: 12 YVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTA 71

Query: 69 LDAIEKLQGATVERMELYVGPFIRRADR 96
            A+E   G   +  +L V    ++   
Sbjct: 72 KAAVEWFDGKDFQGSKLKVSLARKKPPM 99

>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 = 36.7 bits (84), Expect = 8e-04
 Identities = 10/41 (24%), Positives = 20/41 (48%)

Query: 98  QEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKD 138
            E S  + +YV+ L+D +T + L + F + G +     +  
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQ 43

>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 = 40.5 bits (94), Expect = 2e-05
 Identities = 11/71 (15%), Positives = 28/71 (39%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDI-QSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ 76
          ++ N   +     +  +      +  S ++   +   S+ + ++  ++ E A   +EKL 
Sbjct: 5  WMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLN 64

Query: 77 GATVERMELYV 87
          G  +E   L  
Sbjct: 65 GLKIEGYTLVT 75

>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 = 34.4 bits (78), Expect = 0.003
 Identities = 3/26 (11%), Positives = 10/26 (38%)

Query: 106 LYVKNLDDDMTEEILVEKFSEFGKIT 131
           L++ N     T+  + +   +   + 
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVA 29

>d1g9la_ a.144.1.1 (A:) poly(A) binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 144

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 22/101 (21%), Positives = 37/101 (36%), Gaps = 21/101 (20%)

Query: 281 PPPPSPLFLMAPDSVTQYRGAMMNGHANFPMPLMLSNLQKPSYNYPISQPRAGQAAANNL 340
           P   +     A  +V QY+ A    +    +               + QP         L
Sbjct: 2   PLGSAAAATPAVRTVPQYKYAAGVRNPQQHLN--------AQPQVTMQQPAVHVQGQEPL 53

Query: 341 TNGNHRAAASNENLSSMLVATSPDERKDILGQRLYPLVKKL 381
           T             +SML +  P E+K +LG+RL+PL++ +
Sbjct: 54  T-------------ASMLASAPPQEQKQMLGERLFPLIQAM 81

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 40.1 bits (93), Expect = 3e-05
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAIEKLQ 76
          FV ++       ++ + F  +G+I++  + + +    SKGY  V+Y T + AL A E L 
Sbjct: 11 FVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN 70

Query: 77 GATVERMELYV 87
          GA +    + V
Sbjct: 71 GAEIMGQTIQV 81

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V NL+  +  + + Q+FS+ G  +S K++  +   +  Y FV++     A  A+  + G
Sbjct: 12 YVGNLSRDVTEVLILQLFSQIGPCKSCKMIT-EHTSNDPYCFVEFYEHRDAAAALAAMNG 70

Query: 78 ATVERMELYV 87
            +   E+ V
Sbjct: 71 RKILGKEVKV 80

>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 = 36.9 bits (85), Expect = 4e-04
 Identities = 16/89 (17%), Positives = 30/89 (33%), Gaps = 22/89 (24%)

Query: 97  IQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDANGTSKG----------- 145
           +++      LYV NL  D+TE ++++ FS+ G   S  +  +                  
Sbjct: 2   MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDA 61

Query: 146 -----------FGSKVLYVARAQKKAERK 163
                         K + V  A   + +K
Sbjct: 62  AAALAAMNGRKILGKEVKVNWATTPSSQK 90

>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 = 39.7 bits (92), Expect = 4e-05
 Identities = 16/76 (21%), Positives = 27/76 (35%), Gaps = 6/76 (7%)

Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDA 71
          SG     VKNL    +  ++H +   +              ++K   FV     E A +A
Sbjct: 3  SGSSGILVKNLPQDSNCQEVHDLLKDYDL------KYCYVDRNKRTAFVTLLNGEQAQNA 56

Query: 72 IEKLQGATVERMELYV 87
          I+     +    +L V
Sbjct: 57 IQMFHQYSFRGKDLIV 72

>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 = 39.5 bits (92), Expect = 5e-05
 Identities = 9/59 (15%), Positives = 19/59 (32%), Gaps = 4/59 (6%)

Query: 34 IFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE----RMELYVG 88
          +  +       + ++  +    G   V +  PE A   I+ L G          + + G
Sbjct: 36 LRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDG 94

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (90), Expect = 1e-04
 Identities = 18/108 (16%), Positives = 32/108 (29%), Gaps = 23/108 (21%)

Query: 97  IQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVIS-------------------- 136
           ++E       +  +LDD    E L   FS  G+I  +                       
Sbjct: 5   LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGK 64

Query: 137 -KDANGTSKGFGSKVLYVARAQKKAERKAILRAQFERMRKERAELYKN 183
            KDAN        +   V     + E +     +    ++E    +K+
Sbjct: 65  AKDANN--GNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWKS 110

>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 = 37.9 bits (87), Expect = 3e-04
 Identities = 15/89 (16%), Positives = 28/89 (31%), Gaps = 6/89 (6%)

Query: 12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTP-ESALD 70
           G    F  +L        LH +FS  G+I+    V          G + +    + AL 
Sbjct: 9  IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-----KEGIILFKEKAKEALG 63

Query: 71 AIEKLQGATVERMELYVGPFIRRADRIQE 99
            +      ++     V   +   +  +E
Sbjct: 64 KAKDANNGNLQLRNKEVTWEVLEGEVEKE 92

>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 = 38.6 bits (89), Expect = 2e-04
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEG-KSKGYGFVQYSTPESALDAIEKLQ 76
          FV  L     +  L + F  FGDI+ + V+  ++  KS+GYGFV  +   +A  A +   
Sbjct: 14 FVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN 73

Query: 77 G 77
           
Sbjct: 74 P 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 = 37.4 bits (86), Expect = 2e-04
 Identities = 13/69 (18%), Positives = 29/69 (42%), Gaps = 5/69 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIE--- 73
          FV  L+       +   F +FG +  + ++  +   + +G+GFV + + +      E   
Sbjct: 3  FVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHF 62

Query: 74 -KLQGATVE 81
           ++    VE
Sbjct: 63 HEINNKMVE 71

>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 = 37.4 bits (86), Expect = 3e-04
 Identities = 11/70 (15%), Positives = 27/70 (38%), Gaps = 4/70 (5%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE---- 73
          ++K   +      + +     G + + ++  +     KG  FV + + ESA   +E    
Sbjct: 10 YIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQ 69

Query: 74 KLQGATVERM 83
          K +   +  +
Sbjct: 70 KYKETDLLIL 79

>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 = 37.4 bits (86), Expect = 3e-04
 Identities = 27/89 (30%), Positives = 40/89 (44%), Gaps = 2/89 (2%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGK-SKGYGFVQYSTPESALDAIEKLQ 76
           FV N+       +L  IFS+ G + S ++V  +E    KGYGF +Y   E+AL A+  L 
Sbjct: 12  FVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLN 71

Query: 77  GATVERMELYVGPFIRRADRIQEGSSFNN 105
           G       L V       ++ +E  S   
Sbjct: 72  GREFSGRALRVDNAASEKNK-EELKSLGT 99

>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 = 37.0 bits (85), Expect = 5e-04
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 5/63 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
              L + +   +L  +  K G + +  +  ++      Y F +Y T E +  A   L G
Sbjct: 24 ANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP-----YSFARYRTTEESKRAYVTLNG 78

Query: 78 ATV 80
            V
Sbjct: 79 KEV 81

>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 = 36.3 bits (83), Expect = 5e-04
 Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
          +++ L     +  L ++   +G I S+K ++ +   K KGYGFV + +P +A  A+  L+
Sbjct: 2  YIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALK 61

Query: 77 GATVE 81
           + V+
Sbjct: 62 ASGVQ 66

>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 = 36.6 bits (84), Expect = 7e-04
 Identities = 13/86 (15%), Positives = 29/86 (33%), Gaps = 2/86 (2%)

Query: 18  FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQE-GKSKGYGFVQYSTPESALDAIEKLQ 76
           F+ NL   +    + + F                  + KG+G+ ++   +S   +   L 
Sbjct: 19  FLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSL-LSALSLN 77

Query: 77  GATVERMELYVGPFIRRADRIQEGSS 102
             ++    + V    +  D+    SS
Sbjct: 78  EESLGNKRIRVDVADQAQDKDSGPSS 103

>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 = 36.8 bits (84), Expect = 0.001
 Identities = 28/96 (29%), Positives = 45/96 (46%), Gaps = 3/96 (3%)

Query: 16  NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGY-GFVQYSTPESALDAIEK 74
           N  V  + +T+D ++L Q+F ++G I+S K+V  +E +     GFV++ +  SA  AI  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 75  LQGATVERMELYVGPFIRRADR--IQEGSSFNNLYV 108
           L G  +    L V        R  I       N Y+
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139

>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 = 35.0 bits (80), Expect = 0.001
 Identities = 21/70 (30%), Positives = 29/70 (41%), Gaps = 7/70 (10%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
          +V     T   L+    FS FG+I             +   FV Y   ESA  A+ +L G
Sbjct: 9  YVYGEDMTPTLLR--GAFSPFGNIIDL-----SMDPPRNCAFVTYEKMESADQAVAELNG 61

Query: 78 ATVERMELYV 87
            VE ++L V
Sbjct: 62 TQVESVQLKV 71

>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 = 34.5 bits (79), Expect = 0.003
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 6/77 (7%)

Query: 18 FVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQG 77
           V        +  L Q F+++G+I    +       +  +  ++Y +   A  A+ K   
Sbjct: 8  TVFGFPQASASYILLQ-FAQYGNILKHVMS-----NTGNWMHIRYQSKLQARKALSKDGR 61

Query: 78 ATVERMELYVGPFIRRA 94
             E + + V P I + 
Sbjct: 62 IFGESIMIGVKPCIDKN 78

>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 = 34.2 bits (77), Expect = 0.004
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL 75
          N F+ NL       +L    S+        VV  + G ++ +G+V + + E    A+ +L
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-EL 73

Query: 76 QGATVERMELYV 87
           G  V   E+ +
Sbjct: 74 TGLKVFGNEIKL 85

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	398
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.94
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.86
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.85
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.85
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.85
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.85
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.85
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.84
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.84
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.84
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.84
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.83
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.83
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.83
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.83
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.82
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.82
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.82
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.81
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.81
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.81
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.81
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.8
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.8
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.8
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.8
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.79
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.79
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.79
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.78
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.78
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.78
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.77
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.76
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.76
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.76
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.76
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.76
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.75
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.75
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.75
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.75
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.74
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.74
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.74
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.74
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.74
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.73
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.73
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.73
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.72
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.72
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.72
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.72
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.72
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.71
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.7
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.7
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.69
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.67
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.67
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.67
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.66
d1g9la_	144	poly(A) binding protein {Human (Homo sapiens) [Tax	99.66
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	99.66
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.65
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.65
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.65
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.64
d1nmra_	85	poly(A) binding protein {Protozoan (Trypanosoma cr	99.63
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.62
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.52
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.49
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.47
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.45
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.41
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.39
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.39
d1ifwa_	92	poly(A) binding protein {Baker's yeast (Saccharomy	99.38
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.38
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.38
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.37
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.37
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.36
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.36
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.36
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.36
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.35
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.35
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.34
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.34
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.34
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.33
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.32
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.32
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.32
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.32
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.32
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.31
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.3
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.3
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.28
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.28
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.28
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.26
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.26
d1i2ta_	61	hyperplastic discs protein {Human (Homo sapiens) [	99.25
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.25
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.24
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.24
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.23
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.22
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.22
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.21
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.2
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.2
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.18
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.14
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.13
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.12
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.12
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.11
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.1
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.08
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.08
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.07
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.07
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.07
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.05
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.05
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.04
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.02
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.02
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.02
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.01
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.01
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.0
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.99
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	98.99
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	98.98
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.98
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.96
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.95
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	98.95
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.95
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.94
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.94
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.91
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	98.9
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	98.88
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	98.88
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.84
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.84
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.82
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.82
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.82
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.8
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.78
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.61
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.61
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.5
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.34
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.29
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.67
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.65
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.33
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.76
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	91.41
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	82.9

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=1.2e-25  Score=196.69  Aligned_cols=125  Identities=23%  Similarity=0.426  Sum_probs=99.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      .++|||+|||.++|+++|+++|++||.|.+|+++++. +|.++|||||+|.+.++|.+|++ +++..+.++.+.+.....
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            4689999999999999999999999999999999998 99999999999999999999998 577888888888877665


Q ss_pred             cccccccC--CCCceEEeeCCCccccHHHHHHHHccCCCEEEEEEeeCC
Q 039806           93 RADRIQEG--SSFNNLYVKNLDDDMTEEILVEKFSEFGKITSLVISKDA  139 (398)
Q Consensus        93 ~~~~~~~~--~~~~~lfV~nLp~~~tee~L~~~F~~fG~I~~~~i~~d~  139 (398)
                      +.......  ...++|||+|||+++|+++|+++|+.||.|..+.+..|.
T Consensus        85 ~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~  133 (183)
T d1u1qa_          85 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR  133 (183)
T ss_dssp             TTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT
T ss_pred             cccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeeccc
Confidence            55443222  255667777777777777666666666666665555543

>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=99.87  E-value=4.9e-23  Score=158.71  Aligned_cols=89  Identities=47%  Similarity=0.766  Sum_probs=82.9

Q ss_pred             ccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806            7 SEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus         7 ~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      |+.|+++.++|||+|||.++|+++|+++|+.||.|.+|+|..+.. .++|||||+|++.++|++||+.|||..|+|+.|.
T Consensus         1 Ps~r~s~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~   79 (89)
T d1cvja2           1 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF   79 (89)
T ss_dssp             THHHHTTTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEE
T ss_pred             CCCccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            678889999999999999999999999999999999999999874 4789999999999999999999999999999999


Q ss_pred             eecccccccc
Q 039806           87 VGPFIRRADR   96 (398)
Q Consensus        87 V~~~~~~~~~   96 (398)
                      |.++.++.+|
T Consensus        80 V~~a~~~~~R   89 (89)
T d1cvja2          80 VGRFKSRKER   89 (89)
T ss_dssp             EEECCCTTTC
T ss_pred             EEECCCCCCC
Confidence            9999877653

>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=99.86  E-value=3.2e-22  Score=154.39  Aligned_cols=88  Identities=24%  Similarity=0.365  Sum_probs=82.4

Q ss_pred             ccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEe
Q 039806            7 SEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMEL   85 (398)
Q Consensus         7 ~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i   85 (398)
                      |+.+..+.++|||+|||.++|+++|+++|+.||.|.+|+|..|. +|.+||||||+|.+.++|++||+.|||..|+|+.|
T Consensus         1 P~~~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i   80 (90)
T d2cq0a1           1 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLIL   80 (90)
T ss_dssp             SCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            45566778899999999999999999999999999999999998 89999999999999999999999999999999999


Q ss_pred             eeecccccc
Q 039806           86 YVGPFIRRA   94 (398)
Q Consensus        86 ~V~~~~~~~   94 (398)
                      .|.++.++.
T Consensus        81 ~v~~akp~~   89 (90)
T d2cq0a1          81 NVEWAKPST   89 (90)
T ss_dssp             EEEESSCCC
T ss_pred             EEEeeeCCC
Confidence            999987654

>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=99.85  E-value=1.8e-21  Score=149.50  Aligned_cols=83  Identities=25%  Similarity=0.377  Sum_probs=77.9

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ..+..+|||+|||.++|+++|+++|+.||.|.+|+|+.|+ +|+++|||||+|.+.++|++|++.|||..|.|+.|+|++
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456799999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             cccc
Q 039806           90 FIRR   93 (398)
Q Consensus        90 ~~~~   93 (398)
                      +.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            8764

>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=99.85  E-value=8.5e-22  Score=152.89  Aligned_cols=87  Identities=18%  Similarity=0.290  Sum_probs=80.9

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      ....+..++|||+|||.++|+++|+++|++||.|.+|+|+.|. +|.++|||||+|.+.++|++||+.|||..|+|++|+
T Consensus         3 ~~~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   82 (93)
T d1x5ua1           3 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIR   82 (93)
T ss_dssp             CCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCE
T ss_pred             CCcCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3445567899999999999999999999999999999999998 899999999999999999999999999999999999


Q ss_pred             eecccccc
Q 039806           87 VGPFIRRA   94 (398)
Q Consensus        87 V~~~~~~~   94 (398)
                      |.++.++.
T Consensus        83 V~~A~~~~   90 (93)
T d1x5ua1          83 VNKASAHN   90 (93)
T ss_dssp             EEETTTTS
T ss_pred             EEEcCCCC
Confidence            99987654

>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=99.85  E-value=2e-21  Score=153.38  Aligned_cols=85  Identities=31%  Similarity=0.466  Sum_probs=80.2

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+++.+. +|.+||||||+|.+.++|+.||+.|||..|.|+.|+|.++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            455789999999999999999999999999999999998 8999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      .++.++
T Consensus        96 ~~k~~~  101 (102)
T d2cpza1          96 RSKNDS  101 (102)
T ss_dssp             CCSCCC
T ss_pred             CCCCCC
Confidence            877654

>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=99.85  E-value=1.4e-21  Score=147.98  Aligned_cols=79  Identities=27%  Similarity=0.397  Sum_probs=75.5

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      +++|||+|||.++|+++|+++|++||.|.+|+|.+|+ +|+++|||||+|.+.++|++||+.|||..+.|+.|+|.++.+
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            4689999999999999999999999999999999988 899999999999999999999999999999999999998753

>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=99.85  E-value=1.9e-21  Score=145.79  Aligned_cols=77  Identities=21%  Similarity=0.447  Sum_probs=74.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ++|||+|||.++|+++|+++|+.||.|.+|+|..|++|+++|||||+|.+.++|++|++.+||..++|++|+|+++.
T Consensus         1 grl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           1 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999998875

>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=99.84  E-value=2.1e-21  Score=152.49  Aligned_cols=86  Identities=29%  Similarity=0.478  Sum_probs=81.0

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      .+++++|||+|||.++|+++|+++|++||.|.+|+|+.|. +|+++|||||+|.+.++|++||+.||+..|+|+.|+|.+
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            4567889999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      +..+.+.
T Consensus        85 a~~~~~~   91 (99)
T d1whwa_          85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             CCCCCcc
Confidence            9876654

>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=99.84  E-value=2.8e-21  Score=145.61  Aligned_cols=77  Identities=21%  Similarity=0.307  Sum_probs=74.4

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ++|||+|||.++|+++|+++|+.||.|.+|+|++|+ +|+++|||||+|.+.++|..|++.|||..+.|+.|+|.++.
T Consensus         1 aslfV~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           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            479999999999999999999999999999999998 89999999999999999999999999999999999999875

>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=99.84  E-value=1.2e-21  Score=150.83  Aligned_cols=83  Identities=24%  Similarity=0.359  Sum_probs=78.2

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+|+.|+ +|+++|||||+|.+.++|++||+.|||..|+|+.|.|.++.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45789999999999999999999999999999999998 89999999999999999999999999999999999999987


Q ss_pred             cccc
Q 039806           92 RRAD   95 (398)
Q Consensus        92 ~~~~   95 (398)
                      ++..
T Consensus        84 p~~~   87 (89)
T d2cqba1          84 PMRI   87 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=5.7e-21  Score=148.17  Aligned_cols=83  Identities=19%  Similarity=0.257  Sum_probs=78.2

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ..+++|||+|||.++|+++|+++|+.||.|.+|+|+.|+ +|.++|||||+|.+.++|..||+.|||..|+|+.|+|.++
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            356799999999999999999999999999999999998 8999999999999999999999999999999999999998


Q ss_pred             cccc
Q 039806           91 IRRA   94 (398)
Q Consensus        91 ~~~~   94 (398)
                      ....
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            6543

>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=99.84  E-value=4.3e-21  Score=160.21  Aligned_cols=84  Identities=32%  Similarity=0.557  Sum_probs=79.3

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+|+.|+ +|++||||||+|.+.++|.+||+.|||..|+|++|+|.++.
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            45689999999999999999999999999999999998 89999999999999999999999999999999999999988


Q ss_pred             ccccc
Q 039806           92 RRADR   96 (398)
Q Consensus        92 ~~~~~   96 (398)
                      .+..+
T Consensus       121 ~~~~~  125 (139)
T d1u6fa1         121 SGHQR  125 (139)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76655

>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=99.84  E-value=7.1e-21  Score=144.07  Aligned_cols=78  Identities=31%  Similarity=0.523  Sum_probs=74.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ++|||+|||.++|+++|+++|++||.|.+|++.+|. +|.++|||||+|.+.++|++|++.|||..|.|+.|+|.++.+
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            479999999999999999999999999999999988 899999999999999999999999999999999999998764

>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=99.84  E-value=2.6e-21  Score=149.24  Aligned_cols=85  Identities=31%  Similarity=0.527  Sum_probs=79.8

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ++.++|||+|||.++|+++|+++|+.||.|.+|+++.+. +|.++|||||+|.+.++|++||+.|||..|+|+.|+|+++
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            467889999999999999999999999999999999987 8999999999999999999999999999999999999998


Q ss_pred             cccccc
Q 039806           91 IRRADR   96 (398)
Q Consensus        91 ~~~~~~   96 (398)
                      .++.++
T Consensus        83 ~~~~~~   88 (90)
T d1x5sa1          83 GKSSDN   88 (90)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            776544

>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=99.83  E-value=1.2e-20  Score=143.24  Aligned_cols=75  Identities=25%  Similarity=0.387  Sum_probs=72.1

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      .+++|||+|||.++|+++|+++|++||.|.+|+|..|+ +|+++|||||+|.+.++|++||+.|||..|+|++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            35689999999999999999999999999999999998 8999999999999999999999999999999999987

>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=99.83  E-value=5.8e-21  Score=148.41  Aligned_cols=85  Identities=19%  Similarity=0.383  Sum_probs=78.6

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC--CCCceeEEEEEecCHHHHHHHHHHh-cCCeecceEee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ--EGKSKGYGFVQYSTPESALDAIEKL-QGATVERMELY   86 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~--~g~skg~aFV~F~~~e~A~~Ai~~l-ng~~l~gk~i~   86 (398)
                      ++..+++|||+|||.++|+++|+++|+.||.|.+|+|++|.  +|+++|||||+|.+.++|.+||+.| |+..|+|++|.
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~   83 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   83 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEE
Confidence            45567889999999999999999999999999999999885  7999999999999999999999998 89999999999


Q ss_pred             eecccccc
Q 039806           87 VGPFIRRA   94 (398)
Q Consensus        87 V~~~~~~~   94 (398)
                      |.++..+.
T Consensus        84 V~~A~~~~   91 (94)
T d2cpha1          84 LEWADSEV   91 (94)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCC
Confidence            99987654

>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=99.83  E-value=1.2e-20  Score=145.35  Aligned_cols=81  Identities=20%  Similarity=0.314  Sum_probs=75.0

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+|+.|. +|.+||||||+|.+.++|++||+.  ...|+|+.|.|.++.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCC
Confidence            45789999999999999999999999999999999998 899999999999999999999984  558999999999988


Q ss_pred             cccc
Q 039806           92 RRAD   95 (398)
Q Consensus        92 ~~~~   95 (398)
                      ++..
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            7654

>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=99.83  E-value=3.5e-21  Score=146.81  Aligned_cols=80  Identities=24%  Similarity=0.413  Sum_probs=76.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRR   93 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~   93 (398)
                      .+|||+|||.++|+++|+++|+.||.|.+|+|+.|+ +|.++|||||+|.+.++|+.|++.|||..|.|+.|.|.++...
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            479999999999999999999999999999999998 8999999999999999999999999999999999999998754


Q ss_pred             c
Q 039806           94 A   94 (398)
Q Consensus        94 ~   94 (398)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.5e-21  Score=153.51  Aligned_cols=90  Identities=29%  Similarity=0.503  Sum_probs=81.0

Q ss_pred             CccccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceE
Q 039806            6 NSEARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERME   84 (398)
Q Consensus         6 d~~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~   84 (398)
                      ||+..+ ..++|||+|||.++|+++|+++|+.||.|.+|+|+.+. +|+++|||||+|.+.++|++|++.|||..|.|+.
T Consensus         1 dP~~~~-~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~   79 (104)
T d1p1ta_           1 DPAVDR-SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRA   79 (104)
T ss_dssp             CCCSHH-HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSC
T ss_pred             CCCCCC-CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            454544 35689999999999999999999999999999999998 8999999999999999999999999999999999


Q ss_pred             eeeecccccccc
Q 039806           85 LYVGPFIRRADR   96 (398)
Q Consensus        85 i~V~~~~~~~~~   96 (398)
                      |+|.++..+..+
T Consensus        80 i~V~~a~~~~~~   91 (104)
T d1p1ta_          80 LRVDNAASEKNK   91 (104)
T ss_dssp             BEEEETTCTTHH
T ss_pred             EEEEECCCCCCc
Confidence            999998765433

>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=99.83  E-value=1.5e-20  Score=143.26  Aligned_cols=77  Identities=31%  Similarity=0.508  Sum_probs=72.2

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecc--eEeeeecc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVER--MELYVGPF   90 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g--k~i~V~~~   90 (398)
                      .++|||+|||.++|+++|+++|++||+|.+|+|+.|+ +|.++|||||+|.+.++|++|++.|||..+.|  ++|.|.++
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            4689999999999999999999999999999999998 89999999999999999999999999999987  55888764

>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=99.82  E-value=2.2e-20  Score=141.99  Aligned_cols=77  Identities=21%  Similarity=0.365  Sum_probs=73.3

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      .++|||+|||.++|+++|+++|+.||.|.+|+|+.|. +|+++|||||+|.+.++|++||+ +++..|+|+.|.|..+.
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            4689999999999999999999999999999999998 89999999999999999999997 69999999999998775

>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=99.82  E-value=1.7e-20  Score=148.20  Aligned_cols=83  Identities=27%  Similarity=0.410  Sum_probs=75.9

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      +..++|||+|||.++|+++|+++|+.||.|.+|+|+.|. +|++||||||+|.+.++|++||+.+|+ .|+|++|.|.++
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            345679999999999999999999999999999999998 899999999999999999999998776 799999999988


Q ss_pred             ccccc
Q 039806           91 IRRAD   95 (398)
Q Consensus        91 ~~~~~   95 (398)
                      ..+..
T Consensus        87 ~~~~~   91 (103)
T d2cqda1          87 YLGAK   91 (103)
T ss_dssp             TTTCC
T ss_pred             CCCCC
Confidence            76543

>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=99.82  E-value=3.9e-21  Score=143.60  Aligned_cols=75  Identities=16%  Similarity=0.328  Sum_probs=71.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      |+|||+|||.++|+++|+++|++||.|.+|+|++|+ +|++||||||+|.+.++|++||+ +|+..|+|+.|.|..+
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            589999999999999999999999999999999999 89999999999999999999997 7999999999999865

>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=99.82  E-value=2.6e-20  Score=141.92  Aligned_cols=78  Identities=32%  Similarity=0.490  Sum_probs=73.3

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecc--eEeeeec
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVER--MELYVGP   89 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g--k~i~V~~   89 (398)
                      ..++|||+|||.++|+++|+++|++||.|.+|+|++|+ +|+++|||||+|.+.++|.+||+.|||..+.|  ++|.|.+
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            35679999999999999999999999999999999998 89999999999999999999999999999976  8899987


Q ss_pred             c
Q 039806           90 F   90 (398)
Q Consensus        90 ~   90 (398)
                      +
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.82  E-value=5.6e-21  Score=150.38  Aligned_cols=82  Identities=22%  Similarity=0.370  Sum_probs=76.6

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      +.++|||+|||.++|+++|+++|+.||.|.+|+|++|. +|++||||||+|.+.++|.+|++ |||..|.|+.|.|.++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            35789999999999999999999999999999999998 89999999999999999999995 99999999999999887


Q ss_pred             cccc
Q 039806           92 RRAD   95 (398)
Q Consensus        92 ~~~~   95 (398)
                      .+..
T Consensus        96 ~~~n   99 (101)
T d2cq4a1          96 AEKN   99 (101)
T ss_dssp             HHHH
T ss_pred             CCCC
Confidence            5543

>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=99.81  E-value=1.4e-20  Score=142.11  Aligned_cols=79  Identities=15%  Similarity=0.220  Sum_probs=69.3

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      .++|||+|||.++|+++|+++|+.||.|..++++.+. +|+++|||||+|.+.++|++||+.|||..++|++|.|.++.+
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            3699999999999999999999999999988888777 899999999999999999999999999999999999998764

>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=99.81  E-value=1.1e-20  Score=143.41  Aligned_cols=79  Identities=29%  Similarity=0.493  Sum_probs=73.9

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEE-EEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccccc
Q 039806           17 AFVKNLASTIDNLKLHQIFSKFGDIQSS-KVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRA   94 (398)
Q Consensus        17 lfV~nLp~~vte~~L~~~F~~~G~I~~v-ki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~~   94 (398)
                      |||+|||.++|+++|+++|++||.|.++ +|++|. +|+++|||||+|.+.++|++||+.+||..++|++|+|.++.++.
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            8999999999999999999999999765 788887 89999999999999999999999999999999999999988765


Q ss_pred             c
Q 039806           95 D   95 (398)
Q Consensus        95 ~   95 (398)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.81  E-value=5.4e-20  Score=141.68  Aligned_cols=83  Identities=20%  Similarity=0.342  Sum_probs=75.7

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+|..|..+ .+|||||+|.+.++|.+|++.+||..|.|+.|+|.++.
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            34568999999999999999999999999999999998743 47999999999999999999999999999999999987


Q ss_pred             cccc
Q 039806           92 RRAD   95 (398)
Q Consensus        92 ~~~~   95 (398)
                      ++..
T Consensus        85 ~~~~   88 (90)
T d2cqia1          85 TPSS   88 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6543

>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=99.81  E-value=1.8e-20  Score=139.25  Aligned_cols=74  Identities=22%  Similarity=0.420  Sum_probs=70.5

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      +|||+|||.++|+++|+++|++||.|.+|+|..|+ +|+++|||||+|.+.++|++||+ +++..|+|+.|.|..+
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            59999999999999999999999999999999998 89999999999999999999997 7999999999999753

>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=99.81  E-value=7.5e-20  Score=141.76  Aligned_cols=82  Identities=32%  Similarity=0.507  Sum_probs=76.1

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|++..|..+ ++|||||+|.+.++|++||+.|||..|+|+.|+|.++.
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            44668999999999999999999999999999999998754 79999999999999999999999999999999999987


Q ss_pred             ccc
Q 039806           92 RRA   94 (398)
Q Consensus        92 ~~~   94 (398)
                      ++.
T Consensus        88 ~r~   90 (93)
T d2cq3a1          88 ARV   90 (93)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            653

>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=99.81  E-value=4.4e-20  Score=140.67  Aligned_cols=77  Identities=38%  Similarity=0.565  Sum_probs=71.9

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CC---CceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EG---KSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        17 lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g---~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      |||+|||.++|+++|+++|+.||.|.+|+|.+++ ++   .+||||||+|.+.++|++|++.+||..|+|+.|.|.++.+
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            8999999999999999999999999999999987 33   5799999999999999999999999999999999999864


Q ss_pred             c
Q 039806           93 R   93 (398)
Q Consensus        93 ~   93 (398)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.80  E-value=3.6e-20  Score=146.16  Aligned_cols=82  Identities=16%  Similarity=0.334  Sum_probs=77.0

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      .++|||+|||.++|+++|+++|++||.|.+|+|.+|. ++.+||||||+|.+.++|++||+ +|+..|+|+.|.|.++.+
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            4789999999999999999999999999999999998 88999999999999999999997 799999999999999887


Q ss_pred             cccc
Q 039806           93 RADR   96 (398)
Q Consensus        93 ~~~~   96 (398)
                      +.++
T Consensus        99 ke~~  102 (103)
T d1x4ba1          99 REES  102 (103)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            6643

>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=99.80  E-value=1.2e-19  Score=136.28  Aligned_cols=76  Identities=20%  Similarity=0.393  Sum_probs=72.3

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      .++|||+|||.++|+++|+++|+.||.|.++++..|+ ++.++|||||+|.+.|+|++|++ +||..|+|+.|.|..+
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            4689999999999999999999999999999999998 89999999999999999999996 8999999999999865

>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=99.80  E-value=9e-20  Score=143.55  Aligned_cols=82  Identities=21%  Similarity=0.398  Sum_probs=76.6

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ..+.++|||+|||.++|+++|+++|+.||.|.++++..+.++.++|||||+|.+.++|++||+.|||..|.|+++.|.++
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            34457899999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             cc
Q 039806           91 IR   92 (398)
Q Consensus        91 ~~   92 (398)
                      .+
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=99.80  E-value=1.2e-19  Score=146.07  Aligned_cols=103  Identities=23%  Similarity=0.275  Sum_probs=86.7

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      .+++|||+|||.++|+++|+++|+.||.|.+|++..+  +.++|||||+|.+.++|..||+.|||..|.|+.|.|.++..
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~--~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4578999999999999999999999999999999764  56799999999999999999999999999999999998765


Q ss_pred             cccccccCCCCceEEeeCCCccccHHHHHHHHccCCC
Q 039806           93 RADRIQEGSSFNNLYVKNLDDDMTEEILVEKFSEFGK  129 (398)
Q Consensus        93 ~~~~~~~~~~~~~lfV~nLp~~~tee~L~~~F~~fG~  129 (398)
                      .....            .......++++..+.+++|.
T Consensus        84 ~~~~~------------~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          84 NRAFQ------------KMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             HHHTT------------TSCHHHHHHHHHHHHHHHCC
T ss_pred             Cchhh------------hhHHHHHHHHHHHHHHHhCC
Confidence            43221            12233456778888888774

>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=99.79  E-value=1.1e-20  Score=145.90  Aligned_cols=85  Identities=22%  Similarity=0.263  Sum_probs=77.3

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      ........+|||+|||.++|+++|+++|+.||.|.+|+|..+.+|++||||||+|.+.++|++||+ +||..|+|++|.|
T Consensus         7 ~~~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V   85 (91)
T d1fjeb1           7 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL   85 (91)
T ss_dssp             SSSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEE
T ss_pred             CCCCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEE
Confidence            344455679999999999999999999999999999999877799999999999999999999996 9999999999999


Q ss_pred             eccccc
Q 039806           88 GPFIRR   93 (398)
Q Consensus        88 ~~~~~~   93 (398)
                      +++..|
T Consensus        86 ~~ak~k   91 (91)
T d1fjeb1          86 EKPKGR   91 (91)
T ss_dssp             ECCCCS
T ss_pred             EecCCC
Confidence            998653

>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=99.79  E-value=4.7e-20  Score=140.78  Aligned_cols=80  Identities=18%  Similarity=0.285  Sum_probs=71.0

Q ss_pred             CcceEEEcCCCCCCc-HHHHHHHHhccCCeeEEEEEEcC--CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           13 GIGNAFVKNLASTID-NLKLHQIFSKFGDIQSSKVVVSQ--EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        13 ~~~~lfV~nLp~~vt-e~~L~~~F~~~G~I~~vki~~d~--~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      +.++|||+|||.++| +++|+++|+.||.|.+|+|..+.  +|+++|||||+|.+.++|++||+ +||..|+|+.|.|.+
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            467999999999876 56699999999999999998754  89999999999999999999996 999999999999999


Q ss_pred             cccc
Q 039806           90 FIRR   93 (398)
Q Consensus        90 ~~~~   93 (398)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8754

>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=99.79  E-value=3.4e-20  Score=137.61  Aligned_cols=74  Identities=19%  Similarity=0.355  Sum_probs=69.8

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      +|||+|||.++|+++|+++|++||.|.+|+|+.|+ ++++||||||+|.+.++|++||+ .++..|+|+.|.|..+
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999998 89999999999999999999997 4788999999998754

>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=99.79  E-value=2.1e-19  Score=140.52  Aligned_cols=84  Identities=25%  Similarity=0.438  Sum_probs=77.4

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhc------CCeecceE
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQ------GATVERME   84 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~ln------g~~l~gk~   84 (398)
                      .+.++|||+|||.++|+++|+++|+.||.|.++++..+. ++.++|||||+|.+.++|.+||+.+|      |..|.|+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            456799999999999999999999999999999999988 88999999999999999999999887      67889999


Q ss_pred             eeeeccccccc
Q 039806           85 LYVGPFIRRAD   95 (398)
Q Consensus        85 i~V~~~~~~~~   95 (398)
                      |.|.++.++.+
T Consensus        86 l~v~~a~~k~~   96 (98)
T d1x4ha1          86 LKVDLAVTRDE   96 (98)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCc
Confidence            99999887654

>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=99.78  E-value=2.6e-19  Score=140.86  Aligned_cols=85  Identities=22%  Similarity=0.343  Sum_probs=77.0

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCe--------eEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDI--------QSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVER   82 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I--------~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g   82 (398)
                      ...++|||+|||.++|+++|+++|+.||.|        ..+++..|. +|+++|||||+|.+.++|.+||+.|||..|+|
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            356799999999999999999999999987        456777777 89999999999999999999999999999999


Q ss_pred             eEeeeecccccccc
Q 039806           83 MELYVGPFIRRADR   96 (398)
Q Consensus        83 k~i~V~~~~~~~~~   96 (398)
                      +.|+|.++.++..+
T Consensus        86 r~i~V~~a~~~~p~   99 (101)
T d2cpea1          86 SKLKVSLARKKPPM   99 (101)
T ss_dssp             EECEEECSSCCCCS
T ss_pred             EEEEEEEcCCCCCC
Confidence            99999999876543

>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=99.78  E-value=4.5e-19  Score=134.92  Aligned_cols=76  Identities=16%  Similarity=0.188  Sum_probs=72.5

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      .++|||+|||.++|+++|+++|+.||.|.+|+|..+.+|++||||||+|.+.++|++||+ +++..+.|+.|.|.+.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   81 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEc
Confidence            468999999999999999999999999999999998899999999999999999999997 7999999999999874

>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=99.78  E-value=1.2e-19  Score=134.79  Aligned_cols=74  Identities=15%  Similarity=0.363  Sum_probs=70.7

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      +|||+|||.++|+++|+++|+.||.|.+|.+..++ ++.++|||||+|.+.++|++|++ +||..|+|++|.|.++
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            59999999999999999999999999999999988 89999999999999999999997 9999999999999764

>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=99.77  E-value=9.2e-20  Score=143.73  Aligned_cols=84  Identities=18%  Similarity=0.318  Sum_probs=79.4

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      .+++|||+|||.++|+++|+++|+.||.|.+|++..+. +|+++|||||+|.+.++|.+||+.|||..|.|+.|.|.++.
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            46799999999999999999999999999999999887 89999999999999999999999999999999999999998


Q ss_pred             ccccc
Q 039806           92 RRADR   96 (398)
Q Consensus        92 ~~~~~   96 (398)
                      ++.++
T Consensus        97 ~k~~r  101 (102)
T d2cpxa1          97 NKKQR  101 (102)
T ss_dssp             CCSCC
T ss_pred             CcccC
Confidence            77654

>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=99.76  E-value=2.2e-19  Score=135.08  Aligned_cols=77  Identities=25%  Similarity=0.390  Sum_probs=70.8

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCC-eecceEeeeeccccc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA-TVERMELYVGPFIRR   93 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~-~l~gk~i~V~~~~~~   93 (398)
                      .+|||+|||.++|+++|+++|++||.|.++++..     +||||||+|.+.++|++|++.|||. .++|+.|+|+++.++
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 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec-----ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            4799999999999999999999999998888866     6799999999999999999999996 699999999999887


Q ss_pred             ccc
Q 039806           94 ADR   96 (398)
Q Consensus        94 ~~~   96 (398)
                      ..+
T Consensus        77 ~~r   79 (80)
T d2cqha1          77 KLR   79 (80)
T ss_dssp             CCC
T ss_pred             CcC
Confidence            654

>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=99.76  E-value=6.1e-19  Score=137.39  Aligned_cols=85  Identities=20%  Similarity=0.326  Sum_probs=76.0

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      +.+....++|||+|||.++|+++|+++|+.||.|..++.    +++++|||||+|.+.++|++|++.|||..|+|+.|+|
T Consensus        10 ~~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V   85 (96)
T d1fjca_          10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             TSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEE
T ss_pred             cCcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEE
Confidence            445566789999999999999999999999998876643    6789999999999999999999999999999999999


Q ss_pred             ecccccccc
Q 039806           88 GPFIRRADR   96 (398)
Q Consensus        88 ~~~~~~~~~   96 (398)
                      .++.++...
T Consensus        86 ~~a~~k~~~   94 (96)
T d1fjca_          86 YYTGEKGGT   94 (96)
T ss_dssp             EECSSSCCC
T ss_pred             EEeCCCCCC
Confidence            999876543

>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=99.76  E-value=8.7e-19  Score=133.64  Aligned_cols=80  Identities=15%  Similarity=0.184  Sum_probs=72.8

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeE-EEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQS-SKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~-vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      .+.....|||+|||.++|++||+++|+.||.|.+ +.+..+.+|+++|||||+|.+.++|++||+.||+..|.|++|+|.
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            4445678999999999999999999999999876 566667799999999999999999999999999999999999997


Q ss_pred             c
Q 039806           89 P   89 (398)
Q Consensus        89 ~   89 (398)
                      .
T Consensus        85 l   85 (86)
T d2cqpa1          85 L   85 (86)
T ss_dssp             E
T ss_pred             E
Confidence            5

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.2e-18  Score=135.65  Aligned_cols=76  Identities=32%  Similarity=0.397  Sum_probs=71.1

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ..++|||+|||.++|+++|+++|+.||.|.+|+|..|     ||||||+|.+.++|.+||+.|||..|.|+.|+|.|+.+
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4578999999999999999999999999999999864     69999999999999999999999999999999999865


Q ss_pred             c
Q 039806           93 R   93 (398)
Q Consensus        93 ~   93 (398)
                      +
T Consensus        92 ~   92 (96)
T d1x4ga1          92 S   92 (96)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2.5e-19  Score=131.91  Aligned_cols=70  Identities=26%  Similarity=0.539  Sum_probs=67.6

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEee
Q 039806           17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELY   86 (398)
Q Consensus        17 lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~   86 (398)
                      |||+|||.++|+++|+++|+.||.|.++++..++ ++.++|||||+|.+.++|++|++.|||..|+|+.|+
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            7999999999999999999999999999999998 899999999999999999999999999999998764

>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=99.76  E-value=2.3e-18  Score=133.77  Aligned_cols=80  Identities=21%  Similarity=0.309  Sum_probs=72.6

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      +..++|||+|||.++|+++|+++|+.||.|..|++..+  +.++|||||+|++.++|+.||+.|||..|.|++|+|+++.
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            45678999999999999999999999999999887554  4578999999999999999999999999999999999986


Q ss_pred             cc
Q 039806           92 RR   93 (398)
Q Consensus        92 ~~   93 (398)
                      ..
T Consensus        90 ~~   91 (95)
T d1x4aa1          90 SG   91 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.75  E-value=6.4e-19  Score=135.22  Aligned_cols=80  Identities=25%  Similarity=0.354  Sum_probs=71.4

Q ss_pred             ccCCCcceEEEcCCCCCCcHHHH---HHHHhccCCeeEEEEEEcC-CCCc---eeEEEEEecCHHHHHHHHHHhcCCeec
Q 039806            9 ARLSGIGNAFVKNLASTIDNLKL---HQIFSKFGDIQSSKVVVSQ-EGKS---KGYGFVQYSTPESALDAIEKLQGATVE   81 (398)
Q Consensus         9 ~~~~~~~~lfV~nLp~~vte~~L---~~~F~~~G~I~~vki~~d~-~g~s---kg~aFV~F~~~e~A~~Ai~~lng~~l~   81 (398)
                      .|--..++|||+|||+++|+++|   +++|++||.|.+|+|.+|+ ++.+   +|||||+|++.++|.+||+.|||..|+
T Consensus         3 ~Rviq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~   82 (89)
T d2cpia1           3 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   82 (89)
T ss_dssp             CCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             eeEEecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEEC
Confidence            44445668999999999999999   7789999999999999987 5444   489999999999999999999999999


Q ss_pred             ceEeeee
Q 039806           82 RMELYVG   88 (398)
Q Consensus        82 gk~i~V~   88 (398)
                      |+.|+|.
T Consensus        83 gr~lkvS   89 (89)
T d2cpia1          83 GRTLKAS   89 (89)
T ss_dssp             TEEEEEE
T ss_pred             CEEEEEC
Confidence            9999874

>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=99.75  E-value=2e-18  Score=136.45  Aligned_cols=83  Identities=19%  Similarity=0.347  Sum_probs=74.6

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC--CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ--EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~--~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ...++|||+|||.++|+++|+++|+.|| |.+++++.+.  +|+++|||||+|.+.++|++|++ ||+..|+|+.|+|.+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            4568999999999999999999999999 8888888876  78999999999999999987775 999999999999999


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      +.++..+
T Consensus        91 a~~~~~~   97 (104)
T d1wi8a_          91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8776544

>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=99.75  E-value=7.2e-19  Score=136.96  Aligned_cols=84  Identities=18%  Similarity=0.174  Sum_probs=75.2

Q ss_pred             cceEEEcCCCCCCcHHHHHHHHhccCC-eeEEEEEEcC--CCCceeEEEEEecCHHHHHHHHHHhcC--CeecceEeeee
Q 039806           14 IGNAFVKNLASTIDNLKLHQIFSKFGD-IQSSKVVVSQ--EGKSKGYGFVQYSTPESALDAIEKLQG--ATVERMELYVG   88 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~~F~~~G~-I~~vki~~d~--~g~skg~aFV~F~~~e~A~~Ai~~lng--~~l~gk~i~V~   88 (398)
                      +++|||+|||.++|+++|+++|+.||. |.+|++..|.  +|+++|||||+|.+.++|.+|++.|++  ..++|+.|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            468999999999999999999999996 9999999886  688999999999999999999999864  46679999999


Q ss_pred             ccccccccc
Q 039806           89 PFIRRADRI   97 (398)
Q Consensus        89 ~~~~~~~~~   97 (398)
                      ++.++.+..
T Consensus        81 ~A~p~~~~~   89 (96)
T d2disa1          81 WAEPEIDVD   89 (96)
T ss_dssp             ESCSSCSTT
T ss_pred             EcCCCCCCC
Confidence            998766553

>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=99.75  E-value=9.7e-19  Score=133.31  Aligned_cols=78  Identities=24%  Similarity=0.333  Sum_probs=71.7

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ++.++|||+|||.++++++|+++|+.||.|.+|++.+     .+|||||+|++.++|++|++.|||..|+|+.|+|+++.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~-----~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           6 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-----DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET-----TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeec-----ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3456899999999999999999999999999999976     46899999999999999999999999999999999987


Q ss_pred             ccc
Q 039806           92 RRA   94 (398)
Q Consensus        92 ~~~   94 (398)
                      .+.
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            543

>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=99.74  E-value=1.8e-18  Score=137.87  Aligned_cols=77  Identities=22%  Similarity=0.328  Sum_probs=70.9

Q ss_pred             CcceEEEcCCC-CCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLA-STIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp-~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      |+++|||+||+ ..+|+++|+++|+.||.|.+|+|+.|    ++|||||+|++.++|.+||+.|||..|.|+.|.|.++.
T Consensus         1 g~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~----~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           1 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT----TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEec----ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            57899999996 46999999999999999999999886    47899999999999999999999999999999999986


Q ss_pred             cc
Q 039806           92 RR   93 (398)
Q Consensus        92 ~~   93 (398)
                      .+
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.74  E-value=2.9e-18  Score=136.46  Aligned_cols=81  Identities=27%  Similarity=0.279  Sum_probs=73.2

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCee--cceEeeee
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATV--ERMELYVG   88 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l--~gk~i~V~   88 (398)
                      .+...+|||+|||.++|+++|+++|+.||.|.+|+|..++   ++|||||+|.+.++|++||+.|||..|  .+++|.|.
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~---~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC---CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            4567799999999999999999999999999999999875   689999999999999999999999988  47888888


Q ss_pred             cccccc
Q 039806           89 PFIRRA   94 (398)
Q Consensus        89 ~~~~~~   94 (398)
                      ++..+.
T Consensus        81 ~s~~~~   86 (108)
T d2adba1          81 FSKLTS   86 (108)
T ss_dssp             ECSSCS
T ss_pred             ecCCcc
Confidence            876544

>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=99.74  E-value=2.4e-18  Score=134.32  Aligned_cols=76  Identities=28%  Similarity=0.408  Sum_probs=69.3

Q ss_pred             CCcceEEEcCCC-CCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           12 SGIGNAFVKNLA-STIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp-~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ...++|||+||+ ..+++++|+++|++||.|.+|+|       +||||||+|++.++|++||+.|||..|.|+.|+|.++
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 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE-------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE-------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            345679999997 57889999999999999999999       6799999999999999999999999999999999998


Q ss_pred             cccc
Q 039806           91 IRRA   94 (398)
Q Consensus        91 ~~~~   94 (398)
                      ..+.
T Consensus        86 ~~~~   89 (98)
T d1wf2a_          86 AEPK   89 (98)
T ss_dssp             TSCC
T ss_pred             CCCC
Confidence            7543

>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=99.74  E-value=2e-18  Score=135.91  Aligned_cols=87  Identities=13%  Similarity=0.128  Sum_probs=77.4

Q ss_pred             cccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeee
Q 039806            8 EARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus         8 ~~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      +.+.+...+|||+|||+++|++||+++|+.|| |.+|.++.+.+|.++|||||+|.+.++|++|++ +|+..|+||.|.|
T Consensus         9 ~~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V   86 (102)
T d1weza_           9 SFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVEL   86 (102)
T ss_dssp             SCCCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEE
T ss_pred             CCcCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEE
Confidence            34455667999999999999999999999998 558999999999999999999999999999997 8999999999999


Q ss_pred             ecccccccc
Q 039806           88 GPFIRRADR   96 (398)
Q Consensus        88 ~~~~~~~~~   96 (398)
                      .++..+...
T Consensus        87 ~~s~~~~~~   95 (102)
T d1weza_          87 FLNSTAGTS   95 (102)
T ss_dssp             EEECCCCCC
T ss_pred             EEcCCCCCC
Confidence            988765533

>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=99.74  E-value=5.3e-18  Score=129.17  Aligned_cols=78  Identities=21%  Similarity=0.307  Sum_probs=71.3

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      +..++|||+|||.++|+++|+++|+.||.|..+++..     ++|||||+|.+.++|.+|++.|||..|.|+.|.|.++.
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-----~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-----ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            3467999999999999999999999999998888744     78999999999999999999999999999999999987


Q ss_pred             ccc
Q 039806           92 RRA   94 (398)
Q Consensus        92 ~~~   94 (398)
                      ++.
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.73  E-value=2e-18  Score=138.01  Aligned_cols=77  Identities=18%  Similarity=0.212  Sum_probs=70.7

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...++|||+|||.++|+++|+++|+.||.|.+|+|.     .++|||||+|.+.++|.+||+.|||..|.|+.|+|.++.
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~-----~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-----SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee-----ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            346799999999999999999999999999999884     368999999999999999999999999999999999876


Q ss_pred             cc
Q 039806           92 RR   93 (398)
Q Consensus        92 ~~   93 (398)
                      ..
T Consensus        83 ~~   84 (111)
T d1whxa_          83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=99.73  E-value=4.4e-18  Score=126.09  Aligned_cols=74  Identities=23%  Similarity=0.301  Sum_probs=68.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ++|||+|||.++++++|+++|+.||.|.+|++..++++. +|||||+|+++++|++|++ +|+..|+|+.|.|..+
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-FRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            489999999999999999999999999999999998654 4799999999999999996 8999999999999764

>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=99.73  E-value=3.9e-18  Score=129.05  Aligned_cols=76  Identities=20%  Similarity=0.298  Sum_probs=69.2

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCee-cceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATV-ERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l-~gk~i~V~~~   90 (398)
                      ..+++|||+|||.++|+++|+++|+.||.|.+|++..+    .+|||||+|.+.++|.+|++.|||..| +|+.|+|.++
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~a   81 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA   81 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEe
Confidence            34679999999999999999999999999999999764    468999999999999999999999988 4689999987


Q ss_pred             c
Q 039806           91 I   91 (398)
Q Consensus        91 ~   91 (398)
                      .
T Consensus        82 k   82 (83)
T d2b0ga1          82 K   82 (83)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.73  E-value=5.8e-18  Score=133.72  Aligned_cols=86  Identities=19%  Similarity=0.214  Sum_probs=75.5

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      ...+...|||+|||.++|++||+++|+.+|.|..+.++.+. +++++|||||+|.++++|++|++ +|+..|.||.|.|.
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEE
Confidence            34556689999999999999999999999998886555555 99999999999999999999997 89999999999999


Q ss_pred             cccccccc
Q 039806           89 PFIRRADR   96 (398)
Q Consensus        89 ~~~~~~~~   96 (398)
                      ++.++..+
T Consensus        90 ~~~~~~~~   97 (104)
T d1wg5a_          90 KSSRAEVR   97 (104)
T ss_dssp             EECTTTSC
T ss_pred             ECCHHHhc
Confidence            88766543

>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=99.72  E-value=2.5e-18  Score=132.48  Aligned_cols=81  Identities=26%  Similarity=0.344  Sum_probs=72.6

Q ss_pred             cceEEEcCCCCCCcHHHHHH----HHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           14 IGNAFVKNLASTIDNLKLHQ----IFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        14 ~~~lfV~nLp~~vte~~L~~----~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      +++|||+|||.++|++||++    +|+.||+|.+|++..  ++.++|||||+|++.++|.+|++.+||..++|+.|.|.+
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            57999999999999999864    689999999998754  567899999999999999999999999999999999999


Q ss_pred             ccccccc
Q 039806           90 FIRRADR   96 (398)
Q Consensus        90 ~~~~~~~   96 (398)
                      +..+.+.
T Consensus        81 ak~~~~~   87 (91)
T d1nu4a_          81 AKTDSDI   87 (91)
T ss_dssp             CSSCCTH
T ss_pred             eCCCchh
Confidence            9876543

>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=99.72  E-value=4.1e-18  Score=130.38  Aligned_cols=77  Identities=23%  Similarity=0.317  Sum_probs=67.9

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      +++++|||+|||.++|++||+++|+.|| +..+.+     +++||||||+|.+.++|++||+.||+..|+|+.|.|+++.
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-LKYCYV-----DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE-----EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee-----eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            5678999999999999999999999999 333444     3478999999999999999999999999999999999985


Q ss_pred             ccc
Q 039806           92 RRA   94 (398)
Q Consensus        92 ~~~   94 (398)
                      .+.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            443

>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=99.72  E-value=7.4e-18  Score=128.94  Aligned_cols=78  Identities=18%  Similarity=0.249  Sum_probs=69.9

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCee-cceEeeeecc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATV-ERMELYVGPF   90 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l-~gk~i~V~~~   90 (398)
                      ..+++|||+|||.++|+++|+++|+.||.|.++++..+   +++|||||+|++.++|.+|+..|||..| +|+.|+|+++
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            34679999999999999999999999999988877654   4678999999999999999999999988 5899999987


Q ss_pred             cc
Q 039806           91 IR   92 (398)
Q Consensus        91 ~~   92 (398)
                      +.
T Consensus        85 k~   86 (88)
T d2adca2          85 KS   86 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>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=99.72  E-value=1.8e-18  Score=132.41  Aligned_cols=79  Identities=15%  Similarity=0.320  Sum_probs=71.3

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      +++++|||+|||.++|+++|+++|++||.|.+|++..    .++|||||+|++.++|++||.  ++..|+|++|.|.++.
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 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            5678999999999999999999999999999998753    478999999999999999996  7889999999999997


Q ss_pred             ccccc
Q 039806           92 RRADR   96 (398)
Q Consensus        92 ~~~~~   96 (398)
                      ++...
T Consensus        77 ~k~~~   81 (88)
T d1wf0a_          77 PKHNS   81 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76544

>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=99.72  E-value=2.8e-18  Score=131.01  Aligned_cols=74  Identities=20%  Similarity=0.223  Sum_probs=68.1

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccccccc
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIRRAD   95 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~~~~   95 (398)
                      +|||+|||.++|+++|+++|++||.|.+|+|..      +|||||+|.+.++|++||+.|||..|.|+.|.|.++..+..
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~~   75 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   75 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEEC
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhcccccccccc------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCcC
Confidence            699999999999999999999999999999864      38999999999999999999999999999999988765443

>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=99.71  E-value=6.1e-18  Score=126.69  Aligned_cols=74  Identities=27%  Similarity=0.347  Sum_probs=67.9

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ..++|||+||+  +|+++|+++|++||.|.+|++.+     .+|||||+|.+.++|.+|++.|||..++|++|+|.++.+
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--MTPTLLRGAFSPFGNIIDLSMDP-----PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeecc-----CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            35689999996  99999999999999999999965     568999999999999999999999999999999999865


Q ss_pred             c
Q 039806           93 R   93 (398)
Q Consensus        93 ~   93 (398)
                      +
T Consensus        77 ~   77 (79)
T d2bz2a1          77 Q   77 (79)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.70  E-value=1.7e-17  Score=129.38  Aligned_cols=78  Identities=21%  Similarity=0.195  Sum_probs=71.3

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      ...+|||+|||.+++++||+++|+.||.|.+|+|.      ++|||||+|.+.++|++||+.|||..|.|+.|+|.+...
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~------~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~   87 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ------KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRV   87 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE------TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhccccccccc------ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEec
Confidence            45689999999999999999999999999999985      458999999999999999999999999999999998876


Q ss_pred             cccc
Q 039806           93 RADR   96 (398)
Q Consensus        93 ~~~~   96 (398)
                      +.++
T Consensus        88 ~~~~   91 (98)
T d1wg4a_          88 YPER   91 (98)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            5544

>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=99.70  E-value=3.8e-18  Score=134.55  Aligned_cols=81  Identities=17%  Similarity=0.256  Sum_probs=71.7

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEE-EEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSS-KVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~v-ki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...+|||+|||.++|+++|.++|+.||.|..+ .+..+.+|+++|||||+|.+.++|++||+ +|+..|+|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            34579999999999999999999999998774 45455599999999999999999999997 89999999999998876


Q ss_pred             ccc
Q 039806           92 RRA   94 (398)
Q Consensus        92 ~~~   94 (398)
                      .+.
T Consensus        86 ~~~   88 (103)
T d2cpya1          86 LED   88 (103)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>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=99.69  E-value=2.3e-17  Score=122.20  Aligned_cols=70  Identities=24%  Similarity=0.352  Sum_probs=64.1

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecccc
Q 039806           17 AFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFIR   92 (398)
Q Consensus        17 lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~~   92 (398)
                      |||+|||.++|+++|+++|++|| +..+++     ++++|||||+|.+.++|++|++.|||..+.|++|+|+++..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-----~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-----cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            79999999999999999999999 555555     45889999999999999999999999999999999999854

>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=99.67  E-value=1.4e-17  Score=133.23  Aligned_cols=83  Identities=18%  Similarity=0.271  Sum_probs=72.9

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEE-cCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVV-SQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~-d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      .....+|||+|||+++|++||.++|+.||.|..+.++. +.+|.++|||||+|.+.++|++|++ +|+..|+|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            34556899999999999999999999999987655544 4599999999999999999999997 899999999999988


Q ss_pred             ccccc
Q 039806           90 FIRRA   94 (398)
Q Consensus        90 ~~~~~   94 (398)
                      +.++.
T Consensus        94 ~~~~~   98 (112)
T d1wela1          94 ITKKG   98 (112)
T ss_dssp             ECHHH
T ss_pred             cChHH
Confidence            76554

>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=99.67  E-value=9.3e-17  Score=122.70  Aligned_cols=79  Identities=11%  Similarity=0.201  Sum_probs=70.6

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHh--cCCeecceEeeee
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL--QGATVERMELYVG   88 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~l--ng~~l~gk~i~V~   88 (398)
                      ...+++|||+|||.++|+++|+++|+.||.|.+|++..     ++|||||+|++.++|++|++.+  ++..++|+.|+|.
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 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-----GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccc-----cceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            34678999999999999999999999999999999875     4589999999999999999865  5779999999999


Q ss_pred             cccccc
Q 039806           89 PFIRRA   94 (398)
Q Consensus        89 ~~~~~~   94 (398)
                      ++..+.
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            986543

>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=99.67  E-value=1e-16  Score=124.74  Aligned_cols=76  Identities=21%  Similarity=0.326  Sum_probs=69.2

Q ss_pred             CCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecc--eEeeeec
Q 039806           12 SGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVER--MELYVGP   89 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g--k~i~V~~   89 (398)
                      ..+++|||+|||.++|+++|+++|+.||.|.+|++.+     .++||||+|.+.++|.+|++.||+..|.|  ++|+|++
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 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK-----GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS-----SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeec-----cccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            4568999999999999999999999999999999965     46899999999999999999999999986  5799988


Q ss_pred             ccc
Q 039806           90 FIR   92 (398)
Q Consensus        90 ~~~   92 (398)
                      +.+
T Consensus        90 ak~   92 (97)
T d1whya_          90 AKS   92 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.66  E-value=1.8e-16  Score=125.03  Aligned_cols=80  Identities=15%  Similarity=0.188  Sum_probs=71.2

Q ss_pred             cCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHh--cCCeecceEeee
Q 039806           10 RLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL--QGATVERMELYV   87 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~l--ng~~l~gk~i~V   87 (398)
                      +...+++|||+|||.++|+++|+++|+.||.|.+|++.+     .||||||+|++.++|++|++.+  ++..+.|++|+|
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~-----~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-----FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe-----cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            345678999999999999999999999999999999965     5689999999999999999977  556789999999


Q ss_pred             ecccccc
Q 039806           88 GPFIRRA   94 (398)
Q Consensus        88 ~~~~~~~   94 (398)
                      .++..+.
T Consensus        86 ~~s~~~~   92 (104)
T d1wexa_          86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEcCCCc
Confidence            9987644

>d1g9la_ a.144.1.1 (A:) poly(A) binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.3e-17  Score=135.58  Aligned_cols=43  Identities=30%  Similarity=0.549  Sum_probs=40.8

Q ss_pred             hhHHhhhhcCChHHHhhhhhcccchhhhccccceeceeeeeee
Q 039806          352 ENLSSMLVATSPDERKDILGQRLYPLVKKLKVITHIFVKGQFR  394 (398)
Q Consensus       352 ~~~~s~la~a~p~~qk~mLGe~Lyplv~~~~~~~~~~~~~~~~  394 (398)
                      ..++++||+|+|++||+||||+|||||++++|++|+|||||+-
T Consensus        52 pltas~la~a~p~eQkq~LGE~Lyp~I~~~~p~~A~KITGMLL   94 (144)
T d1g9la_          52 PLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLL   94 (144)
T ss_dssp             CCSHHHHTTCTTTTTTTTTTSSSHHHHHHHTTSCCSSHHHHTT
T ss_pred             cccHHHHhhCCHHHHHHHHHHHHHHHHHHhChhhccchhhhhh
Confidence            4689999999999999999999999999999999999999973

>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=99.66  E-value=3.6e-18  Score=134.70  Aligned_cols=76  Identities=12%  Similarity=0.134  Sum_probs=72.4

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeecc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPF   90 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~   90 (398)
                      ++++|+++..+++|++|+++|++||.|.+|+|+++.+|+++|||||+|.+.++|.+|++.|||..++|++|.|+++
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            5688999999999999999999999999999998889999999999999999999999999999999999999864

>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=99.65  E-value=7.7e-17  Score=125.91  Aligned_cols=78  Identities=13%  Similarity=0.126  Sum_probs=69.6

Q ss_pred             CCcceEEEcCCCCC-CcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHH--HhcCCeecceEeeee
Q 039806           12 SGIGNAFVKNLAST-IDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIE--KLQGATVERMELYVG   88 (398)
Q Consensus        12 ~~~~~lfV~nLp~~-vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~--~lng~~l~gk~i~V~   88 (398)
                      ..+++|||+|||.+ +|+++|.++|+.||.|.+|++..     ++|||||+|++.++|.+|++  ++|+..++|+.|+|.
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 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   90 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEee-----cCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEE
Confidence            44678999999975 89999999999999999999975     46899999999999999998  578889999999999


Q ss_pred             cccccc
Q 039806           89 PFIRRA   94 (398)
Q Consensus        89 ~~~~~~   94 (398)
                      ++.++.
T Consensus        91 ~s~~~~   96 (99)
T d1x4fa1          91 LSEKYK   96 (99)
T ss_dssp             EECSCS
T ss_pred             EcCCcc
Confidence            987654

>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=99.65  E-value=1.2e-16  Score=122.30  Aligned_cols=79  Identities=18%  Similarity=0.158  Sum_probs=70.1

Q ss_pred             cCCCcceEEEcCCCCC-CcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHh--cCCeecceEee
Q 039806           10 RLSGIGNAFVKNLAST-IDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKL--QGATVERMELY   86 (398)
Q Consensus        10 ~~~~~~~lfV~nLp~~-vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~l--ng~~l~gk~i~   86 (398)
                      +...++.|||+|||.. +|++||.++|+.||.|.+|++..     .+++|||+|++.++|.+|++.+  ++..+.|++|+
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~-----~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN-----KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECS-----SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeec-----cceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            4556789999999986 89999999999999999999976     4579999999999999999966  67789999999


Q ss_pred             eeccccc
Q 039806           87 VGPFIRR   93 (398)
Q Consensus        87 V~~~~~~   93 (398)
                      |.++.+.
T Consensus        79 V~~s~~~   85 (89)
T d1x4da1          79 VHLSQKY   85 (89)
T ss_dssp             EEEECCC
T ss_pred             EEECCCc
Confidence            9998653

>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=99.65  E-value=1.9e-16  Score=137.49  Aligned_cols=86  Identities=17%  Similarity=0.348  Sum_probs=79.8

Q ss_pred             CCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeec
Q 039806           11 LSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGP   89 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~   89 (398)
                      ....++|||+|||.++|+++|+++|+.||.|..|+|..|. +|.++|||||+|.+.++|++||+ +++..++|+.|.|.+
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEe
Confidence            4456799999999999999999999999999999999998 89999999999999999999997 799999999999999


Q ss_pred             cccccccc
Q 039806           90 FIRRADRI   97 (398)
Q Consensus        90 ~~~~~~~~   97 (398)
                      +.++.++.
T Consensus       173 A~~k~e~~  180 (183)
T d1u1qa_         173 ALSKQEMA  180 (183)
T ss_dssp             CCCHHHHH
T ss_pred             cCCccccc
Confidence            98877654

>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=99.64  E-value=5.5e-17  Score=127.79  Aligned_cols=81  Identities=16%  Similarity=0.071  Sum_probs=71.8

Q ss_pred             CCCcceEEEcCCCCCC-c----HHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEe
Q 039806           11 LSGIGNAFVKNLASTI-D----NLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMEL   85 (398)
Q Consensus        11 ~~~~~~lfV~nLp~~v-t----e~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i   85 (398)
                      .+++++|||+||+.++ +    +++|+++|+.||.|.+|++.+     ++|||||+|++.++|.+|++.|||..|+|+.|
T Consensus         2 ~~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k-----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           2 SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             CSCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-----TTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec-----CCCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            3678899999999886 3    356999999999999999974     67899999999999999999999999999999


Q ss_pred             eeecccccccc
Q 039806           86 YVGPFIRRADR   96 (398)
Q Consensus        86 ~V~~~~~~~~~   96 (398)
                      +|.++..+...
T Consensus        77 ~v~~a~~~~~~   87 (104)
T d1weya_          77 KLYFAQTLHIG   87 (104)
T ss_dssp             EEECCCCSSCC
T ss_pred             EEeecccCCCC
Confidence            99998765443

>d1nmra_ a.144.1.1 (A:) poly(A) binding protein {Protozoan (Trypanosoma cruzi) [TaxId: 5693]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Protozoan (Trypanosoma cruzi) [TaxId: 5693]

Probab=99.63  E-value=6.2e-18  Score=124.83  Aligned_cols=41  Identities=32%  Similarity=0.601  Sum_probs=40.0

Q ss_pred             hHHhhhhcCChHHHhhhhhcccchhhhccccceeceeeeee
Q 039806          353 NLSSMLVATSPDERKDILGQRLYPLVKKLKVITHIFVKGQF  393 (398)
Q Consensus       353 ~~~s~la~a~p~~qk~mLGe~Lyplv~~~~~~~~~~~~~~~  393 (398)
                      .++++||+++|++||+||||+|||+|++++|++|+|||||+
T Consensus        10 ~~a~~la~~~p~eqK~~LGE~Lyp~V~~~~p~~AgKITGML   50 (85)
T d1nmra_          10 NLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGML   50 (85)
T ss_dssp             TTHHHHTTCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHC
T ss_pred             HHHHHHhhCCHHHHHHHHHHHHHHHHHHHCcccccchhHHh
Confidence            58999999999999999999999999999999999999997

>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=99.62  E-value=9.5e-18  Score=128.88  Aligned_cols=76  Identities=12%  Similarity=0.230  Sum_probs=67.0

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEE-----EcC-CCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeee
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVV-----VSQ-EGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVG   88 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~-----~d~-~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~   88 (398)
                      ++|||+|||.++|+++|+++|+.||.|.++.+.     .+. +++++|||||+|.+.|+|++|++ |||..+.|+.|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            689999999999999999999999988776553     233 67899999999999999999996 99999999999997


Q ss_pred             ccc
Q 039806           89 PFI   91 (398)
Q Consensus        89 ~~~   91 (398)
                      .+.
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.52  E-value=3.8e-15  Score=118.98  Aligned_cols=81  Identities=17%  Similarity=0.176  Sum_probs=70.6

Q ss_pred             ccCCCcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCH-HHHHHHHHHhcCCeecceEeee
Q 039806            9 ARLSGIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTP-ESALDAIEKLQGATVERMELYV   87 (398)
Q Consensus         9 ~~~~~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~-e~A~~Ai~~lng~~l~gk~i~V   87 (398)
                      .++.+...+||+|||.++|+++|+++|+.||+|.+|+|+.     .+|||||.|.+. ++|.+|+..+|+..+.++.+.|
T Consensus         6 ~~~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~-----~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v   80 (113)
T d1owxa_           6 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-----GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEV   80 (113)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT-----TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             CCCCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEec-----CCceEEEEecCcHHHHHHHHHHhcCCceecCceEE
Confidence            4567778889999999999999999999999999999975     479999999996 7899999999999988887777


Q ss_pred             ecccccc
Q 039806           88 GPFIRRA   94 (398)
Q Consensus        88 ~~~~~~~   94 (398)
                      .+...+.
T Consensus        81 ~~~~~~~   87 (113)
T d1owxa_          81 TWEVLEG   87 (113)
T ss_dssp             EEEECCH
T ss_pred             EEeeccc
Confidence            7765443

>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=99.49  E-value=2e-14  Score=112.21  Aligned_cols=65  Identities=25%  Similarity=0.338  Sum_probs=58.2

Q ss_pred             CCcceEEEcC--CCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeec
Q 039806           12 SGIGNAFVKN--LASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVE   81 (398)
Q Consensus        12 ~~~~~lfV~n--Lp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~   81 (398)
                      ..+.+|+|.|  ||.++|+++|+++|++||.|.+|++..     .++||||+|.+.++|.+|++.|||..|.
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~-----~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-----TCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeecc-----CccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            3467888855  999999999999999999999998865     4689999999999999999999998773

>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=99.47  E-value=4.2e-14  Score=109.99  Aligned_cols=82  Identities=21%  Similarity=0.272  Sum_probs=70.1

Q ss_pred             cCCCcceEEEcCC--CCCCc---------HHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCC
Q 039806           10 RLSGIGNAFVKNL--ASTID---------NLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGA   78 (398)
Q Consensus        10 ~~~~~~~lfV~nL--p~~vt---------e~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~   78 (398)
                      +...+++|+|+||  +.++.         ++||++.|++||.|.+|++..+.   .+|||||+|++.++|.+|++.|||.
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~---~~G~~fV~f~~~e~A~~A~~~lng~   80 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH---PDGVASVSFRDPEEADYCIQTLDGR   80 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC---TTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC---CccEEEEEECCHHHHHHHHHHhCCc
Confidence            3456789999999  54432         36789999999999999987654   6799999999999999999999999


Q ss_pred             eecceEeeeecccccc
Q 039806           79 TVERMELYVGPFIRRA   94 (398)
Q Consensus        79 ~l~gk~i~V~~~~~~~   94 (398)
                      .++|+.|.|.+...+.
T Consensus        81 ~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          81 WFGGRQITAQAWDGTT   96 (99)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCEEEEEEEeCCcC
Confidence            9999999999876554

>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=99.45  E-value=5.1e-14  Score=105.14  Aligned_cols=74  Identities=16%  Similarity=0.219  Sum_probs=63.3

Q ss_pred             CcceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceE-eeeeccc
Q 039806           13 GIGNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERME-LYVGPFI   91 (398)
Q Consensus        13 ~~~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~-i~V~~~~   91 (398)
                      +.+.|+|.+||++++++.| +.|++||.|.++++.     +++|||||+|.+.++|++||+ +||..|+|+. |.|.+..
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~-----~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS-----NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC-----SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec-----CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            3567999999999997655 579999999999873     467999999999999999996 8999999975 5688776


Q ss_pred             cc
Q 039806           92 RR   93 (398)
Q Consensus        92 ~~   93 (398)
                      .+
T Consensus        76 ~k   77 (81)
T d1wwha1          76 DK   77 (81)
T ss_dssp             CH
T ss_pred             Ch
Confidence            54

>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=99.41  E-value=1e-13  Score=105.88  Aligned_cols=62  Identities=21%  Similarity=0.286  Sum_probs=57.5

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHH
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRI  236 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~  236 (398)
                      ..++++|+|||.++||++|+++|++||.|.+|+|++|. +|++||| ||.|.+.++|.+|+.+.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~   70 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR   70 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC
Confidence            35678999999999999999999999999999999997 7999999 99999999999998643

>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=99.39  E-value=2.4e-13  Score=102.60  Aligned_cols=66  Identities=20%  Similarity=0.318  Sum_probs=60.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .++.++|+|||.++|+++|+++|++||+|++|+|++|+ +|+++|| ||+|.+.++|.+|+..++...
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~   72 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK   72 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCE
Confidence            35678999999999999999999999999999999987 7999999 999999999999998887543

>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=99.39  E-value=2.9e-13  Score=101.66  Aligned_cols=67  Identities=16%  Similarity=0.158  Sum_probs=61.1

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..+++++|+|||.++|+++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+.+++...
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~   75 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME   75 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCE
Confidence            346789999999999999999999999999999999987 7999999 999999999999998877543

>d1ifwa_ a.144.1.1 (A:) poly(A) binding protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: poly(A) binding protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.38  E-value=6.5e-15  Score=110.26  Aligned_cols=41  Identities=15%  Similarity=0.123  Sum_probs=38.0

Q ss_pred             hHHhhhhcCChHHHhhhhhcccchhhhcc--ccceeceeeeee
Q 039806          353 NLSSMLVATSPDERKDILGQRLYPLVKKL--KVITHIFVKGQF  393 (398)
Q Consensus       353 ~~~s~la~a~p~~qk~mLGe~Lyplv~~~--~~~~~~~~~~~~  393 (398)
                      .+++.++++++++||+||||+|||+|+++  +|++|+|||||+
T Consensus         7 ~~~~~~~~~~~~~qk~~LGe~Lyp~V~~~~~~pe~A~KITGML   49 (92)
T d1ifwa_           7 RNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMI   49 (92)
T ss_dssp             SCCSSCCSCSCHHHHHHHHHHHHHHHGGGCCCHHHHHHHHHHH
T ss_pred             CChHHHhhcCHHHHHHHHHHHHHHHHHHhccCccccccchhhh
Confidence            45678899999999999999999999998  899999999997

>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=99.38  E-value=2.2e-13  Score=101.06  Aligned_cols=62  Identities=15%  Similarity=0.215  Sum_probs=58.4

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      .++|+|||.++|+++|+++|++||.|++|+|.+|++|+++|| ||+|.+.++|.+|+..++..
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   64 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGV   64 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCC
Confidence            478899999999999999999999999999999999999999 99999999999999887654

>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=99.38  E-value=1.9e-13  Score=102.43  Aligned_cols=66  Identities=17%  Similarity=0.233  Sum_probs=60.2

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      +++++|+|||.++|+++|+++|++||.|.+|+|.+|. +|+++|| ||+|.+.++|.+|+..++....
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~   69 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV   69 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEE
Confidence            3568999999999999999999999999999999986 8999999 9999999999999988876543

>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=99.37  E-value=3.6e-13  Score=101.62  Aligned_cols=66  Identities=15%  Similarity=0.281  Sum_probs=60.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .++.++|+|||.++++++|+++|++||.|.+|+|++|+ +|+++|| ||+|.+.++|.+|+..++...
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   72 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI   72 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCE
Confidence            34568999999999999999999999999999999986 8999999 999999999999999887543

>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=99.37  E-value=1.6e-13  Score=100.92  Aligned_cols=56  Identities=11%  Similarity=0.302  Sum_probs=53.2

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHH
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      ++|+|||.++|+++|+++|++||.|++|+|++|+ +|+++|| ||+|.+.++|.+|+.
T Consensus         2 lfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~   59 (75)
T d1x0fa1           2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME   59 (75)
T ss_dssp             EEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT
T ss_pred             EEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh
Confidence            6789999999999999999999999999999997 8999999 999999999999974

>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=99.36  E-value=5.1e-13  Score=100.53  Aligned_cols=60  Identities=20%  Similarity=0.278  Sum_probs=56.1

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHH
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      ..++++|+|||.++|+++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~   66 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN   66 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH
Confidence            34679999999999999999999999999999999998 7999999 999999999999975

>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=99.36  E-value=3.3e-13  Score=99.27  Aligned_cols=56  Identities=16%  Similarity=0.285  Sum_probs=53.4

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHH
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      ++|+|||.++||++|+++|++||+|++|+|++|+ +|+++|| ||+|.+.++|++|+.
T Consensus         2 lfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~   59 (75)
T d1hd0a_           2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD   59 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH
T ss_pred             EEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh
Confidence            6789999999999999999999999999999987 8999999 999999999999975

>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=99.36  E-value=3.4e-13  Score=100.51  Aligned_cols=62  Identities=19%  Similarity=0.253  Sum_probs=57.5

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      .++|+|||.++||++|+++|++||.|.+|+|++|+ +|+++|| ||+|.+.++|.+|+..++..
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~   65 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFD   65 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCC
Confidence            47889999999999999999999999999999987 7999999 99999999999999776644

>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=99.36  E-value=4.9e-13  Score=101.56  Aligned_cols=65  Identities=20%  Similarity=0.267  Sum_probs=59.9

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..+++|+|||.++|+++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|++|+..++...
T Consensus         7 ~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~   73 (88)
T d1rk8a_           7 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAE   73 (88)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCE
Confidence            4678899999999999999999999999999999986 8999999 999999999999998877543

>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=99.35  E-value=2e-13  Score=100.99  Aligned_cols=57  Identities=16%  Similarity=0.270  Sum_probs=54.1

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHH
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      .++|+|||.++|+++|+++|++||.|++|+|++|+ +|++||| ||+|.+.++|.+|+.
T Consensus         2 klfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~   60 (77)
T d1uawa_           2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA   60 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH
Confidence            57889999999999999999999999999999988 7999999 999999999999985

>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=99.35  E-value=2.3e-13  Score=103.61  Aligned_cols=66  Identities=15%  Similarity=0.211  Sum_probs=60.7

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++|+++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~   71 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESE   71 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEE
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCE
Confidence            35789999999999999999999999999999999988 7999999 999999999999998877543

>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=99.34  E-value=8.2e-13  Score=99.59  Aligned_cols=60  Identities=15%  Similarity=0.245  Sum_probs=56.8

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHH
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSY  233 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~  233 (398)
                      ..+++++|+|||.++|+++|+++|+.||.|.+|+|.++.+|+++|| ||+|.+.++|.+|+
T Consensus         4 ~~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al   64 (85)
T d1zh5a2           4 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV   64 (85)
T ss_dssp             HHTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHH
T ss_pred             CCcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHH
Confidence            3467899999999999999999999999999999999999999999 99999999999996

>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=99.34  E-value=5.1e-13  Score=100.76  Aligned_cols=63  Identities=10%  Similarity=0.230  Sum_probs=58.5

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .++|+|||.++||++|+++|++||.|++|+|++|+ +|+++|| ||+|.+.++|.+|+..++...
T Consensus         3 rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~   67 (85)
T d2u2fa_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ   67 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCE
Confidence            57899999999999999999999999999999987 7999999 999999999999998776544

>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=99.34  E-value=8.2e-13  Score=98.81  Aligned_cols=64  Identities=17%  Similarity=0.265  Sum_probs=58.7

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ++++|+|||.+++|++|+++|++||.|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~   68 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLR   68 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCE
Confidence            358889999999999999999999999999999987 7899999 999999999999998877543

>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=99.33  E-value=6e-13  Score=102.14  Aligned_cols=66  Identities=14%  Similarity=0.213  Sum_probs=60.9

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .+++++|+|||.++|+++|+++|++||.|++|+|++|. +|.++|| ||+|.+.++|.+|+..++...
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~   75 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIK   75 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCB
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCE
Confidence            35689999999999999999999999999999999987 8999999 999999999999998877554

>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=99.32  E-value=9e-13  Score=101.12  Aligned_cols=67  Identities=13%  Similarity=0.134  Sum_probs=61.1

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..+++++|+|||.++|+++|+++|++||.|++|+|++|. +|.++|| ||+|.+.++|.+|+..++...
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~   73 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTR   73 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCE
Confidence            345689999999999999999999999999999999987 8999999 999999999999998876544

>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=99.32  E-value=7.5e-13  Score=103.16  Aligned_cols=64  Identities=16%  Similarity=0.309  Sum_probs=58.1

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .++++|+|||.++|+++|+++|+.||.|.+|+|++|. +|++||| ||+|.+.++|.+|+ +++...
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~   83 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQR   83 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCE
Confidence            4689999999999999999999999999999999987 7999999 99999999999997 565443

>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=99.32  E-value=4.9e-13  Score=101.97  Aligned_cols=66  Identities=17%  Similarity=0.307  Sum_probs=60.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .+++++|+|||.++++++|+++|++||.|++|+|++|. +|.++|| ||+|.+.++|.+|+..++...
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~   74 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFG   74 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCE
Confidence            45678999999999999999999999999999999987 8999999 999999999999998876543

>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=99.32  E-value=6.8e-13  Score=104.01  Aligned_cols=80  Identities=15%  Similarity=0.152  Sum_probs=68.7

Q ss_pred             CcceEEEcCC--CCCC--------cHHHHHHHHhccCCeeEEEEEEcCCC---CceeEEEEEecCHHHHHHHHHHhcCCe
Q 039806           13 GIGNAFVKNL--ASTI--------DNLKLHQIFSKFGDIQSSKVVVSQEG---KSKGYGFVQYSTPESALDAIEKLQGAT   79 (398)
Q Consensus        13 ~~~~lfV~nL--p~~v--------te~~L~~~F~~~G~I~~vki~~d~~g---~skg~aFV~F~~~e~A~~Ai~~lng~~   79 (398)
                      .++.|.|+||  +.++        ..+||++.|++||.|++|+|.++.++   .++|++||+|.+.++|.+|++.|||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4678999999  5444        23578999999999999999887633   456999999999999999999999999


Q ss_pred             ecceEeeeecccc
Q 039806           80 VERMELYVGPFIR   92 (398)
Q Consensus        80 l~gk~i~V~~~~~   92 (398)
                      ++||.|.|.+...
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999998754

>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=99.32  E-value=8.7e-13  Score=103.21  Aligned_cols=62  Identities=15%  Similarity=0.237  Sum_probs=57.2

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHh
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      .++++|+|||.+++|++|+++|++||.|++|+|++|. +|+++|| ||+|++.++|.+|+..+.
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~   73 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN   73 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSS
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCC
Confidence            3568999999999999999999999999999999987 7999999 999999999999986554

>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=99.31  E-value=6.1e-13  Score=104.30  Aligned_cols=67  Identities=22%  Similarity=0.288  Sum_probs=60.7

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +..++++|+|||.++|+++|+++|++||+|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus         6 ~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~   74 (104)
T d1p1ta_           6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGRE   74 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBS
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCE
Confidence            345789999999999999999999999999999999987 7999999 999999999999988876443

>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=99.30  E-value=9.5e-13  Score=101.20  Aligned_cols=64  Identities=16%  Similarity=0.365  Sum_probs=58.7

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC--CCCccce-EEEecccHHHHHHHHHHh
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD--RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~--~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ...++++|+|||.++++++|+++|++||.|++|+|++|.  +|+++|| ||.|.+.++|.+|+..+.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~   72 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALC   72 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHcc
Confidence            345679999999999999999999999999999998874  7999999 999999999999998873

>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=99.30  E-value=1.2e-12  Score=101.70  Aligned_cols=65  Identities=15%  Similarity=0.205  Sum_probs=59.8

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .+.++|+|||.++++++|+++|++||.|.+|+|++|. +|+++|| ||+|.+.++|.+|+.+++...
T Consensus         8 ~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~   74 (99)
T d1whwa_           8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQV   74 (99)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEE
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCE
Confidence            4568999999999999999999999999999999987 8999999 999999999999998877544

>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=99.28  E-value=2.2e-12  Score=93.95  Aligned_cols=62  Identities=11%  Similarity=0.155  Sum_probs=57.2

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ++|+|||.++|+++|+++|++||.|.++++.+++ ++.++|| ||+|.+.++|.+|+..++...
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~   64 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASG   64 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHT
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCE
Confidence            4789999999999999999999999999999987 8899999 999999999999998877543

>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=99.28  E-value=1.9e-12  Score=101.19  Aligned_cols=59  Identities=19%  Similarity=0.309  Sum_probs=55.2

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHH
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      .++++|+|||.++++++|+++|++||.|++++|.+|. ++.++|| ||+|.+.++|.+|+.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~   80 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA   80 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH
Confidence            4679999999999999999999999999999999987 7889999 999999999998864

>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=99.28  E-value=1.9e-12  Score=101.01  Aligned_cols=65  Identities=14%  Similarity=0.180  Sum_probs=59.8

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .+.++|+|||.++++++|+++|++||.|++|++++|. +|+++|| ||+|.+.++|.+|+.+++...
T Consensus        18 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~   84 (102)
T d2cpza1          18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQ   84 (102)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCE
Confidence            4578999999999999999999999999999999987 8999999 999999999999998877544

>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=99.26  E-value=1.6e-12  Score=107.37  Aligned_cols=65  Identities=25%  Similarity=0.314  Sum_probs=59.9

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .++++|+|||.++|+++|+++|++||+|++|+|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus        42 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~  108 (139)
T d1u6fa1          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFN  108 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCE
Confidence            4579999999999999999999999999999999987 7999999 999999999999998876544

>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=99.26  E-value=1.5e-12  Score=97.11  Aligned_cols=65  Identities=8%  Similarity=0.069  Sum_probs=53.9

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +.+++|+|||.++|+++|+++|++||.|.+++++++. +|+++|| ||+|.+.++|.+|+..++...
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~   67 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLK   67 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCE
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCE
Confidence            3578999999999999999999999999998887765 8999999 999999999999998887654

>d1i2ta_ a.144.1.1 (A:) hyperplastic discs protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: PABP domain-like
superfamily: PABC (PABP) domain
family: PABC (PABP) domain
domain: hyperplastic discs protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=1e-13  Score=95.54  Aligned_cols=28  Identities=29%  Similarity=0.554  Sum_probs=27.4

Q ss_pred             Hhhhhhcccchhhhccccceeceeeeee
Q 039806          366 RKDILGQRLYPLVKKLKVITHIFVKGQF  393 (398)
Q Consensus       366 qk~mLGe~Lyplv~~~~~~~~~~~~~~~  393 (398)
                      ||+||||+|||+|++++|++|+|||||+
T Consensus         1 qk~~LGE~Ly~~V~~~~p~~A~KITGML   28 (61)
T d1i2ta_           1 HRQALGERLYPRVQAMQPAFASKITGML   28 (61)
T ss_dssp             CHHHHHHHHHHHHHHHCGGGHHHHHHHH
T ss_pred             ChHHHHHHhHHHHHHHChhhhcchhHHH
Confidence            8999999999999999999999999996

>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=99.25  E-value=1.9e-12  Score=98.60  Aligned_cols=65  Identities=18%  Similarity=0.292  Sum_probs=59.5

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +++++|+|||.++|+++|+++|++||.|.+|+++++. +|.++|| ||+|.+.++|.+|+..++...
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~   71 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKS   71 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCE
Confidence            4678999999999999999999999999999998876 8999999 999999999999998877543

>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=99.24  E-value=3.5e-12  Score=99.29  Aligned_cols=65  Identities=20%  Similarity=0.241  Sum_probs=60.5

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .++++|+|||.++|+++|+++|++||.|+++++..+.++.++|| ||+|.+.++|.+|+..++...
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~   83 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKF   83 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCE
Confidence            45799999999999999999999999999999999999999999 999999999999998877654

>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=99.24  E-value=3.8e-12  Score=95.76  Aligned_cols=62  Identities=23%  Similarity=0.313  Sum_probs=54.9

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCC-C---Cccce-EEEecccHHHHHHHHHHhccc
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDR-G---ISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~-g---~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      |+|+|||.++|+++|+++|++||.|++|+|++|+. +   .+||| ||+|.+.++|.+|+..++...
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~   67 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHT   67 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCE
Confidence            57899999999999999999999999999998763 2   47899 999999999999998776543

>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=99.23  E-value=8e-12  Score=95.67  Aligned_cols=65  Identities=23%  Similarity=0.321  Sum_probs=58.1

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+|||.++++++|+++|++||.|++|+|++|..+ ++|| ||+|.+.++|.+|+..++...
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~   75 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTV   75 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCE
Confidence            3467899999999999999999999999999999988654 6899 999999999999998877654

>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=99.22  E-value=7.1e-12  Score=92.87  Aligned_cols=60  Identities=20%  Similarity=0.375  Sum_probs=53.5

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHh
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      +.++|+|||.++|+++|+++|++||.|.++++..|+ +++++|| ||+|.+.+++.+|+ ++.
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al-~~~   64 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQK   64 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCS
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhC
Confidence            578999999999999999999999999999999987 8899999 99999987766665 443

>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=99.22  E-value=3.1e-12  Score=95.85  Aligned_cols=62  Identities=29%  Similarity=0.306  Sum_probs=55.5

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEE-EEeeCC-CCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSV-KIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~sv-ki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ++|+|||.++||++|+++|++||.|+++ +|++|. +|+++|| ||+|.+.++|.+|+..++...
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~   65 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQY   65 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCE
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcE
Confidence            5789999999999999999999999775 788886 8999999 999999999999998776544

>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=99.21  E-value=7.3e-12  Score=96.74  Aligned_cols=64  Identities=14%  Similarity=0.217  Sum_probs=58.9

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      .+++++|+|||.++||++|+++|++||.|.+++++.+. ++.++|| ||+|.+.++|.+|+..++.
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~   72 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASL   72 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCT
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHccc
Confidence            35689999999999999999999999999999999887 7889999 9999999999999988764

>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=99.20  E-value=4.3e-12  Score=96.41  Aligned_cols=64  Identities=20%  Similarity=0.235  Sum_probs=56.7

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..+++|+|||.++|+++|+++|++||.|++|+|+.|. +.++|| ||+|.+.++|.+|+.+++...
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~-~~~kg~afV~f~~~~~A~~Ai~~l~g~~   72 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGML   72 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT-TBCCSCEEEEESCHHHHHHHTTSSSEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec-CCCcceeEEEECCHHHHHHHHHHcCCCE
Confidence            3568999999999999999999999999999999886 447899 999999999999987766543

>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=99.20  E-value=6.8e-12  Score=95.46  Aligned_cols=66  Identities=18%  Similarity=0.241  Sum_probs=58.3

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...++++|+|||.++|+++|+++|++||.|++|+|.+|..+ .+|| ||+|.+.++|.+|+..++...
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~   72 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRK   72 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCE
Confidence            34578999999999999999999999999999999998643 3788 999999999999998877554

>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=99.18  E-value=1.7e-11  Score=97.50  Aligned_cols=64  Identities=11%  Similarity=0.187  Sum_probs=57.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .+++++|+|||.++|+++|+++|++||.|++|++..  ++.++|| ||+|.+.++|.+|+..++...
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~--~~~~kG~afV~f~~~~~A~~Ai~~l~g~~   70 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLSGFN   70 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC--STTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc--cCCcCCeEEEEECCHHHHHHHHHHhCCCE
Confidence            457899999999999999999999999999999985  4667899 999999999999998887654

>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=99.14  E-value=8e-12  Score=94.22  Aligned_cols=62  Identities=16%  Similarity=0.267  Sum_probs=52.0

Q ss_pred             hhhccccCCCcccC-HHHHHHHhhcCCCeEEEEEeeCC--CCCccce-EEEecccHHHHHHHHHHhc
Q 039806          176 ERAELYKNINDEVD-EIELKQYFSQCGTISSVKIMRTD--RGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       176 ~~~~~v~nL~~~vt-ee~L~~~F~~fG~I~svki~~d~--~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      .++++|+|||.+++ +++|+++|++||.|++|+|..++  +|+++|| ||+|.+.++|.+|+ +++.
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al-~~n~   69 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNR   69 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTT
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHH-hcCC
Confidence            46889999999876 56799999999999999997753  8899999 99999999999996 4543

>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=99.13  E-value=1.6e-11  Score=89.91  Aligned_cols=58  Identities=14%  Similarity=0.242  Sum_probs=53.0

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHh
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ++|+|||.++||++|+++|++||.|+++.++++. +|.++|| ||+|.+.++|.+|+ ++.
T Consensus         2 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al-~~~   61 (75)
T d2msta_           2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIH   61 (75)
T ss_dssp             EEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHH-HCS
T ss_pred             EEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHH-hcC
Confidence            6789999999999999999999999999998887 7899999 99999999998886 443

>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=99.12  E-value=1.5e-11  Score=94.62  Aligned_cols=62  Identities=8%  Similarity=0.094  Sum_probs=56.2

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCC-eEEEEEeeCC--CCCccce-EEEecccHHHHHHHHHHhc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGT-ISSVKIMRTD--RGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~-I~svki~~d~--~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ..++|+|||.++|+++|+++|++||. |++|+|++|.  +|+++|| ||+|.+.++|.+|+..++.
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~   67 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMP   67 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTT
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcC
Confidence            45889999999999999999999996 9999999885  6889999 9999999999999877654

>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=99.12  E-value=1.9e-12  Score=98.83  Aligned_cols=63  Identities=11%  Similarity=0.101  Sum_probs=57.4

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ..+++|+|||.++|+++|+++|++||.|.+|+|+.+.+|+++|| ||+|.+.++|.+|+ +++..
T Consensus        13 ~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al-~~~g~   76 (91)
T d1fjeb1          13 PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGL   76 (91)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGE
T ss_pred             CcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHH-hcCCc
Confidence            45788999999999999999999999999999988889999999 99999999999997 55544

>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=99.11  E-value=4.1e-11  Score=87.80  Aligned_cols=55  Identities=18%  Similarity=0.301  Sum_probs=50.2

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHH
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSY  233 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~  233 (398)
                      +++|+|||.++++++|+++|+.||.|++|++.+++.+. +|| ||+|.+.++|.+|+
T Consensus         2 tv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~-~~~afV~F~~~~~a~~Al   57 (75)
T d2ghpa2           2 TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAI   57 (75)
T ss_dssp             EEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHH
T ss_pred             EEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHH
Confidence            57889999999999999999999999999999987655 467 99999999999995

>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=99.10  E-value=2.4e-11  Score=92.19  Aligned_cols=64  Identities=13%  Similarity=0.183  Sum_probs=55.3

Q ss_pred             hhccccCCCcccCHHHH---HHHhhcCCCeEEEEEeeCC-CCCc---cce-EEEecccHHHHHHHHHHhccc
Q 039806          177 RAELYKNINDEVDEIEL---KQYFSQCGTISSVKIMRTD-RGIS---KGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L---~~~F~~fG~I~svki~~d~-~g~s---kGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +.++|+|||.++++++|   +++|++||.|++|+|++|+ ++.+   +|| ||+|.+.++|.+|+..+....
T Consensus         9 n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~   80 (89)
T d2cpia1           9 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVV   80 (89)
T ss_dssp             SCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             CEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCE
Confidence            56788999999999999   7789999999999999987 4443   467 999999999999998887543

>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=99.08  E-value=5.9e-11  Score=93.32  Aligned_cols=62  Identities=16%  Similarity=0.094  Sum_probs=55.3

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ..++|+||+.++|+++|+++|++||.|++|+|+++   +++|| ||+|.+.++|.+|+..++....
T Consensus         8 ~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~---~~~g~aFV~f~~~e~A~~Ai~~ln~~~l   70 (108)
T d2adba1           8 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNI   70 (108)
T ss_dssp             EEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE---TTEEEEEEEESCHHHHHHHHHHHHSCCS
T ss_pred             EEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee---CCCCeEEEEECCHHHHHHHHHHHCCCEe
Confidence            45678999999999999999999999999999976   35788 9999999999999998886653

>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=99.08  E-value=5e-11  Score=91.70  Aligned_cols=60  Identities=13%  Similarity=0.236  Sum_probs=54.5

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .++++|+||+.++++++|+++|++||.|++|+|++|     ||| ||.|.+.++|.+|+..++...
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~   78 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTT   78 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCE
Confidence            457899999999999999999999999999999965     788 999999999999998887554

>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=99.07  E-value=4.5e-11  Score=94.34  Aligned_cols=65  Identities=18%  Similarity=0.241  Sum_probs=57.0

Q ss_pred             hhhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccccC
Q 039806          173 MRKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQG  242 (398)
Q Consensus       173 ~~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~~  242 (398)
                      .+.+++++|+|||.++++++|+++|++||.|++|+|.     +++|| ||.|.+.++|.+|+..++.....
T Consensus         7 ~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~-----~~kg~afV~f~~~~~A~~A~~~lng~~~~   72 (111)
T d1whxa_           7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLAYSKFH   72 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-----SSSSCEEEEESCHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee-----ccCceEEEEEcCHHHHHHHHHHHcCCccC
Confidence            3456789999999999999999999999999999985     45788 99999999999999988876543

>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=99.07  E-value=9.1e-11  Score=87.62  Aligned_cols=64  Identities=13%  Similarity=0.173  Sum_probs=56.2

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      .++++++|+|||.++|+++|+++|++||.|++|+++++    .+|| ||+|.+.++|.+|+..++....
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~   70 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSNAAKEALQGFKI   70 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHHHHHHHhCCcEe
Confidence            34678999999999999999999999999999999865    3567 9999999999999988876443

>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=99.07  E-value=3.9e-11  Score=90.30  Aligned_cols=65  Identities=14%  Similarity=0.185  Sum_probs=58.3

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEE-EEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISS-VKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~s-vki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ..++++|||.++++++|+++|+.||.|.+ +.+..+++|+++|| ||+|.+.++|.+|+.+++....
T Consensus        10 ~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l   76 (86)
T d2cqpa1          10 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI   76 (86)
T ss_dssp             EEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEE
Confidence            45788999999999999999999999976 57777889999999 9999999999999998876553

>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=99.05  E-value=6.7e-11  Score=93.05  Aligned_cols=61  Identities=21%  Similarity=0.274  Sum_probs=53.3

Q ss_pred             hhhccccCCC-cccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNIN-DEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~-~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +++++|+||+ ..+|+++|+++|++||.|.+|+|++|.    +|| ||+|.+.++|.+|+..++...
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~----kg~afV~f~~~~~A~~ai~~lng~~   64 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHK   64 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCB
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCE
Confidence            3678999996 469999999999999999999999874    566 999999999999998877543

>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=99.05  E-value=5.7e-11  Score=89.62  Aligned_cols=58  Identities=10%  Similarity=0.157  Sum_probs=52.4

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      .++|+|||.++++++|+++|++||.|++|+|.+|      || ||+|.+.++|.+|+..++....
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~   60 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKF   60 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBC
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc------ceeeEEeCCHHHHHHHHHHhCCCEE
Confidence            5789999999999999999999999999999744      67 9999999999999998876653

>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=99.04  E-value=1.7e-10  Score=87.03  Aligned_cols=64  Identities=14%  Similarity=0.120  Sum_probs=55.6

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ++++++|+|||.++++++|+++|++||.|.++++..   ++++|| ||+|.+.++|.+|+.+++....
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~---~~~~~~afV~f~~~~~A~~A~~~l~~~~i   73 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF---QKDRKMALIQMGSVEEAVQALIDLHNHDL   73 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC---SSSTTCEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee---ecccceeEEEECCHHHHHHHHHhccCCEe
Confidence            357899999999999999999999999999988764   345677 9999999999999998876543

>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=99.02  E-value=9.3e-11  Score=91.45  Aligned_cols=62  Identities=19%  Similarity=0.251  Sum_probs=52.9

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC--CCCccce-EEEecccHHHHHHHHHHhc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD--RGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~--~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ...+++|+|||.++||++|+++|+.|| |++++++.+.  +|+++|| ||+|.+.++|++| ++++.
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~-~~~~~   78 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA-LSLNE   78 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHH-HGGGT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHH-HHcCC
Confidence            346789999999999999999999999 8888888765  7889999 9999999988644 45554

>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=99.02  E-value=8.9e-11  Score=91.28  Aligned_cols=61  Identities=13%  Similarity=0.116  Sum_probs=54.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHh
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ...+++|+|||+++||++|+++|+.|| |++|.++++.+|+++|| ||+|.+.++|.+|+ ++.
T Consensus        14 ~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al-~~~   75 (102)
T d1weza_          14 TGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKD   75 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHH-HcC
Confidence            345788899999999999999999998 56899999999999999 99999999999995 444

>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=99.02  E-value=1.6e-10  Score=88.50  Aligned_cols=65  Identities=6%  Similarity=0.103  Sum_probs=56.1

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +.+++++|+|||.++|+++|+++|++||.|+++++.++  +.++|| ||+|.+.++|.+|+..++...
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~   77 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYD   77 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCE
Confidence            34567999999999999999999999999999998755  445777 999999999999998887544

>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=99.01  E-value=1.6e-10  Score=90.17  Aligned_cols=59  Identities=14%  Similarity=0.112  Sum_probs=51.3

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEE-eeCCCCCccce-EEEecccHHHHHHHH
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKI-MRTDRGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki-~~d~~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      +.+++|+|||+++||++|+++|+.||.|.++.+ ..+.+++++|| ||+|++.++|.+|+.
T Consensus        15 ~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~   75 (104)
T d1wg5a_          15 DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK   75 (104)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh
Confidence            446888999999999999999999999988544 55569999999 999999999987763

>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=99.01  E-value=1.8e-10  Score=86.59  Aligned_cols=60  Identities=15%  Similarity=0.260  Sum_probs=54.0

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      +.++|+|||.++++++|+++|++||+|.+|++.++     +|| ||.|.+.++|.+|+..++....
T Consensus         9 ~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i   69 (86)
T d2cpja1           9 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPL   69 (86)
T ss_dssp             TEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCB
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEE
Confidence            46889999999999999999999999999999854     677 9999999999999998876543

>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=99.00  E-value=8.6e-11  Score=91.07  Aligned_cols=67  Identities=19%  Similarity=0.324  Sum_probs=58.3

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeE--------EEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTIS--------SVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~--------svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ..++++|+|||.++|+++|+++|+.||.|.        .+++.+|. +|+++|| ||+|.+.++|.+|+..++....
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            456899999999999999999999999984        56666766 7899999 9999999999999998876543

>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=98.99  E-value=2.1e-10  Score=88.21  Aligned_cols=62  Identities=6%  Similarity=0.106  Sum_probs=55.3

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      +.++++|+||+.++++++|+++|++||.|++|++.++     ++| ||+|++.++|.+|+..++....
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i   78 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPL   78 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEe
Confidence            4578999999999999999999999999999999854     556 9999999999999999886553

>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=98.99  E-value=2.4e-11  Score=94.52  Aligned_cols=65  Identities=14%  Similarity=0.142  Sum_probs=59.4

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      ++++++|+|||.++++++|+++|++||.|.++++..+. +|+++|| ||.|.+.++|.+|+..++..
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~   83 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGY   83 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCC
Confidence            45789999999999999999999999999999998876 8999999 99999999999999877643

>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=98.98  E-value=8.9e-11  Score=91.56  Aligned_cols=62  Identities=8%  Similarity=0.061  Sum_probs=55.7

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +.++++.++++||+|+++|++||.|++|+|+++.+|+++|| ||.|.+.++|.+|+..+....
T Consensus        30 ~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~   92 (104)
T d1jmta_          30 VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRW   92 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCE
T ss_pred             HHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCE
Confidence            44567778899999999999999999999999999999999 999999999999998877543

>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=98.98  E-value=8.1e-11  Score=88.95  Aligned_cols=56  Identities=18%  Similarity=0.248  Sum_probs=49.9

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHH
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYL  234 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l  234 (398)
                      ..++++|+|||.++||++|+++|++||.|.+|++..    .++|| ||+|.+.++|.+|+.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~----~~~gfafV~f~~~~~a~~a~~   60 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSLCG   60 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS----SCCSCCEEECSCHHHHHHTTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee----ccCceEEEEECCHHHHHHHHh
Confidence            457899999999999999999999999999998863    46788 999999999998864

>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=98.96  E-value=9.1e-11  Score=89.23  Aligned_cols=64  Identities=17%  Similarity=0.264  Sum_probs=55.3

Q ss_pred             hhhhccccCCCcccCHHHHHH----HhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQ----YFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~----~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ++++++|+|||.++++++|++    +|++||+|++|++.+  +++++|| ||+|.+.++|.+|+.+++...
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~   70 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFP   70 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCE
Confidence            467899999999999999864    689999999999853  5678888 999999999999998887543

>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=98.95  E-value=4.5e-10  Score=84.70  Aligned_cols=60  Identities=15%  Similarity=0.167  Sum_probs=53.4

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      .++++++|+|||.++++++|+++|++||.|.++++.++     +|| ||+|.+.++|.+|+..++.
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~   66 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSA   66 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHcc
Confidence            45778999999999999999999999999999999844     567 9999999999999877653

>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=98.95  E-value=1.1e-10  Score=86.54  Aligned_cols=56  Identities=11%  Similarity=0.077  Sum_probs=50.8

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      .++|+|||.++|+++|+++|++||.|.++++.+     ++|| ||+|.+.++|.+|+..++.
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~-----~rg~aFV~f~~~~~A~~Ai~~lng   59 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLSG   59 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-----ETTEEEECCSCHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec-----ccceEEEEECCHHHHHHHHHHhCC
Confidence            588999999999999999999999999888874     4788 9999999999999988764

>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=98.95  E-value=1.8e-10  Score=89.65  Aligned_cols=61  Identities=15%  Similarity=0.251  Sum_probs=53.5

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEE-EEEeeCCCCCccce-EEEecccHHHHHHHHHHh
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISS-VKIMRTDRGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~s-vki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      ..+++|+|||+++|+++|+++|+.||.|.. +.+..+.+|+++|| ||+|.+.++|.+|+ ++.
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al-~~n   70 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-RLH   70 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHG-GGC
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHH-hcC
Confidence            356888999999999999999999999987 55666679999999 99999999999996 443

>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=98.94  E-value=5.4e-10  Score=87.05  Aligned_cols=60  Identities=15%  Similarity=0.138  Sum_probs=53.2

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ...++++|+|||.++||++|+++|++||.|++|++.+     .||| ||+|.+.++|.+|+..++.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~-----~k~~AfV~f~~~e~A~~ai~~~~~   73 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-----FKRQALVEFENIDSAKECVTFAAD   73 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe-----cceeEEEEeCCHHHHHHHHHHHcC
Confidence            3467789999999999999999999999999999974     4677 9999999999999987654

>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=98.94  E-value=5e-10  Score=86.26  Aligned_cols=60  Identities=10%  Similarity=0.123  Sum_probs=53.5

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ...+++|+|||.++++++|+++|++||+|++|+|.      ++|| ||+|.+.++|.+|+.+++...
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~------~~g~afV~f~~~~~a~~Ai~~lng~~   74 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQ------KDGMGMVEYLRKEDMEYALRKLDDTK   74 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEE------TTTEEEEEESSHHHHHHHHHHHSSEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhccccccccc------ccceEEEEECCHHHHHHHHHHhCCCE
Confidence            34568999999999999999999999999999996      3578 999999999999998887554

>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=98.91  E-value=3e-10  Score=87.17  Aligned_cols=63  Identities=27%  Similarity=0.260  Sum_probs=55.4

Q ss_pred             hhhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +..++++|+|||.++|+++|+++|++||.|..++.    +|+++|| ||+|.+.++|.+|+..++...
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~   77 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAE   77 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCE
Confidence            44678999999999999999999999999877653    6889999 999999999999998887544

>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=98.90  E-value=5e-10  Score=82.66  Aligned_cols=59  Identities=10%  Similarity=0.111  Sum_probs=51.7

Q ss_pred             hhhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      ..++++|+||+  +|+++|+++|++||.|++|++.+     .+|| ||+|.+.++|.+|+..+....
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~-----~~~~afV~f~~~~~A~~Ai~~lng~~   63 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP-----PRNCAFVTYEKMESADQAVAELNGTQ   63 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCB
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeecc-----CCCEEEEEEcccHHHHHHHHHhCCCE
Confidence            35678999996  99999999999999999999974     4677 999999999999999887554

>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=98.88  E-value=8.8e-10  Score=82.65  Aligned_cols=60  Identities=5%  Similarity=-0.014  Sum_probs=53.6

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .++++|+|||.++++++|+++|++||.|..+++.     +++|| ||.|.+.++|.+|+..++...
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~-----~~rg~afV~f~~~~~A~~Ai~~l~~~~   68 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVHFSNREDAVEAMKALNGKV   68 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE-----ECSSEEEEEESSHHHHHHHHHHHSSEE
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc-----cccEEEEEEeCCHHHHHHHHHHcCCCE
Confidence            4678999999999999999999999999988875     45788 999999999999998887544

>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=98.88  E-value=5.1e-10  Score=86.18  Aligned_cols=59  Identities=17%  Similarity=0.208  Sum_probs=51.6

Q ss_pred             hhhhccccCCC-cccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNIN-DEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL~-~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .+.+++|+||+ ..+++++|+++|++||.|++|+|.       ||| ||+|.+.++|.+|+..++...
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-------rg~aFV~f~~~~~A~~Ai~~lng~~   74 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGEDGRM   74 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-------TEEEEEEESSHHHHHHHHHTTTTCE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-------CCeEEEEECCHHHHHHHHHHcCCCE
Confidence            34578999997 578899999999999999999993       788 999999999999998877544

>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=98.84  E-value=5.6e-10  Score=86.46  Aligned_cols=63  Identities=11%  Similarity=0.212  Sum_probs=54.0

Q ss_pred             hhhhhccc--cCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          174 RKERAELY--KNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       174 ~~~~~~~v--~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      .+.++++|  +||+.++|+++|+++|++||.|++|+++++     +|| ||.|.+.++|.+|+.+++....
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            44566777  459999999999999999999999998854     556 9999999999999999886654

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.84  E-value=3.9e-10  Score=89.07  Aligned_cols=62  Identities=10%  Similarity=0.119  Sum_probs=53.0

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEE-EEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSV-KIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~sv-ki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ..+++|+|||+++|+++|+++|+.||.|.++ .+..+.+|.++|| ||+|.+.++|.+|+ +++.
T Consensus        18 ~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al-~~~~   81 (112)
T d1wela1          18 GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHK   81 (112)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHH-TSCS
T ss_pred             CeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHH-HcCC
Confidence            4578889999999999999999999999775 4555669999999 99999999998776 4443

>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=98.82  E-value=3.7e-09  Score=77.02  Aligned_cols=57  Identities=11%  Similarity=0.187  Sum_probs=49.1

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      ++|+|||.++++++|+++|++|| +.++++     ++++|| ||.|.+.++|.+|+..++....
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-----~~~~g~afv~f~~~~~A~~Ai~~ln~~~~   58 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----DKYKGTAFVTLLNGEQAEAAINTFHQSRL   58 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTEES
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-----cccceeEEEEECCHHHHHHHHHHhCCccC
Confidence            46899999999999999999999 666665     357888 9999999999999998876543

>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=98.82  E-value=1.3e-09  Score=82.07  Aligned_cols=60  Identities=8%  Similarity=0.109  Sum_probs=50.8

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhcccc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQ  241 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~  241 (398)
                      .++++|+|||.++++++|+++|++|| +..+++     ++++|| ||+|.+.++|.+|+.+++....
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~-----~~~kg~afV~f~~~~~A~~Ai~~ln~~~~   65 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-----DRNKRTAFVTLLNGEQAQNAIQMFHQYSF   65 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE-----EGGGTEEEECCSCHHHHHHHHHHHTTEEE
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee-----eccCCceEEEECCHHHHHHHHHHhCCCEE
Confidence            46789999999999999999999999 333444     356888 9999999999999998887653

>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=98.82  E-value=2.1e-09  Score=84.93  Aligned_cols=57  Identities=14%  Similarity=0.198  Sum_probs=48.1

Q ss_pred             ccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEeccc-HHHHHHHHHHhccc
Q 039806          179 ELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQT-KRERTSYLRIMYAK  240 (398)
Q Consensus       179 ~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~-~ea~~A~l~~q~~q  240 (398)
                      .+++||++++|+++|+++|++||+|.+|+|+++     +|| ||.|.++ ++|..|...+....
T Consensus        14 ~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~   72 (113)
T d1owxa_          14 KFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGN   72 (113)
T ss_dssp             EEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSC
T ss_pred             EEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCc
Confidence            355999999999999999999999999999844     677 9999997 56777877766543

>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=98.80  E-value=1.4e-09  Score=83.81  Aligned_cols=58  Identities=12%  Similarity=0.154  Sum_probs=50.6

Q ss_pred             hhhhccccCCCcc-cCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHh
Q 039806          175 KERAELYKNINDE-VDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       175 ~~~~~~v~nL~~~-vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      .+++++|+|||.+ +|+++|+++|++||.|.+|+++++     +|| ||+|.+.++|.+|+....
T Consensus        17 ~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~   76 (99)
T d1x4fa1          17 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCL   76 (99)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHh
Confidence            4567899999975 899999999999999999999854     577 999999999999986443

>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=98.78  E-value=1.9e-09  Score=81.37  Aligned_cols=59  Identities=15%  Similarity=0.127  Sum_probs=51.3

Q ss_pred             hhhhhccccCCCcc-cCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHh
Q 039806          174 RKERAELYKNINDE-VDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIM  237 (398)
Q Consensus       174 ~~~~~~~v~nL~~~-vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q  237 (398)
                      +..++++|+|||.. +|+++|+++|++||.|.+|+++++     +++ ||.|++.++|..|+..++
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~   66 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYT   66 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHh
Confidence            45678999999986 889999999999999999999855     344 899999999999987664

>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=98.61  E-value=4.8e-10  Score=84.87  Aligned_cols=62  Identities=10%  Similarity=0.074  Sum_probs=51.8

Q ss_pred             hhccccCCCcccCHHHHHHHhhcCCCeEEEEEee------CCCCCccce-EEEecccHHHHHHHHHHhcc
Q 039806          177 RAELYKNINDEVDEIELKQYFSQCGTISSVKIMR------TDRGISKGH-CMAIAQTKRERTSYLRIMYA  239 (398)
Q Consensus       177 ~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~------d~~g~skGf-fV~f~~~~ea~~A~l~~q~~  239 (398)
                      |.++|+|||.++||++|+++|++||.|.++.+..      ..+++++|| ||+|.+.++|.+|+ +++..
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~   70 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGI   70 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCc
Confidence            5689999999999999999999999988776642      236789999 99999999998885 45433

>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=98.61  E-value=7.5e-09  Score=80.31  Aligned_cols=62  Identities=13%  Similarity=0.119  Sum_probs=52.4

Q ss_pred             hhhccccCCCccc-CH----HHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccccC
Q 039806          176 ERAELYKNINDEV-DE----IELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAKQG  242 (398)
Q Consensus       176 ~~~~~v~nL~~~v-te----e~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q~~  242 (398)
                      ...|+|+||++++ ++    ++|+++|++||.|++++++     +++|| ||+|.+.++|.+|+.+++.....
T Consensus         5 ~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~-----k~~~~afV~f~~~~~A~~Ai~~lng~~~~   72 (104)
T d1weya_           5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-----KSFKRVRINFSNPLSAADARLRLHKTEFL   72 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE-----TTTTEEEEECSSTTHHHHHHHTSTTSEET
T ss_pred             CceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEe-----cCCCEEEEEECCHHHHHHHHHHhcccccC
Confidence            4678999999987 33    5699999999999999998     34666 99999999999999999876543

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.50  E-value=7.4e-08  Score=70.91  Aligned_cols=56  Identities=11%  Similarity=-0.004  Sum_probs=46.4

Q ss_pred             hhhccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhc
Q 039806          176 ERAELYKNINDEVDEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMY  238 (398)
Q Consensus       176 ~~~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~  238 (398)
                      ++.+.|.++|.+.+++.| ++|++||+|+++++.     +++|| ||.|+++++|.+|+ ++..
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~-----~~~~~~fV~f~~~~~A~~Al-~~nG   60 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS-----NTGNWMHIRYQSKLQARKAL-SKDG   60 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC-----SSSSEEEEEESSHHHHHHHH-TTTT
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEec-----CCCCEEEEEEcccHHHHHHH-hcCC
Confidence            456778999999997766 479999999999985     45788 99999999999997 3443

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.34  E-value=1.6e-07  Score=72.51  Aligned_cols=66  Identities=15%  Similarity=0.138  Sum_probs=52.2

Q ss_pred             hhhhccccCC--Ccc--------cCHHHHHHHhhcCCCeEEEEEeeCCCC---Cccce-EEEecccHHHHHHHHHHhccc
Q 039806          175 KERAELYKNI--NDE--------VDEIELKQYFSQCGTISSVKIMRTDRG---ISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       175 ~~~~~~v~nL--~~~--------vtee~L~~~F~~fG~I~svki~~d~~g---~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +++.+.++||  +.+        ...++|++.|++||.|++|+|.++..+   ..+|+ ||.|.+.++|.+|+..++...
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            3566777787  222        234789999999999999999987643   34577 999999999999999998754

>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=98.29  E-value=2.2e-07  Score=71.12  Aligned_cols=64  Identities=16%  Similarity=0.178  Sum_probs=51.5

Q ss_pred             hhhhhccccCC--Cccc---------CHHHHHHHhhcCCCeEEEEEeeCCCCCccce-EEEecccHHHHHHHHHHhccc
Q 039806          174 RKERAELYKNI--NDEV---------DEIELKQYFSQCGTISSVKIMRTDRGISKGH-CMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       174 ~~~~~~~v~nL--~~~v---------tee~L~~~F~~fG~I~svki~~d~~g~skGf-fV~f~~~~ea~~A~l~~q~~q  240 (398)
                      +.+++++++||  +.++         .+++|++.|++||.|++|++..+   ..+|| ||.|++.++|.+|+..++...
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            34577888898  4433         23789999999999999998754   56788 999999999999998887543

>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=97.67  E-value=0.00011  Score=50.68  Aligned_cols=66  Identities=15%  Similarity=0.257  Sum_probs=55.9

Q ss_pred             CCCcHHH----HHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecceEeeeeccc
Q 039806           24 STIDNLK----LHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVERMELYVGPFI   91 (398)
Q Consensus        24 ~~vte~~----L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~gk~i~V~~~~   91 (398)
                      ...++++    |.+.|+++|.|+++.|..-.+|..  .|-|.-.+..+|..|+..|+...|++|+|.|.++.
T Consensus         2 ~~L~~kelqq~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           2 YRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             TTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CcCCHHHHHHHHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            3455555    556799999999999977667766  59999999999999999999999999999998764

>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=97.65  E-value=5.6e-05  Score=54.96  Aligned_cols=70  Identities=17%  Similarity=0.279  Sum_probs=57.8

Q ss_pred             CCcceEEEcCCCCCCcH---------HHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhcCCeecc
Q 039806           12 SGIGNAFVKNLASTIDN---------LKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQGATVER   82 (398)
Q Consensus        12 ~~~~~lfV~nLp~~vte---------~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~lng~~l~g   82 (398)
                      ...++|.|.=...+.++         .+|.+.|+.||+|.-|+++.|       -.+|.|.+-++|.+|++ ++|..+.|
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al~-l~g~~v~G   84 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHhc-cCCeEEcc
Confidence            45668888655544433         368889999999999999775       49999999999999998 89999999


Q ss_pred             eEeeeec
Q 039806           83 MELYVGP   89 (398)
Q Consensus        83 k~i~V~~   89 (398)
                      +.|.|..
T Consensus        85 ~~l~It~   91 (95)
T d1ufwa_          85 RAVKISG   91 (95)
T ss_dssp             EEEEEEC
T ss_pred             eEEEEec
Confidence            9999865

>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=97.33  E-value=0.00054  Score=50.34  Aligned_cols=68  Identities=7%  Similarity=0.174  Sum_probs=57.1

Q ss_pred             ceEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcC-C-CC-ceeEEEEEecCHHHHHHHHHHhcCCeecc
Q 039806           15 GNAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQ-E-GK-SKGYGFVQYSTPESALDAIEKLQGATVER   82 (398)
Q Consensus        15 ~~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~-~-g~-skg~aFV~F~~~e~A~~Ai~~lng~~l~g   82 (398)
                      ++|-|+.||++.||+++.+.++..|.+.......-+ + +. .-.-|||.|.+.++.....+..+|..+-+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            579999999999999999999999998887766654 2 22 22469999999999999999999988754

>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=94.76  E-value=0.059  Score=39.31  Aligned_cols=54  Identities=26%  Similarity=0.362  Sum_probs=45.3

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEEEcCCCCceeEEEEEecCHHHHHHHHHHhc
Q 039806           16 NAFVKNLASTIDNLKLHQIFSKFGDIQSSKVVVSQEGKSKGYGFVQYSTPESALDAIEKLQ   76 (398)
Q Consensus        16 ~lfV~nLp~~vte~~L~~~F~~~G~I~~vki~~d~~g~skg~aFV~F~~~e~A~~Ai~~ln   76 (398)
                      -||.-..|+.....||.++|+.||.|. |..+.|-      -|||...+.|+|+.++..++
T Consensus        17 HVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          17 HVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT------EEEEECSCHHHHHHHHHHHH
T ss_pred             eeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc------eEEEEecCHHHHHHHHHHhc
Confidence            589999999999999999999999884 4444432      49999999999999987554

>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=91.41  E-value=0.17  Score=36.40  Aligned_cols=58  Identities=5%  Similarity=-0.008  Sum_probs=44.3

Q ss_pred             hccccCCCcccCHHHHHHHhhcCCCeEEEEEeeCC-CCCccce---EEEecccHHHHHHHHH
Q 039806          178 AELYKNINDEVDEIELKQYFSQCGTISSVKIMRTD-RGISKGH---CMAIAQTKRERTSYLR  235 (398)
Q Consensus       178 ~~~v~nL~~~vtee~L~~~F~~fG~I~svki~~d~-~g~skGf---fV~f~~~~ea~~A~l~  235 (398)
                      ++.|++||+..||+++.+.++..|.+........+ +-+..-+   ||.|.+.++...-...
T Consensus         3 KvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~   64 (91)
T d1uw4a_           3 KVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDR   64 (91)
T ss_dssp             EEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHH
T ss_pred             eEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHH
Confidence            46779999999999999999999999988777644 2222222   9999999987654443

>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=82.90  E-value=1.1  Score=30.21  Aligned_cols=50  Identities=14%  Similarity=0.143  Sum_probs=41.2

Q ss_pred             HHHHHHHhhcCCCeEEEEEeeCCCCCccceEEEecccHHHHHHHHHHhccc
Q 039806          190 EIELKQYFSQCGTISSVKIMRTDRGISKGHCMAIAQTKRERTSYLRIMYAK  240 (398)
Q Consensus       190 ee~L~~~F~~fG~I~svki~~d~~g~skGffV~f~~~~ea~~A~l~~q~~q  240 (398)
                      .+.|.+.|+++|.|.++.|....+|..+. -|...+..||.-|+..+|-..
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~~dg~~~A-~V~v~~~q~A~~~v~~LhR~K   59 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPHTDYQLKA-VVQMENLQDAIGAVNSLHRYK   59 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSCCSTTCCE-EEEESSHHHHHHHHHHHTTEE
T ss_pred             HHHHHHHHHhheeEEEEEEEeccCCcEEE-EEEcCCHHHHHHHHHHHHHHh
Confidence            45677789999999999998766776666 599999999999998887544