Citrus Sinensis ID: 012257

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------
Protein Sequence
MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPRMPMYPPVAPGLGQQLFYGQGPPIIPPQVIYSFLLIDYFNALVLLMI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEEcccccccccEEEEEcccHHHHHHHHHHHcccccccEEEEEEEEcccccccccccccEEEccccccccHHHHHHHHHccccccEEEEEEccccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEcccccccccccccccccccEEEEccccccccHHHHHHHHccccccEEEEEEEccccccccEEEEEcccHHHHHHHHHHHcccEEccEEEEEEcccccHHHHHHHHHHHHHHHHHccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEcccccccEEEEEEcccHHHHHHHHHHHcccEEccEEEEEEEccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccEEEEEc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccEEEEEccccccccHHHHHHHHcccccEEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEEEcccccHcccccEEEEEEcccccccHHHHHHHHHHcccEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEccccHHHHHHHHHccccEEEEEEcccccccHHHHHHHHHHcccEEEEEEEEcccccccccEEEEcccHHHHHHHHHHHccccccccEEEEEccccHHHHHHHHHHHHHHHHHHHHHHccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEcccccccccEEEEEccHHHHHHHHHHHcccccccccEEHHHHHcHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHccccEcccc
Coil and Loop (DISEMBL)
maqvqvqpqapvavaaqpspatngiannggvgdaRQFVSTSLyvgdldlsvndsQLYDLFNQMGQVVSVRVCRdlstrrslgygyvnyNAAHEATRALdelnftplngkpirimysyrdptirksgagnifiknldksidnkalhdtfstFGNILSCKVatdslgqsrgygfvqfdneESAKSAIDKLNGmllndkqvfvgpflrkqerestadktrfnnvyvknlsettteDDLKKIFGEFGIITSTavmrdadgkskcfgfvnfddpddaARSVEAlngkkfddkewyvgKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEfgtitsckvmrdpngisrgsgfVAFSTAEEASKALTEmngkmvvskPLYVALAQRKEERRARLQAQFsqmrppvgprmpmyppvapglgqqlfygqgppiippqviYSFLLIDYFNALVLLMI
Flexible Loop (DISEMBL)
maqvqvqpqapvavaaqpspatNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATraldelnftplngKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLrkqerestadktrfnnvyvknlsettteddlkKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEalngkkfddkewyvGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEfgtitsckvmrdpnGISRGSGFVAFSTAEEASKALtemngkmvvSKPLYVALAQRKEERRARLQAqfsqmrppvgprMPMYPPVAPGLGQQLFYGQGPPIIPPQVIYSFLLIDYFNALVLLMI
Low Complexity Region (SEG)
MaqvqvqpqapvavaaqpspaTNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQmrppvgprmpmyppvAPGLGQQLFYgqgppiippqVIYSFLLIDYFNALVLLMI
Disordered region (IsUnstruct)
*****************************GVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDN*****SAIDKLNGMLLNDKQVFVGPFLR***********RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDD*********ALNGKKFDDKEWYVGK************************KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFS***************MVVSKPLYVAL********************************APGLGQQLFYGQGPPIIPPQVIYSFLLIDYFNALVLLM*
Disordered Region (DISOPRED)
*****************************************LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI****************IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVG******************NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYV******************************LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL***********************************L**QLFYG*********************ALVLLMI
Disordered Region (DISEMBL)
****************QPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPRMPMYPPVAPGLGQQLFYGQGPPIIPPQVIYSFLLIDYFNALVLLMI
Disordered Region (DISPRO)
************************************FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPRMPMYPPVAPGLGQQLFYGQGPPIIPPQVIYSFLLIDYFNALVLLMI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHi
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHi
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPRMPMYPPVAPGLGQQLFYGQGPPIIPPQVIYSFLLIDYFNALVLLMI
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	467	2.2.26 [Sep-21-2011]
P42731	629	Polyadenylate-binding pro	yes	no	0.957	0.710	0.696	0.0
O64380	660	Polyadenylate-binding pro	no	no	0.935	0.662	0.565	1e-136
Q05196	682	Polyadenylate-binding pro	no	no	0.871	0.596	0.576	1e-134
P29341	636	Polyadenylate-binding pro	yes	no	0.809	0.594	0.575	1e-126
Q9EPH8	636	Polyadenylate-binding pro	yes	no	0.809	0.594	0.575	1e-126
P11940	636	Polyadenylate-binding pro	yes	no	0.809	0.594	0.575	1e-126
P61286	636	Polyadenylate-binding pro	yes	no	0.809	0.594	0.575	1e-126
Q5R8F7	636	Polyadenylate-binding pro	yes	no	0.809	0.594	0.573	1e-125
Q13310	644	Polyadenylate-binding pro	no	no	0.809	0.586	0.575	1e-125
P31209	653	Polyadenylate-binding pro	yes	no	0.800	0.572	0.555	1e-125

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

 Score =  672 bits (1733), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/461 (69%), Positives = 387/461 (83%), Gaps = 14/461 (3%)

Query: 1   MAQVQVQPQAP--VAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYD 58
           MAQVQ+Q Q P     A   +PAT+G A       A QF +TSLYVGDLD +V DSQL+D
Sbjct: 1   MAQVQLQGQTPNGSTAAVTSAPATSGGAT------ATQFGNTSLYVGDLDFNVTDSQLFD 54

Query: 59  LFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR 118
            F QMG VV+VRVCRDL TRRSLGYGYVN+    +A RA+ ELN+ PL GKPIR+MYS+R
Sbjct: 55  AFGQMGTVVTVRVCRDLVTRRSLGYGYVNFTNPQDAARAIQELNYIPLYGKPIRVMYSHR 114

Query: 119 DPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNE 178
           DP++R+SGAGNIFIKNLD+SID+KALHDTFS+FGNI+SCKVA DS GQS+GYGFVQ+ NE
Sbjct: 115 DPSVRRSGAGNIFIKNLDESIDHKALHDTFSSFGNIVSCKVAVDSSGQSKGYGFVQYANE 174

Query: 179 ESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKI 238
           ESA+ AI+KLNGMLLNDKQV+VGPFLR+QER+STA+KT+F NVYVKNL+E+TT+DDLK  
Sbjct: 175 ESAQKAIEKLNGMLLNDKQVYVGPFLRRQERDSTANKTKFTNVYVKNLAESTTDDDLKNA 234

Query: 239 FGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKY 298
           FGE+G ITS  VM+D +GKSK FGFVNF++ DDAAR+VE+LNG KFDDKEWYVG+AQKK 
Sbjct: 235 FGEYGKITSAVVMKDGEGKSKGFGFVNFENADDAARAVESLNGHKFDDKEWYVGRAQKKS 294

Query: 299 EREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN 358
           ERE EL+ ++EQ+LKE ADKF+  NLYVKNLD SISD+KLKE+FS FGT+TS KVMRDPN
Sbjct: 295 ERETELRVRYEQNLKEAADKFQSSNLYVKNLDPSISDEKLKEIFSPFGTVTSSKVMRDPN 354

Query: 359 GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQ----- 413
           G S+GSGFVAF+T EEA++A+++++GKM+ SKPLYVA+AQRKE+RR RLQAQFSQ     
Sbjct: 355 GTSKGSGFVAFATPEEATEAMSQLSGKMIESKPLYVAIAQRKEDRRVRLQAQFSQVRPVA 414

Query: 414 MRPPVGPRMPMYPPVAPGLGQQLFYGQGPP-IIPPQVIYSF 453
           M+P VGPRMP+YPP  PG+GQQ+FYGQ PP +IPPQ  Y +
Sbjct: 415 MQPSVGPRMPVYPPGGPGIGQQMFYGQAPPAMIPPQPGYGY 455

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

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

 Score =  486 bits (1252), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 258/456 (56%), Positives = 323/456 (70%), Gaps = 19/456 (4%)

Query: 5   QVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMG 64
           Q   Q PV++   PSP          V D +   ++SLY GDLD  V ++ L+DLF  + 
Sbjct: 24  QTSVQVPVSIPL-PSPVV--------VAD-QTHPNSSLYAGDLDPKVTEAHLFDLFKHVA 73

Query: 65  QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRK 124
            VVSVRVCRD   RRSLGY Y+N++  ++A RA++ LN+TPL  +PIRIM S RDP+ R 
Sbjct: 74  NVVSVRVCRD-QNRRSLGYAYINFSNPNDAYRAMEALNYTPLFDRPIRIMLSNRDPSTRL 132

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           SG GNIFIKNLD SIDNKAL +TFS+FG ILSCKVA D  G+S+GYGFVQF+ EESA++A
Sbjct: 133 SGKGNIFIKNLDASIDNKALFETFSSFGTILSCKVAMDVTGRSKGYGFVQFEKEESAQAA 192

Query: 185 IDKLNGMLLNDKQVFVGPFLRKQER--ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEF 242
           IDKLNGML+NDKQVFVG F+R+QER  +      RF NVYVKNL +   ED+L+K FG+F
Sbjct: 193 IDKLNGMLMNDKQVFVGHFIRRQERARDENTPTPRFTNVYVKNLPKEIGEDELRKTFGKF 252

Query: 243 GIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREM 302
           G+I+S  VMRD  G S+CFGFVNF+  + AA +VE +NG    D   YVG+AQKK ERE 
Sbjct: 253 GVISSAVVMRDQSGNSRCFGFVNFECTEAAASAVEKMNGISLGDDVLYVGRAQKKSEREE 312

Query: 303 ELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISR 362
           EL+ KFEQ      +K +G NLY+KNLDDS+ D+KLKE+FSE+G +TS KVM +P G+SR
Sbjct: 313 ELRRKFEQERINRFEKSQGANLYLKNLDDSVDDEKLKEMFSEYGNVTSSKVMLNPQGMSR 372

Query: 363 GSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPRM 422
           G GFVA+S  EEA +AL+EMNGKM+  KPLY+ALAQRKE+RRA LQA FSQ+R P GP  
Sbjct: 373 GFGFVAYSNPEEALRALSEMNGKMIGRKPLYIALAQRKEDRRAHLQALFSQIRAP-GPMS 431

Query: 423 PMY---PPVAPGLGQQLFYGQ-GPPIIPPQVI-YSF 453
             +       PG  Q ++ GQ G  ++P Q I Y F
Sbjct: 432 GFHHPPGGPMPGPPQHMYVGQNGASMVPSQPIGYGF 467

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 =  478 bits (1230), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 245/425 (57%), Positives = 313/425 (73%), Gaps = 18/425 (4%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           ++SLYVGDLD SVN+S L DLFNQ+  V ++RVCRDL T RSLGY YVN+    +A+RA+
Sbjct: 58  NSSLYVGDLDPSVNESHLLDLFNQVAPVHNLRVCRDL-THRSLGYAYVNFANPEDASRAM 116

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCK 158
           + LN+ P+  +PIRIM S RDP+ R SG GN+FIKNLD SIDNKAL++TFS+FG ILSCK
Sbjct: 117 ESLNYAPIRDRPIRIMLSNRDPSTRLSGKGNVFIKNLDASIDNKALYETFSSFGTILSCK 176

Query: 159 VATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQER---ESTADK 215
           VA D +G+S+GYGFVQF+ EE+A++AIDKLNGMLLNDKQVFVG F+R+Q+R   ES A  
Sbjct: 177 VAMDVVGRSKGYGFVQFEKEETAQAAIDKLNGMLLNDKQVFVGHFVRRQDRARSESGAVP 236

Query: 216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARS 275
           + F NVYVKNL +  T+D+LKK FG++G I+S  VM+D  G S+ FGFVNF  P+ AA +
Sbjct: 237 S-FTNVYVKNLPKEITDDELKKTFGKYGDISSAVVMKDQSGNSRSFGFVNFVSPEAAAVA 295

Query: 276 VEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISD 335
           VE +NG    +   YVG+AQKK +RE EL+ KFEQ      +K +G NLY+KNLDDS++D
Sbjct: 296 VEKMNGISLGEDVLYVGRAQKKSDREEELRRKFEQERISRFEKLQGSNLYLKNLDDSVND 355

Query: 336 DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA 395
           +KLKE+FSE+G +TSCKVM +  G+SRG GFVA+S  EEA  A+ EMNGKM+  KPLYVA
Sbjct: 356 EKLKEMFSEYGNVTSCKVMMNSQGLSRGFGFVAYSNPEEALLAMKEMNGKMIGRKPLYVA 415

Query: 396 LAQRKEERRARLQAQFSQMRPPVGPRMPM---------YPPVAP--GLGQQLFYGQ-GPP 443
           LAQRKEER+A LQ+ F+Q+R P G   P+         +PP  P  G    +F G  G  
Sbjct: 416 LAQRKEERQAHLQSLFTQIRSP-GTMSPVPSPMSGFHHHPPGGPMSGPHHPMFIGHNGQG 474

Query: 444 IIPPQ 448
           ++P Q
Sbjct: 475 LVPSQ 479

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 =  451 bits (1161), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 220/382 (57%), Positives = 288/382 (75%), Gaps = 4/382 (1%)

Query: 34  ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
           A  +   SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +
Sbjct: 5   APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64

Query: 94  ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
           A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct: 65  AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124

Query: 154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST- 212
           ILSCKV  D  G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+  
Sbjct: 125 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183

Query: 213 -ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
            A    F NVY+KN  E   ++ LK++FG+FG   S  VM D  GKSK FGFV+F+  +D
Sbjct: 184 GARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDESGKSKGFGFVSFERHED 243

Query: 272 AARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDD 331
           A ++V+ +NGK+ + K+ YVG+AQKK ER+ ELK KFEQ  ++   +++G+NLYVKNLDD
Sbjct: 244 AQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDD 303

Query: 332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
            I D++L++ FS FGTITS KVM +  G S+G GFV FS+ EEA+KA+TEMNG++V +KP
Sbjct: 304 GIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP 362

Query: 392 LYVALAQRKEERRARLQAQFSQ 413
           LYVALAQRKEER+A L  Q+ Q
Sbjct: 363 LYVALAQRKEERQAHLTNQYMQ 384

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|Q9EPH8|PABP1_RAT Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=2 SV=1

 Score =  451 bits (1160), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 220/382 (57%), Positives = 288/382 (75%), Gaps = 4/382 (1%)

Query: 34  ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
           A  +   SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +
Sbjct: 5   APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64

Query: 94  ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
           A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct: 65  AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124

Query: 154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST- 212
           ILSCKV  D  G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+  
Sbjct: 125 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183

Query: 213 -ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
            A    F NVY+KN  E   ++ LK++FG+FG   S  VM D  GKSK FGFV+F+  +D
Sbjct: 184 GARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDESGKSKGFGFVSFERHED 243

Query: 272 AARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDD 331
           A ++V+ +NGK+ + K+ YVG+AQKK ER+ ELK KFEQ  ++   +++G+NLYVKNLDD
Sbjct: 244 AQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDD 303

Query: 332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
            I D++L++ FS FGTITS KVM +  G S+G GFV FS+ EEA+KA+TEMNG++V +KP
Sbjct: 304 GIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP 362

Query: 392 LYVALAQRKEERRARLQAQFSQ 413
           LYVALAQRKEER+A L  Q+ Q
Sbjct: 363 LYVALAQRKEERQAHLTNQYMQ 384

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.

Rattus norvegicus (taxid: 10116)

>sp|P11940|PABP1_HUMAN Polyadenylate-binding protein 1 OS=Homo sapiens GN=PABPC1 PE=1 SV=2

 Score =  450 bits (1158), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 220/382 (57%), Positives = 287/382 (75%), Gaps = 4/382 (1%)

Query: 34  ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
           A  +   SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +
Sbjct: 5   APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64

Query: 94  ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
           A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct: 65  AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124

Query: 154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST- 212
           ILSCKV  D  G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+  
Sbjct: 125 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183

Query: 213 -ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
            A    F NVY+KN  E   ++ LK +FG+FG   S  VM D  GKSK FGFV+F+  +D
Sbjct: 184 GARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHED 243

Query: 272 AARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDD 331
           A ++V+ +NGK+ + K+ YVG+AQKK ER+ ELK KFEQ  ++   +++G+NLYVKNLDD
Sbjct: 244 AQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDD 303

Query: 332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
            I D++L++ FS FGTITS KVM +  G S+G GFV FS+ EEA+KA+TEMNG++V +KP
Sbjct: 304 GIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP 362

Query: 392 LYVALAQRKEERRARLQAQFSQ 413
           LYVALAQRKEER+A L  Q+ Q
Sbjct: 363 LYVALAQRKEERQAHLTNQYMQ 384

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.

Homo sapiens (taxid: 9606)

>sp|P61286|PABP1_BOVIN Polyadenylate-binding protein 1 OS=Bos taurus GN=PABPC1 PE=2 SV=1

 Score =  450 bits (1158), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 220/382 (57%), Positives = 287/382 (75%), Gaps = 4/382 (1%)

Query: 34  ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
           A  +   SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +
Sbjct: 5   APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64

Query: 94  ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
           A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct: 65  AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124

Query: 154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST- 212
           ILSCKV  D  G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+  
Sbjct: 125 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183

Query: 213 -ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
            A    F NVY+KN  E   ++ LK +FG+FG   S  VM D  GKSK FGFV+F+  +D
Sbjct: 184 GARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHED 243

Query: 272 AARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDD 331
           A ++V+ +NGK+ + K+ YVG+AQKK ER+ ELK KFEQ  ++   +++G+NLYVKNLDD
Sbjct: 244 AQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDD 303

Query: 332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
            I D++L++ FS FGTITS KVM +  G S+G GFV FS+ EEA+KA+TEMNG++V +KP
Sbjct: 304 GIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP 362

Query: 392 LYVALAQRKEERRARLQAQFSQ 413
           LYVALAQRKEER+A L  Q+ Q
Sbjct: 363 LYVALAQRKEERQAHLTNQYMQ 384

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.

Bos taurus (taxid: 9913)

>sp|Q5R8F7|PABP1_PONAB Polyadenylate-binding protein 1 OS=Pongo abelii GN=PABPC1 PE=2 SV=1

 Score =  449 bits (1155), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 219/382 (57%), Positives = 286/382 (74%), Gaps = 4/382 (1%)

Query: 34  ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
           A  +   SLYVGDL     ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +
Sbjct: 5   APSYPMASLYVGDLHPDATEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64

Query: 94  ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
           A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct: 65  AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124

Query: 154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST- 212
           ILSCKV  D  G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+  
Sbjct: 125 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183

Query: 213 -ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
            A    F NVY+KN  E   ++ LK +FG+FG   S  VM D  GKSK FGFV+F+  +D
Sbjct: 184 GARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHED 243

Query: 272 AARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDD 331
           A ++V+ +NGK+ + K+ YVG+AQKK ER+ ELK KFEQ  ++   +++G+NLYVKNLDD
Sbjct: 244 AQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDD 303

Query: 332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
            I D++L++ FS FGTITS KVM +  G S+G GFV FS+ EEA+KA+TEMNG++V +KP
Sbjct: 304 GIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP 362

Query: 392 LYVALAQRKEERRARLQAQFSQ 413
           LYVALAQRKEER+A L  Q+ Q
Sbjct: 363 LYVALAQRKEERQAHLTNQYMQ 384

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.

Pongo abelii (taxid: 9601)

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

 Score =  448 bits (1152), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 220/382 (57%), Positives = 287/382 (75%), Gaps = 4/382 (1%)

Query: 34  ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
           A  +   SLYVGDL   V ++ LY+ F+  G V+S+RVCRD+ TRRSLGY YVN+    +
Sbjct: 5   ASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPAD 64

Query: 94  ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
           A RALD +NF  + GKPIRIM+S RDP++RKSG GN+FIKNLDKSIDNKAL+DTFS FGN
Sbjct: 65  AERALDTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGN 124

Query: 154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST- 212
           ILSCKV  D  G S+GY FV F+ +E+A  AI+K+NGMLLND++VFVG F  ++ERE+  
Sbjct: 125 ILSCKVVCDENG-SKGYAFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183

Query: 213 -ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
            A    F NVY+KN  E   ++ LK++F +FG   S  VMRD +GKSK FGFV+++  +D
Sbjct: 184 GAKAKEFTNVYIKNFGEEVDDESLKELFSQFGKTLSVKVMRDPNGKSKGFGFVSYEKHED 243

Query: 272 AARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDD 331
           A ++VE +NGK+   K  +VG+AQKK ER+ ELK KFEQ  +E   +++G+NLY+KNLDD
Sbjct: 244 ANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKFEQLKQERISRYQGVNLYIKNLDD 303

Query: 332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
           +I D+KL++ FS FG+ITS KVM + +G S+G GFV FS+ EEA+KA+TEMNG++V SKP
Sbjct: 304 TIDDEKLRKEFSPFGSITSAKVMLE-DGRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKP 362

Query: 392 LYVALAQRKEERRARLQAQFSQ 413
           LYVALAQRKEER+A L  Q+ Q
Sbjct: 363 LYVALAQRKEERKAHLTNQYMQ 384

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

 Score =  447 bits (1149), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 209/376 (55%), Positives = 285/376 (75%), Gaps = 2/376 (0%)

Query: 38  VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
            S SLYVG+LD SV ++ L++LFN +G V S+RVCRD  TRRSLGY YVN++   +  +A
Sbjct: 78  TSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKA 137

Query: 98  LDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSC 157
           LDELN+T + G+P RIM+S RDP++RK G GN+FIKNLD +IDNKALHDTFS FG ILSC
Sbjct: 138 LDELNYTLIKGRPCRIMWSQRDPSLRKMGTGNVFIKNLDPAIDNKALHDTFSAFGKILSC 197

Query: 158 KVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTAD--K 215
           KVA D LG ++GYGFV FD+ ESA +AI+ +NGMLLNDK+V+VG  + ++ER+S  +  K
Sbjct: 198 KVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHHVSRRERQSKVEALK 257

Query: 216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARS 275
             F NVY+KNL    TE +   +FG+FG ITS ++++D + K + FGFVN+ + + A ++
Sbjct: 258 ANFTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKA 317

Query: 276 VEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISD 335
           V+ LN K++  K+ YVG+AQKK+ERE EL+ ++EQ   E  +K++G+NL++KNL D + D
Sbjct: 318 VDELNDKEYKGKKLYVGRAQKKHEREEELRKRYEQMKLEKMNKYQGVNLFIKNLQDEVDD 377

Query: 336 DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA 395
           ++LK  FS FGTITS K+M D  G S+G GFV ++T EEA+KA+TEMN +M+  KPLYVA
Sbjct: 378 ERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVA 437

Query: 396 LAQRKEERRARLQAQF 411
           LAQRKE RR++L+AQ 
Sbjct: 438 LAQRKEVRRSQLEAQI 453

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

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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	467
359386152	652	poly A-binding protein 2 [Citrus sinensi	0.970	0.694	0.988	0.0
317106693	642	JHL03K20.3 [Jatropha curcas]	0.946	0.688	0.810	0.0
317106694	642	JHL03K20.4 [Jatropha curcas]	0.946	0.688	0.801	0.0
225438781	654	PREDICTED: polyadenylate-binding protein	0.895	0.639	0.818	0.0
356499763	646	PREDICTED: polyadenylate-binding protein	0.944	0.682	0.760	0.0
302142286	621	unnamed protein product [Vitis vinifera]	0.922	0.694	0.782	0.0
225458678	640	PREDICTED: polyadenylate-binding protein	0.922	0.673	0.782	0.0
356521524	651	PREDICTED: polyadenylate-binding protein	0.950	0.682	0.760	0.0
386780450	657	poly(A)-binding protein [Nicotiana tabac	0.965	0.686	0.753	0.0
357475273	654	Poly(A)-binding protein [Medicago trunca	0.957	0.683	0.762	0.0

>gi|359386152|gb|AEV43365.1| poly A-binding protein 2 [Citrus sinensis]

 Score =  924 bits (2389), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 448/453 (98%), Positives = 450/453 (99%)

Query: 1   MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLF 60
           MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLF
Sbjct: 1   MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLF 60

Query: 61  NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP 120
           NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP
Sbjct: 61  NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP 120

Query: 121 TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEES 180
           TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEES
Sbjct: 121 TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEES 180

Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240
           AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG
Sbjct: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240

Query: 241 EFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           EFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER
Sbjct: 241 EFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300

Query: 301 EMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI 360
           EMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI
Sbjct: 301 EMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI 360

Query: 361 SRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGP 420
           SRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGP
Sbjct: 361 SRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGP 420

Query: 421 RMPMYPPVAPGLGQQLFYGQGPPIIPPQVIYSF 453
           RMPMYPPVAPGLGQQLFYGQGPPIIPPQ  + +
Sbjct: 421 RMPMYPPVAPGLGQQLFYGQGPPIIPPQPGFGY 453

Source: Citrus sinensis

Species: Citrus sinensis

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|317106693|dbj|BAJ53194.1| JHL03K20.3 [Jatropha curcas]

 Score =  769 bits (1986), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/458 (81%), Positives = 412/458 (89%), Gaps = 16/458 (3%)

Query: 1   MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLF 60
           M+QVQ QPQ PV+       A  G+A+NGG     QFVSTSLYVGDL+ +V ++QLYDLF
Sbjct: 1   MSQVQSQPQGPVS-------APVGMASNGG----NQFVSTSLYVGDLEQNVTETQLYDLF 49

Query: 61  NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP 120
           NQ+GQ+VS+RVCRDL++RRSLGYGYVNYN  H+A +AL+ LNFTP+NGKPIRIMYSYRDP
Sbjct: 50  NQLGQIVSIRVCRDLTSRRSLGYGYVNYNNVHDAAQALEVLNFTPVNGKPIRIMYSYRDP 109

Query: 121 TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEES 180
           TIRKSGAGNI+IKNLDK+IDNKALHDTFS FGNILSCKVATDS GQS GYGFVQFDNEES
Sbjct: 110 TIRKSGAGNIYIKNLDKAIDNKALHDTFSAFGNILSCKVATDSAGQSLGYGFVQFDNEES 169

Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240
           AK+AIDKLNGMLLNDKQV+VGPFLR+QERES  DKT+FNNVYVKNLSETTTE+DLKKIFG
Sbjct: 170 AKNAIDKLNGMLLNDKQVYVGPFLRRQERESGTDKTKFNNVYVKNLSETTTEEDLKKIFG 229

Query: 241 EFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           E+G ITS  VMRD DGKS+CFGFVNF++PDDAARSVEALNGK FD+KEWYVGKAQKK ER
Sbjct: 230 EYGAITSAVVMRDGDGKSRCFGFVNFENPDDAARSVEALNGKTFDEKEWYVGKAQKKSER 289

Query: 301 EMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI 360
           E+ELKG+FEQ+LKET DKFEGLNLYVKNLDDSI+DDKLKELFSEFGTITSCKVMRDPNG+
Sbjct: 290 EVELKGQFEQTLKETVDKFEGLNLYVKNLDDSITDDKLKELFSEFGTITSCKVMRDPNGV 349

Query: 361 SRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR----P 416
           S+GSGFVA+STAEEASKALTEMNGKM+VSKPLYVALAQRKEERRARLQAQFSQMR    P
Sbjct: 350 SKGSGFVAYSTAEEASKALTEMNGKMIVSKPLYVALAQRKEERRARLQAQFSQMRPAMAP 409

Query: 417 PVGPRMPMYPPVAPGLGQQLFYGQGPP-IIPPQVIYSF 453
            VGPRMPMYP   PG+GQQLFYGQGPP I+PPQ  + +
Sbjct: 410 AVGPRMPMYPHGTPGIGQQLFYGQGPPAIVPPQPGFGY 447

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|317106694|dbj|BAJ53195.1| JHL03K20.4 [Jatropha curcas]

 Score =  766 bits (1979), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 367/458 (80%), Positives = 410/458 (89%), Gaps = 16/458 (3%)

Query: 1   MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLF 60
           MAQVQVQPQAPV+       A NG+ +NG      QFV TSLYVGDL+ +V ++QLYDLF
Sbjct: 1   MAQVQVQPQAPVS-------APNGVVSNG----VNQFVPTSLYVGDLEQNVTETQLYDLF 49

Query: 61  NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP 120
           NQ GQVVS+RVCRDL++RRSLGYGYVNYN  H+A +A++ LNFTP+NGKPIRIMYSYRDP
Sbjct: 50  NQHGQVVSIRVCRDLTSRRSLGYGYVNYNNVHDAAQAIEVLNFTPVNGKPIRIMYSYRDP 109

Query: 121 TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEES 180
           TIRKSG GNI+IKNLDK+IDNKALHDTFS FG+ILSCKVATDSLGQS GYGFVQFDNEES
Sbjct: 110 TIRKSGTGNIYIKNLDKAIDNKALHDTFSAFGSILSCKVATDSLGQSLGYGFVQFDNEES 169

Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240
           AK+AIDKLNGMLLNDKQV+VGPFLRKQERES  DK  FNNVYVKNLSETTTE+DLKKIFG
Sbjct: 170 AKNAIDKLNGMLLNDKQVYVGPFLRKQERESAIDKATFNNVYVKNLSETTTEEDLKKIFG 229

Query: 241 EFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           E+G ITS  VMRD +GKS+CFGFVNF++PDDAA+SVEALNGK FD+KEWYVGKAQKK ER
Sbjct: 230 EYGTITSAVVMRDGNGKSRCFGFVNFENPDDAAQSVEALNGKTFDEKEWYVGKAQKKSER 289

Query: 301 EMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI 360
           E+ELKG+FEQ+LKET DKF+GLNLYVKNLDDSI+DDKLKELFSEFGTITSCKVMRDPNG+
Sbjct: 290 EVELKGRFEQTLKETVDKFQGLNLYVKNLDDSITDDKLKELFSEFGTITSCKVMRDPNGV 349

Query: 361 SRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR----P 416
           SRGSGFVAFSTAEEAS+ALTEMNGKMVVSKPLYVALAQRKEERRARLQAQ+SQ+R    P
Sbjct: 350 SRGSGFVAFSTAEEASRALTEMNGKMVVSKPLYVALAQRKEERRARLQAQYSQIRPAMAP 409

Query: 417 PVGPRMPMYPPVAPGLGQQLFYGQGPP-IIPPQVIYSF 453
           P+GPRMP+YPP  PG+G QLFYGQGPP I+PPQ  + +
Sbjct: 410 PIGPRMPIYPPGTPGIGHQLFYGQGPPAIVPPQPGFGY 447

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225438781|ref|XP_002283105.1| PREDICTED: polyadenylate-binding protein 2 [Vitis vinifera] gi|296082381|emb|CBI21386.3| unnamed protein product [Vitis vinifera]

 Score =  721 bits (1862), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 347/424 (81%), Positives = 382/424 (90%), Gaps = 6/424 (1%)

Query: 36  QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEAT 95
           QFVSTSLYVGDL+ +V DS LYDLF Q+G VVSVRVCRDLSTRRSLGYGYVNY    +A 
Sbjct: 28  QFVSTSLYVGDLESNVTDSHLYDLFGQLGPVVSVRVCRDLSTRRSLGYGYVNYGNTQDAA 87

Query: 96  RALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNIL 155
           RALD LNFTPLNGKPIRIMYS+RDP+IR+SG  NIFIKNLDK+IDNKAL+DTFSTFG IL
Sbjct: 88  RALDMLNFTPLNGKPIRIMYSFRDPSIRRSGTANIFIKNLDKAIDNKALYDTFSTFGAIL 147

Query: 156 SCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADK 215
           SCK+ATD+ GQS+GYGFVQFDNEESAK+A DKLNGMLLNDKQV+VGPF+RKQERES  +K
Sbjct: 148 SCKIATDASGQSKGYGFVQFDNEESAKNATDKLNGMLLNDKQVYVGPFVRKQERESATNK 207

Query: 216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARS 275
           T+FNNVYVKNL E+TT++DLK IFGE+G ITS  VM+D DGKSKCFGFVNF++ DDAARS
Sbjct: 208 TKFNNVYVKNLLESTTDEDLKNIFGEYGPITSAVVMQDGDGKSKCFGFVNFENADDAARS 267

Query: 276 VEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISD 335
           VEALNGKKFDDKEWYVGKAQKK ERE+ELKG+FEQSLKE  DKF+GLNLYVKNLDDSI+D
Sbjct: 268 VEALNGKKFDDKEWYVGKAQKKTEREVELKGRFEQSLKEAVDKFQGLNLYVKNLDDSIAD 327

Query: 336 DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA 395
           DKL+ELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEAS+AL +MNGKMV SKPLYVA
Sbjct: 328 DKLRELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASRALADMNGKMVASKPLYVA 387

Query: 396 LAQRKEERRARLQAQFSQMRPP-----VGPRMPMYPPVAPGLGQQLFYGQGPP-IIPPQV 449
           LAQRKE+RRARLQAQFSQMRP      VGPRM MYPP APGLGQQLFYGQGPP +IPPQ 
Sbjct: 388 LAQRKEDRRARLQAQFSQMRPAAMAPSVGPRMSMYPPGAPGLGQQLFYGQGPPALIPPQP 447

Query: 450 IYSF 453
            + +
Sbjct: 448 GFGY 451

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356499763|ref|XP_003518706.1| PREDICTED: polyadenylate-binding protein 2-like [Glycine max]

 Score =  716 bits (1849), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 349/459 (76%), Positives = 392/459 (85%), Gaps = 18/459 (3%)

Query: 1   MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLF 60
           MAQVQV PQ  +                 G     QFV+TSLYVGDLD +V D+QLYDLF
Sbjct: 1   MAQVQVPPQNAIPGPNG------------GGAAGNQFVTTSLYVGDLDPNVTDAQLYDLF 48

Query: 61  NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP 120
           NQ+GQVVSVRVCRDL++RRSLGYGYVN++   +A RALD LNFTPLN +PIRIMYS+RDP
Sbjct: 49  NQLGQVVSVRVCRDLTSRRSLGYGYVNFSNPQDAARALDVLNFTPLNNRPIRIMYSHRDP 108

Query: 121 TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEES 180
           +IRKSG GNIFIKNLD++ID+KALHDTFSTFGNILSCKVATDS GQS+GYGFVQFDNEES
Sbjct: 109 SIRKSGQGNIFIKNLDRAIDHKALHDTFSTFGNILSCKVATDSSGQSKGYGFVQFDNEES 168

Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240
           A+ AI+KLNGMLLNDKQV+VGPFLRKQERESTADK +FNNV+VKNLSE+TT+D+LK +FG
Sbjct: 169 AQKAIEKLNGMLLNDKQVYVGPFLRKQERESTADKAKFNNVFVKNLSESTTDDELKNVFG 228

Query: 241 EFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           EFG ITS  VMRD DGKSKCFGFVNF++ DDAAR+VEALNGKKFDDKEWYVGKAQKK ER
Sbjct: 229 EFGTITSAVVMRDGDGKSKCFGFVNFENADDAARAVEALNGKKFDDKEWYVGKAQKKSER 288

Query: 301 EMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI 360
           E ELK +FEQS+KE ADK++G NLYVKNLDDS+ DDKLKELFS FGTITSCKVMRDPNGI
Sbjct: 289 ENELKQRFEQSMKEAADKYQGANLYVKNLDDSLGDDKLKELFSPFGTITSCKVMRDPNGI 348

Query: 361 SRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR----- 415
           SRGSGFVAFST +EAS+AL EMNGKMVVSKPLYV LAQRKE+RRARLQAQF+QMR     
Sbjct: 349 SRGSGFVAFSTPDEASRALLEMNGKMVVSKPLYVTLAQRKEDRRARLQAQFAQMRPVGMP 408

Query: 416 PPVGPRMPMYPPVAPGLGQQLFYGQGPP-IIPPQVIYSF 453
           P VGPR+PMYPP  PG+GQQ+FY QGPP IIP Q  + +
Sbjct: 409 PSVGPRVPMYPPGGPGIGQQIFYAQGPPAIIPSQPGFGY 447

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302142286|emb|CBI19489.3| unnamed protein product [Vitis vinifera]

 Score =  716 bits (1848), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 359/459 (78%), Positives = 396/459 (86%), Gaps = 28/459 (6%)

Query: 1   MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLF 60
           MAQ+Q       A  A P    NG+AN           + SLYVGDLD+++ DSQLYDLF
Sbjct: 1   MAQIQ-------AAVAGP----NGVAN-----------TASLYVGDLDVNITDSQLYDLF 38

Query: 61  NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP 120
            Q GQV+SVRVCRDLSTRRSLGYGYVNY+   +A RALD LNFTPLNGKPIRIMYS+RDP
Sbjct: 39  IQAGQVLSVRVCRDLSTRRSLGYGYVNYSNPQDAARALDLLNFTPLNGKPIRIMYSHRDP 98

Query: 121 TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEES 180
           +IRKSG  NIFIKNLDKSIDNKALHDTFS FGNILSCK+ATD  GQS+GYGFVQFDNEES
Sbjct: 99  SIRKSGTANIFIKNLDKSIDNKALHDTFSAFGNILSCKIATDPSGQSKGYGFVQFDNEES 158

Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240
           A++AIDKLNGML+NDKQV+VG FLRKQERE+  +KT+FNNVYVKNLSE+TTE+DLK IFG
Sbjct: 159 AQNAIDKLNGMLINDKQVYVGQFLRKQERETALNKTKFNNVYVKNLSESTTEEDLKNIFG 218

Query: 241 EFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           EFGIITS  VMRD DGKSKCFGFVNF++ DDAA +VEALNGKKFD+KEWYVGKAQKKYER
Sbjct: 219 EFGIITSVVVMRDGDGKSKCFGFVNFENADDAAEAVEALNGKKFDEKEWYVGKAQKKYER 278

Query: 301 EMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI 360
           E+ELKG+FEQS+KE  DKF+G+NLY+KNLDDSI DDKLKELFSEFGTITSCKVMRDP+GI
Sbjct: 279 ELELKGRFEQSMKEVVDKFQGVNLYIKNLDDSIGDDKLKELFSEFGTITSCKVMRDPSGI 338

Query: 361 SRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR----- 415
           SRGSGFVAFST+EEAS+ALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR     
Sbjct: 339 SRGSGFVAFSTSEEASRALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPVSMA 398

Query: 416 PPVGPRMPMYPPVAPGLGQQLFYGQGPP-IIPPQVIYSF 453
           P V PRMPMYPP APGLGQQLFYGQGPP IIPPQ  + +
Sbjct: 399 PSVAPRMPMYPPGAPGLGQQLFYGQGPPAIIPPQAGFGY 437

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225458678|ref|XP_002284923.1| PREDICTED: polyadenylate-binding protein 2 [Vitis vinifera] gi|147773643|emb|CAN76464.1| hypothetical protein VITISV_017035 [Vitis vinifera]

 Score =  716 bits (1847), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 359/459 (78%), Positives = 396/459 (86%), Gaps = 28/459 (6%)

Query: 1   MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLF 60
           MAQ+Q       A  A P    NG+AN           + SLYVGDLD+++ DSQLYDLF
Sbjct: 1   MAQIQ-------AAVAGP----NGVAN-----------TASLYVGDLDVNITDSQLYDLF 38

Query: 61  NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP 120
            Q GQV+SVRVCRDLSTRRSLGYGYVNY+   +A RALD LNFTPLNGKPIRIMYS+RDP
Sbjct: 39  IQAGQVLSVRVCRDLSTRRSLGYGYVNYSNPQDAARALDLLNFTPLNGKPIRIMYSHRDP 98

Query: 121 TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEES 180
           +IRKSG  NIFIKNLDKSIDNKALHDTFS FGNILSCK+ATD  GQS+GYGFVQFDNEES
Sbjct: 99  SIRKSGTANIFIKNLDKSIDNKALHDTFSAFGNILSCKIATDPSGQSKGYGFVQFDNEES 158

Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240
           A++AIDKLNGML+NDKQV+VG FLRKQERE+  +KT+FNNVYVKNLSE+TTE+DLK IFG
Sbjct: 159 AQNAIDKLNGMLINDKQVYVGQFLRKQERETALNKTKFNNVYVKNLSESTTEEDLKNIFG 218

Query: 241 EFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           EFGIITS  VMRD DGKSKCFGFVNF++ DDAA +VEALNGKKFD+KEWYVGKAQKKYER
Sbjct: 219 EFGIITSVVVMRDGDGKSKCFGFVNFENADDAAEAVEALNGKKFDEKEWYVGKAQKKYER 278

Query: 301 EMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI 360
           E+ELKG+FEQS+KE  DKF+G+NLY+KNLDDSI DDKLKELFSEFGTITSCKVMRDP+GI
Sbjct: 279 ELELKGRFEQSMKEVVDKFQGVNLYIKNLDDSIGDDKLKELFSEFGTITSCKVMRDPSGI 338

Query: 361 SRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR----- 415
           SRGSGFVAFST+EEAS+ALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR     
Sbjct: 339 SRGSGFVAFSTSEEASRALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPVSMA 398

Query: 416 PPVGPRMPMYPPVAPGLGQQLFYGQGPP-IIPPQVIYSF 453
           P V PRMPMYPP APGLGQQLFYGQGPP IIPPQ  + +
Sbjct: 399 PSVAPRMPMYPPGAPGLGQQLFYGQGPPAIIPPQAGFGY 437

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521524|ref|XP_003529405.1| PREDICTED: polyadenylate-binding protein 2-like [Glycine max]

 Score =  711 bits (1835), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 349/459 (76%), Positives = 390/459 (84%), Gaps = 15/459 (3%)

Query: 1   MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLF 60
           MAQVQV PQ  +                G  G   QFV+TSLYVGDLD +V D+QLYDLF
Sbjct: 1   MAQVQVPPQNAMPGPN---------GGGGAGGAGNQFVTTSLYVGDLDPNVTDAQLYDLF 51

Query: 61  NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP 120
           NQ+GQVVSVRVCRDL++RRSLGYGYVN++   +A RALD LNFTPLN +PIRIMYS+RDP
Sbjct: 52  NQLGQVVSVRVCRDLTSRRSLGYGYVNFSNPQDAARALDVLNFTPLNNRPIRIMYSHRDP 111

Query: 121 TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEES 180
           +IRKSG GNIFIKNLD++ID+KALHDTFSTFGNILSCKVATDS GQS+GYGFVQFDNEES
Sbjct: 112 SIRKSGQGNIFIKNLDRAIDHKALHDTFSTFGNILSCKVATDSSGQSKGYGFVQFDNEES 171

Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240
           A+ AI+KLNGMLLNDKQV+VGPFLRKQERES ADK +FNNV+VKNLSE+TT+D+LK  FG
Sbjct: 172 AQKAIEKLNGMLLNDKQVYVGPFLRKQERESAADKAKFNNVFVKNLSESTTDDELKNTFG 231

Query: 241 EFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           EFG ITS  VMRD DGKSKCFGFVNF++ DDAAR+VEALNGK FDDKEWYVGKAQKK ER
Sbjct: 232 EFGTITSAVVMRDGDGKSKCFGFVNFENADDAARAVEALNGKNFDDKEWYVGKAQKKSER 291

Query: 301 EMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI 360
           E ELK +FEQS+KE ADK++G NLYVKNLDDSI D+KLKELFS FGTITSCKVMRDPNG+
Sbjct: 292 ENELKQRFEQSMKEAADKYQGANLYVKNLDDSIGDEKLKELFSPFGTITSCKVMRDPNGL 351

Query: 361 SRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR----- 415
           SRGSGFVAFST EEAS+AL EMNGKMVVSKPLYV LAQRKE+RRARLQAQF+QMR     
Sbjct: 352 SRGSGFVAFSTPEEASRALLEMNGKMVVSKPLYVTLAQRKEDRRARLQAQFAQMRPVGMP 411

Query: 416 PPVGPRMPMYPPVAPGLGQQLFYGQGPP-IIPPQVIYSF 453
           P VGPR+PMYPP  PG+GQQLFY QGPP IIP Q  + +
Sbjct: 412 PSVGPRVPMYPPGGPGIGQQLFYSQGPPAIIPSQPGFGY 450

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|386780450|dbj|BAM15222.1| poly(A)-binding protein [Nicotiana tabacum]

 Score =  710 bits (1833), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 346/459 (75%), Positives = 398/459 (86%), Gaps = 8/459 (1%)

Query: 1   MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLF 60
           MAQ+QVQ Q+PVA       A  G A            STSLYVGDL+ +V DSQLYDLF
Sbjct: 1   MAQIQVQHQSPVAGGNGVVAAAVGGAAAVATPGG--LTSTSLYVGDLEFNVTDSQLYDLF 58

Query: 61  NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP 120
           NQ+GQVVSVRVCRDLSTRRSLGYGYVNY+  ++A+RA++ LNFTP+NGK IR+MYS+RDP
Sbjct: 59  NQVGQVVSVRVCRDLSTRRSLGYGYVNYSNPNDASRAMEMLNFTPVNGKSIRVMYSHRDP 118

Query: 121 TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEES 180
           T+RKSG+ NIFIKNLDKSIDNKALHDTFS+FGNILSCK+ATDS GQS+GYGFVQ+DNEES
Sbjct: 119 TLRKSGSANIFIKNLDKSIDNKALHDTFSSFGNILSCKIATDSNGQSKGYGFVQYDNEES 178

Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240
           A+ AIDKLNGML+NDKQV+VG FLRKQEREST   T+F NVYVKNLSE+TT+D+LKK+FG
Sbjct: 179 AQGAIDKLNGMLMNDKQVYVGHFLRKQERESTTGMTKFQNVYVKNLSESTTDDELKKVFG 238

Query: 241 EFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           EFG ITS  VMRDADGKSKCFGF+NF+  +DAA++VE+LNGKKFDDKEWYVGKAQKK ER
Sbjct: 239 EFGNITSAVVMRDADGKSKCFGFINFETAEDAAKAVESLNGKKFDDKEWYVGKAQKKSER 298

Query: 301 EMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI 360
           E ELK KFEQ+ KE  DK++GLNLYVKNLDD+I D+KLKELFSEFGTITSCKVMRDP+GI
Sbjct: 299 EQELKSKFEQTAKEAVDKYQGLNLYVKNLDDTIDDEKLKELFSEFGTITSCKVMRDPSGI 358

Query: 361 SRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR----- 415
           SRGSGFVAFST+EEAS+AL+EMNGKM+VSKPLYVALAQRKEERRA+LQAQFSQ+R     
Sbjct: 359 SRGSGFVAFSTSEEASRALSEMNGKMIVSKPLYVALAQRKEERRAKLQAQFSQLRPVAMP 418

Query: 416 PPVGPRMPMYPPVAPGLGQQLFYGQGPP-IIPPQVIYSF 453
           P + PRMP+YPP APG+GQQLFYGQGPP +IPPQ  + +
Sbjct: 419 PSLAPRMPIYPPGAPGIGQQLFYGQGPPAMIPPQAGFGY 457

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357475273|ref|XP_003607922.1| Poly(A)-binding protein [Medicago truncatula] gi|355508977|gb|AES90119.1| Poly(A)-binding protein [Medicago truncatula]

 Score =  710 bits (1833), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 350/459 (76%), Positives = 390/459 (84%), Gaps = 12/459 (2%)

Query: 1   MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLF 60
           MAQVQVQPQ      A   P   G A     G    FV+TSLYVGDLD++V DSQLYDLF
Sbjct: 1   MAQVQVQPQN-----AMTGP-NGGAAAAAAAGGGGNFVTTSLYVGDLDMNVTDSQLYDLF 54

Query: 61  NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP 120
           NQ+GQVVSVRVCRDL+TRRSLGYGYVNY+   +A RALD LNFTPLN +PIRIMYS+RDP
Sbjct: 55  NQLGQVVSVRVCRDLTTRRSLGYGYVNYSNPQDAARALDVLNFTPLNNRPIRIMYSHRDP 114

Query: 121 TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEES 180
           +IRKSG GNIFIKNLDK+ID+KALHDTFS+FGNILSCKVA D  GQS+GYGFVQFD EE+
Sbjct: 115 SIRKSGQGNIFIKNLDKAIDHKALHDTFSSFGNILSCKVAVDGSGQSKGYGFVQFDTEEA 174

Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240
           A+ AI+KLNGMLLNDKQV+VGPFLRKQEREST D+ +FNNV+VKNLSE+TT+D+LKK FG
Sbjct: 175 AQKAIEKLNGMLLNDKQVYVGPFLRKQERESTGDRAKFNNVFVKNLSESTTDDELKKTFG 234

Query: 241 EFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           EFG ITS  VMRD DGKSKCFGFVNF+  DDAAR+VEALNGKK DDKEWYVGKAQKK ER
Sbjct: 235 EFGTITSAVVMRDGDGKSKCFGFVNFESTDDAARAVEALNGKKIDDKEWYVGKAQKKSER 294

Query: 301 EMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI 360
           E ELK KFEQS+KE ADK++G NLYVKNLDDSI+D+KLKELFS +GTITSCKVMRDPNG+
Sbjct: 295 EHELKIKFEQSMKEAADKYQGANLYVKNLDDSIADEKLKELFSSYGTITSCKVMRDPNGV 354

Query: 361 SRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR----- 415
           SRGSGFVAFST EEAS+AL EMNGKMV SKPLYV LAQRKE+RRARLQAQF+QMR     
Sbjct: 355 SRGSGFVAFSTPEEASRALLEMNGKMVASKPLYVTLAQRKEDRRARLQAQFAQMRPVSMP 414

Query: 416 PPVGPRMPMYPPVAPGLGQQLFYGQGPP-IIPPQVIYSF 453
           P V PRMPMYPP  PG+GQQ+FYGQGPP IIP Q  + +
Sbjct: 415 PSVAPRMPMYPPGGPGMGQQIFYGQGPPAIIPSQPGFGY 453

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	467
TAIR|locus:2124261	629	PAB2 "AT4G34110" [Arabidopsis	0.890	0.661	0.689	8e-156
TAIR|locus:2012161	671	PAB8 "AT1G49760" [Arabidopsis	0.867	0.603	0.692	1.4e-151
TAIR|locus:2058573	662	PAB4 "AT2G23350" [Arabidopsis	0.892	0.629	0.669	2e-150
TAIR|locus:2199700	660	PAB3 "poly(A) binding protein	0.800	0.566	0.620	1.7e-121
MGI|MGI:1349722	636	Pabpc1 "poly(A) binding protei	0.809	0.594	0.575	1.3e-114
RGD|619838	636	Pabpc1 "poly(A) binding protei	0.809	0.594	0.575	1.3e-114
UNIPROTKB|P61286	636	PABPC1 "Polyadenylate-binding	0.809	0.594	0.575	2.2e-114
UNIPROTKB|J9P326	636	PABPC1 "Uncharacterized protei	0.809	0.594	0.575	2.2e-114
UNIPROTKB|P11940	636	PABPC1 "Polyadenylate-binding	0.809	0.594	0.575	2.2e-114
UNIPROTKB|F2Z557	636	PABPC1 "Uncharacterized protei	0.809	0.594	0.575	2.2e-114

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

 Score = 1519 (539.8 bits), Expect = 8.0e-156, P = 8.0e-156
 Identities = 291/422 (68%), Positives = 352/422 (83%)

Query:    22 TNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSL 81
             T+  A +GG   A QF +TSLYVGDLD +V DSQL+D F QMG VV+VRVCRDL TRRSL
Sbjct:    19 TSAPATSGGA-TATQFGNTSLYVGDLDFNVTDSQLFDAFGQMGTVVTVRVCRDLVTRRSL 77

Query:    82 GYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDN 141
             GYGYVN+    +A RA+ ELN+ PL GKPIR+MYS+RDP++R+SGAGNIFIKNLD+SID+
Sbjct:    78 GYGYVNFTNPQDAARAIQELNYIPLYGKPIRVMYSHRDPSVRRSGAGNIFIKNLDESIDH 137

Query:   142 KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVG 201
             KALHDTFS+FGNI+SCKVA DS GQS+GYGFVQ+ NEESA+ AI+KLNGMLLNDKQV+VG
Sbjct:   138 KALHDTFSSFGNIVSCKVAVDSSGQSKGYGFVQYANEESAQKAIEKLNGMLLNDKQVYVG 197

Query:   202 PFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCF 261
             PFLR+QER+STA+KT+F NVYVKNL+E+TT+DDLK  FGE+G ITS  VM+D +GKSK F
Sbjct:   198 PFLRRQERDSTANKTKFTNVYVKNLAESTTDDDLKNAFGEYGKITSAVVMKDGEGKSKGF 257

Query:   262 GFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEG 321
             GFVNF++ DDAAR+VE+LNG KFDDKEWYVG+AQKK ERE EL+ ++EQ+LKE ADKF+ 
Sbjct:   258 GFVNFENADDAARAVESLNGHKFDDKEWYVGRAQKKSERETELRVRYEQNLKEAADKFQS 317

Query:   322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
              NLYVKNLD SISD+KLKE+FS FGT+TS KVMRDPNG S+GSGFVAF+T EEA++A+++
Sbjct:   318 SNLYVKNLDPSISDEKLKEIFSPFGTVTSSKVMRDPNGTSKGSGFVAFATPEEATEAMSQ 377

Query:   382 MNGKMVVSKPLYVALAQRKEERRARLQAQFSQXXXXXXXXXXXXXX-----XAPGLGQQL 436
             ++GKM+ SKPLYVA+AQRKE+RR RLQAQFSQ                     PG+GQQ+
Sbjct:   378 LSGKMIESKPLYVAIAQRKEDRRVRLQAQFSQVRPVAMQPSVGPRMPVYPPGGPGIGQQM 437

Query:   437 FY 438
             FY
Sbjct:   438 FY 439

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

 Score = 1479 (525.7 bits), Expect = 1.4e-151, P = 1.4e-151
 Identities = 284/410 (69%), Positives = 341/410 (83%)

Query:    34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
             A Q  +TSLYVGDLD +V DSQL++ F Q GQVVSVRVCRD++TRRSLGYGYVNY    +
Sbjct:    39 AAQQGTTSLYVGDLDATVTDSQLFEAFTQAGQVVSVRVCRDMTTRRSLGYGYVNYATPQD 98

Query:    94 ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
             A+RAL+ELNF  LNG+ IR+MYS RDP++RKSG GNIFIKNLDKSID+KALH+TFS FG 
Sbjct:    99 ASRALNELNFMALNGRAIRVMYSVRDPSLRKSGVGNIFIKNLDKSIDHKALHETFSAFGP 158

Query:   154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTA 213
             ILSCKVA D  GQS+GYGFVQ+D +E+A+ AIDKLNGMLLNDKQV+VGPF+ K +R+ + 
Sbjct:   159 ILSCKVAVDPSGQSKGYGFVQYDTDEAAQGAIDKLNGMLLNDKQVYVGPFVHKLQRDPSG 218

Query:   214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAA 273
             +K +F NVYVKNLSE+ ++++L K+FGEFG+ TS  +MRD +GKSK FGFVNF++ DDAA
Sbjct:   219 EKVKFTNVYVKNLSESLSDEELNKVFGEFGVTTSCVIMRDGEGKSKGFGFVNFENSDDAA 278

Query:   274 RSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSI 333
             R+V+ALNGK FDDKEW+VGKAQKK ERE ELK KFEQSLKE ADK +G NLYVKNLD+S+
Sbjct:   279 RAVDALNGKTFDDKEWFVGKAQKKSERETELKQKFEQSLKEAADKSQGSNLYVKNLDESV 338

Query:   334 SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY 393
             +DDKL+E F+ FGTITSCKVMRDP+G+SRGSGFVAFST EEA++A+TEMNGKM+V+KPLY
Sbjct:   339 TDDKLREHFAPFGTITSCKVMRDPSGVSRGSGFVAFSTPEEATRAITEMNGKMIVTKPLY 398

Query:   394 VALAQRKEERRARLQAQFSQXXXXXX--XXXXXXXXXAPG---LGQQLFY 438
             VALAQRKE+R+ARLQAQFSQ                  PG   +GQQLFY
Sbjct:   399 VALAQRKEDRKARLQAQFSQMRPVNMPPAVGPRMQMYPPGGPPMGQQLFY 448

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

TAIR|locus:2058573 PAB4 "AT2G23350" [Arabidopsis thaliana (taxid:3702)]

 Score = 1468 (521.8 bits), Expect = 2.0e-150, P = 2.0e-150
 Identities = 282/421 (66%), Positives = 335/421 (79%)

Query:    22 TNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSL 81
             T GI   GG          SLYVGDLD +V DSQLYD F ++ QVVSVRVCRD +T  SL
Sbjct:    28 TPGIGVGGGGDGVTHGALCSLYVGDLDFNVTDSQLYDYFTEVCQVVSVRVCRDAATNTSL 87

Query:    82 GYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDN 141
             GYGYVNY+   +A +A+ +LN++ LNGK IRI YS RD + R+SG GN+F+KNLDKS+DN
Sbjct:    88 GYGYVNYSNTDDAEKAMQKLNYSYLNGKMIRITYSSRDSSARRSGVGNLFVKNLDKSVDN 147

Query:   142 KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVG 201
             K LH+ FS  G I+SCKVATD +GQSRGYGFVQFD E+SAK+AI+KLNG +LNDKQ+FVG
Sbjct:   148 KTLHEAFSGCGTIVSCKVATDHMGQSRGYGFVQFDTEDSAKNAIEKLNGKVLNDKQIFVG 207

Query:   202 PFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCF 261
             PFLRK+ERES ADK +F NVYVKNLSE TT+D+LK  FG++G I+S  VMRD DGKS+CF
Sbjct:   208 PFLRKEERESAADKMKFTNVYVKNLSEATTDDELKTTFGQYGSISSAVVMRDGDGKSRCF 267

Query:   262 GFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEG 321
             GFVNF++P+DAAR+VEALNGKKFDDKEWYVGKAQKK ERE+EL  ++EQ   +  +KF+G
Sbjct:   268 GFVNFENPEDAARAVEALNGKKFDDKEWYVGKAQKKSERELELSRRYEQGSSDGGNKFDG 327

Query:   322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
             LNLYVKNLDD+++D+KL+ELF+EFGTITSCKVMRDP+G S+GSGFVAFS A EAS+ L E
Sbjct:   328 LNLYVKNLDDTVTDEKLRELFAEFGTITSCKVMRDPSGTSKGSGFVAFSAASEASRVLNE 387

Query:   382 MNGKMVVSKPLYVALAQRKEERRARLQAQFSQXXXXXXXXXX----XXXXXAPGLGQQLF 437
             MNGKMV  KPLYVALAQRKEERRA+LQAQFSQ                   APGLGQQ+F
Sbjct:   388 MNGKMVGGKPLYVALAQRKEERRAKLQAQFSQMRPAFIPGVGPRMPIFTGGAPGLGQQIF 447

Query:   438 Y 438
             Y
Sbjct:   448 Y 448

GO:0003723 "RNA binding" evidence=ISS

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

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

GO:0005829 "cytosol" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

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

 Score = 1195 (425.7 bits), Expect = 1.7e-121, P = 1.7e-121
 Identities = 234/377 (62%), Positives = 290/377 (76%)

Query:    39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             ++SLY GDLD  V ++ L+DLF  +  VVSVRVCRD   RRSLGY Y+N++  ++A RA+
Sbjct:    48 NSSLYAGDLDPKVTEAHLFDLFKHVANVVSVRVCRD-QNRRSLGYAYINFSNPNDAYRAM 106

Query:    99 DELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCK 158
             + LN+TPL  +PIRIM S RDP+ R SG GNIFIKNLD SIDNKAL +TFS+FG ILSCK
Sbjct:   107 EALNYTPLFDRPIRIMLSNRDPSTRLSGKGNIFIKNLDASIDNKALFETFSSFGTILSCK 166

Query:   159 VATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQER--ESTADKT 216
             VA D  G+S+GYGFVQF+ EESA++AIDKLNGML+NDKQVFVG F+R+QER  +      
Sbjct:   167 VAMDVTGRSKGYGFVQFEKEESAQAAIDKLNGMLMNDKQVFVGHFIRRQERARDENTPTP 226

Query:   217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSV 276
             RF NVYVKNL +   ED+L+K FG+FG+I+S  VMRD  G S+CFGFVNF+  + AA +V
Sbjct:   227 RFTNVYVKNLPKEIGEDELRKTFGKFGVISSAVVMRDQSGNSRCFGFVNFECTEAAASAV 286

Query:   277 EALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDD 336
             E +NG    D   YVG+AQKK ERE EL+ KFEQ      +K +G NLY+KNLDDS+ D+
Sbjct:   287 EKMNGISLGDDVLYVGRAQKKSEREEELRRKFEQERINRFEKSQGANLYLKNLDDSVDDE 346

Query:   337 KLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL 396
             KLKE+FSE+G +TS KVM +P G+SRG GFVA+S  EEA +AL+EMNGKM+  KPLY+AL
Sbjct:   347 KLKEMFSEYGNVTSSKVMLNPQGMSRGFGFVAYSNPEEALRALSEMNGKMIGRKPLYIAL 406

Query:   397 AQRKEERRARLQAQFSQ 413
             AQRKE+RRA LQA FSQ
Sbjct:   407 AQRKEDRRAHLQALFSQ 423

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

MGI|MGI:1349722 Pabpc1 "poly(A) binding protein, cytoplasmic 1" [Mus musculus (taxid:10090)]

 Score = 1130 (402.8 bits), Expect = 1.3e-114, P = 1.3e-114
 Identities = 220/382 (57%), Positives = 288/382 (75%)

Query:    34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
             A  +   SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +
Sbjct:     5 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64

Query:    94 ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
             A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct:    65 AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124

Query:   154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST- 212
             ILSCKV  D  G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+  
Sbjct:   125 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183

Query:   213 -ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
              A    F NVY+KN  E   ++ LK++FG+FG   S  VM D  GKSK FGFV+F+  +D
Sbjct:   184 GARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDESGKSKGFGFVSFERHED 243

Query:   272 AARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDD 331
             A ++V+ +NGK+ + K+ YVG+AQKK ER+ ELK KFEQ  ++   +++G+NLYVKNLDD
Sbjct:   244 AQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDD 303

Query:   332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
              I D++L++ FS FGTITS KVM +  G S+G GFV FS+ EEA+KA+TEMNG++V +KP
Sbjct:   304 GIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP 362

Query:   392 LYVALAQRKEERRARLQAQFSQ 413
             LYVALAQRKEER+A L  Q+ Q
Sbjct:   363 LYVALAQRKEERQAHLTNQYMQ 384

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008022 "protein C-terminus binding" evidence=ISO

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

GO:2000623 "negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=ISO

RGD|619838 Pabpc1 "poly(A) binding protein, cytoplasmic 1" [Rattus norvegicus (taxid:10116)]

 Score = 1130 (402.8 bits), Expect = 1.3e-114, P = 1.3e-114
 Identities = 220/382 (57%), Positives = 288/382 (75%)

Query:    34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
             A  +   SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +
Sbjct:     5 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64

Query:    94 ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
             A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct:    65 AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124

Query:   154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST- 212
             ILSCKV  D  G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+  
Sbjct:   125 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183

Query:   213 -ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
              A    F NVY+KN  E   ++ LK++FG+FG   S  VM D  GKSK FGFV+F+  +D
Sbjct:   184 GARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDESGKSKGFGFVSFERHED 243

Query:   272 AARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDD 331
             A ++V+ +NGK+ + K+ YVG+AQKK ER+ ELK KFEQ  ++   +++G+NLYVKNLDD
Sbjct:   244 AQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDD 303

Query:   332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
              I D++L++ FS FGTITS KVM +  G S+G GFV FS+ EEA+KA+TEMNG++V +KP
Sbjct:   304 GIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP 362

Query:   392 LYVALAQRKEERRARLQAQFSQ 413
             LYVALAQRKEER+A L  Q+ Q
Sbjct:   363 LYVALAQRKEERQAHLTNQYMQ 384

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0003729 "mRNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008022 "protein C-terminus binding" evidence=ISO

GO:0008143 "poly(A) RNA binding" evidence=ISO;ISS

GO:0008380 "RNA splicing" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=ISO;ISS

GO:0030529 "ribonucleoprotein complex" evidence=ISO;ISS

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

GO:2000623 "negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=ISO;ISS

UNIPROTKB|P61286 PABPC1 "Polyadenylate-binding protein 1" [Bos taurus (taxid:9913)]

 Score = 1128 (402.1 bits), Expect = 2.2e-114, P = 2.2e-114
 Identities = 220/382 (57%), Positives = 287/382 (75%)

Query:    34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
             A  +   SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +
Sbjct:     5 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64

Query:    94 ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
             A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct:    65 AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124

Query:   154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST- 212
             ILSCKV  D  G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+  
Sbjct:   125 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183

Query:   213 -ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
              A    F NVY+KN  E   ++ LK +FG+FG   S  VM D  GKSK FGFV+F+  +D
Sbjct:   184 GARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHED 243

Query:   272 AARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDD 331
             A ++V+ +NGK+ + K+ YVG+AQKK ER+ ELK KFEQ  ++   +++G+NLYVKNLDD
Sbjct:   244 AQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDD 303

Query:   332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
              I D++L++ FS FGTITS KVM +  G S+G GFV FS+ EEA+KA+TEMNG++V +KP
Sbjct:   304 GIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP 362

Query:   392 LYVALAQRKEERRARLQAQFSQ 413
             LYVALAQRKEER+A L  Q+ Q
Sbjct:   363 LYVALAQRKEERQAHLTNQYMQ 384

GO:0005515 "protein binding" evidence=IPI

GO:0010494 "cytoplasmic stress granule" evidence=ISS

GO:2000623 "negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=ISS

GO:0030529 "ribonucleoprotein complex" evidence=ISS

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

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

GO:0008022 "protein C-terminus binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|J9P326 PABPC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1128 (402.1 bits), Expect = 2.2e-114, P = 2.2e-114
 Identities = 220/382 (57%), Positives = 287/382 (75%)

Query:    34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
             A  +   SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +
Sbjct:     5 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64

Query:    94 ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
             A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct:    65 AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124

Query:   154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST- 212
             ILSCKV  D  G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+  
Sbjct:   125 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183

Query:   213 -ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
              A    F NVY+KN  E   ++ LK +FG+FG   S  VM D  GKSK FGFV+F+  +D
Sbjct:   184 GARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHED 243

Query:   272 AARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDD 331
             A ++V+ +NGK+ + K+ YVG+AQKK ER+ ELK KFEQ  ++   +++G+NLYVKNLDD
Sbjct:   244 AQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDD 303

Query:   332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
              I D++L++ FS FGTITS KVM +  G S+G GFV FS+ EEA+KA+TEMNG++V +KP
Sbjct:   304 GIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP 362

Query:   392 LYVALAQRKEERRARLQAQFSQ 413
             LYVALAQRKEER+A L  Q+ Q
Sbjct:   363 LYVALAQRKEERQAHLTNQYMQ 384

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|P11940 PABPC1 "Polyadenylate-binding protein 1" [Homo sapiens (taxid:9606)]

 Score = 1128 (402.1 bits), Expect = 2.2e-114, P = 2.2e-114
 Identities = 220/382 (57%), Positives = 287/382 (75%)

Query:    34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
             A  +   SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +
Sbjct:     5 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64

Query:    94 ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
             A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct:    65 AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124

Query:   154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST- 212
             ILSCKV  D  G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+  
Sbjct:   125 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183

Query:   213 -ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
              A    F NVY+KN  E   ++ LK +FG+FG   S  VM D  GKSK FGFV+F+  +D
Sbjct:   184 GARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHED 243

Query:   272 AARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDD 331
             A ++V+ +NGK+ + K+ YVG+AQKK ER+ ELK KFEQ  ++   +++G+NLYVKNLDD
Sbjct:   244 AQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDD 303

Query:   332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
              I D++L++ FS FGTITS KVM +  G S+G GFV FS+ EEA+KA+TEMNG++V +KP
Sbjct:   304 GIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP 362

Query:   392 LYVALAQRKEERRARLQAQFSQ 413
             LYVALAQRKEER+A L  Q+ Q
Sbjct:   363 LYVALAQRKEERQAHLTNQYMQ 384

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0006378 "mRNA polyadenylation" evidence=TAS

GO:0005737 "cytoplasm" evidence=IDA;TAS

GO:0048255 "mRNA stabilization" evidence=TAS

GO:0008494 "translation activator activity" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0008022 "protein C-terminus binding" evidence=IPI

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC

GO:2000623 "negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IDA

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=TAS

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=TAS

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006412 "translation" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

GO:0045727 "positive regulation of translation" evidence=TAS

UNIPROTKB|F2Z557 PABPC1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 1128 (402.1 bits), Expect = 2.2e-114, P = 2.2e-114
 Identities = 220/382 (57%), Positives = 287/382 (75%)

Query:    34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
             A  +   SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +
Sbjct:     5 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64

Query:    94 ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
             A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct:    65 AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124

Query:   154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST- 212
             ILSCKV  D  G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+  
Sbjct:   125 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183

Query:   213 -ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
              A    F NVY+KN  E   ++ LK +FG+FG   S  VM D  GKSK FGFV+F+  +D
Sbjct:   184 GARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHED 243

Query:   272 AARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDD 331
             A ++V+ +NGK+ + K+ YVG+AQKK ER+ ELK KFEQ  ++   +++G+NLYVKNLDD
Sbjct:   244 AQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDD 303

Query:   332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
              I D++L++ FS FGTITS KVM +  G S+G GFV FS+ EEA+KA+TEMNG++V +KP
Sbjct:   304 GIDDERLRKEFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP 362

Query:   392 LYVALAQRKEERRARLQAQFSQ 413
             LYVALAQRKEER+A L  Q+ Q
Sbjct:   363 LYVALAQRKEERQAHLTNQYMQ 384

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P42731	PABP2_ARATH	No assigned EC number	0.6963	0.9571	0.7106	yes	no
Q6FKG4	PABP_CANGA	No assigned EC number	0.5535	0.8094	0.6528	yes	no
Q6CSV3	PABP_KLULA	No assigned EC number	0.5466	0.7987	0.6300	yes	no
Q54BM2	PAP1A_DICDI	No assigned EC number	0.5226	0.8650	0.7150	yes	no
P04147	PABP_YEAST	No assigned EC number	0.5366	0.8072	0.6533	yes	no
Q74ZS6	PABP_ASHGO	No assigned EC number	0.5165	0.8565	0.6837	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	467
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.0
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-59
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	8e-50
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	7e-49
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-44
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-39
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	4e-32
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-26
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-26
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	8e-25
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	8e-24
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-23
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-22
smart00360	73	smart00360, RRM, RNA recognition motif	1e-22
smart00360	73	smart00360, RRM, RNA recognition motif	1e-22
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-22
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-22
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-21
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-21
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	7e-21
smart00360	73	smart00360, RRM, RNA recognition motif	8e-21
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	1e-20
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-20
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-20
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-20
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-19
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-19
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	4e-19
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-18
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-18
smart00360	73	smart00360, RRM, RNA recognition motif	5e-18
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-18
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-17
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-17
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-16
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-16
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-16
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-16
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-16
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-16
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	2e-16
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-16
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	8e-16
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-15
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-15
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-15
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	3e-15
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	4e-15
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-15
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	9e-15
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-14
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-14
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-14
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-14
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-14
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-14
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-14
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-14
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-14
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	4e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	8e-14
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	9e-14
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	9e-14
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-13
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-13
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-13
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-13
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-13
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-13
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-13
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-13
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-13
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-13
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	2e-13
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	3e-13
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	3e-13
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	4e-13
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-13
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-13
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	5e-13
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	7e-13
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	8e-13
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	9e-13
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	9e-13
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-12
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-12
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-12
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-12
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-12
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-12
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-12
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-12
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-12
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-12
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	1e-12
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-12
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	2e-12
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	2e-12
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-12
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-12
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	3e-12
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	4e-12
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	4e-12
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	4e-12
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	4e-12
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-12
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	5e-12
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	5e-12
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	5e-12
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	5e-12
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	5e-12
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	5e-12
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	6e-12
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	7e-12
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	7e-12
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	7e-12
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	8e-12
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	8e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	8e-12
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	9e-12
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	9e-12
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	9e-12
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-11
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-11
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-11
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-11
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-11
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	2e-11
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-11
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	3e-11
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	3e-11
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-11
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-11
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-11
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	3e-11
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	3e-11
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-11
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	3e-11
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	4e-11
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	4e-11
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	4e-11
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	4e-11
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	5e-11
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	5e-11
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	6e-11
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	6e-11
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	6e-11
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	7e-11
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	7e-11
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	7e-11
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	7e-11
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	8e-11
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	8e-11
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	9e-11
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-10
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-10
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-10
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-10
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-10
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	1e-10
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-10
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	1e-10
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	1e-10
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-10
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-10
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-10
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-10
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-10
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-10
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	2e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-10
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	2e-10
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	2e-10
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-10
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-10
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-10
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-10
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-10
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-10
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	3e-10
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	3e-10
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-10
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-10
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	4e-10
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	4e-10
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-10
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	4e-10
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-10
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	4e-10
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	4e-10
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	5e-10
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	5e-10
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	5e-10
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	5e-10
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	6e-10
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	6e-10
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	6e-10
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	6e-10
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	6e-10
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	6e-10
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	7e-10
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	8e-10
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	8e-10
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	8e-10
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	9e-10
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-09
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-09
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-09
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	1e-09
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	1e-09
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-09
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-09
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	1e-09
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	1e-09
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-09
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	1e-09
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	1e-09
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-09
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-09
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-09
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-09
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-09
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	2e-09
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-09
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	2e-09
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-09
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	2e-09
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-09
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	3e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-09
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-09
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	3e-09
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-09
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	3e-09
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	3e-09
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-09
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	3e-09
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	3e-09
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	4e-09
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	4e-09
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	4e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-09
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	4e-09
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-09
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	4e-09
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	5e-09
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	5e-09
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	5e-09
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	5e-09
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	5e-09
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	5e-09
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	6e-09
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	6e-09
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	6e-09
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	6e-09
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	6e-09
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	6e-09
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	6e-09
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	6e-09
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	6e-09
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	6e-09
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	6e-09
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	6e-09
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	7e-09
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	7e-09
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	7e-09
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	7e-09
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	7e-09
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	7e-09
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	7e-09
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	8e-09
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	8e-09
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	8e-09
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	8e-09
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	8e-09
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	8e-09
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	9e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-08
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-08
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	1e-08
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-08
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-08
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	1e-08
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-08
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	1e-08
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	1e-08
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	1e-08
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	1e-08
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	1e-08
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	1e-08
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	1e-08
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	1e-08
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-08
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-08
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-08
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-08
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-08
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-08
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-08
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	2e-08
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-08
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-08
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-08
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-08
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	2e-08
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-08
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	3e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	3e-08
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	3e-08
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	3e-08
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-08
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	3e-08
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	3e-08
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	3e-08
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	3e-08
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	3e-08
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-08
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	4e-08
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	4e-08
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	4e-08
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-08
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	4e-08
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	4e-08
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	4e-08
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-08
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	5e-08
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	5e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	5e-08
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	5e-08
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	5e-08
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	5e-08
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	6e-08
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	6e-08
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	6e-08
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	6e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	6e-08
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	6e-08
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	7e-08
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	7e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	7e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	8e-08
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	8e-08
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	8e-08
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	8e-08
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	8e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	8e-08
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	8e-08
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	8e-08
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	8e-08
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	8e-08
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	9e-08
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	9e-08
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-07
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-07
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	1e-07
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	1e-07
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	1e-07
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-07
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	1e-07
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	1e-07
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	1e-07
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	1e-07
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-07
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	1e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	1e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-07
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	1e-07
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	1e-07
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	1e-07
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	1e-07
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	1e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-07
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	2e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-07
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-07
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	2e-07
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	2e-07
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	2e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-07
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	2e-07
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	2e-07
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	2e-07
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	2e-07
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-07
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-07
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-07
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	2e-07
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	2e-07
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-07
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-07
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	2e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-07
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	3e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	3e-07
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	3e-07
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-07
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	3e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	3e-07
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	3e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	3e-07
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	3e-07
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	3e-07
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	3e-07
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-07
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	3e-07
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	3e-07
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	4e-07
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	4e-07
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-07
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	4e-07
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	4e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	4e-07
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	4e-07
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	4e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	4e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-07
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	5e-07
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	5e-07
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	5e-07
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	5e-07
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	5e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	5e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	5e-07
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	5e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-07
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	5e-07
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	5e-07
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	6e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	6e-07
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	6e-07
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	7e-07
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	7e-07
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	7e-07
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	7e-07
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	7e-07
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	8e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	8e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	8e-07
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	8e-07
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	9e-07
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	9e-07
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	9e-07
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-06
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	1e-06
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	1e-06
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-06
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-06
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	1e-06
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-06
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	1e-06
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	1e-06
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	1e-06
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	1e-06
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-06
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	1e-06
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	1e-06
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-06
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-06
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	1e-06
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	1e-06
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	1e-06
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	1e-06
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	1e-06
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	1e-06
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-06
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-06
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-06
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-06
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-06
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-06
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	2e-06
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-06
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	2e-06
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-06
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	2e-06
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	2e-06
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	2e-06
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	2e-06
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	2e-06
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	2e-06
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	2e-06
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	2e-06
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	2e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	3e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-06
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	3e-06
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	3e-06
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	3e-06
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	3e-06
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	3e-06
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	3e-06
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	3e-06
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	3e-06
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	3e-06
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	3e-06
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	3e-06
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	3e-06
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	3e-06
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-06
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	3e-06
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	3e-06
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	3e-06
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	3e-06
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	3e-06
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	3e-06
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	3e-06
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	3e-06
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	4e-06
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-06
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	4e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-06
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-06
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	4e-06
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	4e-06
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	4e-06
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	4e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	4e-06
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	4e-06
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	5e-06
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	5e-06
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	5e-06
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	5e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	5e-06
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	5e-06
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	5e-06
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	5e-06
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	5e-06
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	5e-06
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	5e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	6e-06
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	6e-06
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	6e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	6e-06
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	6e-06
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	7e-06
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	7e-06
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	7e-06
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	7e-06
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	7e-06
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	7e-06
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	7e-06
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	7e-06
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	8e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	8e-06
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	8e-06
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	8e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	8e-06
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	8e-06
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	8e-06
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	9e-06
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	9e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	9e-06
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	9e-06
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	9e-06
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	9e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	9e-06
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	9e-06
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	9e-06
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	9e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	9e-06
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	9e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-05
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-05
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	1e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-05
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	1e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	1e-05
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	1e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	1e-05
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	1e-05
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	1e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	1e-05
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	1e-05
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	1e-05
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	1e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-05
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-05
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	2e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	2e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-05
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	2e-05
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	2e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	2e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-05
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	2e-05
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	2e-05
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	2e-05
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	2e-05
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	2e-05
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	2e-05
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	2e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	2e-05
cd12478	91	cd12478, RRM1_U2B, RNA recognition motif 1 in U2 s	2e-05
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-05
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	2e-05
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	2e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	2e-05
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	2e-05
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	2e-05
cd12626	77	cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in	2e-05
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	3e-05
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	3e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	3e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	3e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	3e-05
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	3e-05
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	3e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	3e-05
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	3e-05
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	3e-05
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	3e-05
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	3e-05
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	3e-05
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	3e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	3e-05
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	3e-05
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	3e-05
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	3e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	3e-05
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	3e-05
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	3e-05
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	3e-05
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	3e-05
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	3e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	4e-05
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	4e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-05
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	4e-05
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	4e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	4e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	4e-05
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	4e-05
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	4e-05
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	4e-05
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	4e-05
cd12349	74	cd12349, RRM2_SHARP, RNA recognition motif 2 in SM	4e-05
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	5e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	5e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	5e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	5e-05
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	5e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	5e-05
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	5e-05
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	6e-05
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	6e-05
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	6e-05
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	6e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	6e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	6e-05
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	6e-05
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	6e-05
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	6e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	7e-05
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	7e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	7e-05
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	7e-05
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	8e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	8e-05
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	8e-05
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	8e-05
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	8e-05
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	8e-05
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	8e-05
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	8e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	9e-05
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	9e-05
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	9e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	9e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	9e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	9e-05
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	9e-05
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	9e-05
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	9e-05
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	1e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	1e-04
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	1e-04
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	1e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-04
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	1e-04
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	1e-04
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	1e-04
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	1e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	1e-04
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	1e-04
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	1e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	1e-04
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	1e-04
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	1e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	1e-04
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	1e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-04
cd12356	79	cd12356, RRM_PPARGC1B, RNA recognition motif in pe	1e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	1e-04
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	1e-04
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	1e-04
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	1e-04
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	1e-04
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	1e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	1e-04
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	1e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-04
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	2e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-04
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-04
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-04
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	2e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-04
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	2e-04
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	2e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	2e-04
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	2e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-04
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	2e-04
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	2e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-04
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	2e-04
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	2e-04
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	2e-04
cd12611	81	cd12611, RRM1_NGR1_NAM8_like, RNA recognition moti	2e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	2e-04
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	2e-04
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	2e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-04
cd12425	76	cd12425, RRM4_PTBP1_like, RNA recognition motif 4	2e-04
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	2e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	3e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	3e-04
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	3e-04
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	3e-04
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	3e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-04
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	3e-04
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	3e-04
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	3e-04
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	3e-04
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	3e-04
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	3e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	3e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	3e-04
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	3e-04
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	3e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	3e-04
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	3e-04
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	3e-04
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	3e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	4e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	4e-04
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	4e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	4e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	4e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	4e-04
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	4e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	4e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	4e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	4e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	4e-04
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	4e-04
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	4e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	4e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	4e-04
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	4e-04
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	4e-04
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	5e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	5e-04
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	5e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	5e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	5e-04
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	5e-04
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	5e-04
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	5e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	5e-04
cd12605	69	cd12605, RRM_RALYL, RNA recognition motif in verte	5e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	6e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	6e-04
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	6e-04
cd12477	89	cd12477, RRM1_U1A, RNA recognition motif 1 found i	6e-04
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	6e-04
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	6e-04
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	6e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	6e-04
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	6e-04
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	6e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	6e-04
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	6e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	7e-04
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	7e-04
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	7e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	7e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	7e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	7e-04
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	7e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	7e-04
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	7e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	8e-04
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	8e-04
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	8e-04
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	8e-04
cd12600	72	cd12600, RRM2_SRSF4_like, RNA recognition motif 2	8e-04
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	8e-04
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	8e-04
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	9e-04
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	9e-04
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	9e-04
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	9e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	9e-04
cd12527	71	cd12527, RRM2_EAR1_like, RNA recognition motif 2 i	9e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	0.001
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	0.001
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	0.001
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	0.001
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	0.001
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	0.001
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	0.001
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	0.001
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	0.001
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	0.001
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	0.001
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	0.001
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	0.001
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.001
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	0.001
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	0.001
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	0.001
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.001
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	0.001
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	0.001
cd12356	79	cd12356, RRM_PPARGC1B, RNA recognition motif in pe	0.001
cd12611	81	cd12611, RRM1_NGR1_NAM8_like, RNA recognition moti	0.001
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	0.001
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	0.001
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	0.001
cd12624	91	cd12624, RRM_PRC, RNA recognition motif in peroxis	0.001
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	0.001
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	0.001
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	0.001
cd12569	72	cd12569, RRM4_RBM19, RNA recognition motif 4 in RN	0.001
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.002
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	0.002
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	0.002
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.002
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.002
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.002
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.002
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	0.002
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	0.002
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	0.002
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.002
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	0.002
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	0.002
cd12476	78	cd12476, RRM1_SNF, RNA recognition motif 1 found i	0.002
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	0.002
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	0.002
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	0.002
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	0.002
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	0.002
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	0.002
cd12540	105	cd12540, RRM_U2AFBPL, RNA recognition motif in U2	0.002
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	0.002
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	0.002
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	0.002
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	0.002
cd12388	70	cd12388, RRM1_RAVER, RNA recognition motif 1 in ri	0.002
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	0.002
cd12625	77	cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in	0.002
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	0.002
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	0.003
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	0.003
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	0.003
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	0.003
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	0.003
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	0.003
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	0.003
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	0.003
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	0.003
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.003
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	0.003
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	0.003
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	0.003
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.003
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.003
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	0.003
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	0.003
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	0.003
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	0.003
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	0.003
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	0.003
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	0.003
cd12259	76	cd12259, RRM_SRSF11_SREK1, RNA recognition motif i	0.003
cd12487	78	cd12487, RRM1_DND1, RNA recognition motif 1 found	0.003
cd12452	88	cd12452, RRM_ARP_like, RNA recognition motif in ye	0.003
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	0.003
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	0.004
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	0.004
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	0.004
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	0.004
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	0.004
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	0.004
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	0.004
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	0.004
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	0.004
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	0.004
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	0.004
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	0.004
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	0.004
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	0.004
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	0.004
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	0.004
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.004
cd12423	74	cd12423, RRM3_PTBP1_like, RNA recognition motif 3	0.004
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	0.004
cd12374	85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	0.004
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	0.004

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

 Score =  584 bits (1507), Expect = 0.0
 Identities = 248/406 (61%), Positives = 314/406 (77%), Gaps = 6/406 (1%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           SLYVGDLD  V +++LYDLF   G V+SVRVCRD  TRRSLGYGYVN+    +A RAL+ 
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 101 LNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVA 160
           +NF  L GKPIRIM+S RDP++R+SG GNIF+KNLDKS+DNKAL DTFS FGNILSCKVA
Sbjct: 62  MNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVA 121

Query: 161 TDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNN 220
           TD  G+SRGYGFV F+ EESAK+AI K+NGMLLNDK+V+VG F++K ERE+   K +F N
Sbjct: 122 TDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLK-KFTN 180

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YVKNL  +  ED L+++F +FG ITS AVM+D  G+S+ F FVNF+  +DAA++VE +N
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMN 240

Query: 281 GKKFDD----KEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDD 336
           GKK       K+ YVG+AQK+ ERE EL+ KFE+  +E   K +G+NLYVKNLDD+++D+
Sbjct: 241 GKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDE 300

Query: 337 KLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL 396
           KL+ELFSE G ITS KVM D  G+SRG GFV FS  EEA++A+TEM+G+M+  KPLYVAL
Sbjct: 301 KLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVAL 360

Query: 397 AQRKEERRARLQAQFSQMRPPVGPRMPMYPPVAPGLGQQLFYGQGP 442
           AQRKE+RRA LQ QF Q++P    ++PM  P+   +GQ  +YGQGP
Sbjct: 361 AQRKEQRRAHLQDQFMQLQPR-MRQLPMGSPMGGAMGQPPYYGQGP 405

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

 Score =  204 bits (520), Expect = 2e-59
 Identities = 95/297 (31%), Positives = 160/297 (53%), Gaps = 20/297 (6%)

Query: 33  DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAH 92
             R+    +++V +LD SV++  L+D F++ G ++S +V  D    +S GYG+V++    
Sbjct: 82  SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEE 140

Query: 93  EATRALDELNFTPLNGKPI---RIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFS 149
            A  A+ ++N   LN K +   R +  +           N+++KNLD S++   L + F+
Sbjct: 141 SAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFA 200

Query: 150 TFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNG----MLLNDKQVFVGPF-- 203
            FG I S  V  D  G+SRG+ FV F+  E A  A++++NG    +    K+++VG    
Sbjct: 201 KFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQK 260

Query: 204 ----------LRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD 253
                       ++ ++    K +  N+YVKNL +T T++ L+++F E G ITS  VM D
Sbjct: 261 RAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD 320

Query: 254 ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQ 310
             G S+ FGFV F +P++A R+V  ++G+    K  YV  AQ+K +R   L+ +F Q
Sbjct: 321 EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQ 377

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 =  163 bits (416), Expect = 8e-50
 Identities = 61/77 (79%), Positives = 68/77 (88%)

Query: 126 GAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
           G GNIFIKNLDKSIDNKAL+DTFS FGNILSCKVATD  G S+GYGFV F+ EE+A  AI
Sbjct: 1   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAI 60

Query: 186 DKLNGMLLNDKQVFVGP 202
           +K+NGMLLNDK+VFVGP
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|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score =  161 bits (410), Expect = 7e-49
 Identities = 55/79 (69%), Positives = 66/79 (83%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
           G+NLYVKNLDDSI D++L+E FS FGTITS KVM D  G S+G GFV FS+ EEA+KA+T
Sbjct: 1   GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVT 60

Query: 381 EMNGKMVVSKPLYVALAQR 399
           EMNG+++  KPLYVALAQR
Sbjct: 61  EMNGRIIGGKPLYVALAQR 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|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score =  149 bits (379), Expect = 3e-44
 Identities = 49/80 (61%), Positives = 60/80 (75%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           SLYVGDL   V ++ LY++F+  G V+S+RVCRDL TRRSLGY YVN+    +A RALD 
Sbjct: 1   SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDT 60

Query: 101 LNFTPLNGKPIRIMYSYRDP 120
           LNF  + GKPIRIM+S RDP
Sbjct: 61  LNFDVIKGKPIRIMWSQRDP 80

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

 Score =  136 bits (345), Expect = 2e-39
 Identities = 45/80 (56%), Positives = 62/80 (77%)

Query: 218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
           F NVYVKNL E   ++ LK++FG++G ITS  VM+D +GKSK FGFVNF++ + A ++VE
Sbjct: 1   FTNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVE 60

Query: 278 ALNGKKFDDKEWYVGKAQKK 297
            LNGK+ + K+ YVG+AQKK
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 =  117 bits (295), Expect = 4e-32
 Identities = 44/78 (56%), Positives = 55/78 (70%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           N+YVKNL + + D+KLKELF ++G ITS KVM+D  G S+G GFV F   E A KA+ E+
Sbjct: 3   NVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 383 NGKMVVSKPLYVALAQRK 400
           NGK V  K LYV  AQ+K
Sbjct: 63  NGKEVNGKKLYVGRAQKK 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|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score =  101 bits (255), Expect = 1e-26
 Identities = 34/77 (44%), Positives = 49/77 (63%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           N+YVKNL ++  ++ L++ F  FG ITS  VM D  G+SK FGFV F  P++A ++V  +
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 280 NGKKFDDKEWYVGKAQK 296
           NG+    K  YV  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|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score =  101 bits (254), Expect = 2e-26
 Identities = 34/73 (46%), Positives = 48/73 (65%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           N+++KNLD SI +  L + FS FG I SCKV  D NG S+G GFV F T E A +A+ ++
Sbjct: 4   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 383 NGKMVVSKPLYVA 395
           NG ++  K ++V 
Sbjct: 64  NGMLLNDKKVFVG 76

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

 Score =  103 bits (258), Expect = 8e-25
 Identities = 63/306 (20%), Positives = 125/306 (40%), Gaps = 15/306 (4%)

Query: 111 IRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDT-FSTFGNILSCKVATDSLGQSRG 169
                     +  +S             +  K  +          L+ +V +  +     
Sbjct: 1   KESKNLKGPHSSFESVKPEDIESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEIS 60

Query: 170 YGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTR------FNNVYV 223
               +       K   ++      + ++ +   F  +  R S + K+R       N ++V
Sbjct: 61  PPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFV 120

Query: 224 KNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGK 282
            NL    TE+DL+++F +FG +    ++RD + GKS+ F FV F+  + A +++E LNGK
Sbjct: 121 GNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGK 180

Query: 283 KFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFE------GLNLYVKNLDDSISDD 336
           + + +   V KAQ   +   EL    + S  +   + +        NLYV NL    +++
Sbjct: 181 ELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEE 240

Query: 337 KLKELFSEFGTITSCKVMRDPNG-ISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA 395
           +L +LF   G I    +    +G I +   FV    +++A ++ +  N K ++ +    A
Sbjct: 241 ELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKKKILGRGPRKA 300

Query: 396 LAQRKE 401
            +Q + 
Sbjct: 301 FSQPRL 306

Length = 306

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score =  101 bits (254), Expect = 8e-24
 Identities = 60/219 (27%), Positives = 111/219 (50%), Gaps = 23/219 (10%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +T T+++++ +F   G I S  ++RD   G+S  +GFVN+  P+DA ++V +
Sbjct: 5   NLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS 64

Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
           LNG +  +K   V  A                  + ++D  +G NLYV  L  +++  +L
Sbjct: 65  LNGLRLQNKTIKVSYA------------------RPSSDSIKGANLYVSGLPKTMTQHEL 106

Query: 339 KELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMV--VSKPLYVA 395
           + +FS FG I + +++ D   G+S+G GF+ F   +EA +A+  +NG      ++P+ V 
Sbjct: 107 ESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVK 166

Query: 396 LAQRKEERRAR-LQAQFSQMRPPVGPRMPMYPPVAPGLG 433
            A       ++ L +Q   ++ P   R+P+   +     
Sbjct: 167 FANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGI 205

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

 Score = 98.9 bits (246), Expect = 9e-23
 Identities = 56/157 (35%), Positives = 89/157 (56%), Gaps = 8/157 (5%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           N+ +  L +++  + +   F++ G I SCK+  D   GQS GYGFV +   E A+ A++ 
Sbjct: 5   NLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS 64

Query: 188 LNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFG-IIT 246
           LNG+ L +K + V  + R      ++D  +  N+YV  L +T T+ +L+ IF  FG IIT
Sbjct: 65  LNGLRLQNKTIKVS-YAR-----PSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIIT 118

Query: 247 STAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKK 283
           S  +  +  G SK  GF+ FD  D+A R+++ LNG  
Sbjct: 119 SRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTT 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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 91.1 bits (227), Expect = 1e-22
 Identities = 31/73 (42%), Positives = 53/73 (72%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           N+++KNL + +D++ L + F  +G I S KV  D  G+S+G+GFV F+N E+A+ A+++L
Sbjct: 3   NVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 189 NGMLLNDKQVFVG 201
           NG  +N K+++VG
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|214636 smart00360, RRM, RNA recognition motif

 Score = 91.1 bits (227), Expect = 1e-22
 Identities = 31/73 (42%), Positives = 50/73 (68%), Gaps = 1/73 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
            ++V NL   TTE++L+++F +FG + S  ++RD + GKSK F FV F+  +DA +++EA
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 279 LNGKKFDDKEWYV 291
           LNGK+ D +   V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 90.7 bits (226), Expect = 1e-22
 Identities = 31/73 (42%), Positives = 48/73 (65%), Gaps = 1/73 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            L+V NL    ++++L+ELFS+FG + S +++RD   G S+G  FV F + E+A KAL  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 382 MNGKMVVSKPLYV 394
           +NGK +  +PL V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 89.6 bits (223), Expect = 3e-22
 Identities = 33/70 (47%), Positives = 48/70 (68%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V NL   TTE+DLK +F +FG I S  ++RD  G+SK F FV F+D +DA +++EALN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 281 GKKFDDKEWY 290
           GK+   +E  
Sbjct: 61  GKELGGRELR 70

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

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 96.9 bits (241), Expect = 5e-22
 Identities = 52/152 (34%), Positives = 87/152 (57%), Gaps = 3/152 (1%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+L V  L  ++   ++  LF  +G++ S ++ RD  T +SLGYG+VNY    +A +A++
Sbjct: 4   TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVN 63

Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKV 159
            LN   L  K I++  SY  P+       N+++  L K++    L   FS FG I++ ++
Sbjct: 64  SLNGLRLQNKTIKV--SYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRI 121

Query: 160 ATDSL-GQSRGYGFVQFDNEESAKSAIDKLNG 190
            +D++ G S+G GF++FD  + A  AI  LNG
Sbjct: 122 LSDNVTGLSKGVGFIRFDKRDEADRAIKTLNG 153

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

 Score = 87.7 bits (218), Expect = 2e-21
 Identities = 35/71 (49%), Positives = 52/71 (73%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V NL   TTE+DL+++F +FG I S  ++RD DGKSK F FV F+ P+DA +++EALN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 281 GKKFDDKEWYV 291
           GK+ D ++  V
Sbjct: 61  GKELDGRKLKV 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 87.0 bits (216), Expect = 3e-21
 Identities = 31/71 (43%), Positives = 47/71 (66%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V NL    +++ L+ELFS+FG I S +++RD +G S+G  FV F + E+A KAL  +N
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 384 GKMVVSKPLYV 394
           GK +  + L V
Sbjct: 61  GKELDGRKLKV 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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 85.7 bits (213), Expect = 7e-21
 Identities = 26/69 (37%), Positives = 43/69 (62%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+ NL      + L D FS FG I S ++  D  G+S+G+ FV+F++EE A+ A++ LN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 190 GMLLNDKQV 198
           G  L  +++
Sbjct: 61  GKELGGREL 69

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

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

 Score = 85.7 bits (213), Expect = 8e-21
 Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
            +F+ NL      + L + FS FG + S ++  D   G+S+G+ FV+F++EE A+ A++ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 188 LNGMLLNDKQVFV 200
           LNG  L+ + + V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 85.3 bits (212), Expect = 1e-20
 Identities = 28/74 (37%), Positives = 44/74 (59%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           N+++KNL ++     L   F  FG I S  V  D +G SK +GFV+F+  + A R++E +
Sbjct: 4   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 280 NGKKFDDKEWYVGK 293
           NG   +DK+ +VG 
Sbjct: 64  NGMLLNDKKVFVGP 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 85.0 bits (211), Expect = 1e-20
 Identities = 25/71 (35%), Positives = 44/71 (61%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+ NL      + L + FS FG I S ++  D  G+S+G+ FV+F++ E A+ A++ LN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 190 GMLLNDKQVFV 200
           G  L+ +++ V
Sbjct: 61  GKELDGRKLKV 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|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding proteins

 Score = 85.0 bits (211), Expect = 2e-20
 Identities = 33/73 (45%), Positives = 50/73 (68%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           N+++KNLD SID++ L + FS FG I S KV TD  G+S+G+GFV F + E A  A+ ++
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 189 NGMLLNDKQVFVG 201
           NG ++  K ++V 
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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 92.7 bits (230), Expect = 3e-20
 Identities = 58/208 (27%), Positives = 91/208 (43%), Gaps = 9/208 (4%)

Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGF 263
           R  +   T  +     V+V  L+    E DL + F + G +     ++D +  +SK   +
Sbjct: 76  RNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAY 135

Query: 264 VNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLN 323
           V F D  ++     AL G+    +   V  +Q   E+    K    Q           L 
Sbjct: 136 VEFYD-VESVIKALALTGQMLLGRPIIVQSSQA--EKNRAAKAATHQPGDIPNF----LK 188

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           LYV NL  +I++ +L+++F  FG I   ++ RDP  G S+G GF+ F  AEEA +AL  M
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248

Query: 383 NGKMVVSKPLYVALAQRKEERRARLQAQ 410
           NG  +  +P+ V  AQ            
Sbjct: 249 NGFELAGRPIKVGYAQDSTYLLDAANTF 276

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 81.9 bits (203), Expect = 2e-19
 Identities = 30/70 (42%), Positives = 44/70 (62%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V NL    +++ LK+LFS+FG I S +++RD  G S+G  FV F   E+A KAL  +N
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 384 GKMVVSKPLY 393
           GK +  + L 
Sbjct: 61  GKELGGRELR 70

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

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

 Score = 88.9 bits (220), Expect = 2e-19
 Identities = 70/232 (30%), Positives = 105/232 (45%), Gaps = 31/232 (13%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+ +L  +F   G I +  +MRD   G S  + FV+F    D+ R+++ 
Sbjct: 109 NLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKN 168

Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
           LNG    +K   V  A+   E           S+K+T       NLYV NL  +I+DD+L
Sbjct: 169 LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 210

Query: 339 KELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMV--VSKPLYVA 395
             +F ++G I    ++RD   G  RG  FV F+  EEA +A++ +N  +    S+PL V 
Sbjct: 211 DTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVR 270

Query: 396 LAQRKEERRARLQAQFSQMRPPVGPRMPMYPPVAPGLGQQLFYGQGPPIIPP 447
           LA+  E  +A+     SQM       M        G       G G     P
Sbjct: 271 LAE--EHGKAKAHHYMSQMGHGNMGNMGHGNMGMAG-------GSGMNPPNP 313

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

 Score = 81.2 bits (201), Expect = 4e-19
 Identities = 33/77 (42%), Positives = 51/77 (66%), Gaps = 3/77 (3%)

Query: 126 GAGNIFIKNLDKSIDNKALHDTFSTFGNIL-SCKVATD-SLGQSRGYGFVQFDNEESAKS 183
           GA N+FI NLD  +D K L+DTFS FG IL + K+  D   G S+G+ F+ +D+ E++ +
Sbjct: 1   GA-NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDA 59

Query: 184 AIDKLNGMLLNDKQVFV 200
           AI+ +NG  L ++ + V
Sbjct: 60  AIEAMNGQYLCNRPITV 76

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

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

 Score = 86.6 bits (214), Expect = 1e-18
 Identities = 53/180 (29%), Positives = 88/180 (48%), Gaps = 7/180 (3%)

Query: 18  PSPATNGIANNGGVGDARQFVS----TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCR 73
            + A+    N+ G G +    +    T+L V  L   + D +LY LF  +G + + R+ R
Sbjct: 82  ANMASTNSLNSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMR 141

Query: 74  DLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIK 133
           D  T  S GY +V++ +  ++ RA+  LN   +  K  R+  SY  P        N+++ 
Sbjct: 142 DYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNK--RLKVSYARPGGESIKDTNLYVT 199

Query: 134 NLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKLNGML 192
           NL ++I +  L   F  +G I+   +  D L G  RG  FV+F+  E A+ AI  LN ++
Sbjct: 200 NLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVI 259

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 86.6 bits (214), Expect = 1e-18
 Identities = 50/165 (30%), Positives = 84/165 (50%), Gaps = 8/165 (4%)

Query: 118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFD 176
            D     +   N+ +  L + + ++ L+  F T G I +C++  D   G S GY FV F 
Sbjct: 98  SDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFG 157

Query: 177 NEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLK 236
           +E  ++ AI  LNG+ + +K++ V  + R        +  +  N+YV NL  T T+D L 
Sbjct: 158 SEADSQRAIKNLNGITVRNKRLKVS-YAR-----PGGESIKDTNLYVTNLPRTITDDQLD 211

Query: 237 KIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEALN 280
            IFG++G I    ++RD   G  +   FV F+  ++A  ++ ALN
Sbjct: 212 TIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALN 256

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

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

 Score = 78.0 bits (193), Expect = 5e-18
 Identities = 26/73 (35%), Positives = 49/73 (67%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L+VG+L     + +L +LF++ G+V SVR+ RD  T +S G+ +V + +  +A +AL+ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 101 LNFTPLNGKPIRI 113
           LN   L+G+P+++
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>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 = 77.6 bits (192), Expect = 7e-18
 Identities = 30/80 (37%), Positives = 48/80 (60%), Gaps = 1/80 (1%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKAL 379
           G  L+V  L    ++ +L+ LFS+FG +    +M+DP  G SRG GFV F + E+A  A+
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 380 TEMNGKMVVSKPLYVALAQR 399
            ++NGK +  + + V  A+R
Sbjct: 61  RDLNGKELEGRVIKVEKAKR 80

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

 Score = 77.3 bits (191), Expect = 1e-17
 Identities = 28/74 (37%), Positives = 43/74 (58%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           + VKNL   +++D+L+E F   G +T  KVMR  +G SR  GFV F + E+A +A+   N
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 384 GKMVVSKPLYVALA 397
              + +  + V LA
Sbjct: 63  KTFIDTSKISVELA 76

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

 Score = 77.3 bits (191), Expect = 1e-17
 Identities = 34/77 (44%), Positives = 50/77 (64%), Gaps = 1/77 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           NLYV NL  +++++ LK+LF +FG +TS +V+ D   G SRG GFV   TAEEA+ A+ +
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 382 MNGKMVVSKPLYVALAQ 398
           +NG     + L V  A+
Sbjct: 61  LNGTDFGGRTLTVNEAR 77

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|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 = 74.2 bits (183), Expect = 1e-16
 Identities = 29/79 (36%), Positives = 49/79 (62%), Gaps = 1/79 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVE 277
           N ++V  LS  TTE +L+ +F +FG +    +M+D   G+S+ FGFV F+  +DA  ++ 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 278 ALNGKKFDDKEWYVGKAQK 296
            LNGK+ + +   V KA++
Sbjct: 62  DLNGKELEGRVIKVEKAKR 80

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

 Score = 74.2 bits (183), Expect = 1e-16
 Identities = 32/78 (41%), Positives = 49/78 (62%), Gaps = 1/78 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
           N+YV NL    TE+DLK +FG+FG +TS  V+ D + G+S+ FGFV  +  ++A  ++E 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 279 LNGKKFDDKEWYVGKAQK 296
           LNG  F  +   V +A+ 
Sbjct: 61  LNGTDFGGRTLTVNEARP 78

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

>gnl|CDD|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 = 74.2 bits (183), Expect = 1e-16
 Identities = 29/72 (40%), Positives = 46/72 (63%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKL 188
           +FI +L     ++ L+  F+ FGN++S KV  D   GQS+ +GFV +DN ESA++AI  +
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 189 NGMLLNDKQVFV 200
           NG  +  K++ V
Sbjct: 61  NGFQVGGKRLKV 72

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

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

 Score = 80.0 bits (196), Expect = 2e-16
 Identities = 45/215 (20%), Positives = 86/215 (40%), Gaps = 7/215 (3%)

Query: 202 PFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCF 261
                +   S+ +  +  ++    L+E   +++   +        +  V           
Sbjct: 2   ESKNLKGPHSSFESVKPEDIESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEISP 61

Query: 262 GFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEG 321
                    +     E    ++ D +  Y  + +++  R  E     ++S +E       
Sbjct: 62  PSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENN----- 116

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALT 380
             L+V NL   ++++ L+ELF +FG +   +++RD   G SRG  FV F + E A KA+ 
Sbjct: 117 -TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175

Query: 381 EMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR 415
           E+NGK +  +PL V  AQ   + R+ L        
Sbjct: 176 ELNGKELEGRPLRVQKAQPASQPRSELSNNLDASF 210

Length = 306

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

 Score = 73.9 bits (182), Expect = 2e-16
 Identities = 30/83 (36%), Positives = 52/83 (62%), Gaps = 2/83 (2%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTI-TSCKVMRDP-NGISRGSGFVAFSTAEEASKA 378
           G NL++ NLD  + +  L + FS FG I  + K+MRDP  G S+G  F+++ + E +  A
Sbjct: 1   GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA 60

Query: 379 LTEMNGKMVVSKPLYVALAQRKE 401
           +  MNG+ + ++P+ V+ A +K+
Sbjct: 61  IEAMNGQYLCNRPITVSYAFKKD 83

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

 Score = 73.8 bits (182), Expect = 2e-16
 Identities = 28/65 (43%), Positives = 38/65 (58%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           + VKNL +  TED L++ F   G +T   VMR  DGKS+ FGFV F   +DA ++V+  N
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 281 GKKFD 285
               D
Sbjct: 63  KTFID 67

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

 Score = 73.5 bits (181), Expect = 2e-16
 Identities = 30/71 (42%), Positives = 40/71 (56%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L VKNL   I +DKL++LF  FGTIT  ++    +G  R  GFV + T EEA KAL   N
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 384 GKMVVSKPLYV 394
              + +  + V
Sbjct: 63  NSFIDTSKITV 73

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

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

 Score = 73.1 bits (180), Expect = 3e-16
 Identities = 29/77 (37%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V NL  S   D L+E F E G +   ++ +D +G S+G G V F+T E A KAL E +
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL-EKS 60

Query: 384 GKMVVSKPLYVALAQRK 400
           G+ ++ + + V LA  +
Sbjct: 61  GEELLGREIRVDLATER 77

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

 Score = 79.2 bits (195), Expect = 8e-16
 Identities = 90/381 (23%), Positives = 157/381 (41%), Gaps = 49/381 (12%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +++V  L L   +  LY+ F+++G+V  V+  +D ++RRS G  YV +    E+      
Sbjct: 91  TVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEF-YDVESVIKALA 149

Query: 101 LNFTPLNGKPIRIMYSYRDPTIRKSGAGN----------IFIKNLDKSIDNKALHDTFST 150
           L    L G+PI +  S  +       A +          +++ NL  +I  + L   F  
Sbjct: 150 LTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEP 209

Query: 151 FGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQER 209
           FG+I   ++  D   G+S+G+GF+QF + E AK A++ +NG  L  + + VG + +    
Sbjct: 210 FGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVG-YAQDSTY 268

Query: 210 ESTADKTRFN----NVYVKNLSETTTEDDLKKI----FGEFGIITSTAVMRDADGKSKCF 261
              A  T  +        KNL+    E  ++K+         +I  T        K +  
Sbjct: 269 LLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRD 328

Query: 262 GFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEG 321
           G ++ + P   A    A+  +           A       + L   F+ + +E       
Sbjct: 329 GIIDPNIPSRYATGALAIMARNSFVPSTNNNLAT----TCLVLSNMFDPATEEE------ 378

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
                 N D+ I DD +KE  S++G +    V    N  S G  ++ FS+ + A  A   
Sbjct: 379 -----PNFDNEILDD-VKEECSKYGGVVHIYVD-TKN--SAGKIYLKFSSVDAALAAFQA 429

Query: 382 MN-----GKMV----VSKPLY 393
           +N     GKM+    V   +Y
Sbjct: 430 LNGRYFGGKMITAAFVVNDVY 450

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 71.1 bits (175), Expect = 1e-15
 Identities = 26/71 (36%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG+L     +  L DLF++ G + S+R+ RD  T RS G+ +V +    +A +AL+ L
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 102 NFTPLNGKPIR 112
           N   L G+ +R
Sbjct: 60  NGKELGGRELR 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 71.5 bits (176), Expect = 1e-15
 Identities = 31/72 (43%), Positives = 43/72 (59%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYVG+L  +V +  L DLF Q G+V S RV  D  T RS G+G+V    A EA  A+++L
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 102 NFTPLNGKPIRI 113
           N T   G+ + +
Sbjct: 62  NGTDFGGRTLTV 73

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

 Score = 70.0 bits (172), Expect = 3e-15
 Identities = 31/72 (43%), Positives = 47/72 (65%), Gaps = 1/72 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           LYV NL  +I++D L+ +F  FG I   ++ RDP  G S+G GF+ F+ AE+A KAL ++
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 383 NGKMVVSKPLYV 394
           NG  +  +P+ V
Sbjct: 61  NGFELAGRPIKV 72

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

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

 Score = 70.0 bits (172), Expect = 3e-15
 Identities = 28/78 (35%), Positives = 45/78 (57%), Gaps = 1/78 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           L+V+NL    +D++L+E FSE G I  C V++D      RG G+V F+  E+A +AL E 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 383 NGKMVVSKPLYVALAQRK 400
                  + ++V  A++K
Sbjct: 62  KKTKFGGRKIHVEFAKKK 79

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

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 77.4 bits (190), Expect = 4e-15
 Identities = 50/165 (30%), Positives = 83/165 (50%), Gaps = 9/165 (5%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
           VYV ++S    ED +++ F  FG I S  +  D A GK K F FV ++ P+ A  ++E +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 280 NGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLK 339
           NG+    +   VG+        M         ++E A KF    +YV ++   +S+  +K
Sbjct: 170 NGQMLGGRNIKVGRPSN-----MPQAQPIIDMVQEEAKKFN--RIYVASVHPDLSETDIK 222

Query: 340 ELFSEFGTITSCKVMRDPNGIS-RGSGFVAFSTAEEASKALTEMN 383
            +F  FG I  C++ R P G   +G GF+ ++  +  S+A+  MN
Sbjct: 223 SVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN 267

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

 Score = 69.5 bits (171), Expect = 4e-15
 Identities = 28/64 (43%), Positives = 41/64 (64%), Gaps = 1/64 (1%)

Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALNG 281
           V NLSE   EDDL+++F  FG I+   + +D + G+S+ F FV F   +DA R++E LNG
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

Query: 282 KKFD 285
             +D
Sbjct: 64  FGYD 67

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

 Score = 68.5 bits (168), Expect = 9e-15
 Identities = 23/72 (31%), Positives = 45/72 (62%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG+L     +  L +LF++ G++ SVR+ RD    +S G+ +V + +  +A +AL+ L
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 102 NFTPLNGKPIRI 113
           N   L+G+ +++
Sbjct: 60  NGKELDGRKLKV 71

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

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 68.2 bits (167), Expect = 1e-14
 Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           +++V +L   I  + L+  F+ FG I+  +V++D   G S+G GFV+F   E+A  A+  
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 382 MNGKMVVSKPL 392
           MNG+ +  + +
Sbjct: 61  MNGQWLGGRAI 71

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 68.1 bits (167), Expect = 1e-14
 Identities = 27/71 (38%), Positives = 43/71 (60%), Gaps = 2/71 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LYV NLD ++++D L ELFS+ G I SCK++R+         FV +     A+ AL  MN
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP--YAFVEYYDHRSAAAALQTMN 58

Query: 384 GKMVVSKPLYV 394
           G++++ + + V
Sbjct: 59  GRLILGQEIKV 69

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

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

 Score = 67.6 bits (166), Expect = 2e-14
 Identities = 27/78 (34%), Positives = 45/78 (57%), Gaps = 1/78 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
           ++V+NL   TT++ L++ F E G I    V++D    K + FG+V F   +DA R++E  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 280 NGKKFDDKEWYVGKAQKK 297
              KF  ++ +V  A+KK
Sbjct: 62  KKTKFGGRKIHVEFAKKK 79

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

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

 Score = 67.6 bits (166), Expect = 2e-14
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 7/74 (9%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LYV+NL  S ++++L+ELFSE+G +   K ++D         FV F   ++A KA+ EMN
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEEMN 56

Query: 384 GKMVVSKPLYVALA 397
           GK +   P+ V+LA
Sbjct: 57  GKELEGSPIEVSLA 70

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

 Score = 67.6 bits (166), Expect = 2e-14
 Identities = 29/72 (40%), Positives = 45/72 (62%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           +YVG+LD  V +  L++LF Q G VV+V + +D  T+   GYG+V + +  +A  A+  +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 102 NFTPLNGKPIRI 113
           N   L GKPIR+
Sbjct: 61  NMIKLYGKPIRV 72

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

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

 Score = 67.7 bits (166), Expect = 2e-14
 Identities = 27/74 (36%), Positives = 43/74 (58%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L V+NL    ++  LK+LFS FG +    + R P+G  +G  FV F++  +A KA+  +N
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 384 GKMVVSKPLYVALA 397
           GK +  +P+ V  A
Sbjct: 62  GKKIKGRPVAVDWA 75

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

 Score = 67.4 bits (165), Expect = 3e-14
 Identities = 30/76 (39%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           NL V  L  +++ D+++ LFS  G I SCK++RD   G S G GFV +   E+A KA+  
Sbjct: 3   NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINT 62

Query: 382 MNGKMVVSKPLYVALA 397
           +NG  + +K + V+ A
Sbjct: 63  LNGLRLQNKTIKVSYA 78

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|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 = 66.9 bits (164), Expect = 4e-14
 Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID 186
             +F+  L      K L   FS FG +    +  D   G+SRG+GFV F++ E A +AI 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 187 KLNGMLLNDKQVFV 200
            LNG  L  + + V
Sbjct: 62  DLNGKELEGRVIKV 75

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 67.0 bits (164), Expect = 4e-14
 Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDK 187
           +IF+ +L   ID + L   F+ FG I   +V  D   G+S+GYGFV F  +E A++AI  
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 188 LNGMLLNDKQV 198
           +NG  L  + +
Sbjct: 61  MNGQWLGGRAI 71

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

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

 Score = 66.8 bits (164), Expect = 4e-14
 Identities = 24/70 (34%), Positives = 45/70 (64%), Gaps = 1/70 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LYV+NL  S++++ L+E FS +G +   +++R+ +   RG  FV F++ E+A  AL ++N
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 384 GKMVVSKPLY 393
           G ++  + L 
Sbjct: 60  GLVLDGRTLR 69

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

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

 Score = 66.9 bits (164), Expect = 4e-14
 Identities = 33/76 (43%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSE-FGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           L+V +L   + D +L E FS+ + +    KV+ D NG SRG GFV FS   E  +ALTEM
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTEM 63

Query: 383 NGKMVV-SKPLYVALA 397
            G   +  KP+ V+LA
Sbjct: 64  QGASGLGGKPIRVSLA 79

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

 Score = 66.1 bits (162), Expect = 8e-14
 Identities = 27/65 (41%), Positives = 37/65 (56%)

Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGK 282
           V+NL    TE DLKK+F  FG +    + R  DGK K F FV F    DA ++++ +NGK
Sbjct: 4   VRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGK 63

Query: 283 KFDDK 287
           K   +
Sbjct: 64  KIKGR 68

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

 Score = 71.5 bits (174), Expect = 9e-14
 Identities = 41/175 (23%), Positives = 75/175 (42%), Gaps = 23/175 (13%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           + +L+VG+L   V +  L +LF + G V  VR+ RD  T +S G+ +V + +   A +A+
Sbjct: 115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAI 174

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAGN----------------------IFIKNLD 136
           +ELN   L G+P+R+  +      R   + N                      +++ NL 
Sbjct: 175 EELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLP 234

Query: 137 KSIDNKALHDTFSTFGNILSCKVATDSLG-QSRGYGFVQFDNEESAKSAIDKLNG 190
                + L D F + G+I+   +     G   +   FV  +  + A  +  + N 
Sbjct: 235 LKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNK 289

Length = 306

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

 Score = 65.9 bits (161), Expect = 9e-14
 Identities = 26/71 (36%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
            +F+ NL  S+D++ L   F  FG ++  +V TD   G+SRG+G+V F++ E AK AI+ 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 188 LNGMLLNDKQV 198
           ++G  L+ + +
Sbjct: 61  MDGKELDGRPI 71

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

>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 65.6 bits (161), Expect = 1e-13
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           LYV +L   +++  L E+FS  G + S +V RD     S G  +V F    +A +AL  +
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 383 NGKMVVSKPLYVALAQR 399
           N  ++  KP+ +  +QR
Sbjct: 62  NFDVIKGKPIRIMWSQR 78

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

 Score = 65.4 bits (160), Expect = 1e-13
 Identities = 29/61 (47%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALN 280
           YV NL    TEDDL+ IF  FG I    + RD + G+SK +GF+ F D +DA +++E LN
Sbjct: 2   YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 281 G 281
           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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 65.3 bits (160), Expect = 1e-13
 Identities = 23/67 (34%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV+NL  + TE+DL++ F  +G +    ++R+ D + + F FV F  P+DA  +++ LN
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 281 GKKFDDK 287
           G   D +
Sbjct: 60  GLVLDGR 66

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

>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 = 64.6 bits (158), Expect = 2e-13
 Identities = 28/72 (38%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           L++ +L +  +D  L +LF+ FG + S KV  D N G S+  GFV++   E A  A+  M
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 383 NGKMVVSKPLYV 394
           NG  V  K L V
Sbjct: 61  NGFQVGGKRLKV 72

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 65.1 bits (159), Expect = 2e-13
 Identities = 23/72 (31%), Positives = 39/72 (54%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VGDL   ++   L   F   G++   RV +D+ T +S GYG+V++    +A  A+  +
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 102 NFTPLNGKPIRI 113
           N   L G+ IR 
Sbjct: 62  NGQWLGGRAIRT 73

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 = 65.1 bits (159), Expect = 2e-13
 Identities = 30/76 (39%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
            L+V NL  S+ D+ LK  F +FGT+   +V+ D   G SRG G+V F + E+A KA+  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 382 MNGKMVVSKPLYVALA 397
           M+GK +  +P+ V  +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 65.1 bits (159), Expect = 2e-13
 Identities = 29/76 (38%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           NL V  L   ++ ++L+ LF   G I SCK++RD   G S G GFV +    +A KA+  
Sbjct: 2   NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT 61

Query: 382 MNGKMVVSKPLYVALA 397
           +NG  + +K L V+ A
Sbjct: 62  LNGFEIRNKRLKVSYA 77

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

 Score = 65.1 bits (159), Expect = 2e-13
 Identities = 23/69 (33%), Positives = 42/69 (60%), Gaps = 1/69 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+++L+ +F   G I S  ++RD   G+S  +GFV++ D +DA +++  
Sbjct: 2   NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT 61

Query: 279 LNGKKFDDK 287
           LNG +  +K
Sbjct: 62  LNGFEIRNK 70

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|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 = 65.0 bits (159), Expect = 2e-13
 Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEALN 280
           +V+NL  TTTE++L+++F  FG I+   +  D    +SK F FV+F  P+ A ++   L+
Sbjct: 3   FVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELD 62

Query: 281 GKKFD 285
           G  F 
Sbjct: 63  GSIFQ 67

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

 Score = 64.9 bits (159), Expect = 2e-13
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 4/74 (5%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           VYV NL    T+ +L+  F ++G + S  V R+  G    F FV F+DP DA  +V AL+
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPG----FAFVEFEDPRDAEDAVRALD 57

Query: 281 GKKFDDKEWYVGKA 294
           G++       V  +
Sbjct: 58  GRRICGNRVRVELS 71

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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 72.0 bits (176), Expect = 2e-13
 Identities = 75/289 (25%), Positives = 117/289 (40%), Gaps = 64/289 (22%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+  + + +    L   F   G I   ++  D  GQ+RGY FV F  +E AK A+  LN
Sbjct: 61  VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLN 120

Query: 190 ------GMLL------NDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKK 237
                 G LL      ++ ++FVG   + ++RE                          +
Sbjct: 121 NYEIRPGRLLGVCISVDNCRLFVGGIPKNKKRE--------------------------E 154

Query: 238 IFGEFGIIT----STAVMRDADGKSK--CFGFVNFDDPDDAARSVEALNGKKFDDKEWYV 291
           I  EF  +T       V   A  K K   F FV ++    AA +   L   +   + W  
Sbjct: 155 ILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRI--QLWGH 212

Query: 292 GKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEF--GTIT 349
             A    E E E+       +K          LYV+NL  + +++ +++ FSEF  G + 
Sbjct: 213 VIAVDWAEPEEEVDEDVMAKVKI---------LYVRNLMTTTTEEIIEKSFSEFKPGKVE 263

Query: 350 SCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ 398
             K +RD         FV F   E+A KA+ E+NGK +    + V LA+
Sbjct: 264 RVKKIRD-------YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAK 305

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

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

 Score = 64.6 bits (158), Expect = 3e-13
 Identities = 22/68 (32%), Positives = 43/68 (63%), Gaps = 7/68 (10%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV+NL  +TTE+ L+++F E+G +     ++D       + FV+F++ DDA +++E +N
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEEMN 56

Query: 281 GKKFDDKE 288
           GK+ +   
Sbjct: 57  GKELEGSP 64

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

 Score = 64.3 bits (157), Expect = 3e-13
 Identities = 26/71 (36%), Positives = 39/71 (54%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++V NLD  +   KLKE+F   G +    +  D  G SRG G V F    EA +A++  N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 384 GKMVVSKPLYV 394
           G+M+  +P+ V
Sbjct: 61  GQMLFDRPMRV 71

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

 Score = 64.2 bits (157), Expect = 4e-13
 Identities = 27/70 (38%), Positives = 45/70 (64%), Gaps = 1/70 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYV +LD S++D +L + F+  G + S +V  D    RS G+G+V +++  EAT+A+ E+
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKG-RSKGFGFVCFSSPEEATKAVTEM 62

Query: 102 NFTPLNGKPI 111
           N   + GKP+
Sbjct: 63  NGRIIGGKPL 72

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

 Score = 70.4 bits (172), Expect = 4e-13
 Identities = 59/260 (22%), Positives = 108/260 (41%), Gaps = 24/260 (9%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +LYV  L  ++   +L  +F+  GQ+++ R+  D  T  S G G++ ++   EA RA+  
Sbjct: 91  NLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKT 150

Query: 101 LNFTPLNG--KPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCK 158
           LN T  +G  +PI + ++  +P+   S      +  L+   + +      ST        
Sbjct: 151 LNGTTPSGCTEPITVKFA-NNPSSSNS---KGLLSQLEAVQNPQTTRVPLSTILTAAGIG 206

Query: 159 VATDSLGQSR-------GYGFVQFDNEESAKSAIDKLNGMLLNDKQV---FVGPFLRKQE 208
               +  + R            Q      A+    +       D Q      G  +    
Sbjct: 207 PMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQI---- 262

Query: 209 RESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFD 267
               A       ++V NLS  T E  L ++FG FG + +  ++RD    + K +GFV+  
Sbjct: 263 ---AASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMT 319

Query: 268 DPDDAARSVEALNGKKFDDK 287
           + D+AA ++ +LNG    ++
Sbjct: 320 NYDEAAMAILSLNGYTLGNR 339

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|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 = 64.2 bits (157), Expect = 5e-13
 Identities = 22/74 (29%), Positives = 40/74 (54%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
             L+V  L     + +L  LF++ G+V  V + +D  T  S G+G+V + +  +A  A+ 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 100 ELNFTPLNGKPIRI 113
           +LN   L G+ I++
Sbjct: 62  DLNGKELEGRVIKV 75

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

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

 Score = 64.2 bits (157), Expect = 5e-13
 Identities = 22/57 (38%), Positives = 38/57 (66%), Gaps = 1/57 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKAL 379
           ++++NL    ++++LKELFS+FG +   ++++D   G S+G+ FV F T E A K L
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59

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

 Score = 63.4 bits (155), Expect = 7e-13
 Identities = 27/70 (38%), Positives = 45/70 (64%), Gaps = 1/70 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           ++V +L + ++D+ L   FS++ +    KV+RD   G S+G GFV+FS   +  KA+ EM
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 383 NGKMVVSKPL 392
           NGK V ++P+
Sbjct: 69  NGKYVGNRPI 78

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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 63.5 bits (155), Expect = 8e-13
 Identities = 27/74 (36%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVV-SVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           S++VGDL   V D  L + F      V   +V  D  T RS GYG+V +    E  RAL 
Sbjct: 3   SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALT 62

Query: 100 ELNFTPLNGKPIRI 113
           E+N    + +P+R+
Sbjct: 63  EMNGVYCSSRPMRV 76

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

 Score = 63.0 bits (154), Expect = 9e-13
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKL 188
           +++  L + +D K LH  F  FG+I   ++  D    + RG+ FV+F+  E A +AID +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 189 NGMLLNDKQVFV 200
           N   L  + + V
Sbjct: 61  NESELFGRTIRV 72

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

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

 Score = 63.1 bits (154), Expect = 9e-13
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           IF+  +      + L D FS FG++   K+ TD  G S+GYGFV F+ +E A+  +   N
Sbjct: 5   IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAMGN 64

Query: 190 GMLLNDKQVFVGPFLRK 206
            +    K++ +GP +RK
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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 62.6 bits (153), Expect = 1e-12
 Identities = 28/73 (38%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+++ NL  ++  + L D F  FG + S +V TD   G+SRG+GFV+ +  E A +AI+K
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 188 LNGMLLNDKQVFV 200
           LNG     + + V
Sbjct: 61  LNGTDFGGRTLTV 73

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

 Score = 62.3 bits (152), Expect = 1e-12
 Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V NLS +  +DDL++ F E G +    + +D DG+SK FG V F   + A +++E  +
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-KS 60

Query: 281 GKKFDDKEWYVGKAQKK 297
           G++   +E  V  A ++
Sbjct: 61  GEELLGREIRVDLATER 77

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

 Score = 62.8 bits (153), Expect = 1e-12
 Identities = 27/77 (35%), Positives = 47/77 (61%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+L V  L  ++   ++  LF+ +G++ S ++ RD  T +SLGYG+VNY    +A +A++
Sbjct: 2   TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61

Query: 100 ELNFTPLNGKPIRIMYS 116
            LN   L  K I++ Y+
Sbjct: 62  TLNGLRLQNKTIKVSYA 78

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

 Score = 62.4 bits (152), Expect = 1e-12
 Identities = 25/69 (36%), Positives = 43/69 (62%), Gaps = 1/69 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+D+++ +F   G I S  ++RD   G+S  +GFVN+ DP+DA +++  
Sbjct: 3   NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINT 62

Query: 279 LNGKKFDDK 287
           LNG +  +K
Sbjct: 63  LNGLRLQNK 71

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 = 63.1 bits (154), Expect = 1e-12
 Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 4/79 (5%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVM----RDPNGISRGSGFVAFSTAEEASKA 378
            L++ NLD  +++  L +LFS++G I     +        G  RG  FV F T EEA KA
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 379 LTEMNGKMVVSKPLYVALA 397
           L  +NGK  + K L V  A
Sbjct: 61  LKSLNGKTALGKKLVVRWA 79

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

 Score = 63.1 bits (154), Expect = 1e-12
 Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 3/78 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           NLYV  L  +++  +L+ LFS +G I + +++ D   G+SRG GF+ F    EA +A+  
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 382 MNGKMVV--SKPLYVALA 397
           +NG +    ++P+ V  A
Sbjct: 62  LNGTIPPGATEPITVKFA 79

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

 Score = 62.8 bits (153), Expect = 1e-12
 Identities = 27/76 (35%), Positives = 47/76 (61%), Gaps = 1/76 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
           NL +  L  +++D++ + LF   G + +CK++RD   G S G GFV + +AE+A +A+  
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 382 MNGKMVVSKPLYVALA 397
           +NG  + +K + VA A
Sbjct: 62  LNGLQLQNKRIKVAYA 77

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

 Score = 62.7 bits (153), Expect = 1e-12
 Identities = 25/71 (35%), Positives = 40/71 (56%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++V+NL  S++   LK+LF E G +    V  D +G S+G G V F + E+A +A+   N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 384 GKMVVSKPLYV 394
           G  +  + L V
Sbjct: 61  GYDLEGRELEV 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|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 62.9 bits (153), Expect = 1e-12
 Identities = 25/73 (34%), Positives = 42/73 (57%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +++VGDL   V D+ L+  F+        RV  D+ + RS GYG+V++ +  +A  A++E
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 101 LNFTPLNGKPIRI 113
           +N   L  +PIR 
Sbjct: 61  MNGKWLGSRPIRC 73

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

 Score = 62.5 bits (152), Expect = 1e-12
 Identities = 28/71 (39%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           N++V +L   ++D  L   FS F + +  +VM D   G SRG GFV+F + ++A  A+ E
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 382 MNGKMVVSKPL 392
           MNGK + S+P+
Sbjct: 61  MNGKWLGSRPI 71

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

>gnl|CDD|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 = 62.7 bits (153), Expect = 1e-12
 Identities = 27/62 (43%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEF-GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           L VKNL  S+++ +LKE FS+  G IT  K++R  +G SR   F+ + T EEA KA    
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYF 62

Query: 383 NG 384
           N 
Sbjct: 63  NN 64

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

 Score = 62.4 bits (152), Expect = 2e-12
 Identities = 29/75 (38%), Positives = 47/75 (62%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG+L  SV+D  L   F + G VV  RV  D  T RS G+GYV++ +  +A +A++ +
Sbjct: 2   LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 102 NFTPLNGKPIRIMYS 116
           +   L+G+PI + +S
Sbjct: 62  DGKELDGRPINVDFS 76

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

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

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 28/68 (41%), Positives = 41/68 (60%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V+NL  + T  DLK +F E G +    V  D DG+SK FG V F+ P+DA R++E  N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 281 GKKFDDKE 288
           G   + +E
Sbjct: 61  GYDLEGRE 68

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

 Score = 62.3 bits (152), Expect = 2e-12
 Identities = 27/61 (44%), Positives = 36/61 (59%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L V NLD  +SDD +KELF+EFG +    V  D +G S G+  V F    +A KA+ + N
Sbjct: 3   LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQYN 62

Query: 384 G 384
           G
Sbjct: 63  G 63

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

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

 Score = 64.3 bits (156), Expect = 2e-12
 Identities = 33/93 (35%), Positives = 52/93 (55%)

Query: 36  QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEAT 95
           + +ST L++G L    +D+ L D F   G VV  +V  D  T RS G+G+VN+N    AT
Sbjct: 31  RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAAT 90

Query: 96  RALDELNFTPLNGKPIRIMYSYRDPTIRKSGAG 128
            A+ E++   LNG+ IR+  +   P+  ++  G
Sbjct: 91  AAISEMDGKELNGRHIRVNPANDRPSAPRAYGG 123

Length = 144

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

 Score = 62.3 bits (151), Expect = 2e-12
 Identities = 29/78 (37%), Positives = 49/78 (62%), Gaps = 3/78 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NLYV  L  +++  +L++LFS++G I + +++RD   G+SRG GF+ F    EA +A+  
Sbjct: 2   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 382 MNGKMVV--SKPLYVALA 397
           +NG+     S+P+ V  A
Sbjct: 62  LNGQKPEGASEPITVKFA 79

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

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 25/68 (36%), Positives = 40/68 (58%), Gaps = 1/68 (1%)

Query: 134 NLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKLNGML 192
            L      + L + FS +G I   +V  D   G+SRG+GFV F++ E AK A ++LNGM 
Sbjct: 6   GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGME 65

Query: 193 LNDKQVFV 200
           ++ +++ V
Sbjct: 66  IDGRRIRV 73

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

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

 Score = 61.1 bits (149), Expect = 4e-12
 Identities = 22/61 (36%), Positives = 32/61 (52%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           I +KNL K +    L + F + G +   KV     G+SR +GFV F +EE A+ A+   N
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 190 G 190
            
Sbjct: 63  K 63

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

 Score = 61.3 bits (149), Expect = 4e-12
 Identities = 28/73 (38%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+ +  L +++    +   FS+ G I SCK+  D + GQS GYGFV + + E A+ AI+ 
Sbjct: 3   NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINT 62

Query: 188 LNGMLLNDKQVFV 200
           LNG+ L +K + V
Sbjct: 63  LNGLRLQNKTIKV 75

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 67.7 bits (165), Expect = 4e-12
 Identities = 72/295 (24%), Positives = 132/295 (44%), Gaps = 45/295 (15%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
             ++VG +   + + +L  LF + G +  +R+  D S +   GY +V +    EA  A+ 
Sbjct: 59  CEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNR-GYAFVTFCGKEEAKEAVK 117

Query: 100 ELN-FTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFS--TFG--NI 154
            LN +    G+ + +  S  +          +F+  + K+   + + + FS  T G  ++
Sbjct: 118 LLNNYEIRPGRLLGVCISVDN--------CRLFVGGIPKNKKREEILEEFSKVTEGVVDV 169

Query: 155 LSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL--NGMLLNDKQVFVGPFLRKQEREST 212
           +    A D   ++RG+ FV++++  +A  A  KL    + L    + V       E E  
Sbjct: 170 IVYHSAADKK-KNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAV----DWAEPEEE 224

Query: 213 ADKTRFNNV---YVKNLSETTTEDDLKKIFGEF--GIITSTAVMRDADGKSKCFGFVNFD 267
            D+     V   YV+NL  TTTE+ ++K F EF  G +     +RD       + FV+F+
Sbjct: 225 VDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD-------YAFVHFE 277

Query: 268 DPDDAARSVEALNGKKFD------------DKEWYVGKAQKKYEREMELKGKFEQ 310
           D +DA ++++ LNGK+ +            DK+ YV   +    R  E +   + 
Sbjct: 278 DREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQS 332

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

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

 Score = 61.1 bits (149), Expect = 4e-12
 Identities = 28/67 (41%), Positives = 43/67 (64%), Gaps = 1/67 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITST-AVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           NVY++ L   TT++DL+K+   FG I ST A++     K K +GFV+FD P+ A +++E 
Sbjct: 2   NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEG 61

Query: 279 LNGKKFD 285
           LNG+   
Sbjct: 62  LNGRGVQ 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|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 61.3 bits (149), Expect = 4e-12
 Identities = 20/71 (28%), Positives = 40/71 (56%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+  L  S+  + L   F   G + S ++ T+  G+ +G  +V+++NE SA  A+ K++
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64

Query: 190 GMLLNDKQVFV 200
           G  + +K + V
Sbjct: 65  GTEIKEKTISV 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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 60.7 bits (148), Expect = 5e-12
 Identities = 26/62 (41%), Positives = 39/62 (62%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           IF++NL  S+  + L D F   GN+L   V TD+ G+S+G+G V F++ E A+ AI+  N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 190 GM 191
           G 
Sbjct: 61  GY 62

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

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 4/77 (5%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVM--RDPNGISRG--SGFVAFSTAEEASKA 378
           NLYV NL+  ++++ L + F  FG + S K+M  R      R    GFVAF    +A +A
Sbjct: 3   NLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERA 62

Query: 379 LTEMNGKMVVSKPLYVA 395
           L E++GK V+   L + 
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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 61.1 bits (149), Expect = 5e-12
 Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 6/78 (7%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVM--RDADGKSK---CFGFVNFDDPDDAAR 274
           N+YV NL+   TE+ L + FG FG + S  +M  R  + + +   C GFV F +  DA R
Sbjct: 3   NLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNC-GFVAFMNRADAER 61

Query: 275 SVEALNGKKFDDKEWYVG 292
           +++ L+GK     E  +G
Sbjct: 62  ALDELDGKDVMGYELKLG 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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 60.7 bits (148), Expect = 5e-12
 Identities = 26/71 (36%), Positives = 43/71 (60%), Gaps = 1/71 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+ NLD S+    L   FS  G I   ++  +  G+S+GY +V+F+NEES + A+ KL+
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEAL-KLD 60

Query: 190 GMLLNDKQVFV 200
             L+  + +FV
Sbjct: 61  RELIKGRPMFV 71

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

 Score = 61.0 bits (149), Expect = 5e-12
 Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 6/78 (7%)

Query: 324 LYVKNLDDSISDDKLK----ELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           LY+ NL++ I  D+LK     LFS+FG +      +      RG  FV F   E A+ AL
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLK--MRGQAFVVFKDVESATNAL 59

Query: 380 TEMNGKMVVSKPLYVALA 397
             + G     KP+ +  A
Sbjct: 60  RALQGFPFYDKPMRIQYA 77

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

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 60.8 bits (148), Expect = 5e-12
 Identities = 30/72 (41%), Positives = 43/72 (59%), Gaps = 5/72 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
           L++  L    +DD LK  FS++G IT C VM+DPN   SRG GFV F++A E   A+   
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNAR 61

Query: 381 --EMNGKMVVSK 390
             +++G+ V  K
Sbjct: 62  PHKVDGREVEPK 73

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

 Score = 61.1 bits (149), Expect = 6e-12
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 324 LYVKNLDDSISD-DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           L+V  L  +  D   L++LFS+ G  T C++   PNG  RG  FV ++TAE+A +A   +
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQAL 64

Query: 383 NGKMVVSKPLYVA 395
           NG  +   P+ V+
Sbjct: 65  NGHSLQGSPIRVS 77

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|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 60.4 bits (147), Expect = 7e-12
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV NL  T TED L ++F + G I S  ++R+       + FV + D   AA +++ +N
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP--YAFVEYYDHRSAAAALQTMN 58

Query: 281 GKKFDDKEWYVGKA 294
           G+    +E  V  A
Sbjct: 59  GRLILGQEIKVNWA 72

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

 Score = 60.5 bits (147), Expect = 7e-12
 Identities = 26/71 (36%), Positives = 38/71 (53%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           IF+ NLD  +  K L + F   G ++   +  D  G+SRG G VQF++   A  AI   N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 190 GMLLNDKQVFV 200
           G +L D+ + V
Sbjct: 61  GQMLFDRPMRV 71

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|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 = 60.6 bits (148), Expect = 7e-12
 Identities = 28/75 (37%), Positives = 46/75 (61%), Gaps = 4/75 (5%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           L+V  L  + +++ ++ LF E+G I    ++RD + G S+G  FV FS+ EEA KA+  +
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 383 NGKMV---VSKPLYV 394
           +GK+     S+PL V
Sbjct: 62  HGKVTMPGASRPLQV 76

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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 60.8 bits (148), Expect = 8e-12
 Identities = 29/78 (37%), Positives = 46/78 (58%), Gaps = 2/78 (2%)

Query: 322 LNLYVKNLDDSISDDKLKELFSE-FGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKAL 379
            +++V +L   ++D  L+E F   + ++   KV+ DP  G S+G GFV F   +E  +AL
Sbjct: 2   HSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRAL 61

Query: 380 TEMNGKMVVSKPLYVALA 397
           TEMNG    S+P+ V+ A
Sbjct: 62  TEMNGVYCSSRPMRVSPA 79

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

 Score = 60.5 bits (147), Expect = 8e-12
 Identities = 28/65 (43%), Positives = 43/65 (66%), Gaps = 1/65 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           ++V+NL  +  EDDL+K+F +FG ++   V  D   GKSK F +V F DP+DA ++ + L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 280 NGKKF 284
           +GK F
Sbjct: 65  DGKVF 69

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|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 = 60.3 bits (147), Expect = 8e-12
 Identities = 22/74 (29%), Positives = 41/74 (55%)

Query: 43  YVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN 102
           +VG++     + QL ++F+++G VVS R+  D  T +  GYG+  +     A  A+  LN
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 103 FTPLNGKPIRIMYS 116
               NG+ +R+ ++
Sbjct: 62  GYEFNGRALRVDFA 75

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

>gnl|CDD|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 = 60.3 bits (147), Expect = 9e-12
 Identities = 25/68 (36%), Positives = 44/68 (64%), Gaps = 1/68 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           +++ +L    T+ DL ++F  FG + S  V  D + G+SKCFGFV++D+P+ A  +++A+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 280 NGKKFDDK 287
           NG +   K
Sbjct: 61  NGFQVGGK 68

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

 Score = 60.4 bits (147), Expect = 9e-12
 Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           N+ +  L + +  + L   F   G I SCK+  D   GQS GYGFV + +E  A+ AI+ 
Sbjct: 2   NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT 61

Query: 188 LNGMLLNDKQVFV 200
           LNG  + +K++ 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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 60.4 bits (147), Expect = 9e-12
 Identities = 23/67 (34%), Positives = 40/67 (59%), Gaps = 1/67 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+++  L K++  + L   FS +G I++ ++  D++ G SRG GF++FD    A+ AI  
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 188 LNGMLLN 194
           LNG +  
Sbjct: 62  LNGTIPP 68

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

 Score = 60.3 bits (147), Expect = 1e-11
 Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFG------IITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
           ++VKNL+  TTE+ LKK F + G      I             S  +GFV F   + A +
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 275 SVEALNGKKFDD 286
           +++ L G   D 
Sbjct: 63  ALKRLQGTVLDG 74

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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 59.5 bits (145), Expect = 1e-11
 Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 5/69 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE- 381
           L++  L    +++ L+E FS++G +  C +M+DP  G SRG GFV F+      K L   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 382 ---MNGKMV 387
              ++G+ +
Sbjct: 61  PHVLDGREI 69

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

 Score = 59.2 bits (144), Expect = 2e-11
 Identities = 27/72 (37%), Positives = 46/72 (63%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYVG+L  ++ +  L  +F   G++  V++ RD  T RS GYG++ +  A +A +AL++L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 102 NFTPLNGKPIRI 113
           N   L G+PI++
Sbjct: 61  NGFELAGRPIKV 72

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

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

 Score = 59.6 bits (145), Expect = 2e-11
 Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEALNG 281
           V  LS  TTE DL+++F  +G I    V+ D   G+S+ FGFV F+  +DA  + E LNG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

Query: 282 KKFDDKE 288
            + D + 
Sbjct: 64  MEIDGRR 70

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|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 = 59.9 bits (145), Expect = 2e-11
 Identities = 28/77 (36%), Positives = 50/77 (64%), Gaps = 1/77 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEAL 279
           +++  LS  T E  L+++F ++G I+   V++D + + S+ FGFV F++PDDA  ++ A+
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 280 NGKKFDDKEWYVGKAQK 296
           NGK  D ++  V +A K
Sbjct: 63  NGKSVDGRQIRVDQAGK 79

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

 Score = 59.4 bits (144), Expect = 2e-11
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 3/77 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V  L    +++ ++ +F+ FG+I  C V+RD NG SRG  FV F++ + A  A+  M+
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 63

Query: 384 GKMVV---SKPLYVALA 397
               +   S PL V  A
Sbjct: 64  HSQTMEGCSSPLVVKFA 80

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

 Score = 59.2 bits (144), Expect = 2e-11
 Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           I++ ++   +    +   F  FG I SC +A D   G+ +GYGF++++N +SA+ AI  +
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 189 NGMLLNDKQVFVG 201
           N   L  +Q+ VG
Sbjct: 63  NLFDLGGQQLRVG 75

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

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 20/65 (30%), Positives = 36/65 (55%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           NLY+ NL   + +  L+ +   +G + S +++RD  G SRG GF    + E+    +++ 
Sbjct: 2   NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKF 61

Query: 383 NGKMV 387
           NGK +
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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
            ++V NL     E  L ++F  FG +T+  V+RD    K K +GFV   + ++A  ++ +
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 279 LNGKKFDDK 287
           LNG +   +
Sbjct: 63  LNGYRLGGR 71

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

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 22/78 (28%), Positives = 48/78 (61%), Gaps = 1/78 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVV-SVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           L++G+LD  V++  LYD F+  G ++ + ++ RD  T  S G+ +++Y++   +  A++ 
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 101 LNFTPLNGKPIRIMYSYR 118
           +N   L  +PI + Y+++
Sbjct: 64  MNGQYLCNRPITVSYAFK 81

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

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 4/76 (5%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKV----ATDSLGQSRGYGFVQFDNEESAKSA 184
            ++I NLD  +    L   FS +G I         +    GQ RGY FV F+ +E A+ A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 185 IDKLNGMLLNDKQVFV 200
           +  LNG     K++ V
Sbjct: 61  LKSLNGKTALGKKLVV 76

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

 Score = 58.7 bits (142), Expect = 3e-11
 Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           NIF+ +L   + +  L   FS F +    +V  D   G+SRGYGFV F +++ A++AI++
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 188 LNGMLLNDKQV 198
           +NG  L  + +
Sbjct: 61  MNGKWLGSRPI 71

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

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

 Score = 59.2 bits (144), Expect = 3e-11
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVAT------DSLGQSRGYGFVQFDNEESAKS 183
           +F+KNL+     + L   F   G + S  +A            S GYGFV+F ++E+A+ 
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 184 AIDKLNGMLLNDKQV 198
           A+ +L G +L+   +
Sbjct: 63  ALKRLQGTVLDGHAL 77

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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 5/67 (7%)

Query: 226 LSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA----LN 280
           LS  TTE+ L++ F ++G +    +M+D   G+S+ FGFV F DP    + + A    L+
Sbjct: 6   LSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPHVLD 65

Query: 281 GKKFDDK 287
           G++ D K
Sbjct: 66  GREIDPK 72

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|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 = 59.0 bits (143), Expect = 3e-11
 Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 3/77 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V  L    ++D ++ LF  FGTI  C ++R P+G S+G  FV FS+  EA  A+  ++
Sbjct: 4   LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63

Query: 384 GKMVV---SKPLYVALA 397
           G   +   S  L V  A
Sbjct: 64  GSQTMPGASSSLVVKFA 80

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

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 24/72 (33%), Positives = 43/72 (59%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L++GDL+  ++++ +Y  F + G+V SV++ R+  T +S GYG+V +     A +AL  
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 101 LNFTPLNGKPIR 112
           LN  P+     R
Sbjct: 61  LNGKPIPNTQQR 72

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

 Score = 58.7 bits (143), Expect = 3e-11
 Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           L+V  L  +++ D LKE+FS +GT+    +  D    + RG  +V F + E+A KA+  M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 383 NG 384
           +G
Sbjct: 61  DG 62

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

 Score = 58.7 bits (142), Expect = 3e-11
 Identities = 28/78 (35%), Positives = 47/78 (60%), Gaps = 1/78 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           L+V+NL  S++ + L + FS+   I    V+ DP  G SRG GFV F+  E+A +AL ++
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 383 NGKMVVSKPLYVALAQRK 400
             K +  + L + +A+R+
Sbjct: 62  KNKKLHGRILRLDIAERR 79

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

 Score = 58.2 bits (141), Expect = 4e-11
 Identities = 26/76 (34%), Positives = 49/76 (64%), Gaps = 1/76 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
            ++V NLS +  ++ LK  F +FG +    V+ D + G+S+ FG+V+F+ P+DA +++EA
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 279 LNGKKFDDKEWYVGKA 294
           ++GK+ D +   V  +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 58.8 bits (142), Expect = 4e-11
 Identities = 29/78 (37%), Positives = 46/78 (58%), Gaps = 3/78 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NLYV NL   +++D+L+++F  +G I  C ++RD   G+ RG  FV +   EEA  A++ 
Sbjct: 2   NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 382 MNGKMV--VSKPLYVALA 397
           +NG +    + PL V  A
Sbjct: 62  LNGTIPPGSTMPLSVRYA 79

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

 Score = 58.4 bits (142), Expect = 4e-11
 Identities = 24/73 (32%), Positives = 41/73 (56%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L V NL   ++++ L+ELF   G +   K+  D +G S G+  V F   E+A +A+ + N
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFN 62

Query: 384 GKMVVSKPLYVAL 396
           G ++  +P+ V L
Sbjct: 63  GVLLDGQPMQVEL 75

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

>gnl|CDD|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 = 58.7 bits (142), Expect = 4e-11
 Identities = 29/73 (39%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           N+FI +L +   +  L   F  FGN++S KV  D +  QS+ +GFV FDN  SA++AI  
Sbjct: 6   NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA 65

Query: 188 LNGMLLNDKQVFV 200
           +NG  +  K++ V
Sbjct: 66  MNGFQIGMKRLKV 78

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

 Score = 58.4 bits (142), Expect = 5e-11
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 6/70 (8%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN------GISRGSGFVAFSTAEEASK 377
           L+VKNL+   +++ LK+ F + G + S  + +  +       +S G GFV F + E A K
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 378 ALTEMNGKMV 387
           AL  + G ++
Sbjct: 63  ALKRLQGTVL 72

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

 Score = 57.8 bits (140), Expect = 5e-11
 Identities = 26/72 (36%), Positives = 44/72 (61%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG+L    ++  +Y+ F + G++ SVR+  D  + R  G+GYV +++   A  ALD L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 102 NFTPLNGKPIRI 113
             T L G+P+R+
Sbjct: 61  GGTDLLGRPVRL 72

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

 Score = 58.2 bits (141), Expect = 6e-11
 Identities = 26/77 (33%), Positives = 44/77 (57%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+L +  L  ++ D +   LF  +G V + ++ RD  T  S G+G+V+Y +A +A RA+ 
Sbjct: 1   TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 100 ELNFTPLNGKPIRIMYS 116
            LN   L  K I++ Y+
Sbjct: 61  TLNGLQLQNKRIKVAYA 77

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

 Score = 60.1 bits (145), Expect = 6e-11
 Identities = 29/74 (39%), Positives = 47/74 (63%), Gaps = 1/74 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +FI  L    D+ +L D F+ FG+++  KV  D   G+SRG+GFV F++E +A +AI ++
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 189 NGMLLNDKQVFVGP 202
           +G  LN + + V P
Sbjct: 97  DGKELNGRHIRVNP 110

Length = 144

>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 = 58.4 bits (142), Expect = 6e-11
 Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 6/87 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
           ++V  LS  TTE+ L+++F  +G I    ++RD   G SK + FV ++   DA R+    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 280 NGKKFDDKEWYVGKAQKKYEREMELKG 306
           +    D  E +V      +ERE  L G
Sbjct: 66  HKLVIDGSEIFV-----DFERERTLPG 87

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

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

 Score = 58.0 bits (141), Expect = 7e-11
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +F++NL     ++ L + FS  G I  C V  D    + RG+G+V F  EE AK A+++ 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 189 NGMLLNDKQVFV 200
                  +++ V
Sbjct: 62  KKTKFGGRKIHV 73

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

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 63.9 bits (155), Expect = 7e-11
 Identities = 39/172 (22%), Positives = 84/172 (48%), Gaps = 7/172 (4%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           +++ ++   +    +   F  FG I S  ++ D   G+ +G+ FV+++  E+A+ A++++
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 189 NGMLLNDKQVFVG-----PFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFG 243
           NG +L  + + VG     P  +        +  +FN +YV ++    +E D+K +F  FG
Sbjct: 170 NGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFG 229

Query: 244 IITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA 294
            I    + R   G   K +GF+ +++    + ++ ++N      +   VGK 
Sbjct: 230 EIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC 281

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

 Score = 58.1 bits (141), Expect = 7e-11
 Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFST-FGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +F+ +L   +D+  L++ FS  + +    KV  D  G SRGYGFV+F +E   K A+ ++
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTEM 63

Query: 189 NG 190
            G
Sbjct: 64  QG 65

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|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 = 57.6 bits (140), Expect = 7e-11
 Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 5/70 (7%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            +++ NL   +  + L  TFS FG I   +V  D     +GY FV+FD  E+A +AI  +
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAV 56

Query: 189 NGMLLNDKQV 198
           NG  +N + V
Sbjct: 57  NGTSINGQTV 66

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

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

 Score = 57.7 bits (140), Expect = 8e-11
 Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+ NL  S +   L + F   G ++  ++A D  G+S+G+G V+F  EE A+ A++K +
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEK-S 60

Query: 190 GMLLNDKQVFV 200
           G  L  +++ V
Sbjct: 61  GEELLGREIRV 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|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 57.5 bits (140), Expect = 8e-11
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 326 VKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEMNG 384
           V NL +   +D L+ELF  FG I+   + +D   G SRG  FV F T E+A +A+ ++NG
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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 57.3 bits (139), Expect = 9e-11
 Identities = 23/71 (32%), Positives = 47/71 (66%), Gaps = 1/71 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++V NLD S+ +D+L++LFS+ G IT  +++++  G S+G  +V F   E   +AL  ++
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALK-LD 60

Query: 384 GKMVVSKPLYV 394
            +++  +P++V
Sbjct: 61  RELIKGRPMFV 71

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

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

 Score = 57.2 bits (139), Expect = 1e-10
 Identities = 21/72 (29%), Positives = 39/72 (54%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYVG L   V++  L+  F   G +  +++  D  T++  G+ +V +    +A  A+D +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 102 NFTPLNGKPIRI 113
           N + L G+ IR+
Sbjct: 61  NESELFGRTIRV 72

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

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

 Score = 57.2 bits (139), Expect = 1e-10
 Identities = 23/70 (32%), Positives = 40/70 (57%)

Query: 47  LDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL 106
           L L   +  L ++F++ G +  V+V  D  T RS G+G+V + +  +A  A + LN   +
Sbjct: 7   LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEI 66

Query: 107 NGKPIRIMYS 116
           +G+ IR+ YS
Sbjct: 67  DGRRIRVDYS 76

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

>gnl|CDD|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 = 57.2 bits (139), Expect = 1e-10
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
            VYV NL    TE++L++ F  FG I    V +D     K + FV FD  + AA ++ A+
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAV 56

Query: 280 NGKKFDDK 287
           NG   + +
Sbjct: 57  NGTSINGQ 64

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

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 26/64 (40%), Positives = 40/64 (62%), Gaps = 1/64 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVEAL 279
           VYV NL  + T +DL KIF ++G +    +++D +  KSK   F+ F D +DA + V+AL
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 280 NGKK 283
           N K+
Sbjct: 64  NNKE 67

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

 Score = 57.6 bits (140), Expect = 1e-10
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 6/76 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGI--ITSTAVMRD-ADGKSKCFGFVNFDDPDDAARS 275
           N + ++ L   TTE+D+ +         I    ++RD   G S+ F FV F   +DA + 
Sbjct: 3   NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQW 62

Query: 276 VEALNGK---KFDDKE 288
           ++ALN       D + 
Sbjct: 63  MDALNNLDPFVIDGRV 78

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

 Score = 57.2 bits (139), Expect = 1e-10
 Identities = 17/66 (25%), Positives = 33/66 (50%), Gaps = 3/66 (4%)

Query: 324 LYVKNLDDSISDDKLKELFSEFG--TITSCKVMRDP-NGISRGSGFVAFSTAEEASKALT 380
           L ++ LD   +++ + +  S      I   +++RD   G SRG  FV F + E+A++ + 
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64

Query: 381 EMNGKM 386
            +N   
Sbjct: 65  ALNNLD 70

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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 57.1 bits (138), Expect = 1e-10
 Identities = 26/64 (40%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKA 378
           +   L+V  L+   SD  L+  F+ +G +T C VM DPN   SRG GF+ FS+A+EA +A
Sbjct: 1   QLCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

Query: 379 LTEM 382
           +   
Sbjct: 61  MEAQ 64

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

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           L V NL    +D++ +EL S FG +  C ++     G S+G GFV +++   A KA  ++
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 383 NGKMVVSKPLYVALA 397
           +GK +  + L V  A
Sbjct: 62  DGKQIGGRKLQVDWA 76

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

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 57.4 bits (138), Expect = 1e-10
 Identities = 24/69 (34%), Positives = 40/69 (57%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           NLY+ NL  S+ + +L+ +   FG + S +++RD NG+SRG GF    + E+    +   
Sbjct: 3   NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHF 62

Query: 383 NGKMVVSKP 391
           NGK + + P
Sbjct: 63  NGKYLKTPP 71

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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 57.1 bits (138), Expect = 1e-10
 Identities = 28/76 (36%), Positives = 43/76 (56%), Gaps = 2/76 (2%)

Query: 324 LYVKNLDDSISDDKLKELF-SEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           ++V +L   +++  L  LF S F +  S K+M DP  G+SRG GFV FS   +  +AL E
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 382 MNGKMVVSKPLYVALA 397
           M G     +P+ ++ A
Sbjct: 64  MQGVYCGGRPMRISTA 79

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

 Score = 56.4 bits (137), Expect = 2e-10
 Identities = 25/72 (34%), Positives = 46/72 (63%), Gaps = 1/72 (1%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T++YV +L   ++D +L +LF + G++ S +V +D    +S G+G+VN+     A +A++
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVE 60

Query: 100 ELNFTPLNGKPI 111
           ELN   +NGK +
Sbjct: 61  ELNGKEVNGKKL 72

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

>gnl|CDD|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 = 56.5 bits (137), Expect = 2e-10
 Identities = 20/62 (32%), Positives = 34/62 (54%)

Query: 52  NDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI 111
            D  LY LF   G V+S +V  D +T +S  +G+V+Y+    A  A+  +N   + GK +
Sbjct: 11  TDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRL 70

Query: 112 RI 113
           ++
Sbjct: 71  KV 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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 25/76 (32%), Positives = 44/76 (57%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+L V  L   +   +L  LF  +G + S ++ RD  T +SLGYG+V+Y   ++A +A++
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 100 ELNFTPLNGKPIRIMY 115
            LN   +  K +++ Y
Sbjct: 61  TLNGFEIRNKRLKVSY 76

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

>gnl|CDD|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 = 56.2 bits (136), Expect = 2e-10
 Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           L+V+NL  + ++++L+ELF  FG I+   +  D     S+G  FV+F   E A KA +E+
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 383 NGKMVVSKPLYV 394
           +G +   + L+V
Sbjct: 62  DGSIFQGRLLHV 73

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

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

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 25/79 (31%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N ++V  +   TTE++L+  F  FG +    ++ D  G SK +GFV F+  +DA + + A
Sbjct: 3   NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEK-ILA 61

Query: 279 LNGKKFDDKEWYVGKAQKK 297
           +    F  K+  +G A +K
Sbjct: 62  MGNLNFRGKKLNIGPAIRK 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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 1/65 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N+YV  L +T T+ +L+ +F  +G IITS  +  +  G S+  GF+ FD   +A R+++A
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 279 LNGKK 283
           LNG  
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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 23/65 (35%), Positives = 36/65 (55%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           N++I NL   +D + L      +G ++S ++  DS GQSRG GF + ++ E  +  I K 
Sbjct: 2   NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKF 61

Query: 189 NGMLL 193
           NG  L
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|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 = 56.5 bits (137), Expect = 2e-10
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 5/65 (7%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            +YV NL   +++++L+  FS FG I   +V +D     +G  FV F T E A+ A+  +
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAV 56

Query: 383 NGKMV 387
           NG  +
Sbjct: 57  NGTSI 61

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

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

 Score = 57.0 bits (137), Expect = 2e-10
 Identities = 27/73 (36%), Positives = 43/73 (58%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++V NLD  +   KLKE+FS  GT+    +  D +G SRG G V F    EA +A++  N
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62

Query: 384 GKMVVSKPLYVAL 396
           G+ +  +P++V +
Sbjct: 63  GQFLFDRPMHVKM 75

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|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 57.0 bits (137), Expect = 2e-10
 Identities = 24/69 (34%), Positives = 40/69 (57%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           NLY+ NL  S+ + +L+ +   FG + S +++RD +G SRG GF    + E+    +T  
Sbjct: 2   NLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEAIITHF 61

Query: 383 NGKMVVSKP 391
           NGK + + P
Sbjct: 62  NGKYIKTPP 70

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

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 5/75 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKS----KCFGFVNFDDPDDAARSV 276
           +YV+NL     EDDL+ IF +FG + S  + +  D K       F FV F D   A  ++
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 277 EALNGKKFDDKEWYV 291
           + LNG +   ++  V
Sbjct: 63  Q-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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 26/61 (42%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           IF+  L     + +L   FS FG I    V TD   G+SRGYGFV F ++ESA+ A    
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62

Query: 189 N 189
           N
Sbjct: 63  N 63

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

>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 56.4 bits (137), Expect = 3e-10
 Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEALN 280
           YV +L    TE  L +IF   G + S  V RD    +S  + +VNF +P DA R+++ LN
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 55.8 bits (135), Expect = 3e-10
 Identities = 22/64 (34%), Positives = 40/64 (62%), Gaps = 1/64 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           +++V +LS     + L+  F  FG I+   V++D   GKSK +GFV+F   +DA  ++++
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 279 LNGK 282
           +NG+
Sbjct: 61  MNGQ 64

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

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           V+++NL    TE++LK++F +FG +    +++D   G SK   FV F   + A + +EA 
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 280 NGKKFDD 286
           +  +   
Sbjct: 63  DNAEDSG 69

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

 Score = 56.0 bits (136), Expect = 3e-10
 Identities = 17/69 (24%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
           ++V  L+    +D LK+IF  +G +    +  D      + + +V F+ P+DA ++++ +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 280 NGKKFDDKE 288
           +G + D +E
Sbjct: 61  DGGQIDGQE 69

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

 Score = 56.2 bits (136), Expect = 3e-10
 Identities = 27/69 (39%), Positives = 42/69 (60%), Gaps = 3/69 (4%)

Query: 332 SISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVS- 389
           S+++D L+E F+ FG I    V++D     S+G  +V F+ A  A++A+ EMNGK +   
Sbjct: 13  SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72

Query: 390 -KPLYVALA 397
            KPL V +A
Sbjct: 73  TKPLKVLIA 81

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

 Score = 55.6 bits (134), Expect = 3e-10
 Identities = 23/68 (33%), Positives = 39/68 (57%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV NL    TED LK+IF   G + +  ++ D + K   +GFV +    DA  +++ LN
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 281 GKKFDDKE 288
           G++ ++ E
Sbjct: 61  GRQIENNE 68

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|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 = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           +++ NL  +I    L   F  FG I   ++  D   G+S+GYGF+QF + E AK A+++L
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 189 NGMLLNDKQVFVG 201
           NG  L  + + VG
Sbjct: 61  NGFELAGRPIKVG 73

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

 Score = 55.9 bits (135), Expect = 4e-10
 Identities = 20/74 (27%), Positives = 45/74 (60%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V  L  S++ ++L++LF + G + S +++ + +G  +G  +V +     AS+A+ +M+
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64

Query: 384 GKMVVSKPLYVALA 397
           G  +  K + VA++
Sbjct: 65  GTEIKEKTISVAIS 78

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

 Score = 55.8 bits (135), Expect = 4e-10
 Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKAL 379
           G  ++V NL     +  L +LFS FG +T+ KV+RD      +G GFV  +  EEA  A+
Sbjct: 1   GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

Query: 380 TEMNGKMVVSKPLYVAL 396
             +NG  +  + L V+ 
Sbjct: 61  ASLNGYRLGGRVLQVSF 77

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

 Score = 56.1 bits (136), Expect = 4e-10
 Identities = 19/72 (26%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           +F+  L      + L + FS +G+I   ++  D + G S+GY FV++++E  A  A    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 189 NGMLLNDKQVFV 200
           + ++++  ++FV
Sbjct: 66  HKLVIDGSEIFV 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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITS----CKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +YV+NLD  + +D L+ +FS+FG + S     K       ++ G  FV F  A  A  AL
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 380 TEMNGKMVVSKPLYVAL 396
            ++NG  +  + + V+L
Sbjct: 63  -QLNGTELGGRKISVSL 78

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

 Score = 55.8 bits (134), Expect = 4e-10
 Identities = 26/73 (35%), Positives = 44/73 (60%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++V NLD  +   KLKE+FS  G +    ++ D +G SRG G V F    EA +A++  N
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFN 62

Query: 384 GKMVVSKPLYVAL 396
           G+++  +P++V +
Sbjct: 63  GQLLFDRPMHVKM 75

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

 Score = 55.6 bits (135), Expect = 4e-10
 Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           S++VG+L   + + +L   F   G V +VR+ RD  T    G+GYV +        AL +
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-K 59

Query: 101 LNFTPLNGKPIRIM 114
           LN   L G+ IR+ 
Sbjct: 60  LNGIKLKGRKIRVK 73

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

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

 Score = 55.6 bits (134), Expect = 4e-10
 Identities = 26/79 (32%), Positives = 46/79 (58%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N ++V  +   T E+DL+K F ++G +    ++ D  G SK +GFV F+  +DA + ++ 
Sbjct: 3   NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQE 62

Query: 279 LNGKKFDDKEWYVGKAQKK 297
            N   F DK+  +G+A +K
Sbjct: 63  ANRLCFRDKKLNIGQAIRK 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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 55.9 bits (134), Expect = 4e-10
 Identities = 29/77 (37%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+++ K +FG  G I S  ++RD   G+S  +GFVN+ DP+DA +++  
Sbjct: 5   NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 279 LNGKKFDDKEWYVGKAQ 295
           LNG K   K   V  A+
Sbjct: 65  LNGLKLQTKTIKVSYAR 81

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

 Score = 55.3 bits (134), Expect = 5e-10
 Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           N++I+ L  +  ++ L      FG I+S K   D    + +GYGFV FD+ E+A  AI+ 
Sbjct: 2   NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEG 61

Query: 188 LNGM 191
           LNG 
Sbjct: 62  LNGR 65

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

 Score = 55.5 bits (134), Expect = 5e-10
 Identities = 16/69 (23%), Positives = 42/69 (60%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           + ++V  L  + T+++L+K+F + G++ S  ++ +  GK K   +V +++   A+++V  
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLK 62

Query: 279 LNGKKFDDK 287
           ++G +  +K
Sbjct: 63  MDGTEIKEK 71

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

 Score = 55.7 bits (135), Expect = 5e-10
 Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKS-IDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +F+  L K+  D   L   FS  G    C++A    GQ RG+ FV++   E A+ A   L
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQAL 64

Query: 189 NGMLLNDKQVFV 200
           NG  L    + V
Sbjct: 65  NGHSLQGSPIRV 76

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

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

 Score = 55.4 bits (134), Expect = 5e-10
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L+VG+LD  V +  LY+LF Q G +  V++ +D +  +   + +V +        A+  
Sbjct: 3   TLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAIQL 61

Query: 101 LNFTPLNGKPIRI 113
           LN   L G+ +RI
Sbjct: 62  LNGIRLFGRELRI 74

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

>gnl|CDD|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 = 54.9 bits (133), Expect = 6e-10
 Identities = 26/65 (40%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           V+V N+    TE+ L +IF E G + S  ++ D D GK K +GF  F+D + AA ++  L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 280 NGKKF 284
           NG +F
Sbjct: 61  NGYEF 65

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

 Score = 55.0 bits (133), Expect = 6e-10
 Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
           N +YV ++    +EDD+K +F  FG I S ++  D + GK K +GF+ +++P  A  ++ 
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 278 ALNGKKFDDKEWYVGKA 294
           ++N      ++  VGKA
Sbjct: 61  SMNLFDLGGQQLRVGKA 77

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

 Score = 55.2 bits (133), Expect = 6e-10
 Identities = 25/77 (32%), Positives = 42/77 (54%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           IF+  +D   +   L   FS +G +   K+  D  G S+GYGFV F+ +E A+  + + N
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEAN 64

Query: 190 GMLLNDKQVFVGPFLRK 206
            +   DK++ +G  +RK
Sbjct: 65  RLCFRDKKLNIGQAIRK 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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 55.0 bits (133), Expect = 6e-10
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSV--- 276
           ++V  L E  TE+DL++ F ++G + S  ++ D + GK + F FV FDD D   + V   
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQK 61

Query: 277 -EALNGKKFDDK 287
              +NG + + K
Sbjct: 62  YHTINGHRVEVK 73

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

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

 Score = 54.9 bits (133), Expect = 6e-10
 Identities = 25/66 (37%), Positives = 37/66 (56%), Gaps = 8/66 (12%)

Query: 130 IFIKNLDKSIDNKA-LHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +F+ NL+    +K  L + FS +G IL   +        +GYGFVQFDNEE A++A+   
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISL-------HKGYGFVQFDNEEDARAAVAGE 55

Query: 189 NGMLLN 194
           NG  + 
Sbjct: 56  NGREIA 61

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

 Score = 55.1 bits (132), Expect = 6e-10
 Identities = 30/77 (38%), Positives = 46/77 (59%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+L V  L  ++   +L  LF+ +G+V S ++ RD     SLGYG+VNY  A +A RA++
Sbjct: 2   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61

Query: 100 ELNFTPLNGKPIRIMYS 116
            LN   L  K I++ Y+
Sbjct: 62  TLNGLRLQSKTIKVSYA 78

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

 Score = 55.3 bits (134), Expect = 7e-10
 Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 3/81 (3%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITS-TAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           V+V N+ E  ++D ++K+  + G + S   V   + GK K FGF  F+DP+ A R++  L
Sbjct: 3   VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLL 62

Query: 280 NGKKFDDKEWYV--GKAQKKY 298
           NG +   K+  V      +K 
Sbjct: 63  NGLELGGKKLLVKVDAKTRKL 83

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

 Score = 54.9 bits (132), Expect = 8e-10
 Identities = 23/65 (35%), Positives = 43/65 (66%), Gaps = 1/65 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           N+YV  L +T T+ +L+++F ++G I ++ ++RD   G S+  GF+ FD   +A  +++ 
Sbjct: 2   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 279 LNGKK 283
           LNG+K
Sbjct: 62  LNGQK 66

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|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 = 54.6 bits (132), Expect = 8e-10
 Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +F+ N+      + L + FS  G ++S ++ TD   G+ +GYGF +F++ E+A SAI  L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 189 NGMLLNDKQVFVGP 202
           NG   N + + V  
Sbjct: 61  NGYEFNGRALRVDF 74

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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 55.1 bits (132), Expect = 8e-10
 Identities = 23/69 (33%), Positives = 40/69 (57%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           NLY+ NL  S+ + +L+ +   FG + S +++RD +G SRG GF    + E+    ++  
Sbjct: 2   NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHF 61

Query: 383 NGKMVVSKP 391
           NGK + + P
Sbjct: 62  NGKFIKTPP 70

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

 Score = 54.5 bits (132), Expect = 9e-10
 Identities = 21/68 (30%), Positives = 36/68 (52%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           + V NL    TE+DL+++FG  G +    +  D  G+S+    V F+  +DA R+++  N
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFN 62

Query: 281 GKKFDDKE 288
           G   D + 
Sbjct: 63  GVLLDGQP 70

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|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 54.5 bits (132), Expect = 1e-09
 Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 131 FIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKLN 189
           ++ +L   +    L++ FS  G +LS +V  D +  +S GY +V F N   A+ A+D LN
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 190 GMLLNDK 196
             ++  K
Sbjct: 63  FDVIKGK 69

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 20/69 (28%), Positives = 44/69 (63%), Gaps = 1/69 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           ++++NL  S+  + L + FS +G +   ++  +   + RG+ FV+F + E A++A+ KLN
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 190 GMLLNDKQV 198
           G++L+ + +
Sbjct: 60  GLVLDGRTL 68

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

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

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYV +L  SV +  L + F+  G+V  VR+ R+    R  G+ +V + +  +A  AL +L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKL 58

Query: 102 NFTPLNGKPIR 112
           N   L+G+ +R
Sbjct: 59  NGLVLDGRTLR 69

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

>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 = 20/71 (28%), Positives = 35/71 (49%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V NL        LK++F   G +    +  D +GKS+  G V F+ P +A +++   N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 281 GKKFDDKEWYV 291
           G+   D+   V
Sbjct: 61  GQMLFDRPMRV 71

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|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 = 54.2 bits (131), Expect = 1e-09
 Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 223 VKNLSETTTEDDLKKIFGEF-GIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNG 281
           VKNL  + TE +LK+ F +  G IT   ++R  DGKS+   F+ +   ++A ++ +  N 
Sbjct: 5   VKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYFNN 64

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|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 = 54.5 bits (131), Expect = 1e-09
 Identities = 23/72 (31%), Positives = 42/72 (58%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L++G L    N+  L  +F++ GQ+  V V +D  T+RS G+G+V +    +A  A+  +
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 102 NFTPLNGKPIRI 113
           N   ++G+ IR+
Sbjct: 63  NGKSVDGRQIRV 74

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

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

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 24/63 (38%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           L++ +L+  + +  +   F+E G +TS K++R+   G S G GFV F+T E A +AL  +
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 383 NGK 385
           NGK
Sbjct: 62  NGK 64

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 54.7 bits (131), Expect = 1e-09
 Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
           L++  L    +D+ L+  F ++GT+T C VMRDPN   SRG GFV +S+ EE   A+   
Sbjct: 5   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNAR 64

Query: 381 --EMNGKMVVSK 390
             +++G++V  K
Sbjct: 65  PHKVDGRVVEPK 76

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 54.7 bits (132), Expect = 1e-09
 Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 6/77 (7%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGI----ITSTAVMRDADGKSKCFG--FVNFDDPDDAAR 274
           VY+ NLS +++E+DL++   +F      I S  V      + +  G  +  F  P+ A +
Sbjct: 2   VYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEK 61

Query: 275 SVEALNGKKFDDKEWYV 291
            V+ LNGK F +++ +V
Sbjct: 62  VVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

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

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 21/67 (31%), Positives = 43/67 (64%), Gaps = 7/67 (10%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V NL + TT ++L+ +F ++G +T   V+++       +GFV+ ++ +DA  +++ALN
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN-------YGFVHMEEEEDAEDAIKALN 54

Query: 281 GKKFDDK 287
           G +F  K
Sbjct: 55  GYEFMGK 61

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|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 5/68 (7%)

Query: 332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
            ++++ LK+ FS FG I +  + ++     +  GFV F   E A +A+ E+NG  V    
Sbjct: 13  GLTEEILKKAFSPFGNIINISMEKE-----KNCGFVTFEKMESADRAIAELNGTTVQGVQ 67

Query: 392 LYVALAQR 399
           L V+LA++
Sbjct: 68  LKVSLARK 75

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

 Score = 54.4 bits (130), Expect = 1e-09
 Identities = 29/77 (37%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+++LK +FG  G I S  ++RD   G+S  +GFVN+ DP DA +++  
Sbjct: 6   NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65

Query: 279 LNGKKFDDKEWYVGKAQ 295
           LNG +   K   V  A+
Sbjct: 66  LNGLRLQTKTIKVSYAR 82

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

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVE 277
           N ++V  L+  TT++DL+ IF  FG I S  V+RD   G S  + F+ F+  +D   +  
Sbjct: 4   NVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYF 63

Query: 278 ALNGKKFDDKEWYV 291
            ++    DD+  +V
Sbjct: 64  KMDNVLIDDRRIHV 77

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

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

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 4/57 (7%)

Query: 144 LHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
           L+  FS FGN+   K+    L +  G+ FV+F  EE+A+ A+  LNG+L   + + V
Sbjct: 1   LYKLFSPFGNVEKIKL----LKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53

(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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 23/75 (30%), Positives = 44/75 (58%), Gaps = 2/75 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFST-FGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           IF+ +L   + +  L +TF   + ++   KV  D + G+S+GYGFV+F +E+    A+ +
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 188 LNGMLLNDKQVFVGP 202
           +NG+  + + + V P
Sbjct: 64  MNGVYCSSRPMRVSP 78

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

 Score = 54.1 bits (130), Expect = 2e-09
 Identities = 27/68 (39%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKL 188
           +F++NL  S+  + L D FS    I    V TD   G+SRGYGFV F   E A+ A+ KL
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 189 NGMLLNDK 196
               L+ +
Sbjct: 62  KNKKLHGR 69

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 53.7 bits (129), Expect = 2e-09
 Identities = 23/73 (31%), Positives = 37/73 (50%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L+V +L  SV    L D F+ +  +    V  D  T  S GYG+V +    +A  AL +
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60

Query: 101 LNFTPLNGKPIRI 113
           L    L+G+ +R+
Sbjct: 61  LKNKKLHGRILRL 73

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 7/71 (9%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V NL D+ + ++L+ LF ++GT+T C V+++        GFV     E+A  A+  +N
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN-------YGFVHMEEEEDAEDAIKALN 54

Query: 384 GKMVVSKPLYV 394
           G   + K + V
Sbjct: 55  GYEFMGKRINV 65

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

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

 Score = 53.8 bits (129), Expect = 2e-09
 Identities = 28/73 (38%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           N+FI +L +   +  L  TF  FGN++S KV  D     S+ +GFV +DN +SA++AI  
Sbjct: 6   NLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQA 65

Query: 188 LNGMLLNDKQVFV 200
           +NG  +  K++ 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|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 54.1 bits (131), Expect = 2e-09
 Identities = 23/55 (41%), Positives = 33/55 (60%), Gaps = 2/55 (3%)

Query: 235 LKKIFGEFGIITSTAVM--RDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDK 287
           L+KIF +FG+     +    D  GK+K + FV F  P++A  +V+ALNG K D K
Sbjct: 24  LRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKLDKK 78

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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 54.0 bits (129), Expect = 2e-09
 Identities = 29/72 (40%), Positives = 44/72 (61%), Gaps = 5/72 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
           L++  L    +DD L+E F ++GT+T C VMRDP    SRG GFV +S  EE   A++  
Sbjct: 5   LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSAR 64

Query: 381 --EMNGKMVVSK 390
             +++G++V  K
Sbjct: 65  PHKVDGRVVEPK 76

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 53.5 bits (129), Expect = 2e-09
 Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           +L V  L    ++  LK+ FS FG +   +V +DP  G S+G GFV F+  E+  K L++
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

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

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 53.5 bits (128), Expect = 2e-09
 Identities = 25/77 (32%), Positives = 44/77 (57%), Gaps = 3/77 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFST---AEEASKALT 380
           L++  +    +++ ++ +FS FG I  C+++R P+G+SRG  FV F+T   A+ A KA+ 
Sbjct: 4   LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63

Query: 381 EMNGKMVVSKPLYVALA 397
           +       S P+ V  A
Sbjct: 64  QAQTMEGCSSPIVVKFA 80

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), 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 binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 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 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 preferentially binds 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 contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also 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 = 81

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 58.4 bits (141), Expect = 3e-09
 Identities = 32/119 (26%), Positives = 55/119 (46%), Gaps = 4/119 (3%)

Query: 1   MAQVQVQPQAPVAVAAQPSP-ATNGIANNGGVGDARQFVSTS---LYVGDLDLSVNDSQL 56
             Q Q    A    A + SP AT+G       G        +   ++V +L    +++ L
Sbjct: 227 AHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVL 286

Query: 57  YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY 115
           + LF   G V +V++ RDL+T +  GYG+V+     EA  A+  LN   L  + +++ +
Sbjct: 287 WQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSF 345

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

 Score = 53.1 bits (128), Expect = 3e-09
 Identities = 23/63 (36%), Positives = 35/63 (55%)

Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGK 282
           VKNL +   ED L+K+F  FG IT   +    DGK + FGFV +   ++A ++++  N  
Sbjct: 5   VKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNS 64

Query: 283 KFD 285
             D
Sbjct: 65  FID 67

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

 Score = 53.3 bits (129), Expect = 3e-09
 Identities = 26/60 (43%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 132 IKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKLNG 190
           + NL +  D   L + F  FG I    +A D   GQSRG+ FV F   E A+ AI+KLNG
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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           +YV NL    +  +L++ F ++G + S  V R+P G      FV F    +A  A+  ++
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGF----AFVEFEDPRDAEDAVRALD 57

Query: 384 GKMVVSKPLYVALAQR 399
           G+ +    + V L++ 
Sbjct: 58  GRRICGNRVRVELSRG 73

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

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

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           +YV ++   +S+D +K +F  FG I SC +  DP  G  +G GF+ +   + A  A+  M
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 383 NG 384
           N 
Sbjct: 63  NL 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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 52.9 bits (128), Expect = 3e-09
 Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           + +  L ++++   L + FS +G +    +  D      RGY +V+F++ E A+ AI  +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 189 NGMLLNDKQVFV 200
           +G  ++ ++V V
Sbjct: 61  DGGQIDGQEVTV 72

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|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 = 52.9 bits (127), Expect = 3e-09
 Identities = 24/63 (38%), Positives = 41/63 (65%), Gaps = 1/63 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           N+++ +L +   + +L ++F  FG + S  V  D A  +SKCFGFV+FD+P  A  +++A
Sbjct: 6   NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA 65

Query: 279 LNG 281
           +NG
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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
           ++V  L    +DD L++ FS+FG I    V+ D   G SRG GFV F   E A +A  + 
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62

Query: 383 NGKMVVSKPLYVALA 397
           N  ++  +   V LA
Sbjct: 63  N-PIIDGRKANVNLA 76

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

 Score = 52.9 bits (128), Expect = 3e-09
 Identities = 21/71 (29%), Positives = 42/71 (59%), Gaps = 2/71 (2%)

Query: 325 YVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMN 383
           +V NL   I +++L++ F + G + + +++RD   GI +G G+V F T +  + AL ++N
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KLN 61

Query: 384 GKMVVSKPLYV 394
           G  +  + + V
Sbjct: 62  GIKLKGRKIRV 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|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 53.6 bits (128), Expect = 3e-09
 Identities = 28/77 (36%), Positives = 46/77 (59%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+L V  L  ++   +L  LF  +G++ S ++ RD  T +SLGYG+VNY    +A +A++
Sbjct: 5   TNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 64

Query: 100 ELNFTPLNGKPIRIMYS 116
            LN   L  K I++ Y+
Sbjct: 65  TLNGLRLQTKTIKVSYA 81

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

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 20/54 (37%), Positives = 34/54 (62%), Gaps = 1/54 (1%)

Query: 148 FSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
           FS FG I SC+V  D   G S  Y F++F+ +E  + A  K++ +L++D+++ V
Sbjct: 24  FSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRIHV 77

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

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

 Score = 53.0 bits (127), Expect = 4e-09
 Identities = 25/63 (39%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+++  L K++  K L   FS +G I++ ++  D L G SRG GF++FD    A+ AI  
Sbjct: 2   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 188 LNG 190
           LNG
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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 52.7 bits (127), Expect = 4e-09
 Identities = 25/72 (34%), Positives = 42/72 (58%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++V +L    ++S L+ LF+  G V +V+V RDL+T +  GYG+V      EA  A+  L
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 102 NFTPLNGKPIRI 113
           N   L G+ +++
Sbjct: 64  NGYRLGGRVLQV 75

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

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

 Score = 53.0 bits (127), Expect = 4e-09
 Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+++ NL + +    L   F  +GNI+ C +  D   G  RG  FV++D  E A++AI  
Sbjct: 2   NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 188 LNGML 192
           LNG +
Sbjct: 62  LNGTI 66

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|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 = 23/75 (30%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNI----LSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
           I+++NLD  +D   L   FS FG +    +  K        + G+ FV F +  SA++A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 186 DKLNGMLLNDKQVFV 200
            +LNG  L  +++ V
Sbjct: 63  -QLNGTELGGRKISV 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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 52.8 bits (126), Expect = 4e-09
 Identities = 29/77 (37%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NL V  L  +++ D+L+ LFS  G + S K++RD   G S G GFV +  A++A +A+  
Sbjct: 3   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62

Query: 382 MNGKMVVSKPLYVALAQ 398
           +NG  + SK + V+ A+
Sbjct: 63  LNGLRLQSKTIKVSYAR 79

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 52.1 bits (126), Expect = 4e-09
 Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 4/60 (6%)

Query: 338 LKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA 397
           L +LFS FG +   K+++       G  FV FST E A KA+  +NG +   +PL V  +
Sbjct: 1   LYKLFSPFGNVEKIKLLKK----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

>gnl|CDD|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 = 52.7 bits (127), Expect = 4e-09
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++V  LD ++++D+L+ LF  FG I   K+   P G  +G GFV F     A  A+ ++ 
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKI---PPG--KGCGFVQFVHRAAAEAAIQQLQ 58

Query: 384 GKMVVSKPLYVA 395
           G ++    + ++
Sbjct: 59  GTIIGGSRIRLS 70

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

 Score = 52.6 bits (127), Expect = 5e-09
 Identities = 23/68 (33%), Positives = 42/68 (61%), Gaps = 1/68 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           +++ +LD S+++  LYD F+  G ++S +V  D +   S GYG+V++     A RA++++
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDEN-GGSKGYGFVHFETEEAAVRAIEKV 63

Query: 102 NFTPLNGK 109
           N   LN K
Sbjct: 64  NGMLLNDK 71

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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 52.6 bits (127), Expect = 5e-09
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           +FI  L      ++L + FS +G ++ C +  D + G+SRG+GFV F +  S    +   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 189 NGMLLNDKQV 198
              +L+ +++
Sbjct: 61  P-HVLDGREI 69

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

 Score = 52.6 bits (127), Expect = 5e-09
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +++V  L L V +  LY+ F++ G+V  VR+ RD ++RRS G  YV +        AL  
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-G 59

Query: 101 LNFTPLNGKPIRIM 114
           L    L G+PI + 
Sbjct: 60  LTGQRLLGQPIMVQ 73

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|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 = 52.3 bits (126), Expect = 5e-09
 Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 5/78 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L++ +L   ++++ LK LF E+G I S  ++       RG  +V   T ++A +AL ++ 
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI-----PPRGCAYVCMETRQDAHRALQKLR 59

Query: 384 GKMVVSKPLYVALAQRKE 401
              +  K + VA A  K 
Sbjct: 60  NVKLAGKKIKVAWAPNKG 77

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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 58.0 bits (140), Expect = 5e-09
 Identities = 46/192 (23%), Positives = 82/192 (42%), Gaps = 25/192 (13%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVE 277
           + +Y+ NL     ED +K++   FG + +  +++D A G SK + F  + DP     ++ 
Sbjct: 296 DRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIA 355

Query: 278 ALNGKKFDDKEWYV-----GKAQKKYERE------MELKGKFEQSLKETADK-FEGLNLY 325
           ALNGK   D + +V     G  Q   +          L     QS+ +   K  + + L 
Sbjct: 356 ALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLT 415

Query: 326 VKNLDDSISDDK--------LKELFSEFGTITSCKVMRDPNGISRGSG----FVAFSTAE 373
                D + DD+        +K  FS++G + +  + R     +   G    F+ ++   
Sbjct: 416 NLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVR 475

Query: 374 EASKALTEMNGK 385
            A KA+  MNG+
Sbjct: 476 SAEKAMEGMNGR 487

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 52.4 bits (126), Expect = 5e-09
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 7/78 (8%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
            ++V NL  T TE++L++ F  +G++    + R   G+   + FV F + D A R+  A+
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 280 NGKKFDDKEWYVGKAQKK 297
           +G+       Y+G+ Q K
Sbjct: 64  SGQ-------YIGRNQIK 74

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

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

 Score = 52.7 bits (127), Expect = 6e-09
 Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 2/80 (2%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
           N+++ NL     E  L   F  FG I+ +  +MRD D G SK F F+++D  + +  ++E
Sbjct: 3   NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 278 ALNGKKFDDKEWYVGKAQKK 297
           A+NG+   ++   V  A KK
Sbjct: 63  AMNGQYLCNRPITVSYAFKK 82

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

 Score = 52.3 bits (126), Expect = 6e-09
 Identities = 21/71 (29%), Positives = 34/71 (47%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + +KNL K I    L   F  FG I   ++     G+ R +GFV +  EE A+ A+   N
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFN 62

Query: 190 GMLLNDKQVFV 200
              ++  ++ V
Sbjct: 63  NSFIDTSKITV 73

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

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

 Score = 52.3 bits (126), Expect = 6e-09
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 325 YVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNG 384
           +V  +    ++++L++ FS FG++   K++ D  G+S+G GFV F T E+A K L  M  
Sbjct: 6   FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKIL-AMGN 64

Query: 385 KMVVSKPLYVALAQRK 400
                K L +  A RK
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|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 = 52.2 bits (126), Expect = 6e-09
 Identities = 25/64 (39%), Positives = 42/64 (65%), Gaps = 1/64 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           ++V  L +T TE+D++ +F E+G I    ++RD D G+SK   FV F   ++A +++EAL
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 280 NGKK 283
           +GK 
Sbjct: 62  HGKV 65

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|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 = 52.5 bits (126), Expect = 6e-09
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAID 186
           G +FI  L    + ++L   FS +G I    V  D   Q SRG+GFV F+N + AK A+ 
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 187 KLNGMLLNDKQVFV 200
            +NG  ++ +Q+ V
Sbjct: 61  AMNGKSVDGRQIRV 74

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

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 52.4 bits (125), Expect = 6e-09
 Identities = 29/77 (37%), Positives = 46/77 (59%), Gaps = 1/77 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NL V  L  +++ ++LK LF   G I SCK++RD   G S G GFV +   ++A KA+  
Sbjct: 6   NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65

Query: 382 MNGKMVVSKPLYVALAQ 398
           +NG  + +K + V+ A+
Sbjct: 66  LNGLRLQTKTIKVSYAR 82

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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 52.4 bits (126), Expect = 6e-09
 Identities = 18/72 (25%), Positives = 36/72 (50%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            L+V NL+ +I++++L+  F  +G +    + R P G      FV F   + A +A   M
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 383 NGKMVVSKPLYV 394
           +G+ +    + +
Sbjct: 64  SGQYIGRNQIKI 75

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

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

 Score = 52.5 bits (126), Expect = 6e-09
 Identities = 21/62 (33%), Positives = 37/62 (59%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+  L+K    K + + FS +G +    +  D + QSRG  FV++ ++E A++AI  LN
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 190 GM 191
           G+
Sbjct: 62  GV 63

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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 52.2 bits (125), Expect = 6e-09
 Identities = 27/71 (38%), Positives = 43/71 (60%), Gaps = 4/71 (5%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDP---DDAARSV 276
           +++  L+  TT+D L++ FG+FG +T   VMRD A G+S+ FGF+ F  P   ++  +  
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 277 EALNGKKFDDK 287
             L+GK  D K
Sbjct: 61  HILDGKIIDPK 71

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

 Score = 52.3 bits (126), Expect = 6e-09
 Identities = 20/66 (30%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N++V  LS TT   DLK++F ++G ++ +  V       ++CFGFV     ++AA+ ++ 
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60

Query: 279 LNGKKF 284
           L+  + 
Sbjct: 61  LHRTEL 66

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

 Score = 52.4 bits (126), Expect = 6e-09
 Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             ++V N+     + DL+++FG+FG I    ++ +  G SK FGFV F +  DA R+ E 
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG-SKGFGFVTFANSADADRAREK 59

Query: 279 LNGKKFD 285
           L+G   +
Sbjct: 60  LHGTVVE 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|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 51.9 bits (125), Expect = 6e-09
 Identities = 25/67 (37%), Positives = 42/67 (62%), Gaps = 1/67 (1%)

Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEALNG 281
           V NL+  TT DDL+++F ++G +    + RD   + S+ F FV F D  DA  +++A++G
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 282 KKFDDKE 288
           K+ D +E
Sbjct: 63  KELDGRE 69

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

 Score = 52.2 bits (126), Expect = 7e-09
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 8/73 (10%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEAL 279
           ++V +L    T++ L + F ++       V+RD   GKSK +GFV+F DP+D  ++++ +
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 280 NGKKFDDKEWYVG 292
           NGK       YVG
Sbjct: 69  NGK-------YVG 74

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

 Score = 52.3 bits (126), Expect = 7e-09
 Identities = 30/73 (41%), Positives = 37/73 (50%), Gaps = 3/73 (4%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
            IF+ NL    D   L   FS FG + + KV  D +  + +GYGFV   N E A SAI  
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 188 LNGMLLNDK--QV 198
           LNG  L  +  QV
Sbjct: 63  LNGYRLGGRVLQV 75

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

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

 Score = 52.2 bits (125), Expect = 7e-09
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           N+YV NL    TED+L+KIF  +G I    ++RD + G  +   FV +D  ++A  ++ +
Sbjct: 2   NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 279 LNG 281
           LNG
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|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 52.4 bits (125), Expect = 7e-09
 Identities = 27/73 (36%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+ +  L +++  + L   F + G I SCK+  D + GQS GYGFV + + + A+ AI+ 
Sbjct: 6   NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65

Query: 188 LNGMLLNDKQVFV 200
           LNG+ L  K + 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|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 52.2 bits (125), Expect = 7e-09
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 3/77 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V  L+   ++ +++E+FS +G +    +MRD    SRG  FV +S+ E A  A+  +N
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 384 GKMVV---SKPLYVALA 397
           G   +    +PL V  A
Sbjct: 62  GVYTMRGCDQPLIVRFA 78

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

 Score = 52.3 bits (125), Expect = 7e-09
 Identities = 28/78 (35%), Positives = 49/78 (62%), Gaps = 3/78 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NLYV  L  ++S  ++++LFS++G I + +++ D   GISRG GF+ F    EA +A+  
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62

Query: 382 MNGK--MVVSKPLYVALA 397
           +NG+  +  ++P+ V  A
Sbjct: 63  LNGQKPLGAAEPITVKFA 80

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 52.0 bits (125), Expect = 7e-09
 Identities = 29/71 (40%), Positives = 38/71 (53%), Gaps = 5/71 (7%)

Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDA----ARSV 276
           ++  LS  TT + L++ F +FG I    VMRD   K S+ FGFV F DP       A+  
Sbjct: 2   FIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGP 61

Query: 277 EALNGKKFDDK 287
             L+GKK D K
Sbjct: 62  HELDGKKIDPK 72

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

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

 Score = 51.9 bits (125), Expect = 8e-09
 Identities = 30/75 (40%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQ-MGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           SL+VGDL   V+D QLY+ F++        +V  D     S GYG+V ++   E  RAL 
Sbjct: 3   SLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDESEQKRALT 61

Query: 100 EL-NFTPLNGKPIRI 113
           E+   + L GKPIR+
Sbjct: 62  EMQGASGLGGKPIRV 76

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

 Score = 52.0 bits (125), Expect = 8e-09
 Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           L+V NL     +D + E F E+G I+S ++  DP+ G  +G G+V FS+ E A  AL  +
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 383 NGKMVVSKPL 392
            G  ++ +P+
Sbjct: 61  GGTDLLGRPV 70

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

 Score = 52.0 bits (124), Expect = 8e-09
 Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NL V  L  +++ ++ K LF   G I SCK++RD   G S G GFV +    +A KA+  
Sbjct: 5   NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 382 MNGKMVVSKPLYVALAQ 398
           +NG  + +K + V+ A+
Sbjct: 65  LNGLKLQTKTIKVSYAR 81

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

 Score = 51.5 bits (124), Expect = 8e-09
 Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 7/71 (9%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+ NL  +  ++ L   F  +G +  C V  +       YGFV  + EE A+ AI  LN
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN-------YGFVHMEEEEDAEDAIKALN 54

Query: 190 GMLLNDKQVFV 200
           G     K++ V
Sbjct: 55  GYEFMGKRINV 65

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 52.0 bits (124), Expect = 8e-09
 Identities = 26/68 (38%), Positives = 42/68 (61%), Gaps = 1/68 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           ++V NL+    E  L ++FG FG +T+  V+RD +  K K FGFV   + D+AA ++ +L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 280 NGKKFDDK 287
           NG +  D+
Sbjct: 66  NGYRLGDR 73

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|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 51.8 bits (125), Expect = 8e-09
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 9/81 (11%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-------NGISRGSGFVAFSTAEEAS 376
           LYVKNL   ++++ L  +F  F  + S    ++         G  +G  FV F + E A+
Sbjct: 4   LYVKNLSKRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61

Query: 377 KALTEMNGKMVVSKPLYVALA 397
           KAL  +NG ++  KP+ +   
Sbjct: 62  KALNLVNGYVLKGKPMVIQFG 82

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

 Score = 51.6 bits (124), Expect = 9e-09
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           ++V  L    TE++ K+ F +FG +    +M+D D G+S+ FGFV FD  + A   V + 
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSA 60

Query: 280 NGKKFDDKEWYVGKA 294
              +   K+  V +A
Sbjct: 61  GMLELGGKQVEVKRA 75

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

 Score = 51.4 bits (124), Expect = 1e-08
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 6/77 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDKL 188
           +FI+NL      + L + FS FG +   ++  D L   S+G  FV+F  +ESA+  ++  
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 189 N-----GMLLNDKQVFV 200
           +     G+ L+ +++ V
Sbjct: 63  DNAEDSGLSLDGRRLIV 79

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

 Score = 52.0 bits (125), Expect = 1e-08
 Identities = 21/69 (30%), Positives = 40/69 (57%), Gaps = 1/69 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           N+ +  L +T T+++ + +F   G + +  ++RD   G S  FGFV++   +DA R++  
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 279 LNGKKFDDK 287
           LNG +  +K
Sbjct: 62  LNGLQLQNK 70

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|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 = 51.5 bits (124), Expect = 1e-08
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTF-GNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           + +KNL  S+    L + FS   G I   K+     G+SR   F+ +  EE A+ A D  
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYF 62

Query: 189 NGMLLNDKQVFV 200
           N   +N  ++ V
Sbjct: 63  NNTYINTSKISV 74

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|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 = 51.4 bits (124), Expect = 1e-08
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 131 FIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKLN 189
           F+  L K+   + +   F  +GNI    +  D   GQS+G  FV+F + E A+ AI+ L+
Sbjct: 3   FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALH 62

Query: 190 GM 191
           G 
Sbjct: 63  GK 64

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|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 = 51.8 bits (124), Expect = 1e-08
 Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
           L++  L    ++  L+++FS++G I+   V++D     SRG GFV F   ++A  A+  M
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 383 NGKMVVSKPLYVALAQR 399
           NGK V  + + V  A +
Sbjct: 63  NGKSVDGRQIRVDQAGK 79

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

 Score = 51.7 bits (124), Expect = 1e-08
 Identities = 28/77 (36%), Positives = 45/77 (58%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++V  +D   +++ L++ FS++GT+   K++ D  G+S+G GFV F T E+A K L E N
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEAN 64

Query: 384 GKMVVSKPLYVALAQRK 400
                 K L +  A RK
Sbjct: 65  RLCFRDKKLNIGQAIRK 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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 51.2 bits (123), Expect = 1e-08
 Identities = 22/71 (30%), Positives = 37/71 (52%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V NLD  ++++ L ELF + G +   K+ +DPNG  +   FV F        A+  +N
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 384 GKMVVSKPLYV 394
           G  +  + L +
Sbjct: 64  GIRLFGRELRI 74

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

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

 Score = 51.9 bits (124), Expect = 1e-08
 Identities = 25/63 (39%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEA 278
           N+++ +L +  T+ DL + F  FG + S  V  D     SKCFGFV++D+PD A  +++A
Sbjct: 6   NLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQA 65

Query: 279 LNG 281
           +NG
Sbjct: 66  MNG 68

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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 51.4 bits (123), Expect = 1e-08
 Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 4/71 (5%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAF---STAEEASKAL 379
           +++  L+   +DD L+E F +FG +T C VMRD   G SRG GF+ F    +  E  K  
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 380 TEMNGKMVVSK 390
             ++GK++  K
Sbjct: 61  HILDGKIIDPK 71

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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 51.9 bits (124), Expect = 1e-08
 Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 4/75 (5%)

Query: 208 ERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFD 267
           E +  A++T F    + NL  T TE DL++ F  FG+IT   + R   G++  +GF+ F+
Sbjct: 1   EDDQRANRTLF----LGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFE 56

Query: 268 DPDDAARSVEALNGK 282
           + D A R+  A++GK
Sbjct: 57  NLDMAHRAKLAMSGK 71

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 52.0 bits (124), Expect = 1e-08
 Identities = 27/68 (39%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
           ++V NLS    E  L ++FG FG +T+  V+RD    K K FGFV   + D+AA ++ +L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 280 NGKKFDDK 287
           NG +  D+
Sbjct: 64  NGYRLGDR 71

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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 52.0 bits (124), Expect = 1e-08
 Identities = 26/68 (38%), Positives = 42/68 (61%), Gaps = 1/68 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           ++V NLS  + E  L ++FG FG + +  V+RD +  K K FGFV   + D+AA ++ +L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 280 NGKKFDDK 287
           NG +  D+
Sbjct: 66  NGYRLGDR 73

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 52.2 bits (126), Expect = 1e-08
 Identities = 30/76 (39%), Positives = 40/76 (52%), Gaps = 16/76 (21%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGT---------ITSCKVMRD-----PNGI--SRGSGFV 367
           L ++NL  S+ + KLKELF +  +         I   K+MRD     PNG   S+G GFV
Sbjct: 3   LSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFV 62

Query: 368 AFSTAEEASKALTEMN 383
            F+  E A KAL  +N
Sbjct: 63  EFTNHEHALKALRALN 78

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

 Score = 51.7 bits (123), Expect = 1e-08
 Identities = 27/84 (32%), Positives = 50/84 (59%), Gaps = 3/84 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NLYV  L  +++  +L++LFS++G I + +++ D   G+SRG GF+ F    EA +A+  
Sbjct: 7   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 66

Query: 382 MNGKMV--VSKPLYVALAQRKEER 403
           +NG+     ++P+ V  A    ++
Sbjct: 67  LNGQKPPGATEPITVKFANNPSQK 90

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

 Score = 51.7 bits (123), Expect = 1e-08
 Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+++ + +FG  G I S  ++RD   G+S  +GFVN+ DP DA +++  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 279 LNGKKFDDKEWYVGKAQ 295
           LNG +   K   V  A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

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

 Score = 50.6 bits (121), Expect = 2e-08
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           ++V+NL+ + T++DL   F +   I    V+ D + G+S+ +GFV F   +DA  ++  L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 280 NGKKFDDK 287
             KK   +
Sbjct: 62  KNKKLHGR 69

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

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 23/70 (32%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +F+ NL    D  ++++ F  +G I S ++ TD   G+ +G+G+V+F ++E+A++A+D L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 189 NGMLLNDKQV 198
            G  L  + V
Sbjct: 61  GGTDLLGRPV 70

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|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T++YVG+L   + + +L   F+  G +  VRV +D       GY +V ++    A  A+ 
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIV 54

Query: 100 ELNFTPLNGKPIR 112
            +N T +NG+ ++
Sbjct: 55  AVNGTSINGQTVK 67

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

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

 Score = 51.2 bits (123), Expect = 2e-08
 Identities = 20/74 (27%), Positives = 44/74 (59%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
            +++YV +L  S+ ++ L+ +F++ G+VV V + +D  TR+S G  ++ +    +A + +
Sbjct: 1   KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60

Query: 99  DELNFTPLNGKPIR 112
             LN   L G+ ++
Sbjct: 61  KALNNKELFGRTLK 74

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

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

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 20/72 (27%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVA-TDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           + + NL     ++   +  S FG +  C +  ++S G+S+GYGFV++ ++ SA  A ++L
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 189 NGMLLNDKQVFV 200
           +G  +  +++ V
Sbjct: 62  DGKQIGGRKLQV 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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 51.3 bits (122), Expect = 2e-08
 Identities = 27/77 (35%), Positives = 46/77 (59%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+L V  L  ++   +   LF  +G++ S ++ RD  T +SLGYG+VNY   ++A +A++
Sbjct: 4   TNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAIN 63

Query: 100 ELNFTPLNGKPIRIMYS 116
            LN   L  K I++ Y+
Sbjct: 64  TLNGLKLQTKTIKVSYA 80

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

 Score = 51.2 bits (123), Expect = 2e-08
 Identities = 19/61 (31%), Positives = 32/61 (52%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V NL    TE+ L ++F + G +    + +D +GK K F FV F        +++ LN
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 281 G 281
           G
Sbjct: 64  G 64

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

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
           L+V  L+   +D+ L+ +FS FG I SC+V+RD   G S    F+ F T E+  +A  +M
Sbjct: 6   LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKM 65

Query: 383 NG 384
           + 
Sbjct: 66  DN 67

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 51.3 bits (123), Expect = 2e-08
 Identities = 27/62 (43%), Positives = 34/62 (54%), Gaps = 5/62 (8%)

Query: 334 SDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT----EMNGKMVV 388
           + + L+E FS+FG I  C VMRDP    SRG GFV FS      K L     E++GK + 
Sbjct: 11  TAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELDGKKID 70

Query: 389 SK 390
            K
Sbjct: 71  PK 72

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

>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 = 51.0 bits (122), Expect = 2e-08
 Identities = 25/72 (34%), Positives = 41/72 (56%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VG++     + QL D+F+++G VVS R+  D  T +  GYG+  Y     A  A+  L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 102 NFTPLNGKPIRI 113
           N   LNG+ +R+
Sbjct: 61  NGYELNGRQLRV 72

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

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 51.2 bits (122), Expect = 2e-08
 Identities = 25/68 (36%), Positives = 42/68 (61%), Gaps = 1/68 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           +++ NL +   E  L ++FG FG +T+  V+RD +  K K FGFV   + ++AA ++ +L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 280 NGKKFDDK 287
           NG +  DK
Sbjct: 64  NGYRLGDK 71

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

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           IF+  + +    + +HD F+ FG I +  +  D   G  +GY  ++++ ++ A++AI+ L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 189 NGMLLNDKQVFV 200
           NG  L  + + V
Sbjct: 69  NGKELLGQTISV 80

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

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

 Score = 50.9 bits (121), Expect = 2e-08
 Identities = 27/78 (34%), Positives = 48/78 (61%), Gaps = 3/78 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NLYV  L  +++  +L++LFS++G I + +++ D   G+SRG GF+ F    EA +A+  
Sbjct: 4   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63

Query: 382 MNGKMV--VSKPLYVALA 397
           +NG+     ++P+ V  A
Sbjct: 64  LNGQKPSGAAEPITVKFA 81

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|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 50.6 bits (121), Expect = 2e-08
 Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 6/82 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN------GISRGSGFVAFSTAEEASK 377
           L+VKNL+ S ++  L + F         +V   P+       +S G GFV F T E+A  
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 378 ALTEMNGKMVVSKPLYVALAQR 399
           AL  M+G ++    L V  + R
Sbjct: 63  ALKAMDGFVLDGHTLVVKFSHR 84

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

 Score = 50.3 bits (121), Expect = 3e-08
 Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 1/62 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           LYV  L + + +  L   F  FG I   ++  D      RG  FV F   E+A+ A+  M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 383 NG 384
           N 
Sbjct: 61  NE 62

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

 Score = 50.3 bits (121), Expect = 3e-08
 Identities = 20/67 (29%), Positives = 34/67 (50%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + + NL   +  + L + F   G +   K+  D  G+S G   V F+  E A+ AI + N
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFN 62

Query: 190 GMLLNDK 196
           G+LL+ +
Sbjct: 63  GVLLDGQ 69

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

 Score = 50.6 bits (122), Expect = 3e-08
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 6/77 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGN--ILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID 186
           + ++ LD     + +    S   +  I   ++  D L G SRG+ FV+F + E A   +D
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64

Query: 187 KLNGML---LNDKQVFV 200
            LN +    ++ + V V
Sbjct: 65  ALNNLDPFVIDGRVVRV 81

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

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

 Score = 50.5 bits (120), Expect = 3e-08
 Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+D+L+ +F   G + S  ++RD   G S  +GFVN+ +  DA R++  
Sbjct: 3   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62

Query: 279 LNGKKFDDKEWYVGKAQ 295
           LNG +   K   V  A+
Sbjct: 63  LNGLRLQSKTIKVSYAR 79

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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 50.9 bits (121), Expect = 3e-08
 Identities = 22/65 (33%), Positives = 37/65 (56%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           N++I NL  S+D + L +    FG ++S ++  DS G SRG GF + ++ E  ++ I   
Sbjct: 2   NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHF 61

Query: 189 NGMLL 193
           NG  +
Sbjct: 62  NGKFI 66

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

 Score = 50.9 bits (121), Expect = 3e-08
 Identities = 27/77 (35%), Positives = 45/77 (58%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+L V  L  ++   +   LF  +G++ S ++ RD  T +SLGYG+VNY    +A +A++
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 100 ELNFTPLNGKPIRIMYS 116
            LN   L  K I++ Y+
Sbjct: 63  TLNGLRLQTKTIKVSYA 79

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

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKA 378
           EG  ++V  + +   ++ + + F+EFG I +  +  D   G  +G   + + T +EA  A
Sbjct: 5   EGWIIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAA 64

Query: 379 LTEMNGKMVVSKPLYV 394
           +  +NGK ++ + + V
Sbjct: 65  IEGLNGKELLGQTISV 80

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

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

 Score = 50.6 bits (122), Expect = 3e-08
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKC-FGFVNFDDPDDAARSVEAL 279
           +YV NLS  TTE+ + ++F   G I    +  D   K+ C F FV +   +DA  +V+ L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 280 NGKKFDDK 287
           NG K DD+
Sbjct: 61  NGTKLDDR 68

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

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 50.5 bits (120), Expect = 3e-08
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           ++F+ +L   I    +   F+ FG I   +V  D + G+S+GYGFV F N+  A++AI +
Sbjct: 3   HVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62

Query: 188 LNGMLLNDKQV 198
           + G  L  +Q+
Sbjct: 63  MGGQWLGGRQI 73

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|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 50.5 bits (121), Expect = 3e-08
 Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 2/71 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           +YV ++D  +++++L  LFS  G +  C+V  DPN + R + F+ F+  E A  AL  ++
Sbjct: 5   VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRFA-FIEFTDEEGARAAL-SLS 62

Query: 384 GKMVVSKPLYV 394
           G M+   P+ V
Sbjct: 63  GTMLGFYPVRV 73

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

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

 Score = 50.2 bits (120), Expect = 3e-08
 Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           +Y+ +L     E +LKK F +FG + +  V R    G SK +GF+ F +P+ AA + +++
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 280 NG 281
           N 
Sbjct: 62  NN 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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 50.7 bits (122), Expect = 3e-08
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSV 276
           F  ++V  L+  TTE  L++ F E+G I    ++RD   GK + + F+ F+   D   + 
Sbjct: 1   FKTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAY 60

Query: 277 EALNGKKFDDK 287
           +  +GKK D +
Sbjct: 61  KYADGKKIDGR 71

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

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 1/64 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           N+Y++ L  + +D+ L++L   FG I S K + D      +G GFV F + E A KA+  
Sbjct: 2   NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEG 61

Query: 382 MNGK 385
           +NG+
Sbjct: 62  LNGR 65

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

 Score = 49.8 bits (120), Expect = 4e-08
 Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 7/80 (8%)

Query: 41  SLYVGDLD--LSVND--SQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
           +LY+ +L+  +  ++    LY LF+Q G V+ +   + L  R   G  +V +     AT 
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMR---GQAFVVFKDVESATN 57

Query: 97  ALDELNFTPLNGKPIRIMYS 116
           AL  L   P   KP+RI Y+
Sbjct: 58  ALRALQGFPFYDKPMRIQYA 77

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

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 49.8 bits (119), Expect = 4e-08
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 41  SLYVGDLDLSVNDSQLYDLF-NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           S++VGDL   VN+S L  LF ++     S ++  D  T  S GYG+V ++  ++  RAL 
Sbjct: 3   SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62

Query: 100 ELNFTPLNGKPIRIMYS 116
           E+      G+P+RI  +
Sbjct: 63  EMQGVYCGGRPMRISTA 79

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

 Score = 49.9 bits (120), Expect = 4e-08
 Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
           ++V  L   TT+D L+K F +FG I    V+ D   GKS+ +GFV F D + A R+ +  
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62

Query: 280 NGKKFD 285
           N    D
Sbjct: 63  N-PIID 67

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|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 50.1 bits (119), Expect = 4e-08
 Identities = 29/75 (38%), Positives = 43/75 (57%), Gaps = 10/75 (13%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVM---RDPNGISRGSGFVAFSTAEEASK 377
           G NL+V  L  +     LK LFS++G +   KV+   R P   +R  GFV  ST+EEA+K
Sbjct: 1   GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPG--ARCYGFVTMSTSEEATK 58

Query: 378 AL-----TEMNGKMV 387
            +     TE++G+M+
Sbjct: 59  CINHLHRTELHGRMI 73

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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 49.7 bits (119), Expect = 4e-08
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 5/67 (7%)

Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNG 281
           Y+ NLS    E DL+++F E  I  S+ ++     K   + FV+  D   A +++E LNG
Sbjct: 2   YIGNLSSDVNESDLRQLFEEHKIPVSSVLV-----KKGGYAFVDCPDQSWADKAIEKLNG 56

Query: 282 KKFDDKE 288
           K    K 
Sbjct: 57  KILQGKV 63

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

 Score = 50.1 bits (120), Expect = 4e-08
 Identities = 21/65 (32%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEAL 279
           ++++NL+ T TE+DL+K+F ++G ++   +  D    K K F FV +  P+ A ++   L
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 280 NGKKF 284
           +G  F
Sbjct: 65  DGTVF 69

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

 Score = 49.6 bits (119), Expect = 4e-08
 Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 5/71 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V NL + I++++ KELFS++G ++   + ++     +G GF+   T   A KA  E++
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAELD 58

Query: 384 GKMVVSKPLYV 394
           G M   + L V
Sbjct: 59  GIMRKGRQLRV 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|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 49.2 bits (118), Expect = 5e-08
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +++ NLD+++    L + FS  G I SCK+  +       Y FV++ +  SA +A+  +N
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP--YAFVEYYDHRSAAAALQTMN 58

Query: 190 GMLLNDKQVFVG 201
           G L+  +++ V 
Sbjct: 59  GRLILGQEIKVN 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|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 49.7 bits (119), Expect = 5e-08
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           N+ I  L +++ ++     F   G + +CK+  D   G S G+GFV + + E A+ AI  
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 188 LNGMLLNDKQVFV 200
           LNG+ L +K++ 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|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 49.7 bits (119), Expect = 5e-08
 Identities = 20/64 (31%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V N+     D  L+++F +FG I   +++ +  G S+G GFV F+ + +A +A  +++
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG-SKGFGFVTFANSADADRAREKLH 61

Query: 384 GKMV 387
           G +V
Sbjct: 62  GTVV 65

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

 Score = 49.7 bits (118), Expect = 5e-08
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+ +  L +++  +     F + G I SCK+  D + GQS GYGFV + + + A+ AI+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 188 LNGMLLNDKQVFV 200
           LNG+ L  K + 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|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 49.4 bits (118), Expect = 5e-08
 Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           ++++         A+ + FS +G +   K+ +        + FV+F++ ESA  A D ++
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMIS-------NFAFVEFESLESAIRAKDSVH 54

Query: 190 GMLLNDKQVFV 200
           G +LN+  ++V
Sbjct: 55  GKVLNNNPLYV 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|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 49.5 bits (118), Expect = 5e-08
 Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 7/71 (9%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           IF+ N+  +  +  L   F  FG ++ C    D       Y FV  + EE A +AI+ LN
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKVKD-------YAFVHMEREEEALAAIEALN 55

Query: 190 GMLLNDKQVFV 200
           G  +  +++ V
Sbjct: 56  GKEVKGRRINV 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|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 49.7 bits (119), Expect = 6e-08
 Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 4/73 (5%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           IF+  L   +  +   + FS FG ++  ++  D   G+SRG+GFV FD+E + +      
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFS-- 59

Query: 189 NGML-LNDKQVFV 200
            GML L  KQV V
Sbjct: 60  AGMLELGGKQVEV 72

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

 Score = 49.7 bits (118), Expect = 6e-08
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID 186
            N+++  L K++  K L   FS +G I++ ++  D + G SRG GF++FD    A+ AI 
Sbjct: 3   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 62

Query: 187 KLNG 190
            LNG
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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 49.9 bits (120), Expect = 6e-08
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           +F+  L+       L   F  +G I   ++  D   G+ RGY F++F++E   K+A    
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 189 NGMLLNDKQVFV 200
           +G  ++ ++V V
Sbjct: 64  DGKKIDGRRVLV 75

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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 49.6 bits (118), Expect = 6e-08
 Identities = 24/63 (38%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           N++I  L +++  K + D FS FG I++ +V  D + G SRG  F++FD    A+ AI  
Sbjct: 2   NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 188 LNG 190
            NG
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|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 49.1 bits (118), Expect = 6e-08
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKL 188
           ++I +L        L   FS FG +   +++     G+S+GY FV+F++ E AK   + +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 189 NGMLLNDK 196
           N  LL ++
Sbjct: 62  NNYLLFER 69

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|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 49.7 bits (119), Expect = 6e-08
 Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 6/69 (8%)

Query: 130 IFIKNLDKSIDNKALH----DTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
           +F+ +L  S  +  L     + FS +G ++  KV  D     R Y FVQF N++ AK+A+
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQ--RPYAFVQFTNDDDAKNAL 62

Query: 186 DKLNGMLLN 194
            K  G +L+
Sbjct: 63  AKGQGTILD 71

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

 Score = 49.3 bits (118), Expect = 7e-08
 Identities = 19/66 (28%), Positives = 33/66 (50%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           N+Y+ NL     E DL+ +   +G + ST ++RD+ G+S+  GF   +  +     +   
Sbjct: 2   NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKF 61

Query: 280 NGKKFD 285
           NGK   
Sbjct: 62  NGKYLK 67

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

 Score = 49.1 bits (117), Expect = 7e-08
 Identities = 22/64 (34%), Positives = 37/64 (57%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LYV NLD  +++D LK++F   G + + K++ D N      GFV +  + +A  AL  +N
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 384 GKMV 387
           G+ +
Sbjct: 61  GRQI 64

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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 49.3 bits (118), Expect = 7e-08
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKA 378
            +  +++V  L   ++ ++L E FS  G I    +++  N  +  + F+ F   + A++A
Sbjct: 1   IDKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFA-FIKFEREQAAARA 59

Query: 379 LTEMNGKMVVSKPLYVALAQRKEE 402
           +   N  M+ +K ++V   Q KE 
Sbjct: 60  VESENHSMLKNKTMHV---QYKEI 80

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

 Score = 49.2 bits (118), Expect = 8e-08
 Identities = 22/78 (28%), Positives = 43/78 (55%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L+V +L     D QL + F+++G +    V +D  +++  G+GYV +    +A RAL+E
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 101 LNFTPLNGKPIRIMYSYR 118
              T   G+ I + ++ +
Sbjct: 61  KKKTKFGGRKIHVEFAKK 78

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

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

 Score = 49.1 bits (118), Expect = 8e-08
 Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
           +YV  L+E   E  L   F  FG I    +  D    K + F FV F++P+DAA +++ +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 280 NG 281
           N 
Sbjct: 61  NE 62

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

 Score = 49.0 bits (117), Expect = 8e-08
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
           N++V +LS   T+  L   F  F   +   VM D   G+S+ +GFV+F    DA  ++  
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 279 LNGK 282
           +NGK
Sbjct: 61  MNGK 64

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

 Score = 51.2 bits (122), Expect = 8e-08
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
           L++  L     D  L++ F+ FG +   KV+ D   G SRG GFV F+    A+ A++EM
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 383 NGKMVVSKPLYVALAQRK 400
           +GK +  + + V  A  +
Sbjct: 97  DGKELNGRHIRVNPANDR 114

Length = 144

>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 = 49.4 bits (118), Expect = 8e-08
 Identities = 23/60 (38%), Positives = 35/60 (58%)

Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNG 281
           +V  LS+  TEDD++++F  FG I    ++R  DG SK   FV F    +A  ++ AL+G
Sbjct: 5   FVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALHG 64

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

 Score = 49.1 bits (118), Expect = 8e-08
 Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 5/83 (6%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMG--QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
           + +L +  LDL   +  +    + +    +  VR+ RD  T  S G+ +V + +  +AT+
Sbjct: 2   TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQ 61

Query: 97  ALDELNFTP---LNGKPIRIMYS 116
            +D LN      ++G+ +R+ Y+
Sbjct: 62  WMDALNNLDPFVIDGRVVRVSYA 84

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

 Score = 48.8 bits (117), Expect = 8e-08
 Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAI 185
           +F+  L + +  + L + FS +GN+ S ++ TD   G+ RG+ FV FD+ +     +
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 58

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

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

 Score = 49.0 bits (117), Expect = 8e-08
 Identities = 30/76 (39%), Positives = 39/76 (51%), Gaps = 3/76 (3%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVA-TDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           I+I +L      K L   FS FG + + +VA +   G S+ YGF+QF N E A  A   +
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 189 NGMLLNDK--QVFVGP 202
           N  LL  K  QV V P
Sbjct: 62  NNYLLMGKVLQVHVLP 77

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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 49.3 bits (118), Expect = 8e-08
 Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDA--- 272
           R   ++V  L    TE DL+K F +FG +T   VM D + K  + FGF+ F+  D     
Sbjct: 1   RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

Query: 273 -ARSVEALNGKKFDDK 287
                  +NGKK + K
Sbjct: 61  VNEHFHDINGKKVEVK 76

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

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

 Score = 49.2 bits (118), Expect = 8e-08
 Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LYV+NL   IS ++L +LF ++G I   ++       +RG+ FV +    +A  A   ++
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKE--TRGTAFVVYEDIYDAKNACDHLS 62

Query: 384 G 384
           G
Sbjct: 63  G 63

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

 Score = 49.2 bits (117), Expect = 9e-08
 Identities = 21/63 (33%), Positives = 36/63 (57%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
            +LYV  L  ++   +L  LF+Q G++++ R+ RD  T  S G G++ ++   EA  A+ 
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 100 ELN 102
            LN
Sbjct: 61  GLN 63

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|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 49.0 bits (117), Expect = 9e-08
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA- 278
           ++V  LS  TTEDD+KK F +FG +    +M D    + + FGFV F+  D   +  E  
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

Query: 279 ---LNGKKFDDK 287
              +N K  + K
Sbjct: 62  FHEINNKMVECK 73

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 53.1 bits (127), Expect = 1e-07
 Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKAL 379
           G NL V  L   ++D +L  LF   G I +C++MRD   G S G  FV F +  ++ +A+
Sbjct: 107 GTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAI 166

Query: 380 TEMNGKMVVSKPLYVALAQ 398
             +NG  V +K L V+ A+
Sbjct: 167 KNLNGITVRNKRLKVSYAR 185

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

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 8/68 (11%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKAL 379
           GL+LY        ++  L+E+FS +G I   +V+ D   G SRG GFV F + E+A +A 
Sbjct: 6   GLSLY-------TTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAK 58

Query: 380 TEMNGKMV 387
             +NG  +
Sbjct: 59  ERLNGMEI 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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 48.6 bits (116), Expect = 1e-07
 Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARS 275
           +   ++V  L+  T++  L++ F  +G +T   VM D + K S+ FGF+ F   D+A  +
Sbjct: 1   QLCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

Query: 276 VEA 278
           +EA
Sbjct: 61  MEA 63

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

 Score = 48.5 bits (115), Expect = 1e-07
 Identities = 26/71 (36%), Positives = 35/71 (49%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           IF+ NLD  +  K L + FS  G +    +  D  G+SRG G V F+    A  AI   N
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62

Query: 190 GMLLNDKQVFV 200
           G  L D+ + V
Sbjct: 63  GQFLFDRPMHV 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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 49.0 bits (116), Expect = 1e-07
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+ +  L +++  +     F + G I SCK+  D + GQS GYGFV + +   A  AI+ 
Sbjct: 5   NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 188 LNGMLLNDKQVFV 200
           LNG+ L  K + 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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 48.2 bits (115), Expect = 1e-07
 Identities = 27/68 (39%), Positives = 34/68 (50%), Gaps = 4/68 (5%)

Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALNG 281
           V  L   TTE DLK  F  FG +    V +D   G+SK FGFV F D +D    V+ L+ 
Sbjct: 4   VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQ---VKVLSQ 60

Query: 282 KKFDDKEW 289
           +   D  W
Sbjct: 61  RHMIDGRW 68

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

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

 Score = 48.8 bits (116), Expect = 1e-07
 Identities = 23/64 (35%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID 186
            N+++  L K++  K +   FS +G I++ ++  D + G SRG GF++FD    A+ AI 
Sbjct: 2   ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIK 61

Query: 187 KLNG 190
            LNG
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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 48.8 bits (116), Expect = 1e-07
 Identities = 21/71 (29%), Positives = 38/71 (53%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L++ NLD ++++  L+  F  FG IT   + R   G +   GF+ F   + A +A   M+
Sbjct: 10  LFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMS 69

Query: 384 GKMVVSKPLYV 394
           GK++   P+ +
Sbjct: 70  GKVLRRNPIKI 80

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

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

 Score = 49.0 bits (116), Expect = 1e-07
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID 186
            N+++  L K++  K L   FS +G I++ ++  D + G SRG GF++FD    A+ AI 
Sbjct: 6   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 65

Query: 187 KLNG 190
            LNG
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|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 48.6 bits (115), Expect = 1e-07
 Identities = 25/68 (36%), Positives = 43/68 (63%), Gaps = 1/68 (1%)

Query: 217 RFNNVYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARS 275
           R  N+YV  L +T T+ +L+++F ++G IITS  ++    G S+  GF+ FD   +A  +
Sbjct: 1   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 60

Query: 276 VEALNGKK 283
           ++ LNG+K
Sbjct: 61  IKGLNGQK 68

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

 Score = 48.3 bits (115), Expect = 1e-07
 Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 7/68 (10%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V N+S T T D+L+ +F EFG +     ++D       + FV+ +  ++A  ++EALN
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKVKD-------YAFVHMEREEEALAAIEALN 55

Query: 281 GKKFDDKE 288
           GK+   + 
Sbjct: 56  GKEVKGRR 63

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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 48.5 bits (116), Expect = 1e-07
 Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           IF+  L   +  + L++ FS  G IL   +   +   +  + F++F+ E++A  A++  N
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTN-AFAFIKFEREQAAARAVESEN 64

Query: 190 GMLLNDKQVFV 200
             +L +K + V
Sbjct: 65  HSMLKNKTMHV 75

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

 Score = 48.9 bits (116), Expect = 1e-07
 Identities = 23/68 (33%), Positives = 43/68 (63%), Gaps = 7/68 (10%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V+NL+ T TE+ L+K F EFG +     ++D       + FV+F++ D A R+++ +N
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEERDAAVRAMDEMN 56

Query: 281 GKKFDDKE 288
           GK+ + +E
Sbjct: 57  GKEIEGEE 64

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

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 25/57 (43%), Positives = 36/57 (63%), Gaps = 1/57 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKAL 379
           L+V NL  ++   +LKE FS+FG + SC V  D   G+S+G GFV+FS+ +    AL
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENAL 58

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

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 21/56 (37%), Positives = 33/56 (58%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           L V+N+    +  +L+ELFS FG + S ++ +  +G  RG  FV F T +EA  A+
Sbjct: 3   LIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAM 58

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

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 29/86 (33%), Positives = 43/86 (50%), Gaps = 3/86 (3%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           TSLYV ++  +     L  LF + G +V V +  D  TRR  G+ YV +    +A  AL 
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKS 125
            L+ T   G+ I I ++  D   RK+
Sbjct: 61  YLDRTRFLGREIEIQFAQGD---RKT 83

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 48.5 bits (115), Expect = 1e-07
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 5/73 (6%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID-- 186
           +FI  L      K L +  S FG +L C + TD + G+SRG+GFV F +  S    ++  
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 187 --KLNGMLLNDKQ 197
             KL+G L++ K+
Sbjct: 62  EHKLDGKLIDPKR 74

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 48.7 bits (117), Expect = 1e-07
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++V  +   + +D+L  LF + G I   ++M D +G++RG  FV ++  E A +A+ +++
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 384 GKMV-VSKPLYV 394
              +   K L V
Sbjct: 64  NYEIRPGKRLGV 75

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

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

 Score = 48.5 bits (115), Expect = 1e-07
 Identities = 22/65 (33%), Positives = 42/65 (64%), Gaps = 7/65 (10%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V+NL+ T TE+ L+K FG+FG +     ++D       + F++FD+ D A +++E +N
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 56

Query: 281 GKKFD 285
           GK+ +
Sbjct: 57  GKELE 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|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 48.6 bits (116), Expect = 1e-07
 Identities = 28/73 (38%), Positives = 37/73 (50%), Gaps = 9/73 (12%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGII-----TSTA---VMRDAD-GKSKCFGFVNFDDPDD 271
           V+V NL   TTE DL + FG  GII     T      + +D D G+ K    V +DDP  
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 272 AARSVEALNGKKF 284
           A+ ++E  N K F
Sbjct: 61  ASAAIEWFNNKDF 73

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 48.3 bits (115), Expect = 1e-07
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 7/71 (9%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V N+ E T++++L+ +F  +G + S AVMR        F FV+      A R++E LN
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ-------FAFVHLRGEAAADRAIEELN 55

Query: 281 GKKFDDKEWYV 291
           G++   ++  V
Sbjct: 56  GRELHGRKLVV 66

This subgroup corresponds to the RRM1 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 = 69

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

 Score = 48.3 bits (116), Expect = 2e-07
 Identities = 17/62 (27%), Positives = 35/62 (56%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           ++ V +L    ++  L +LF   G +  V + +D  T +S G+ +V ++   +A RA+++
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 101 LN 102
           LN
Sbjct: 61  LN 62

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

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

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 20/71 (28%), Positives = 34/71 (47%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + ++NL        L   FS FG +    +     G+ +G+ FVQF ++  A+ AI  +N
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 190 GMLLNDKQVFV 200
           G  +  + V V
Sbjct: 62  GKKIKGRPVAV 72

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

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

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 22/72 (30%), Positives = 41/72 (56%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VGDL   V D  L   F++       +V RD  T +S GYG+V+++  ++  +A+ E+
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 102 NFTPLNGKPIRI 113
           N   +  +PI++
Sbjct: 69  NGKYVGNRPIKL 80

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

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 3/59 (5%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           V+V NL  +  ED+L+K+F + G IT   ++++  GKSK + +V F++ +      EAL
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESV---QEAL 57

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

 Score = 48.0 bits (114), Expect = 2e-07
 Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+LYV +L   + + +L  +F   G +V   + RD ST    G  +V Y+   EA  A+ 
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 100 ELNFTPLNGK--PIRIMYS 116
            LN T   G   P+ + Y+
Sbjct: 61  SLNGTIPPGSTMPLSVRYA 79

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|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 48.6 bits (115), Expect = 2e-07
 Identities = 22/65 (33%), Positives = 37/65 (56%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           N++I NL  S+D + L +    FG+++S ++  D+ G SRG GF + ++ E  +  I   
Sbjct: 3   NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHF 62

Query: 189 NGMLL 193
           NG  L
Sbjct: 63  NGKYL 67

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

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 22/73 (30%), Positives = 39/73 (53%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           + V+V NL        LK++F   G++    ++ D DGKS+  G V F+ P +A +++  
Sbjct: 1   STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISM 60

Query: 279 LNGKKFDDKEWYV 291
            NG+   D+  +V
Sbjct: 61  FNGQLLFDRPMHV 73

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

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 26/71 (36%), Positives = 37/71 (52%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+ NLD  +  K L + FS  G ++   +  D  G+SRG G V F+    A  AI   N
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFN 62

Query: 190 GMLLNDKQVFV 200
           G LL D+ + V
Sbjct: 63  GQLLFDRPMHV 73

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG-ISRGSGFVAFSTAEEASKALTEM 382
           L V NL    + D L+ +F ++G +    + RD     SRG  FV F    +A  A+  M
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 383 NGKMVVSKPLYVA 395
           +GK +  + L V 
Sbjct: 61  DGKELDGRELRVQ 73

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

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

 Score = 48.5 bits (115), Expect = 2e-07
 Identities = 22/65 (33%), Positives = 42/65 (64%), Gaps = 1/65 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N+YV  L +T ++ +++++F ++G IITS  ++    G S+  GF+ FD   +A  +++ 
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62

Query: 279 LNGKK 283
           LNG+K
Sbjct: 63  LNGQK 67

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 26/74 (35%), Positives = 35/74 (47%), Gaps = 16/74 (21%)

Query: 132 IKNLDKSIDNKALHDTFSTFGN---------ILSCKVATDS-------LGQSRGYGFVQF 175
           I+NL KS+D K L + F    +         I   K+  D         G+S+GYGFV+F
Sbjct: 5   IRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEF 64

Query: 176 DNEESAKSAIDKLN 189
            N E A  A+  LN
Sbjct: 65  TNHEHALKALRALN 78

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

 Score = 48.2 bits (114), Expect = 2e-07
 Identities = 25/68 (36%), Positives = 43/68 (63%), Gaps = 1/68 (1%)

Query: 217 RFNNVYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARS 275
           R  N+YV  L +T T+ +L+++F ++G IITS  ++    G S+  GF+ FD   +A  +
Sbjct: 4   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 63

Query: 276 VEALNGKK 283
           ++ LNG+K
Sbjct: 64  IKGLNGQK 71

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

 Score = 48.6 bits (115), Expect = 2e-07
 Identities = 27/77 (35%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NL V  L  +++ ++ + LF   G I SCK++RD   G S G GFV +   ++A KA+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 382 MNGKMVVSKPLYVALAQ 398
           +NG  + +K + V+ A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 27/84 (32%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKAL 379
           G  +++ NL     +  L ++F  FG +T+ KV+RD N    +G GFV  +  EEA+ A+
Sbjct: 1   GWCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAI 60

Query: 380 TEMNGKMVVSKPLYVALAQRKEER 403
             +NG  +  K L V+    K  +
Sbjct: 61  ASLNGYRLGDKILQVSFKTSKSHK 84

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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 28/68 (41%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           IFI NL +  D   L   F  FG + + KV  D +  + +G+GFV   N E A  AI  L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 189 NGMLLNDK 196
           NG  L DK
Sbjct: 64  NGYRLGDK 71

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

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 7/73 (9%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LYV+      S+  ++E+FS +G +   K++           FV F + E A +A   ++
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMIS-------NFAFVEFESLESAIRAKDSVH 54

Query: 384 GKMVVSKPLYVAL 396
           GK++ + PLYV  
Sbjct: 55  GKVLNNNPLYVTY 67

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

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +F+ NL  ++ +K L + FS FG + SC V  D   G S+GYGFV F + +  ++A+ K 
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQ 61

Query: 189 NGML 192
             +L
Sbjct: 62  KHIL 65

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

 Score = 48.4 bits (115), Expect = 2e-07
 Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           IF++NL      K L D F+  G++L   +  ++ G+S+G G V+F++ E A+ A   +N
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVRFESPEVAERACRMMN 60

Query: 190 GMLLNDKQVFV 200
           G  LN +++ V
Sbjct: 61  GYKLNGREIDV 71

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

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

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 20/58 (34%), Positives = 31/58 (53%)

Query: 132 IKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +KNL   + N+ L   FS FG +    V  D  G+S G G V+F  +  A++AI + +
Sbjct: 4   VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRCS 61

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|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 48.1 bits (115), Expect = 2e-07
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 325 YVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNG 384
           +V  +D S+S+D LKE FS  G +T  ++  D    +R   FV F+ AE A  AL  ++G
Sbjct: 4   HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR-FAFVEFADAESALSAL-NLSG 61

Query: 385 KMVVSKPLYV 394
            ++   PL V
Sbjct: 62  TLLGGHPLRV 71

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 48.5 bits (115), Expect = 2e-07
 Identities = 27/75 (36%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAI 185
             N+FI +L +   ++ L   F  FGN++S KV  D     S+ +GFV +DN  SA++AI
Sbjct: 7   GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 66

Query: 186 DKLNGMLLNDKQVFV 200
             +NG  +  K++ V
Sbjct: 67  QAMNGFQIGMKRLKV 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|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 5/73 (6%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID-- 186
           +FI  L      K L D FS FG ++ C +  D + G+SRG+GFV F   ES    +D  
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 187 --KLNGMLLNDKQ 197
             KLNG +++ K+
Sbjct: 61  EHKLNGKVIDPKR 73

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 48.1 bits (115), Expect = 2e-07
 Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           VYV+ L +  T + LK +F ++G +   ++ R    G  K F F+ F+ P++A ++ + L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 280 NGKKFDDKEW 289
           N       + 
Sbjct: 62  NNPPETATDK 71

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

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 2/73 (2%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L+VG+L  S     L + F + G+VV VR+ +D    RS G+G+V +     A +AL E
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEFATEEGAQKAL-E 58

Query: 101 LNFTPLNGKPIRI 113
            +   L G+ IR+
Sbjct: 59  KSGEELLGREIRV 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|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 47.2 bits (113), Expect = 3e-07
 Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T L V +LD  V+D  + +LF + G +    V  D S R SLG   V +    +A +A+ 
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGR-SLGTADVVFERRADALKAMK 59

Query: 100 ELNFTPLNGKPIRI 113
           + N  PL+G+P++I
Sbjct: 60  QYNGVPLDGRPMKI 73

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|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 = 47.2 bits (113), Expect = 3e-07
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 325 YVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEMN 383
           +V N+    ++++L E+FSE G + S +++ D + G  +G GF  F   E A+ A+  +N
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 384 GKMVVSKPLYVALA 397
           G     + L V  A
Sbjct: 62  GYEFNGRALRVDFA 75

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

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

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 135 LDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLL 193
           L+  +D   ++  F+  G + S K+  +   G+S GYGFV+F   E+A+ A+  LNG  +
Sbjct: 7   LEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPI 66

Query: 194 -NDKQVF 199
            N +Q F
Sbjct: 67  PNTQQRF 73

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

>gnl|CDD|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 = 47.5 bits (113), Expect = 3e-07
 Identities = 27/76 (35%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKA 378
           EG NL++ +L     D +L ++F  FG + S KV  D     S+  GFV+F     A  A
Sbjct: 3   EGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAA 62

Query: 379 LTEMNGKMVVSKPLYV 394
           +  MNG  +  K L V
Sbjct: 63  IQAMNGFQIGMKRLKV 78

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

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           ++V NLS    ED + + FGE+G I+S  +  D D G+ K FG+V F   + A  +++AL
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 280 NG 281
            G
Sbjct: 61  GG 62

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

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 21/69 (30%), Positives = 37/69 (53%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+ NLD  +  + L++ F   G +   K+  D  G+ + + FV F +E S   AI  LN
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 190 GMLLNDKQV 198
           G+ L  +++
Sbjct: 64  GIRLFGREL 72

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|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 = 47.5 bits (113), Expect = 3e-07
 Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +F+ N+      + L D FS  G ++S ++  D   G+ +GYGF ++ ++E+A SA+  L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 189 NGMLLNDKQVFV 200
           NG  LN +Q+ V
Sbjct: 61  NGYELNGRQLRV 72

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

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 47.4 bits (112), Expect = 3e-07
 Identities = 26/64 (40%), Positives = 41/64 (64%), Gaps = 1/64 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           +V+V +LS   T DD+K  F  FG I+   V++D A GKSK +GFV+F +  DA  +++ 
Sbjct: 3   HVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62

Query: 279 LNGK 282
           + G+
Sbjct: 63  MGGQ 66

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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 48.1 bits (114), Expect = 3e-07
 Identities = 27/83 (32%), Positives = 45/83 (54%), Gaps = 3/83 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
           NLY+  L  +++   ++++FS FG I + +V+ D   G+SRG  F+ F    EA +A+T 
Sbjct: 2   NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 382 MNGKMV--VSKPLYVALAQRKEE 402
            NG      S+P+ V  A    +
Sbjct: 62  FNGHKPPGSSEPITVKFAANPNQ 84

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|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 = 47.2 bits (113), Expect = 3e-07
 Identities = 18/63 (28%), Positives = 33/63 (52%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             + V+N+    T+ +L+++F  FG + S  + +  DG  + F FV F    +A  ++EA
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

Query: 279 LNG 281
           L  
Sbjct: 61  LKS 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|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           I +  +D S+    L + FS  G +   ++  D    +R + FV+F + ESA SA+  L+
Sbjct: 3   IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR-FAFVEFADAESALSAL-NLS 60

Query: 190 GMLLNDKQVFVGP 202
           G LL    + V P
Sbjct: 61  GTLLGGHPLRVSP 73

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

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

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 15/71 (21%), Positives = 33/71 (46%), Gaps = 3/71 (4%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           ++      S     +   F T G +    + + ++   + + F+ F+N E+A+ AI+ LN
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTV---QPHAFITFENLEAAQLAIETLN 58

Query: 190 GMLLNDKQVFV 200
           G  ++   + V
Sbjct: 59  GASVDGNCIKV 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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 47.6 bits (113), Expect = 3e-07
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID-- 186
           +F+  L      K L + FS FG ++ C +  D + G+SRG+GFV F +  S +  +D  
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 187 --KLNGMLLNDKQ 197
             KL+G +++ K+
Sbjct: 61  EHKLDGRVIDPKR 73

This subfamily corresponds to the RRM1 in 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 family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 47.8 bits (113), Expect = 3e-07
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           ++F+ +L   I  + +   F+ FG I   +V  D + G+S+GYGFV F N+  A++AI  
Sbjct: 3   HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62

Query: 188 LNGMLLNDKQV 198
           + G  L  +Q+
Sbjct: 63  MGGQWLGGRQI 73

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|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 = 47.7 bits (114), Expect = 3e-07
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIIT--STAVMRD-ADGKSKCFGFVNFDDPDDAARSVE 277
           +YV NL+  TT++DL+    E G++   S       A+GKSK F +V F     AA   E
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 278 ALNGKKFDDKE 288
            L G++F+ K+
Sbjct: 61  KLEGREFNGKK 71

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|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 47.2 bits (113), Expect = 3e-07
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L V++L   +S+D  ++L   FG  +S +VM    G  + + F  F   + AS+AL+ ++
Sbjct: 2   LLVRHLPPELSEDDKEDLLKHFG-ASSVRVMS-RRGKLKNTAFATFDNEQAASQALSRLH 59

Query: 384 GKMVVSKPLYV 394
              ++ K L V
Sbjct: 60  QLKILGKRLVV 70

This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. . Length = 73

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 47.3 bits (113), Expect = 4e-07
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYVG+LD +V +  L +LF+Q+G + S   C+ +    +  Y +V Y     A  AL  +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKS---CKLIREHGNDPYAFVEYYDHRSAAAALQTM 57

Query: 102 NFTPLNGKPIRI 113
           N   + G+ I++
Sbjct: 58  NGRLILGQEIKV 69

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

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

 Score = 47.1 bits (112), Expect = 4e-07
 Identities = 21/60 (35%), Positives = 32/60 (53%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+  L K  +   +   F+ FG+I  C V  D  GQSRG  FV F + + A +AI  ++
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 63

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

 Score = 46.9 bits (112), Expect = 4e-07
 Identities = 21/75 (28%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           +YV NL  S++++ L ++FS++G +    +++D     S+G  F+ F   E+A K +  +
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 383 NGKMVVSKPLYVALA 397
           N K +  + L  ++A
Sbjct: 64  NNKELFGRTLKCSIA 78

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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 47.5 bits (113), Expect = 4e-07
 Identities = 21/58 (36%), Positives = 36/58 (62%)

Query: 41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           L+VG L+L  +DS L   F + G++    V  D +T+RS G+G++ +++A EA  A+
Sbjct: 4  KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

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|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 47.7 bits (113), Expect = 4e-07
 Identities = 21/62 (33%), Positives = 35/62 (56%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           N++I NL  S+D + L      FG ++S ++  D+ G SRG GF + ++ E  ++ I   
Sbjct: 2   NLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEAIITHF 61

Query: 189 NG 190
           NG
Sbjct: 62  NG 63

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

 Score = 47.2 bits (113), Expect = 4e-07
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           V+V NL     E++L+K F + G + +  ++RD   G  K FG+V F    D+      L
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTK-DSVALALKL 60

Query: 280 NGKKFDDKE 288
           NG K   ++
Sbjct: 61  NGIKLKGRK 69

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 47.4 bits (112), Expect = 4e-07
 Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKAL 379
           G  ++V NL     +  L +LF  FG +T+ KV+RD      +G GFV  +  +EA+ A+
Sbjct: 1   GWCIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAI 60

Query: 380 TEMNGKMVVSKPLYVALAQRKEER 403
             +NG  +  + L V+    K+ +
Sbjct: 61  ASLNGYRLGDRVLQVSFKTSKQHK 84

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

 Score = 47.2 bits (113), Expect = 4e-07
 Identities = 23/72 (31%), Positives = 40/72 (55%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYVG+L     + Q+Y+LF++ G +  + +  D  T+   G+ +V Y    +A  A+  L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 102 NFTPLNGKPIRI 113
           N T L+ + IR+
Sbjct: 61  NGTKLDDRIIRV 72

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

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

 Score = 47.1 bits (112), Expect = 4e-07
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
           +Y+ +L     + +LK+ FS+FGT+ + +V R    G S+  GF+ F   E A+ A   M
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 383 NGKMVVSKPLYV 394
           N  +++ K L V
Sbjct: 62  NNYLLMGKVLQV 73

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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 47.3 bits (113), Expect = 4e-07
 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V  LS   T+++L + F   G I    +++ A+  +  F F+ F+    AAR+VE+ N
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTN-AFAFIKFEREQAAARAVESEN 64

Query: 281 GKKFDDKEWYV 291
                +K  +V
Sbjct: 65  HSMLKNKTMHV 75

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

 Score = 51.1 bits (122), Expect = 5e-07
 Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKAL 379
           G  ++V NL     +  L +LF  FG + + K++RD      +G GFV+ +  +EA+ A+
Sbjct: 269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAI 328

Query: 380 TEMNGKMVVSKPLYVALAQRKEER 403
             +NG  + ++ L V+    K  R
Sbjct: 329 LSLNGYTLGNRVLQVSFKTNKAYR 352

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|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 = 46.9 bits (112), Expect = 5e-07
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           +F++NL  +   + L + F  FG I    +  D    +S+G+ FV F   E A  A  +L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 189 NGMLLNDKQVFVGPFLR 205
                 D  +F G  L 
Sbjct: 62  ------DGSIFQGRLLH 72

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|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 = 46.9 bits (112), Expect = 5e-07
 Identities = 19/73 (26%), Positives = 40/73 (54%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+V +L  +  + +L +LF   G++  V +  D  T+RS G+ +V++     A +A  EL
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 102 NFTPLNGKPIRIM 114
           + +   G+ + ++
Sbjct: 62  DGSIFQGRLLHVL 74

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

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 22/65 (33%), Positives = 35/65 (53%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           + V NL    ++DD+K++F EFG +   AV  D  G+S     V F+   DA ++++  N
Sbjct: 3   LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQYN 62

Query: 281 GKKFD 285
           G   D
Sbjct: 63  GVPLD 67

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

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 227 SETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEALNGKK 283
            ++ TEDDL++ F  FG I    V++D   K SK   +V F     AAR++E +NGK 
Sbjct: 11  GKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKC 68

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

 Score = 46.9 bits (111), Expect = 5e-07
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKA 378
           EG NL++ +L    +D  L + F  FG + S KV  D    +S+  GFV++   + A  A
Sbjct: 3   EGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAA 62

Query: 379 LTEMNGKMVVSKPLYV 394
           +  MNG  + +K L V
Sbjct: 63  IQAMNGFQIGTKRLKV 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|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 = 46.9 bits (112), Expect = 5e-07
 Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           V+V  L    TED+L+ +FG FG I    +        K  GFV F     A  +++ L 
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKI-----PPGKGCGFVQFVHRAAAEAAIQQLQ 58

Query: 281 G 281
           G
Sbjct: 59  G 59

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|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 = 46.5 bits (111), Expect = 5e-07
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+  LD ++    L   F  FG I+  K+        +G GFVQF +  +A++AI +L 
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPP-----GKGCGFVQFVHRAAAEAAIQQLQ 58

Query: 190 GMLL 193
           G ++
Sbjct: 59  GTII 62

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

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

 Score = 47.0 bits (112), Expect = 5e-07
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 10/73 (13%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKV---MRDPNGISRGSGFVAFSTAEEASKAL 379
           NL+V  L  +     LK+LFS++G +   K+    R P   +R  GFV  ++ EEA+K +
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPG--ARCFGFVTMASVEEAAKCI 58

Query: 380 -----TEMNGKMV 387
                TE++G+++
Sbjct: 59  QHLHRTELHGRVI 71

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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 16/75 (21%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           S++VG L   V   +L + F++ G+++ V + +  +   +  + ++ +     A RA++ 
Sbjct: 5   SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAVES 62

Query: 101 LNFTPLNGKPIRIMY 115
            N + L  K + + Y
Sbjct: 63  ENHSMLKNKTMHVQY 77

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 47.1 bits (111), Expect = 5e-07
 Identities = 26/67 (38%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITST-AVMRDADGKSKCFGFVNFDDPDDA 272
           D+    N+Y++ L   TT+ DL K+   +G I ST A++     K K +GFV+FD P  A
Sbjct: 3   DQLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAA 62

Query: 273 ARSVEAL 279
            ++V AL
Sbjct: 63  QKAVSAL 69

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|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 46.7 bits (110), Expect = 5e-07
 Identities = 25/62 (40%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITST-AVMRDADGKSKCFGFVNFDDPDDAARSVE 277
            N+Y++ L   TT+ DL K+   +G I ST A++     K K +GFV+FD P  A ++V 
Sbjct: 2   TNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 61

Query: 278 AL 279
           AL
Sbjct: 62  AL 63

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|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 46.6 bits (111), Expect = 6e-07
 Identities = 20/47 (42%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNF 266
           +++  LS  TT+D LK  F ++G IT   VM+D    +S+ FGFV F
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTF 48

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 47.3 bits (113), Expect = 6e-07
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALT 380
           L L+V  L    +++ L+E+FS +G I   +++RD   G S+G  FV +    +A +A  
Sbjct: 4   LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63

Query: 381 EMN 383
           + +
Sbjct: 64  DAH 66

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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 46.9 bits (112), Expect = 6e-07
 Identities = 23/69 (33%), Positives = 40/69 (57%), Gaps = 1/69 (1%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQ-VVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           SL++GDL+  ++++ +   F  MG+ V+SV++ R+  T    GY +V +     A R L 
Sbjct: 1   SLWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60

Query: 100 ELNFTPLNG 108
           +LN  P+ G
Sbjct: 61  KLNGKPIPG 69

This subgroup corresponds to the RRM1 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 = 84

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

 Score = 46.6 bits (111), Expect = 7e-07
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 2/67 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +FI    KS+    L + F+ FG I    V  D    +S+G  +V+F    SA  A++++
Sbjct: 6   LFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEM 64

Query: 189 NGMLLND 195
           NG  L  
Sbjct: 65  NGKCLGG 71

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

 Score = 46.6 bits (110), Expect = 7e-07
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+ +  L +++    L   FS+ G + S K+  D + G S GYGFV + N + A+ AI+ 
Sbjct: 3   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62

Query: 188 LNGMLLNDKQVFV 200
           LNG+ L  K + 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|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 46.2 bits (110), Expect = 7e-07
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 5/73 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALT-- 380
           ++V  L   +++++ KE FS+FG +   ++M+D + G SRG GFV F +     +  +  
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 381 --EMNGKMVVSKP 391
             E+ GK V  K 
Sbjct: 62  MLELGGKQVEVKR 74

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|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 46.6 bits (111), Expect = 7e-07
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 324 LYVKNLDDSISDDKL----KELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           ++V +L  S SDD+L     E FS++GT+   KV+RD     R   FV F+  ++A  AL
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQ--RPYAFVQFTNDDDAKNAL 62

Query: 380 TEMNGKMVVSKPL 392
            +  G ++  + +
Sbjct: 63  AKGQGTILDGRHI 75

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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 46.4 bits (111), Expect = 7e-07
 Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           VYVK   +  T DD+++ F +FG + +  + RD D K K   FV F   +DA + +E   
Sbjct: 2   VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEK-E 60

Query: 281 GKKFDDKE 288
             K+ +KE
Sbjct: 61  KLKYKEKE 68

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

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

 Score = 48.1 bits (114), Expect = 8e-07
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           +++  LS  T +  L+  F  FG +    V+ D + G+S+ FGFVNF+D   A  ++  +
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 280 NGKKFDDKEWYVGKAQKK 297
           +GK+ + +   V  A  +
Sbjct: 97  DGKELNGRHIRVNPANDR 114

Length = 144

>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 = 46.1 bits (110), Expect = 8e-07
 Identities = 17/61 (27%), Positives = 33/61 (54%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + ++N+      K L + FS FG + S ++     G  RG+ FV+F  ++ A++A++ L 
Sbjct: 3   LIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALK 62

Query: 190 G 190
            
Sbjct: 63  S 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|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 46.6 bits (111), Expect = 8e-07
 Identities = 23/76 (30%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
           +YV+N+++ T  DDL+++FG++G I    +  D    + + F +V F+D  DA  ++  L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 280 NGKKFDDKEWYVGKAQ 295
           +  +F  +E  +  AQ
Sbjct: 63  DRTRFLGREIEIQFAQ 78

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 46.1 bits (109), Expect = 8e-07
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L+VG+L+  V +  LY+LF Q G +  V +C+D    +   +G+V +  +     A+  
Sbjct: 3   TLFVGNLECRVREEILYELFLQAGPLTKVTICKD-KEGKPKSFGFVCFKHSESVPYAIAL 61

Query: 101 LNFTPLNGKPIRI 113
           LN   L G+PI++
Sbjct: 62  LNGIRLYGRPIKV 74

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|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 46.3 bits (110), Expect = 9e-07
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 7/79 (8%)

Query: 39  STSLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEA 94
           S  ++V  L  S +D +L     + F++ G +V V+V RD    R   Y +V +    +A
Sbjct: 2   SACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDW---RQRPYAFVQFTNDDDA 58

Query: 95  TRALDELNFTPLNGKPIRI 113
             AL +   T L+G+ IR 
Sbjct: 59  KNALAKGQGTILDGRHIRC 77

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

 Score = 46.1 bits (110), Expect = 9e-07
 Identities = 22/60 (36%), Positives = 32/60 (53%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L VKNL   +S++ L++ FS+FG +    V+ D  G S G G V FS    A  A+   +
Sbjct: 2   LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRCS 61

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

 Score = 45.8 bits (109), Expect = 9e-07
 Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 7/62 (11%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           VY+  L     E D+++ F  +G I      R+ + K+  FGFV F+DP DA  +V  LN
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRI------REINLKNG-FGFVEFEDPRDADDAVYELN 54

Query: 281 GK 282
           GK
Sbjct: 55  GK 56

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

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

 Score = 46.0 bits (110), Expect = 1e-06
 Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           +YV NLD+ ++++ L ELF + G + +  + +D      +G GFV F + E+A  A+  M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 383 NGKMVVSKPLYV 394
           N   +  KP+ V
Sbjct: 61  NMIKLYGKPIRV 72

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

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 4/71 (5%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +++ NL      + L D F  +G + S  VA        G+ FV+F++   A+ A+  L+
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVAR----NPPGFAFVEFEDPRDAEDAVRALD 57

Query: 190 GMLLNDKQVFV 200
           G  +   +V V
Sbjct: 58  GRRICGNRVRV 68

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

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 7/82 (8%)

Query: 43  YVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN 102
           +VG +     + +L D F++ G V  V++  D     S GYG+V +    +A + L   N
Sbjct: 6   FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAMGN 64

Query: 103 FTPLNGKPIRIMYSYRDPTIRK 124
                GK + I      P IRK
Sbjct: 65  L-NFRGKKLNI-----GPAIRK 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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 22/67 (32%), Positives = 36/67 (53%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYV  L  ++   +L  LF+  G++++ R+  D  T  S G G++ ++   EA RA+  L
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 102 NFTPLNG 108
           N T   G
Sbjct: 63  NGTIPPG 69

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

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

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 6/71 (8%)

Query: 130 IFIKNLDKSID----NKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
           ++I NL++ I      ++L+  FS FG +L   VA+ +L + RG  FV F + ESA +A+
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLDI-VASKTL-KMRGQAFVVFKDVESATNAL 59

Query: 186 DKLNGMLLNDK 196
             L G    DK
Sbjct: 60  RALQGFPFYDK 70

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

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 46.0 bits (109), Expect = 1e-06
 Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 130 IFIKNLDKSIDNKALHDTF-STFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           IF+ +L   ++   L   F S F +  S K+ TD + G SRGYGFV+F +E   + A+ +
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 188 LNGMLLNDKQVFVGP 202
           + G+    + + +  
Sbjct: 64  MQGVYCGGRPMRIST 78

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

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 139 IDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAI 185
              + L D FSTFG +L  +V  D   GQS+G+GFV+F + E     +
Sbjct: 11  TTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58

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

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 45.9 bits (108), Expect = 1e-06
 Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKAL 379
           G  ++V NL     +  L ++F  FG +T+ KV+RD N    +G GFV  +  +EA+ A+
Sbjct: 3   GWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

Query: 380 TEMNGKMVVSKPLYVALAQRKEER 403
             +NG  +  + L V+    K  +
Sbjct: 63  ASLNGYRLGDRVLQVSFKTNKTHK 86

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|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 9/76 (11%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-------DGKSKCFGFVNFDDPDD 271
             +YVKNLS+  TE+DL  IFG F  + S++  ++        +G+ K   FV F   + 
Sbjct: 2   KRLYVKNLSKRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEI 59

Query: 272 AARSVEALNGKKFDDK 287
           A +++  +NG     K
Sbjct: 60  ATKALNLVNGYVLKGK 75

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|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 46.2 bits (109), Expect = 1e-06
 Identities = 22/77 (28%), Positives = 42/77 (54%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VGDL   +    +   F   G++   RV +D++T +S GYG+V++    +A  A+ ++
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 102 NFTPLNGKPIRIMYSYR 118
               L G+ IR  ++ R
Sbjct: 64  GGQWLGGRQIRTNWATR 80

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

 Score = 45.9 bits (109), Expect = 1e-06
 Identities = 20/76 (26%), Positives = 42/76 (55%), Gaps = 9/76 (11%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSC-----KVMRDPNGISRGSGFVAFSTAEEASKA 378
           L+++NL  + +++ L++LFS++G ++       K+ + P G      FV +   E A KA
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGF----AFVTYMIPEHAVKA 60

Query: 379 LTEMNGKMVVSKPLYV 394
             E++G +   + L++
Sbjct: 61  FAELDGTVFQGRLLHL 76

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

 Score = 45.6 bits (108), Expect = 1e-06
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 7/73 (9%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++V N+  + + D+L+ LF EFG +  C  ++D         FV     EEA  A+  +N
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKVKD-------YAFVHMEREEEALAAIEALN 55

Query: 384 GKMVVSKPLYVAL 396
           GK V  + + V L
Sbjct: 56  GKEVKGRRINVEL 68

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

 Score = 45.4 bits (107), Expect = 1e-06
 Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 7/75 (9%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V+NL  +++++ L++ FSEFG +   K ++D         FV F   + A +A+ EMN
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEERDAAVRAMDEMN 56

Query: 384 GKMVVSKPLYVALAQ 398
           GK +  + + + LA+
Sbjct: 57  GKEIEGEEIEIVLAK 71

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

 Score = 45.8 bits (108), Expect = 1e-06
 Identities = 21/75 (28%), Positives = 43/75 (57%), Gaps = 7/75 (9%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V+NL ++++++ L++ F +FG +   K ++D         F+ F   + A KA+ EMN
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 56

Query: 384 GKMVVSKPLYVALAQ 398
           GK +  + + +  A+
Sbjct: 57  GKELEGENIEIVFAK 71

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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 45.6 bits (108), Expect = 1e-06
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           IF+ N+D+    + L   F  +G +LSC V        R + FV    E +A  AI++LN
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVM-------RQFAFVHLRGEAAADRAIEELN 55

Query: 190 GMLLNDKQVFV 200
           G  L+ +++ V
Sbjct: 56  GRELHGRKLVV 66

This subgroup corresponds to the RRM1 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 = 69

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 46.2 bits (109), Expect = 1e-06
 Identities = 25/64 (39%), Positives = 40/64 (62%), Gaps = 1/64 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           +V+V +LS   T +D+K  F  FG I+   V++D A GKSK +GFV+F +  DA  ++  
Sbjct: 3   HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62

Query: 279 LNGK 282
           + G+
Sbjct: 63  MGGQ 66

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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 20/58 (34%), Positives = 33/58 (56%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
           +YVK      + D ++E F +FG + + ++ RD +   +GS FV F T E+A K L +
Sbjct: 2   VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEK 59

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 46.1 bits (109), Expect = 1e-06
 Identities = 22/71 (30%), Positives = 38/71 (53%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V NL+  + ++ L ELF + G +T   + +D  G  +  GFV F  +E    A+  +N
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 384 GKMVVSKPLYV 394
           G  +  +P+ V
Sbjct: 64  GIRLYGRPIKV 74

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|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 = 1e-06
 Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVE 277
           N +++  L    +ED +K++   FG + +  +++D A G SK + F  + DP    +++ 
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

Query: 278 ALNGKKFDDKEWYVGKA 294
            LNG +  DK+  V +A
Sbjct: 61  GLNGMQLGDKKLTVQRA 77

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|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 = 45.7 bits (109), Expect = 1e-06
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           IFI  L   +    + +   +FG + +  +  DS  G S+GY F ++ +      AI  L
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 189 NGMLLNDKQVFV 200
           NGM L DK++ V
Sbjct: 63  NGMQLGDKKLTV 74

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|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 8/79 (10%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTA--------VMRDADGKSKCFGFVNFDDPDDA 272
           +Y+  L +  TED L ++FG  GII            +  D + + K    V +DDP  A
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 273 ARSVEALNGKKFDDKEWYV 291
             ++E  NG +F   +  V
Sbjct: 61  QAAIEWFNGYEFRGNKIKV 79

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

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

 Score = 45.9 bits (109), Expect = 1e-06
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 10/71 (14%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           N+Y+ N+DDS++++KL+  FS++G I S   +R+ N       FV F+    A KA+  +
Sbjct: 5   NVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKN-----CAFVNFTNISNAIKAIDGV 59

Query: 383 NGKMVVSKPLY 393
                 S PL+
Sbjct: 60  K-----SHPLF 65

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 45.8 bits (108), Expect = 1e-06
 Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 9/67 (13%)

Query: 221 VYVKNLSETTTEDDLKKIFGEF--GIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           +YV+NL   T+ED +KK FG+F  G +     +RD       + FV+F   +DA  ++  
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD-------YAFVHFTSREDAVHAMNN 56

Query: 279 LNGKKFD 285
           LNG + +
Sbjct: 57  LNGTELE 63

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 45.9 bits (108), Expect = 1e-06
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALT-- 380
           L++  L    +++ L+  + ++G +T C VMRDP +  SRG GFV FS   E   A+   
Sbjct: 5   LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAAR 64

Query: 381 --EMNGKMVVSK 390
              ++G++V  K
Sbjct: 65  PHTIDGRVVEPK 76

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which 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 A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 45.7 bits (108), Expect = 1e-06
 Identities = 27/65 (41%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++VK LSE TTE+ LK+ F   G I +  V     G SK FGFV+F   +DA  + EA+ 
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAME 60

Query: 281 GKKFD 285
             + D
Sbjct: 61  DGEID 65

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

 Score = 45.4 bits (107), Expect = 1e-06
 Identities = 23/71 (32%), Positives = 46/71 (64%), Gaps = 1/71 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           IF++NL   +  + L + FS  G+++  ++  ++ G+S+G G V+FD+ ESA+ A   +N
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKMEN-GKSKGCGTVRFDSPESAEKACRLMN 60

Query: 190 GMLLNDKQVFV 200
           G+ +N +++ V
Sbjct: 61  GIKINGREIDV 71

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

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 19/57 (33%), Positives = 33/57 (57%)

Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
          L++G L     D  L + F+Q G++    V +D +T+RS G+G+V + +A E   A+
Sbjct: 2  LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM 58

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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L++G L     +  L + F++ G+VV   + +D  T RS G+G+V +       + L   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 102 NFTPLNGKPI 111
               L+G+ I
Sbjct: 61  PHV-LDGREI 69

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 22/75 (29%), Positives = 39/75 (52%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L VG+L L   D Q  +L +  G V    +    ST  S GYG+V Y +   A +A ++L
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 102 NFTPLNGKPIRIMYS 116
           +   + G+ +++ ++
Sbjct: 62  DGKQIGGRKLQVDWA 76

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

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 24/79 (30%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALT 380
            +++V +L   I+ D +K  F+ FG I+  +V++D   G S+G GFV+F    +A  A+ 
Sbjct: 2   FHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61

Query: 381 EMNGKMVVSKPLYVALAQR 399
           +M G+ +  + +    A R
Sbjct: 62  QMGGQWLGGRQIRTNWATR 80

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|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 45.8 bits (108), Expect = 2e-06
 Identities = 28/87 (32%), Positives = 43/87 (49%), Gaps = 1/87 (1%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKA 378
           EG NL++ +L     D  L ++F  FG + S KV  D    +S+  GFV++     A  A
Sbjct: 6   EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 65

Query: 379 LTEMNGKMVVSKPLYVALAQRKEERRA 405
           +  MNG  +  K L V L + K + + 
Sbjct: 66  IQAMNGFQIGMKRLKVQLKRSKNDSKP 92

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|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 23/63 (36%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEA 278
           N+++ +L +   + DL ++F  FG + S  V  D     SKCFGFV++D+P  A  +++A
Sbjct: 9   NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQA 68

Query: 279 LNG 281
           +NG
Sbjct: 69  MNG 71

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|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE- 381
           +++  L    +   LK+ FS+FG +  C +  DP  G SRG GFV F  +E   K + + 
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 382 ---MNGKMVVSK 390
              +NGK++  K
Sbjct: 61  EHKLNGKVIDPK 72

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGIS-RGSGFVAFSTAEEASKALTEM 382
           +YV+ L  + + + LK +FS++GT+    + R  +    +G  F+ F T EEA KA   +
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 383 NGKMV 387
           N    
Sbjct: 62  NNPPE 66

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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 44.9 bits (106), Expect = 2e-06
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALT-- 380
           ++V  L    +   LKE FS+FG +  C +  DP  G SRG GFV F  A    K L   
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 381 --EMNGKMVVSK 390
             +++G+++  K
Sbjct: 61  EHKLDGRVIDPK 72

This subfamily corresponds to the RRM1 in 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 family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALT 380
            +++V +L   I+ + +K  F+ FG I+  +V++D   G S+G GFV+F    +A  A+ 
Sbjct: 2   FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61

Query: 381 EMNGKMVVSKPLYVALAQR 399
            M G+ +  + +    A R
Sbjct: 62  HMGGQWLGGRQIRTNWATR 80

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|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 45.3 bits (107), Expect = 2e-06
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V NL     E+ L ++F + G +T   + +D +GK K FGFV F   +    ++  LN
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 281 G 281
           G
Sbjct: 64  G 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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 45.5 bits (107), Expect = 2e-06
 Identities = 24/59 (40%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALTE 381
           +++  L    S D L++ FS+FG I  C VMRDP    SRG GFV F+      K L +
Sbjct: 2   MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 23/58 (39%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
           ++V NLS  TTED+L+  FG  G I    +M   D GK K F FV+F++ + A  +++
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALK 58

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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 134 NLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNG 190
            + KS+  + LH  F     +  C +  D   G+S+G+ +V + N  SA  A +KLNG
Sbjct: 6   VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNG 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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE- 381
           ++V  L    S   LK+ F++FG +T C +  DPN G SRG GF+ F  A    K L + 
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 382 ---MNGKMVVSK 390
              ++G+++  K
Sbjct: 62  EHRLDGRLIDPK 73

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGK 282
           VKNL   TTE++L+++F +FG +    +       S+    V F +P DA ++ ++L  K
Sbjct: 5   VKNLPFGTTEEELRELFEKFGSLGRLLL-----PPSRTIALVEFLEPSDARKAFKSLAYK 59

Query: 283 KFDDKEWYVGKA 294
           +F     Y+  A
Sbjct: 60  RFKHVPLYLEWA 71

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA- 278
           ++V  LS  TT++ L++ F ++G +    +M+D    +S+ FGFV F DP+     +   
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61

Query: 279 ---LNGKKFDDK 287
              L+G+  D K
Sbjct: 62  PHTLDGRTIDPK 73

This subfamily corresponds to the RRM1 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 form is predominantly nuclear and the nonacetylated form is in cytoplasm. It 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 = 82

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

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 20/56 (35%), Positives = 32/56 (57%)

Query: 132 IKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
           +KNL + + N+ L + FS FG +    V  D  G+  G G V+F  + SA+ A+D+
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|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)

Query: 41  SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
           ++Y+ +L+  +   +L    + +F++ GQ++ + V R L  R   G  +V +     AT 
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 61

Query: 97  ALDELNFTPLNGKPIRIMYSYRDPTI 122
           AL  +   P   KP+RI Y+  D  I
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSDI 87

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

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

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 8/72 (11%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYV +L LS  + QL +LF++ G+V  V+  +D        Y +V++    +A +A++E+
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 102 NFTPLNGKPIRI 113
           N   L G PI +
Sbjct: 56  NGKELEGSPIEV 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|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 = 26/63 (41%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           L+V+NL  S  +D L++LFS+FG ++   V  D  +G S+G  +V F   E+A KA  E+
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 383 NGK 385
           +GK
Sbjct: 65  DGK 67

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|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 45.1 bits (106), Expect = 3e-06
 Identities = 20/63 (31%), Positives = 35/63 (55%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           N+Y+ NL  +  E +L+ +   FG + ST ++RDA+G S+  GF   +  +     ++  
Sbjct: 3   NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHF 62

Query: 280 NGK 282
           NGK
Sbjct: 63  NGK 65

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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 221 VYVKNLSETTTEDDLKKIF-GEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEA 278
           ++V +LS    E DL  +F   F    S  +M D   G S+ +GFV F D +D  R++  
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 279 LNGKKFDDKEWYVGKA 294
           + G     +   +  A
Sbjct: 64  MQGVYCGGRPMRISTA 79

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

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 18/71 (25%), Positives = 34/71 (47%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +++ NLD  +    L   F   G + + K+  D   +   YGFV++     A+ A+  LN
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 190 GMLLNDKQVFV 200
           G  + + ++ V
Sbjct: 61  GRQIENNEIRV 71

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

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

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           ++V N+ + +SDD +++L  + G + S K ++DP+ G  +  GF  F   E A +AL  +
Sbjct: 3   VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLL 62

Query: 383 NGKMVVSKPLYV 394
           NG  +  K 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|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 6/79 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGT----ITSCKVMRDPNGISR--GSGFVAFSTAEEASK 377
           +Y+ NL  S S++ L+E   +F      I S  V    +   R  G  +  FS+ E+A K
Sbjct: 2   VYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEK 61

Query: 378 ALTEMNGKMVVSKPLYVAL 396
            + ++NGK+  ++ L+V L
Sbjct: 62  VVKDLNGKVFKNRKLFVKL 80

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

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

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 17/61 (27%), Positives = 36/61 (59%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V  L++  TE +++++F  +G +    +MRD   +S+   FV +   + A  +++ALN
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 281 G 281
           G
Sbjct: 62  G 62

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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 44.9 bits (106), Expect = 3e-06
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDK- 187
           +FI  L+    + +L + F  FG +  C V  DS  G+SRG+GF+ F   +S    + K 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 188 --LNGMLLNDKQ 197
             L+G +++ K+
Sbjct: 61  HILDGKIIDPKR 72

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLG---YGYVNYNAAHEATRA 97
           +L+V  L  +   + L  LF++ G+VV  ++   ++  RS G   +G+V   +  EA + 
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKI---VTNARSPGARCFGFVTMASVEEAAKC 57

Query: 98  LDELNFTPLNGKPIRI 113
           +  L+ T L+G+ I +
Sbjct: 58  IQHLHRTELHGRVISV 73

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 44.7 bits (105), Expect = 3e-06
 Identities = 28/81 (34%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           IF+ NL    D   L   F  FG + + KV  D +  + +G+GFV   N + A  AI  L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 189 NGMLLNDKQVFVGPFLRKQER 209
           NG  L D+ + V     KQ +
Sbjct: 64  NGYRLGDRVLQVSFKTSKQHK 84

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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 45.1 bits (106), Expect = 3e-06
 Identities = 26/84 (30%), Positives = 43/84 (51%), Gaps = 1/84 (1%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKAL 379
           G  ++V NL     +  L +LF  FG + + KV+RD N    +G GFV  +  +EA+ A+
Sbjct: 3   GWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

Query: 380 TEMNGKMVVSKPLYVALAQRKEER 403
             +NG  +  + L V+    K  +
Sbjct: 63  ASLNGYRLGDRVLQVSFKTNKTHK 86

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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 45.0 bits (106), Expect = 3e-06
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N+Y+  L  T T+ D++ +F  FG II S  ++  A G S+   F+ FD   +A  ++ +
Sbjct: 2   NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 279 LNGKK 283
            NG K
Sbjct: 62  FNGHK 66

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

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           VY+ +L     E +L+K F +FG +T   + R    GKSK + FV F+ P+ A    E +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 280 NG 281
           N 
Sbjct: 62  NN 63

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

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           +Y+ +L     + +L++ FS+FGT+T  ++ R    G S+G  FV F + E A      M
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 383 NGKMVVSKPL 392
           N  ++  + L
Sbjct: 62  NNYLLFERLL 71

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|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 44.7 bits (105), Expect = 3e-06
 Identities = 22/77 (28%), Positives = 41/77 (53%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VGDL   +    +   F   G++   RV +D++T +S GYG+V++    +A  A+  +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 102 NFTPLNGKPIRIMYSYR 118
               L G+ IR  ++ R
Sbjct: 64  GGQWLGGRQIRTNWATR 80

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|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 44.6 bits (105), Expect = 3e-06
 Identities = 21/71 (29%), Positives = 37/71 (52%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+ NL+  +  + L++ F   G +    +  D  G+ + +GFV F + ES   AI  LN
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 190 GMLLNDKQVFV 200
           G+ L  + + V
Sbjct: 64  GIRLYGRPIKV 74

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

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 4/68 (5%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           V V  L E  +  DLK    + G +T   V RD +G     G V F   +D  R++  L+
Sbjct: 3   VVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEG----EGVVEFTSQEDMERALRKLD 58

Query: 281 GKKFDDKE 288
           G +F  + 
Sbjct: 59  GTEFRGRR 66

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 44.9 bits (106), Expect = 3e-06
 Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L+VG+LD  V +  +++LF Q G V+ V++ +D   +    + +VN+        A++ 
Sbjct: 3   TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQ-FAFVNFKHEVSVPYAMNL 61

Query: 101 LNFTPLNGKPIRI 113
           LN   L G+P+ I
Sbjct: 62  LNGIKLYGRPLNI 74

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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 45.7 bits (108), Expect = 3e-06
 Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKAL 379
              L+V+NL    +++ L   FS+FG++     + D   G ++G+GFV F      +  L
Sbjct: 1   DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

This subgroup corresponds to the RRM3 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 = 107

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 45.0 bits (106), Expect = 3e-06
 Identities = 21/63 (33%), Positives = 35/63 (55%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
           G  +++  L   + +D+L  L  + G I   ++M D NG +RG  FV FS  +EA  A+ 
Sbjct: 1   GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIK 60

Query: 381 EMN 383
           ++N
Sbjct: 61  QLN 63

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

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

 Score = 44.6 bits (105), Expect = 3e-06
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 4/62 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           VYV NL     + +L++ F  +G + +  + R+  G    F FV F+DP DA  +V  L+
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG----FAFVEFEDPRDAEDAVRGLD 57

Query: 281 GK 282
           GK
Sbjct: 58  GK 59

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

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

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           I++ NLD +     L + FS  G +   ++A D   Q   Y FV+F  + S  +A+ KLN
Sbjct: 7   IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDE-TQPTRYAFVEFAEQTSVINAL-KLN 64

Query: 190 GMLLNDKQVFV 200
           G +   + + V
Sbjct: 65  GAMFGGRPLKV 75

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

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

 Score = 44.9 bits (106), Expect = 3e-06
 Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 4/81 (4%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESA-KSAIDK 187
           +F+  L   +    L + FS FG +   +V  D   G+ RG+GFV F N +SA K+A+ K
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61

Query: 188 LNGMLLNDKQVFVGPFLRKQE 208
            +   +N  +V V   + K+E
Sbjct: 62  FH--PINGHRVEVKKAVPKEE 80

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

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 3/78 (3%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVC--RDLSTR-RSLGYGYVNYNAAHEAT 95
           +T+LYVG+L+  V +  L   F + G + SV++   R    R R+   G+V +    +A 
Sbjct: 1   TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60

Query: 96  RALDELNFTPLNGKPIRI 113
           RALDEL+   + G  +++
Sbjct: 61  RALDELDGKDVMGYELKL 78

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

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

 Score = 44.2 bits (105), Expect = 4e-06
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMR-DADGKSKCFGFVNFDDPDDAARSVEALN 280
            V NL    T++  +++   FG +    ++  ++ G+SK +GFV +     A ++   L+
Sbjct: 3   CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 281 GKK 283
           GK+
Sbjct: 63  GKQ 65

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

 Score = 44.2 bits (104), Expect = 4e-06
 Identities = 21/71 (29%), Positives = 36/71 (50%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V NL        LK++F   G +    +  D DGKS+  G V F+ P +A +++   N
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62

Query: 281 GKKFDDKEWYV 291
           G+   D+  +V
Sbjct: 63  GQFLFDRPMHV 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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 4/75 (5%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSL---GYGYVNYNAAHEATRAL 98
           +YV +LD  +++  L  +F++ G+V S+R+ +    ++     G+ +V +  A  A  AL
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 99  DELNFTPLNGKPIRI 113
            +LN T L G+ I +
Sbjct: 63  -QLNGTELGGRKISV 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|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 44.4 bits (105), Expect = 4e-06
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           V+V N+    TE+ LK IF E G + S  ++ D + GK K +GF  + D + A  ++  L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 280 NGKKFDDKEWYVGKA 294
           NG + + ++  V  A
Sbjct: 61  NGYELNGRQLRVDNA 75

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|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 27/76 (35%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           ++YV D+D  V + QL  LF+  GQVV  RVC D      L + ++ +     A  AL  
Sbjct: 4   TVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGD--PNSVLRFAFIEFTDEEGARAAL-S 60

Query: 101 LNFTPLNGKPIRIMYS 116
           L+ T L   P+R++ S
Sbjct: 61  LSGTMLGFYPVRVLPS 76

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 44.4 bits (105), Expect = 4e-06
 Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 5/60 (8%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           N+Y+ NL +S S+++L+E   +FG I   K++++     +   FV F +   A K +T +
Sbjct: 5   NVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFLSIANAIKVVTTL 59

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 324 LYVKNLDDSISDDKLK----ELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKA 378
           ++VK  D S+ +D ++    E FS  G IT   +  D   G S+G  ++ F + +   KA
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 379 LTEMNGKMVVSKPLYV 394
           L E++G  +    L V
Sbjct: 62  L-ELDGSDLGGGNLVV 76

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 44.3 bits (104), Expect = 4e-06
 Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEA 278
           N++V  LS  T   DLK +FG++G + S  V+ +A    +KC+G V      + AR +  
Sbjct: 1   NLWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISH 60

Query: 279 LN 280
           L+
Sbjct: 61  LH 62

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains 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. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

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

 Score = 44.0 bits (104), Expect = 4e-06
 Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 5/79 (6%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCR--DLSTRRSLGYGYVNYNAAHEATRA 97
           T + V +L        +  LF+  GQ+ SVRV +  D S R   G+ +V ++ A EA  A
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSAR---GFAFVEFSTAKEALNA 57

Query: 98  LDELNFTPLNGKPIRIMYS 116
           ++ L  T L G+ + + Y+
Sbjct: 58  MNALKDTHLLGRRLVLQYA 76

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

>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 44.6 bits (105), Expect = 4e-06
 Identities = 26/67 (38%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 56  LYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY 115
           LY LF+Q G VV +     L T +  G  +V +     AT AL +L   P  GKP+RI Y
Sbjct: 22  LYALFSQFGHVVDIVA---LKTMKMRGQAFVIFKELSSATNALRQLQGFPFYGKPMRIQY 78

Query: 116 SYRDPTI 122
           +  D  I
Sbjct: 79  AKTDSDI 85

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 91

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

 Score = 43.7 bits (103), Expect = 5e-06
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYVG+LD  V +  L  +F   G V +V++  D    + + YG+V Y+ +H+A  AL  L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 102 NFTPLNGKPIRI 113
           N   +    IR+
Sbjct: 60  NGRQIENNEIRV 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|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 5/57 (8%)

Query: 144 LHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
           L   FS FGNI++      S+ + +  GFV F+  ESA  AI +LNG  +   Q+ V
Sbjct: 19  LKKAFSPFGNIINI-----SMEKEKNCGFVTFEKMESADRAIAELNGTTVQGVQLKV 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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 44.3 bits (104), Expect = 5e-06
 Identities = 25/68 (36%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           IF+ NL    D   L   F  FG + + KV  D +  + +G+GFV   N + A  AI  L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 189 NGMLLNDK 196
           NG  L D+
Sbjct: 66  NGYRLGDR 73

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

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VG L   V + +  + F+Q G+VV  ++ +D  T RS G+G+V +++     R     
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA- 60

Query: 102 NFTPLNGKPIRI 113
               L GK + +
Sbjct: 61  GMLELGGKQVEV 72

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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE- 381
           ++V  L  ++++  L++ FS+FGT+T   VM D      RG GF+ F + +   + + E 
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEH 64

Query: 382 ---MNGKMVVSK 390
              +NGK V  K
Sbjct: 65  FHDINGKKVEVK 76

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

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

 Score = 44.1 bits (104), Expect = 5e-06
 Identities = 19/69 (27%), Positives = 37/69 (53%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+ NLD  +  + + + F   G ++  K+  D  G+ + + FV F +E S   A++ LN
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN 63

Query: 190 GMLLNDKQV 198
           G+ L  + +
Sbjct: 64  GIKLYGRPL 72

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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 44.2 bits (104), Expect = 5e-06
 Identities = 20/69 (28%), Positives = 39/69 (56%)

Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAA 273
           D+    N+++ NL    +E +L++ F ++GII    + R A G+   + F+ F + D A 
Sbjct: 4   DQRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAH 63

Query: 274 RSVEALNGK 282
           R+  A++G+
Sbjct: 64  RAKVAMSGR 72

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B 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. RBM15B belongs 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 = 85

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 44.1 bits (105), Expect = 5e-06
 Identities = 20/73 (27%), Positives = 37/73 (50%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           + ++V N   +  + D++ +F ++G I S         K++ F +V F  P+ AA +V  
Sbjct: 1   STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVAL 60

Query: 279 LNGKKFDDKEWYV 291
           LNGK  +  +  V
Sbjct: 61  LNGKLGEGYKLVV 73

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 44.6 bits (106), Expect = 5e-06
 Identities = 22/75 (29%), Positives = 40/75 (53%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S  +Y+G L   + +  +  +F+Q G++V + + RD  T +S G+ ++ Y        A+
Sbjct: 9   SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAV 68

Query: 99  DELNFTPLNGKPIRI 113
           D LN   L G+ IR+
Sbjct: 69  DNLNGIKLLGRTIRV 83

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|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 43.9 bits (103), Expect = 5e-06
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LYV NL   +++  + +LFS+ G   SCK++ D  G +    FV F     A+ +L  MN
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAG-NDPYCFVEFFEHRHAAASLAAMN 60

Query: 384 GKMVVSKPLYVALA 397
           G+ ++ K + V  A
Sbjct: 61  GRKIMGKEVKVNWA 74

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

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

 Score = 44.0 bits (104), Expect = 5e-06
 Identities = 21/77 (27%), Positives = 44/77 (57%), Gaps = 2/77 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+  +D  +D   +   F+ +G++   K+ TD  G S+GYGFV F ++   +  ++  +
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQKIVE--S 65

Query: 190 GMLLNDKQVFVGPFLRK 206
            +  + K++ +GP +RK
Sbjct: 66  QINFHGKKLKLGPAIRK 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|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 43.7 bits (104), Expect = 6e-06
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           +++ NLD+ +  + L + F   G +++  +  D +    +GYGFV+F +EE A  AI  +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 189 NGMLLNDKQVFV 200
           N + L  K + V
Sbjct: 61  NMIKLYGKPIRV 72

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

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 43.9 bits (103), Expect = 6e-06
 Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEA 278
           N++V  LS TT   DLK +F ++G +    V+ +A    ++C+GFV     ++A + +  
Sbjct: 3   NLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINH 62

Query: 279 LN 280
           L+
Sbjct: 63  LH 64

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

 Score = 43.8 bits (104), Expect = 6e-06
 Identities = 19/72 (26%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           ++++NL   I ++ L+D F  +G I   ++      ++RG  FV +++   AK+A D L+
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTK--ETRGTAFVVYEDIYDAKNACDHLS 62

Query: 190 GMLLNDKQVFVG 201
           G  + ++ + V 
Sbjct: 63  GFNVANRYLVVL 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|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 43.7 bits (103), Expect = 6e-06
 Identities = 23/74 (31%), Positives = 40/74 (54%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           + VKNL    +   ++ LFS +G + S +V +  +  +RG  FV FSTA+EA  A+  + 
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 384 GKMVVSKPLYVALA 397
              ++ + L +  A
Sbjct: 63  DTHLLGRRLVLQYA 76

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

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 44.2 bits (105), Expect = 6e-06
 Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           +Y+  L    TE D+  +F ++G I    ++RD   GKSK F F+ ++D      +V+ L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 280 NGKK 283
           NG K
Sbjct: 72  NGIK 75

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

 Score = 43.8 bits (104), Expect = 7e-06
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 4/77 (5%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVA---TDSL-GQSRGYGFVQFDNEESAKSA 184
           N+++ NL+  +  + L   F  FG + S K+    T+    ++R  GFV F N   A+ A
Sbjct: 3   NLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERA 62

Query: 185 IDKLNGMLLNDKQVFVG 201
           +D+L+G  +   ++ +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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 43.9 bits (103), Expect = 7e-06
 Identities = 22/74 (29%), Positives = 40/74 (54%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++V +L    ++S L+ LF   G V +V+V RD +T +  G+G+V      EA  A+  L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 102 NFTPLNGKPIRIMY 115
           N   L  + +++ +
Sbjct: 64  NGYRLGDRVLQVSF 77

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|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 43.6 bits (102), Expect = 7e-06
 Identities = 21/75 (28%), Positives = 43/75 (57%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             +L+V  L  +   + L +LF++ G+VV  +V  +  +  +  YG+V  + + EAT+ +
Sbjct: 1   GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCI 60

Query: 99  DELNFTPLNGKPIRI 113
           + L+ T L+G+ I +
Sbjct: 61  NHLHRTELHGRMISV 75

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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 43.3 bits (102), Expect = 7e-06
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 7/76 (9%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
           + ++V N+D+  S ++L+ LF  +G + SC VMR          FV       A +A+ E
Sbjct: 1   VKIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ-------FAFVHLRGEAAADRAIEE 53

Query: 382 MNGKMVVSKPLYVALA 397
           +NG+ +  + L V  +
Sbjct: 54  LNGRELHGRKLVVEHS 69

This subgroup corresponds to the RRM1 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 = 69

>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 = 43.4 bits (103), Expect = 7e-06
 Identities = 13/38 (34%), Positives = 23/38 (60%)

Query: 165 GQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGP 202
           G+S+G+ +V+F +E +A +  +KL G   N K+  V  
Sbjct: 39  GKSKGFAYVEFASEAAAAAVKEKLEGREFNGKKCVVTY 76

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

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 43.9 bits (103), Expect = 7e-06
 Identities = 25/62 (40%), Positives = 36/62 (58%), Gaps = 4/62 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           VYV NL     + +L++ FG +G + S  V R+  G    F FV F+DP DAA +V  L+
Sbjct: 7   VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELD 62

Query: 281 GK 282
           G+
Sbjct: 63  GR 64

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 81

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 43.2 bits (102), Expect = 7e-06
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 8/72 (11%)

Query: 221 VYVKNLSE-TTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           ++V      TT E+D++K+F  FG +    + +        F FV F+D +DA +++EAL
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKT-------FAFVEFEDSEDATKALEAL 54

Query: 280 NGKKFDDKEWYV 291
           +G + D     V
Sbjct: 55  HGSRIDGSVLTV 66

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

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

 Score = 43.4 bits (103), Expect = 7e-06
 Identities = 26/72 (36%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L V NLD  ISD +L+ LFS+FG +   K +R    +     FV F     A  AL  +N
Sbjct: 4   LLVFNLDSPISDQELRSLFSQFGEV---KDIR-ETPLRPSQKFVEFYDIRAAEAALDALN 59

Query: 384 GKMVVSKPLYVA 395
           G+  +   L V 
Sbjct: 60  GRPFLGGRLKVK 71

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

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

 Score = 43.6 bits (103), Expect = 8e-06
 Identities = 19/60 (31%), Positives = 35/60 (58%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V  LS+   E+D++ +F  FG I    V+RD +G+S+   FV F     A  +++A++
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 63

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

 Score = 43.5 bits (103), Expect = 8e-06
 Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 2/67 (2%)

Query: 50  SVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG- 108
           SV +  L + F   G++  + V +D  T+ S G  YV +  A  A RA++E+N   L G 
Sbjct: 13  SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72

Query: 109 -KPIRIM 114
            KP++++
Sbjct: 73  TKPLKVL 79

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|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
           +++  L + +S+D++KEL   FG + +  +++D   G+S+G  F  +       +A+  +
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 383 NGKMVVSKPLYVALA 397
           NG  +  K L V  A
Sbjct: 63  NGMQLGDKKLTVQRA 77

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

 Score = 43.6 bits (103), Expect = 8e-06
 Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           +YV ++   + +D +++ FS FG I S  +  DP     +G  FV +   E A  AL +M
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 383 NGKMV 387
           NG M+
Sbjct: 63  NGVML 67

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

 Score = 43.2 bits (102), Expect = 8e-06
 Identities = 21/50 (42%), Positives = 34/50 (68%), Gaps = 1/50 (2%)

Query: 229 TTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
           + TE+DL++ F EFG I   ++++D + G+SK FG+V F  P  AA ++E
Sbjct: 11  SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 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|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 43.7 bits (103), Expect = 8e-06
 Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 324 LYVKNLDDSISD-DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           L ++NL  SI    KLK++F  +G +    + R   G   G  FV     + A  AL   
Sbjct: 3   LIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENT 62

Query: 383 NGKMVVSKPLYVALAQRKE 401
           NG  +  +P+ V  A +K 
Sbjct: 63  NGLEIDGRPVAVDWAVQKN 81

This subgroup corresponds to the RRM2 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 = 83

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

 Score = 43.5 bits (102), Expect = 8e-06
 Identities = 23/56 (41%), Positives = 32/56 (57%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           L VKNL   +S++ L++ FS+FG +    V+ D  G   G GFV F+    A KAL
Sbjct: 2   LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKAL 57

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|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 43.5 bits (102), Expect = 9e-06
 Identities = 20/63 (31%), Positives = 33/63 (52%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           N+Y+ NL  +  E +L+ +   FG + ST ++RDA G S+  GF   +  +     +   
Sbjct: 2   NLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEAIITHF 61

Query: 280 NGK 282
           NGK
Sbjct: 62  NGK 64

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 43.5 bits (102), Expect = 9e-06
 Identities = 20/58 (34%), Positives = 31/58 (53%)

Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
          L++G L     D  L   F Q G +    V RD +T+RS G+G+V Y++  E   A++
Sbjct: 5  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

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

 Score = 42.5 bits (101), Expect = 9e-06
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 4/53 (7%)

Query: 235 LKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDK 287
           L K+F  FG +    +++   G    F FV F   + A ++V+ LNG  F  +
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKPG----FAFVEFSTEEAAEKAVQYLNGVLFGGR 49

(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|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 43.3 bits (103), Expect = 9e-06
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 9/74 (12%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-------GQSRGYGFVQFDNEESAK 182
           +++KNL K +  + L   F  F  + S     +         G+ +G  FV F +EE A 
Sbjct: 4   LYVKNLSKRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61

Query: 183 SAIDKLNGMLLNDK 196
            A++ +NG +L  K
Sbjct: 62  KALNLVNGYVLKGK 75

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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 43.5 bits (102), Expect = 9e-06
 Identities = 25/68 (36%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           IF+ NL    D   L   F  FG + + KV  D +  + +G+GFV   N + A  AI  L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 189 NGMLLNDK 196
           NG  L D+
Sbjct: 66  NGYRLGDR 73

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 43.7 bits (104), Expect = 9e-06
 Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 16/74 (21%)

Query: 223 VKNLSETTTEDDLKKIF----GEF-----GIITSTAVMRDAD-------GKSKCFGFVNF 266
           ++NL ++  E  LK++F     E        I    +MRD         GKSK +GFV F
Sbjct: 5   IRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEF 64

Query: 267 DDPDDAARSVEALN 280
            + + A +++ ALN
Sbjct: 65  TNHEHALKALRALN 78

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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 43.5 bits (103), Expect = 9e-06
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VG L  +V ++ L   F+Q G V  V V  D   +R  G+G++ + +     + ++E 
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE- 63

Query: 102 NFTPLNGKPIRI 113
           +F  +NGK + +
Sbjct: 64  HFHDINGKKVEV 75

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

 Score = 43.5 bits (102), Expect = 9e-06
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++V+NL   ++  KLKE FS+ G +   ++  + NG S+G G V F + E A KA   MN
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME-NGKSKGCGTVRFDSPESAEKACRLMN 60

Query: 384 GKMVVSKPLYVAL 396
           G  +  + + V L
Sbjct: 61  GIKINGREIDVRL 73

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|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 43.2 bits (102), Expect = 9e-06
 Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 1/69 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTF-STFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
            + + NL K +    + + F S  G I    ++ +  G+S G   + F     A  A DK
Sbjct: 1   KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60

Query: 188 LNGMLLNDK 196
            NG + +  
Sbjct: 61  FNGRIDDGN 69

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 42.9 bits (102), Expect = 9e-06
 Identities = 24/57 (42%), Positives = 33/57 (57%), Gaps = 6/57 (10%)

Query: 324 LYVKNL-DDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           L V+N+  +  +  KL E FS+FGTI + +V  +P      S  V FST+EEA KA 
Sbjct: 4   LEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPE-----SALVQFSTSEEAKKAY 55

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 43.3 bits (103), Expect = 9e-06
 Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 2/66 (3%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDA-ARSVEA 278
           ++V  LS + TE DL++ F  FG ++   +++    G  + F +++    +    +    
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 279 LNGKKF 284
           LNG K+
Sbjct: 62  LNGTKW 67

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

 Score = 43.4 bits (102), Expect = 9e-06
 Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSV 276
           ++V  + E T E  L+  F ++G I    +M D   GK + F FV FDD D   + V
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 59

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

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

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 27/78 (34%), Positives = 38/78 (48%), Gaps = 7/78 (8%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRS---LGYGYVNYNAAHEATRAL 98
           L+V  L  SV   +L  LF + G V SVR    L T RS    G  YV Y     A++A+
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVR----LVTNRSGKPKGLAYVEYENESSASQAV 60

Query: 99  DELNFTPLNGKPIRIMYS 116
            +++ T +  K I +  S
Sbjct: 61  LKMDGTEIKEKTISVAIS 78

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 5/82 (6%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCR-----DLSTRRSLGYGYVNYNAAHEA 94
           T+L+V +L+    +  L   F + G V SV + +           S+GYG+V + +   A
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 95  TRALDELNFTPLNGKPIRIMYS 116
            +AL  L  T L+G  + +  S
Sbjct: 61  QKALKRLQGTVLDGHALELKLS 82

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

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKAL 379
           L+V  L + ++++ L+E FS++G + S +++ D   G  RG  FV F   +   K +
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 58

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

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 8/70 (11%)

Query: 324 LYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           ++V NL+ D +S + L+E+FS++G I    +        +G GFV F   E+A  A+   
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISL-------HKGYGFVQFDNEEDARAAVAGE 55

Query: 383 NGKMVVSKPL 392
           NG+ +  + L
Sbjct: 56  NGREIAGQKL 65

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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 43.2 bits (101), Expect = 1e-05
 Identities = 19/63 (30%), Positives = 33/63 (52%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           N+Y+ NL  +  E +L+ +   FG + ST ++RD+ G S+  GF   +  +     +   
Sbjct: 2   NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHF 61

Query: 280 NGK 282
           NGK
Sbjct: 62  NGK 64

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

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + + N+     +  L   F  FG IL  ++  +  G S+G+GFV F N   A  A +KL+
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG-SKGFGFVTFANSADADRAREKLH 61

Query: 190 G 190
           G
Sbjct: 62  G 62

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|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALT-- 380
           ++V  L  + ++D +K+ FS+FG +    +M D      RG GFV F + +   K     
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

Query: 381 --EMNGKMVVSK 390
             E+N KMV  K
Sbjct: 62  FHEINNKMVECK 73

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 5/73 (6%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAID-- 186
           +F+  L      K L D F+ FG +  C +  D + G+SRG+GF+ F +  S +  ++  
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 187 --KLNGMLLNDKQ 197
             +L+G L++ K+
Sbjct: 62  EHRLDGRLIDPKK 74

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

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

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 19/56 (33%), Positives = 31/56 (55%)

Query: 132 IKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
           +KNL   + N+ L   FS FG +    V  D  G+  G GFV+F  + +A+ A+++
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|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSC-KVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           + ++ L  S +++ +++ FS          ++ D +G   G  +V F++ E+A +AL + 
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61

Query: 383 NGKM 386
           N KM
Sbjct: 62  NNKM 65

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 2/66 (3%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGII-TSTAVMRDAD-GKSKCFGFVNFDDPDDAARSV 276
           N + ++ L  + TE+D++      G+      +MR    G S+ F FV F   ++A R +
Sbjct: 3   NTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWM 62

Query: 277 EALNGK 282
           E   GK
Sbjct: 63  ELNQGK 68

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

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

 Score = 43.2 bits (101), Expect = 1e-05
 Identities = 22/56 (39%), Positives = 32/56 (57%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           L V+NL   +S++ L+E FS+FG +    V+ D  G S G G V F++   A KA 
Sbjct: 2   LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAF 57

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|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 43.0 bits (101), Expect = 1e-05
 Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEALNG 281
           V  LS  TTE DL+++F  +G +    V+ D   G+S+ F FV F+  DD+  ++E  NG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 282 KKFDDK 287
            + D +
Sbjct: 64  MELDGR 69

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 326 VKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGIS--RGSGFVAFSTAEEASKALT 380
           V+N+    +  +L+ELFS FG + + ++ +   G    RG GFV F T ++A +A  
Sbjct: 5   VRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61

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|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 132 IKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGY-GFVQFDNEESAKSAIDKLNG 190
           I NL   +    LH  FS +G +   K+      ++ G    VQFD+ ESA++A   LNG
Sbjct: 6   ISNLLYPVTVDVLHQVFSPYGAVE--KILIFE--KNTGVQALVQFDSVESAENAKKALNG 61

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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 42.9 bits (100), Expect = 1e-05
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
           N+Y++ L   TT+ DL K+   +G I ST  + D +  + K +GFV+FD P  A ++V +
Sbjct: 6   NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVAS 65

Query: 279 L 279
           L
Sbjct: 66  L 66

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++V +LD  V   +L ++F   G+VV   +  D    +S G G V +    EA +A+   
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKED-KEGKSRGMGVVQFEHPIEAVQAISMF 59

Query: 102 NFTPLNGKPIRI 113
           N   L  +P+R+
Sbjct: 60  NGQMLFDRPMRV 71

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

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLST----RRSLGYGYVNYNAAHEATRA 97
           L++G+LD  + +  L  LF++ G++          +     +  GY +V +    EA +A
Sbjct: 2   LWIGNLDSRLTEFHLLKLFSKYGKIKKFDF-LFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 98  LDELNFTPLNGKPIRIMY 115
           L  LN     GK + + +
Sbjct: 61  LKSLNGKTALGKKLVVRW 78

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 18/63 (28%), Positives = 35/63 (55%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T++Y+  L  +  D  L  L    G+++S +   D  T +  GYG+V++++   A +A++
Sbjct: 1   TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

Query: 100 ELN 102
            LN
Sbjct: 61  GLN 63

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +++V +LD SV + +L  LF++ G++  VR+ ++    +S GY YV +        AL +
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKN-YKGKSKGYAYVEFENEESVQEAL-K 58

Query: 101 LNFTPLNGKPI 111
           L+   + G+P+
Sbjct: 59  LDRELIKGRPM 69

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L V +L   V +  L +LF ++G+V  V++  D  + RS G   V +    +A RA+ + 
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIKQF 61

Query: 102 NFTPLNGKPIRI 113
           N   L+G+P+++
Sbjct: 62  NGVLLDGQPMQV 73

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

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 20/62 (32%), Positives = 35/62 (56%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L+VG L L   +  L ++F++ G +  +R+ RD+ T  S GY +V Y    +A RA  +
Sbjct: 5   TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64

Query: 101 LN 102
            +
Sbjct: 65  AH 66

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

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 21/63 (33%), Positives = 30/63 (47%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T ++VG L     D  L   F+Q G++    V  D  T +S GYG+V +     A RA  
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 100 ELN 102
           + N
Sbjct: 61  DPN 63

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

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

 Score = 42.1 bits (100), Expect = 2e-05
 Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKL 188
           +F+ NL   I+ + L   F   G++ + ++  D   G  +G+G+V F  ++S   A+ KL
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KL 60

Query: 189 NGMLLNDKQVFV 200
           NG+ L  +++ 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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +F+ N+ + + +  +       G +LS K   D S G+ + +GF +F++ E A  A+  L
Sbjct: 3   VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLL 62

Query: 189 NGMLLNDKQVFV 200
           NG+ L  K++ 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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 41.7 bits (99), Expect = 2e-05
 Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 5/61 (8%)

Query: 56  LYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY 115
           LY LF+  G V  +++ +        G+ +V ++    A +A+  LN     G+P+R+ Y
Sbjct: 1   LYKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 116 S 116
           S
Sbjct: 56  S 56

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

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 19/57 (33%), Positives = 29/57 (50%)

Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
          L++G L     D  L + F + G +    V RD  T+RS G+G+V Y+   E   A+
Sbjct: 5  LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +F+  L   +  + L++ FS  G +   ++  D +  +S+G  +V+F +EES   A+  L
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GL 60

Query: 189 NGMLLN 194
            G  L 
Sbjct: 61  TGQRLL 66

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|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 46.4 bits (110), Expect = 2e-05
 Identities = 58/322 (18%), Positives = 112/322 (34%), Gaps = 83/322 (25%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQ------------MGQVVSVRVCRDLSTRRSLGYGYVNYN 89
           LYVG +     +  + D FN                V SV + ++ +      + ++ + 
Sbjct: 178 LYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKN------FAFLEFR 231

Query: 90  AAHEATRALDELNFTPLNGKPIRI--MYSYRDP-------------------------TI 122
              EAT A+  L+    +   ++I   + Y                            T 
Sbjct: 232 TVEEATFAM-ALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTT 290

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESA 181
                  I+I NL   +    + +   +FG++ +  +  D   G S+GY F ++ +    
Sbjct: 291 VLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVT 350

Query: 182 KSAIDKLNGMLLNDKQVFV--GPFLRKQERESTADKTRFNNVYVKNLS-------ETTTE 232
             AI  LNG    D ++ V        Q    T++      +  K LS          T+
Sbjct: 351 DVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTK 410

Query: 233 -----------------------DDLKKIFGEFGIITSTAVMRDADGKSKCFG----FVN 265
                                  +D+K  F ++G + +  + R    ++   G    F+ 
Sbjct: 411 VVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLE 470

Query: 266 FDDPDDAARSVEALNGKKFDDK 287
           + D   A +++E +NG+KF+D+
Sbjct: 471 YADVRSAEKAMEGMNGRKFNDR 492

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 19/73 (26%), Positives = 34/73 (46%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            +F+ NL+ +I  + L   F  +G +    +     GQ   Y FV+F N + A  A   +
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 189 NGMLLNDKQVFVG 201
           +G  +   Q+ +G
Sbjct: 64  SGQYIGRNQIKIG 76

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 6/77 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS----LGQ--SRGYGFVQFDNEESAKS 183
           +F+KNL+ S  N+ L D F      +  +V T       GQ  S G+GFV F  +E A++
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 184 AIDKLNGMLLNDKQVFV 200
           A+  ++G +L+   + V
Sbjct: 63  ALKAMDGFVLDGHTLVV 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|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 7/71 (9%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV+     T+E  +++IF  +G +    ++         F FV F+  + A R+ ++++
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMI-------SNFAFVEFESLESAIRAKDSVH 54

Query: 281 GKKFDDKEWYV 291
           GK  ++   YV
Sbjct: 55  GKVLNNNPLYV 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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 8/68 (11%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VG++D   +  +L  LF   G V+S  V R         + +V+      A RA++EL
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIEEL 54

Query: 102 NFTPLNGK 109
           N   L+G+
Sbjct: 55  NGRELHGR 62

This subgroup corresponds to the RRM1 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 = 69

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

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V+NL    T   LK  F E G +   A ++  +GKSK  G V F+ P+ A R+   +N
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVL-YADIKMENGKSKGCGVVRFESPEVAERACRMMN 60

Query: 281 GKKFDDKE 288
           G K + +E
Sbjct: 61  GYKLNGRE 68

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

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 14/68 (20%), Positives = 28/68 (41%), Gaps = 3/68 (4%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           VY      +    D+K++F   G +    ++       +   F+ F++ + A  ++E LN
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSR---TVQPHAFITFENLEAAQLAIETLN 58

Query: 281 GKKFDDKE 288
           G   D   
Sbjct: 59  GASVDGNC 66

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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 18/56 (32%), Positives = 29/56 (51%)

Query: 47  LDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN 102
           +  SV   QL+ LF+ +  +    + RD  T +S G+ YV Y+    A  A ++LN
Sbjct: 7   VSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLN 62

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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 2/62 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           L+V  +  S++ ++L  LF     +  C + RDP  G S+G  +V +S    A  A  ++
Sbjct: 3   LFV-VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKL 61

Query: 383 NG 384
           NG
Sbjct: 62  NG 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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAF 369
           L+V  L    + + L+  FS++G +  C +M+D     SRG GFV F
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKF 48

This subfamily corresponds to the RRM1 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 form is predominantly nuclear and the nonacetylated form is in cytoplasm. It 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 = 82

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

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 23/56 (41%), Positives = 30/56 (53%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           L VKNL   +S++ L+E FS FG +    V+ D  G   G G V F+    A KAL
Sbjct: 2   LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKAL 57

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 4/60 (6%)

Query: 326 VKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGK 385
           V  L +  S   LK+   + G +T   V RD  G     G V F++ E+  +AL +++G 
Sbjct: 5   VSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEGE----GVVEFTSQEDMERALRKLDGT 60

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSV--- 276
           ++V  L     E DL + F +FG +    V+ D   GK + FGFV F + D A ++    
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61

Query: 277 -EALNGKKFDDKE 288
              +NG + + K+
Sbjct: 62  FHPINGHRVEVKK 74

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|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B" (U2B") and similar proteins

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 27/82 (32%), Positives = 41/82 (50%), Gaps = 12/82 (14%)

Query: 324 LYVKNLDDSISDDKLKE----LFSEFG---TITSCKVMRDPNGISRGSGFVAFSTAEEAS 376
           +Y+ NL+D I  ++LK     LFS+FG    I + K M+      RG  FV F     A+
Sbjct: 4   IYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTMK-----MRGQAFVIFKELSSAT 58

Query: 377 KALTEMNGKMVVSKPLYVALAQ 398
            AL ++ G     KP+ +  A+
Sbjct: 59  NALRQLQGFPFYGKPMRIQYAK 80

This subgroup corresponds to the RRM1 of U2B" (also termed U2 snRNP B") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA. In addition, the nuclear transport of U2B" is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus. . Length = 91

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

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 18/73 (24%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKL 188
           +++ ++   +    +   FS FG I S  ++ D    + +G+ FV+++  E+A+ A++++
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 189 NGMLLNDKQVFVG 201
           NG++L  + + VG
Sbjct: 63  NGVMLGGRNIKVG 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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 332 SISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKAL 379
           S +++ L+E F EFG I    +++D N G S+G G+V F    +A+ AL
Sbjct: 11  SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59

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|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 323 NLYVKNLDDSISDDKLKELF-SEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
            + V NL   +++ +++E F S+ G I    +  +  G S G   + F  A +A+KA  +
Sbjct: 1   KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60

Query: 382 MNGKMVVSK 390
            NG++    
Sbjct: 61  FNGRIDDGN 69

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

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

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 5/65 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LYV  L + +++  L++ F +FG I S  V+       +   FV F+T E A KA   + 
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITVVP-----RQQCAFVTFTTREAAEKAAERLF 58

Query: 384 GKMVV 388
            K+++
Sbjct: 59  NKLII 63

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

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 21/51 (41%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVM-RDADGKSKCFGFVNFDDPD 270
           ++V NL    TED+LK+ F EFG +    +  +   G+   FGFV FDDP+
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPE 56

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 132 IKNLDKSIDNKALHDTFSTFGNILSC-KVATDSLGQSRGYGFVQFDNEESAKSAIDKLNG 190
           I NL  +   +   +    FGN+  C  V +++ G S+GYGFV++  ++SA  A   L G
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 191 MLLNDKQVFV 200
             L  + ++V
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|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSC-KVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           L + NL  + +  + +EL   FG +  C  V  +  G S+G GFV +   + A++A +++
Sbjct: 2   LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61

Query: 383 NGKMVVSKPLYV 394
            GK + S+ LYV
Sbjct: 62  LGKQLGSRTLYV 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|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2)

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 5/64 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N +Y+ NLS   T +DL+++FG+  +  +  V+  +      + FV++ D + A R++E 
Sbjct: 2   NKLYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLLKSG-----YAFVDYPDQNWAIRAIET 56

Query: 279 LNGK 282
           L+GK
Sbjct: 57  LSGK 60

This subgroup corresponds to the RRM1 of IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also termed hepatocellular carcinoma autoantigen p62, or VICKZ family member 2, which is a ubiquitously expressed RNA-binding protein involved in the stimulation of insulin action. It is predominantly nuclear. SNPs in IGF2BP2 gene are implicated in susceptibility to type 2 diabetes. IGF2BP2 plays an important role in cellular motility; it regulates the expression of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein, through direct binding to their mRNAs. IGF2BP2 may be involved in the regulation of mRNA stability through the interaction with the AU-rich element-binding factor AUF1. IGF2BP2 binds initially to nascent beta-actin transcripts and facilitates the subsequent binding of the shuttling IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. . Length = 77

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

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGE-FGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           ++V +L+    +  L + F + +       V+ D +G S+ +GFV F D  +  R++  +
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTEM 63

Query: 280 NG 281
            G
Sbjct: 64  QG 65

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

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 17/72 (23%), Positives = 35/72 (48%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           +YV  +   +++  +  +F   G++ S  +  D  T +  GYG++ Y     A  A+  +
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 102 NFTPLNGKPIRI 113
           N   L G+ +R+
Sbjct: 63  NLFDLGGQQLRV 74

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 = 41.4 bits (98), Expect = 3e-05
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 8/72 (11%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG+L  +    +L  LF + G V    V ++        YG+V+     +A  A+  L
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKAL 53

Query: 102 NFTPLNGKPIRI 113
           N     GK I +
Sbjct: 54  NGYEFMGKRINV 65

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 21/74 (28%), Positives = 40/74 (54%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++V +L    ++S L+ +F   G V +V+V RD +T +  G+G+V      EA  A+  L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 102 NFTPLNGKPIRIMY 115
           N   L  + +++ +
Sbjct: 66  NGYRLGDRVLQVSF 79

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

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 16/67 (23%), Positives = 34/67 (50%), Gaps = 2/67 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV+NL    + ++L  +FG++G I    +    + +     FV ++D  DA  + + L+
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTA--FVVYEDIYDAKNACDHLS 62

Query: 281 GKKFDDK 287
           G    ++
Sbjct: 63  GFNVANR 69

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

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 42.3 bits (99), Expect = 3e-05
 Identities = 27/83 (32%), Positives = 40/83 (48%), Gaps = 6/83 (7%)

Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK+    +FS FG I    V R  +   RG  FV F     A+ AL
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 63

Query: 380 TEMNGKMVVSKPLYVALAQRKEE 402
             M G     KP+ +  A+   +
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTDSD 86

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

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

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 21/64 (32%), Positives = 33/64 (51%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V NL    TE+ + ++F + G +    + +D DGK K F FVNF        ++  LN
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN 63

Query: 281 GKKF 284
           G K 
Sbjct: 64  GIKL 67

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

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKA 378
           L+V  L   + +  L E FS+FG +   +V+ D   G  RG GFV F   + A KA
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57

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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 41.9 bits (98), Expect = 3e-05
 Identities = 19/73 (26%), Positives = 38/73 (52%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           NL++ NLD ++S+ +L+  F ++G I    + R   G      F+ F   + A +A   M
Sbjct: 10  NLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAM 69

Query: 383 NGKMVVSKPLYVA 395
           +G+++   P+ + 
Sbjct: 70  SGRVIGRNPIKIG 82

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B 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. RBM15B belongs 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 = 85

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 21/66 (31%), Positives = 35/66 (53%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +++ N   S D   + D F  +G ILS +  +    ++R + +VQF + ESA +A+  LN
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALLN 62

Query: 190 GMLLND 195
           G L   
Sbjct: 63  GKLGEG 68

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|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV NLS   TE  + ++F + G   S  ++ D  G    + FV F +   AA S+ A+N
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDP-YCFVEFFEHRHAAASLAAMN 60

Query: 281 GKKFDDKE 288
           G+K   KE
Sbjct: 61  GRKIMGKE 68

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding protein Raly

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 8/65 (12%)

Query: 130 IFIKNLDKSIDNKALHDT-FSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +FI NL+ ++  K+  +T FS +G ++ C V        +GY FVQ+ NE  A+ A+   
Sbjct: 4   VFIGNLNTAVVKKSDVETIFSKYGRVVGCSV-------HKGYAFVQYSNERHARGAVIGE 56

Query: 189 NGMLL 193
           NG +L
Sbjct: 57  NGRVL 61

This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch. . Length = 76

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 42.4 bits (100), Expect = 3e-05
 Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEALN 280
           +V  +     E DL+ +F +FG I    V++D   G  K   F+ +   + A ++  AL+
Sbjct: 9   FVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSALH 68

Query: 281 GKK 283
            +K
Sbjct: 69  EQK 71

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

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

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           ++   +   +  + +  TFS FG I+  +V  D     +GY FV+F++ ESA  AI  +N
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD-----KGYSFVRFNSHESAAHAIVSVN 57

Query: 190 GMLL 193
           G  +
Sbjct: 58  GTTI 61

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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 42.3 bits (99), Expect = 3e-05
 Identities = 24/66 (36%), Positives = 39/66 (59%), Gaps = 1/66 (1%)

Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVEALNG 281
           V  LS  TTE DL+++F ++G I   +++ D    +S+ F FV F++ DDA  + E  NG
Sbjct: 14  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 73

Query: 282 KKFDDK 287
            + D +
Sbjct: 74  MELDGR 79

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 42.1 bits (99), Expect = 3e-05
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
            +L+V NL+ +   D+LK   SEF +  +  V     G S+  G+V F +AE+  KAL E
Sbjct: 1   FSLFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKAL-E 59

Query: 382 MNGKMVVSKPL 392
           + GK ++   +
Sbjct: 60  LTGKKLLGNEI 70

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin 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. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 6/79 (7%)

Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ +  ++LK+    +FS+FG I     ++      RG  FV F     A+ AL
Sbjct: 2   IYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLK--MRGQAFVVFKDISSATNAL 59

Query: 380 TEMNGKMVVSKPLYVALAQ 398
             M G     KP+ +A ++
Sbjct: 60  RSMQGFPFYDKPMRIAYSK 78

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

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

 Score = 41.6 bits (98), Expect = 3e-05
 Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 337 KLKELF-SEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV 394
            LK+LF  + G +T  ++ +D  G SRG G V F   E   KAL  MN   +  + L V
Sbjct: 15  DLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETMNRYELKGRKLVV 73

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

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

 Score = 41.6 bits (98), Expect = 3e-05
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 3/65 (4%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           VY+ NL+   TEDD+++ F     ITS  +  D + G+ K FG V+F D +    +++ L
Sbjct: 2   VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALK-L 59

Query: 280 NGKKF 284
           +G   
Sbjct: 60  DGTVL 64

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

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

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LYV NL   +++  + +LFS+ G   SCK++ +    +    FV F    +A+ AL  MN
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMN 60

Query: 384 GKMVVSKPLYVALA 397
           G+ ++ K + V  A
Sbjct: 61  GRKILGKEVKVNWA 74

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA--L 98
            ++VG+L     +  L+ +F + G +  VR+ RD  T    G+ YV +   +   +A  L
Sbjct: 1   CVFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLL 60

Query: 99  DELNFTPLNGKPIRIM 114
           +E  F P+  + +R+ 
Sbjct: 61  NEKKFPPMLPRELRVS 76

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 19/86 (22%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITST----------------AVMR--DADGKSKCF 261
            V+V NL  TT + DLKK+F +FG I S                 A ++    D K    
Sbjct: 2   TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVN 61

Query: 262 GFVNFDDPDDAARSVEALNGKKFDDK 287
            +V F + + A ++++ LNG +F+  
Sbjct: 62  AYVVFKEEESAEKALK-LNGTEFEGH 86

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|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 3/67 (4%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V NL  + ++++L++LFS        K+     G      FV F     A++AL  + 
Sbjct: 5   LFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGGP---VCFVEFEDVSFATQALNSLQ 61

Query: 384 GKMVVSK 390
           G ++ S 
Sbjct: 62  GAVLSSS 68

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

>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 = 41.9 bits (99), Expect = 3e-05
 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 2/58 (3%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
            +YV  +   TT  +L++ F  FG I    +    DG +  +GFV +    DA R++E
Sbjct: 4   VIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN--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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 41.6 bits (97), Expect = 4e-05
 Identities = 22/74 (29%), Positives = 40/74 (54%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++V +L    ++S L+ LF   G V +V+V RD +T +  G+G+V      EA  A+  L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 102 NFTPLNGKPIRIMY 115
           N   L  + +++ +
Sbjct: 66  NGYRLGDRVLQVSF 79

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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 41.6 bits (97), Expect = 4e-05
 Identities = 20/74 (27%), Positives = 39/74 (52%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           +++ +L    ++  L+ +F   G V +V+V RD +T +  G+G+V      EA  A+  L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 102 NFTPLNGKPIRIMY 115
           N   L  K +++ +
Sbjct: 64  NGYRLGDKILQVSF 77

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

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+ NL   I  +   + FS +G +         L + +G+GF++ D   +A+ A  +L+
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEV-----FLNKEKGFGFIRLDTRTNAEKAKAELD 58

Query: 190 GMLLNDKQVFV 200
           G++   +Q+ V
Sbjct: 59  GIMRKGRQLRV 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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 4/64 (6%)

Query: 130 IFIKNL--DKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
           +F+  +  D   D   L   F   G I   ++  D  G +RGY FV + N+E+A+ A+ +
Sbjct: 4   VFVGKIPRDLFEDE--LVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQ 61

Query: 188 LNGM 191
           L+  
Sbjct: 62  LHNY 65

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 41.6 bits (97), Expect = 4e-05
 Identities = 20/51 (39%), Positives = 32/51 (62%), Gaps = 1/51 (1%)

Query: 217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNF 266
           +F  +++  LS  TTE+ L+  + ++G +T   VMRD A  +S+ FGFV F
Sbjct: 1   QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 51

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which 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 A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 4/63 (6%)

Query: 235 LKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDK----EWY 290
           LKKIFG +G +    + R   GK   F FV      +A  ++E  NG + D +    +W 
Sbjct: 18  LKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDWA 77

Query: 291 VGK 293
           V K
Sbjct: 78  VQK 80

This subgroup corresponds to the RRM2 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 = 83

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVAT-DSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +F+ NL   I    L + F  FGN+L  ++ +    G+   +GFV FD+ E+ +  +   
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 189 NGMLLNDKQVFV 200
                 D ++ V
Sbjct: 66  PIYFRGDHRLNV 77

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

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

 Score = 41.5 bits (97), Expect = 4e-05
 Identities = 19/63 (30%), Positives = 35/63 (55%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
           G  ++V  +   + +D+L  +F   G I   ++M D +G +RG  FV ++   EA +A+ 
Sbjct: 1   GCEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVR 60

Query: 381 EMN 383
           E+N
Sbjct: 61  ELN 63

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

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 4/59 (6%)

Query: 233 DDLKKIFGEFGIITSTAVMRDADGKSKCFG----FVNFDDPDDAARSVEALNGKKFDDK 287
           +D+K+  G++G + S  + R         G    FV F D +DA ++  AL G+KFD +
Sbjct: 26  EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGR 84

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

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 41.5 bits (97), Expect = 4e-05
 Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           +++  L    + + L+E F +FG +  C VMRDP    SRG GFV F       K L +
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 25/64 (39%), Positives = 36/64 (56%), Gaps = 7/64 (10%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           V++  L+    E D+++ F  +G I      RD D K + FGFV FDDP DA  +V  L+
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYGRI------RDIDLK-RGFGFVEFDDPRDADDAVYELD 54

Query: 281 GKKF 284
           GK+ 
Sbjct: 55  GKEL 58

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

>gnl|CDD|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 29/77 (37%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 323 NLYVKNLDDSISDDKLKE-LFSEF---GTITSCKVMRDPNGISRGSGFVAFSTAEEASKA 378
            + VKNL    SD  LK+ LF EF   G +TS KV     G  R    V F   E+A KA
Sbjct: 1   GIIVKNLPLRSSDTSLKDGLFHEFKKHGKVTSVKVHGT--GSER-YAIVFFRKPEDAEKA 57

Query: 379 LTEMNGKMVVSKPLYVA 395
           L    GK+     + V 
Sbjct: 58  LEVSKGKLFFGAEIEVT 74

This subfamily corresponds to the RRM2 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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++V +L  SV    L DLF + G V+   V  D   R S G+G V + +  +A RA++  
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGR-SKGFGTVLFESPEDAQRAIEMF 59

Query: 102 NFTPLNGKPI 111
           N   L G+ +
Sbjct: 60  NGYDLEGREL 69

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

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

 Score = 41.3 bits (97), Expect = 5e-05
 Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 6/83 (7%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VG +D   N++ L   F+Q G V  V++  D +   S GYG+V +    +A + L E 
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAG-VSKGYGFVTFETQEDAQKILQEA 63

Query: 102 NFTPLNGKPIRIMYSYRDPTIRK 124
           N      K + I        IRK
Sbjct: 64  NRLCFRDKKLNI-----GQAIRK 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|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 = 41.1 bits (97), Expect = 5e-05
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 16/79 (20%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRV-----CRDLSTRRSLGYGYVNYNAAHEA 94
           T+++VG LD +V + +L  LF   G++V V++     C           G+V +     A
Sbjct: 2   TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGC-----------GFVQFVHRAAA 50

Query: 95  TRALDELNFTPLNGKPIRI 113
             A+ +L  T + G  IR+
Sbjct: 51  EAAIQQLQGTIIGGSRIRL 69

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

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

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 3/80 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
           LYV+N+ D+   D L+ LF ++G I    +  D      RG  +V F    +A  AL  +
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 383 NGKMVVSKPLYVALAQ--RK 400
           +    + + + +  AQ  RK
Sbjct: 63  DRTRFLGREIEIQFAQGDRK 82

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 41.3 bits (97), Expect = 5e-05
 Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 5/64 (7%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           NVY+ N+ ++ TE+ L+  F ++G I S   +R    +  C  FVNF +  +A ++++ +
Sbjct: 5   NVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLR----EKNC-AFVNFTNISNAIKAIDGV 59

Query: 280 NGKK 283
               
Sbjct: 60  KSHP 63

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 5/73 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA- 278
           ++V  LS  T++ DLK  F +FG +T   +  D + G+S+ FGF+ F D     + +E  
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 279 ---LNGKKFDDKE 288
              L+G+  D K+
Sbjct: 62  EHRLDGRLIDPKK 74

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

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

 Score = 41.0 bits (96), Expect = 5e-05
 Identities = 20/71 (28%), Positives = 37/71 (52%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V NLD  ++++ + ELF + G +   K+ +D +G  +   FV F        A+  +N
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN 63

Query: 384 GKMVVSKPLYV 394
           G  +  +PL +
Sbjct: 64  GIKLYGRPLNI 74

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

 Score = 40.8 bits (95), Expect = 6e-05
 Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 7/69 (10%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F++NL  ++  + L  +FS FG +   K   D       Y FV F+  ++A  A+D++N
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEERDAAVRAMDEMN 56

Query: 190 GMLLNDKQV 198
           G  +  +++
Sbjct: 57  GKEIEGEEI 65

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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 41.2 bits (97), Expect = 6e-05
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFG-NILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           +++ +L+  +D   +   F++ G  +LS K+  + L G   GY FV+F +E +A+  + K
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 188 LNGMLLN 194
           LNG  + 
Sbjct: 62  LNGKPIP 68

This subgroup corresponds to the RRM1 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 = 84

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 40.8 bits (95), Expect = 6e-05
 Identities = 22/50 (44%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDP 269
           +++  LS  T+ D L+  F +FG I    VMRD   K S+ FGFV F DP
Sbjct: 2   MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADP 51

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 41.1 bits (96), Expect = 6e-05
 Identities = 17/64 (26%), Positives = 37/64 (57%), Gaps = 1/64 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEAL 279
           ++V ++  T TE +++ +F E G +   A+++D   G  +   FV +   D+A R++ AL
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 280 NGKK 283
           + ++
Sbjct: 62  HNQR 65

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. 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|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 41.2 bits (96), Expect = 6e-05
 Identities = 25/80 (31%), Positives = 39/80 (48%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           TSL+V ++  +     L   F + G +V V V  D  TRR  G+ Y+ +    +A  AL 
Sbjct: 1   TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60

Query: 100 ELNFTPLNGKPIRIMYSYRD 119
            LN   + G+ I I ++  D
Sbjct: 61  NLNRKWVCGRQIEIQFAQGD 80

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S +L+V +++ +V D +L  LF Q G + ++      +  +  G+  V+Y     A RA 
Sbjct: 1   SRTLFVRNINSNVEDEELRALFEQFGDIRTL-----YTACKHRGFIMVSYYDIRAARRAK 55

Query: 99  DELNFTPLNGKPIRIMYS 116
             L  T L G+ + I +S
Sbjct: 56  RALQGTELGGRKLDIHFS 73

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|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 40.8 bits (95), Expect = 6e-05
 Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 8/65 (12%)

Query: 130 IFIKNLDKSIDNKA-LHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +FI NL+  +  K+ +   FS +G I+ C V        +G+ FVQ+ NE +A++A+   
Sbjct: 4   VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGE 56

Query: 189 NGMLL 193
           +G ++
Sbjct: 57  DGRMI 61

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, 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 hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

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

 Score = 41.0 bits (96), Expect = 6e-05
 Identities = 24/61 (39%), Positives = 36/61 (59%), Gaps = 3/61 (4%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+VKNL  +I+ D+LKE+F +   I   ++    +G S+G  ++ F T  EA KAL E  
Sbjct: 6   LFVKNLPYNITVDELKEVFEDAVDI---RLPSGKDGSSKGIAYIEFKTEAEAEKALEEKQ 62

Query: 384 G 384
           G
Sbjct: 63  G 63

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|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 40.7 bits (96), Expect = 6e-05
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 4/54 (7%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
           V+V  L+E  TE+DL++ F +FG +T   + +        F FV F DP+ A  
Sbjct: 3   VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRA----FAFVTFADPEVAQS 52

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

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

 Score = 41.0 bits (97), Expect = 7e-05
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 6/56 (10%)

Query: 336 DKLKE----LFSEFGTITSCKVM--RDPNGISRGSGFVAFSTAEEASKALTEMNGK 385
           +KLK+    +FS+FG      +    D  G ++G  FV F+T EEA +A+  +NG 
Sbjct: 18  EKLKKVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGY 73

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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 40.4 bits (95), Expect = 7e-05
 Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 8/76 (10%)

Query: 42  LYVGDLDLSVNDSQLYDLF-NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           LY+G+L   VN+S L  LF      V SV V +        GY +V+      A +A+++
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKG-------GYAFVDCPDQSWADKAIEK 53

Query: 101 LNFTPLNGKPIRIMYS 116
           LN   L GK I + +S
Sbjct: 54  LNGKILQGKVIEVEHS 69

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

 Score = 40.5 bits (95), Expect = 7e-05
 Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 8/74 (10%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYV       ++S + ++F+  G V  V++           + +V + +   A RA D +
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMIS--------NFAFVEFESLESAIRAKDSV 53

Query: 102 NFTPLNGKPIRIMY 115
           +   LN  P+ + Y
Sbjct: 54  HGKVLNNNPLYVTY 67

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

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 40.7 bits (95), Expect = 7e-05
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 5/71 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V NL   I+++  K+LF ++G  +   + RD     RG GF+   +   A  A  E++
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELD 58

Query: 384 GKMVVSKPLYV 394
           G ++ ++PL +
Sbjct: 59  GTILKNRPLRI 69

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 18/66 (27%), Positives = 31/66 (46%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
             + + NLD  + +  + + F+ FG +    V  D  G+S G   V F+    A  A+ +
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60

Query: 188 LNGMLL 193
            NG+ L
Sbjct: 61  YNGVPL 66

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|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 = 40.6 bits (96), Expect = 8e-05
 Identities = 18/61 (29%), Positives = 34/61 (55%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG L  +  +  +  LF + G +  V + RD  T +S G  +V +++  EA +A++ L
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 102 N 102
           +
Sbjct: 62  H 62

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|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 = 40.9 bits (96), Expect = 8e-05
 Identities = 19/61 (31%), Positives = 30/61 (49%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+  L K      +   F  FG I  C +     G S+G  FV+F +   A++AI+ L+
Sbjct: 4   LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63

Query: 190 G 190
           G
Sbjct: 64  G 64

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|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 = 40.4 bits (95), Expect = 8e-05
 Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           ++I +L K +  + L + F  +G I S  +        RG  +V  +  + A  A+ KL 
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP-----PRGCAYVCMETRQDAHRALQKLR 59

Query: 190 GMLLNDKQV 198
            + L  K++
Sbjct: 60  NVKLAGKKI 68

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|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 40.8 bits (95), Expect = 8e-05
 Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALT-- 380
           +++  L    S   L E  S FG +  C +  DP  G SRG GFV F  A    K L   
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 381 --EMNGKMVVSK 390
             +++GK++  K
Sbjct: 62  EHKLDGKLIDPK 73

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 40.7 bits (95), Expect = 8e-05
 Identities = 22/60 (36%), Positives = 31/60 (51%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           IFI  L + +    L       G I   ++  D  G +RGY FV F N++ AK+AI +LN
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLN 63

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 40.8 bits (96), Expect = 8e-05
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 4/62 (6%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSC-KVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           I I N+   +  + L    ST+G + +C +V T S   +     V +++ E A+ A++KL
Sbjct: 3   IQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATV---NVTYESPEQAQQAVNKL 59

Query: 189 NG 190
           NG
Sbjct: 60  NG 61

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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 40.8 bits (96), Expect = 8e-05
 Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 3/67 (4%)

Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALN 280
           +V NL   T + DL  IF +   + S  ++RD +  K K F +V F+D +    ++E  +
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDLS-VKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YD 62

Query: 281 GKKFDDK 287
           G  FDD+
Sbjct: 63  GALFDDR 69

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 40.4 bits (95), Expect = 9e-05
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDK 187
           N+++  L  +     L   FS +G ++  K+ T++    +R +GFV   + E A   I  
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60

Query: 188 LNGMLLNDKQVFV 200
           L+   L+ + + V
Sbjct: 61  LHRTELHGRVISV 73

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|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 40.5 bits (95), Expect = 9e-05
 Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +++ ++D+ +  + L   FS  G ++ C+V  D     R + F++F +EE A++A+    
Sbjct: 5   VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLR-FAFIEFTDEEGARAALSLSG 63

Query: 190 GML 192
            ML
Sbjct: 64  TML 66

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

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

 Score = 40.4 bits (94), Expect = 9e-05
 Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V+NL    T   LK+ F + G +   A ++  +GKSK  G V FD P+ A ++   +N
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVM-FAEIKMENGKSKGCGTVRFDSPESAEKACRLMN 60

Query: 281 GKKFDDKE 288
           G K + +E
Sbjct: 61  GIKINGRE 68

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

 Score = 40.5 bits (95), Expect = 9e-05
 Identities = 15/51 (29%), Positives = 27/51 (52%)

Query: 50  SVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           S  +  L + F + G +  V + +D +T  S G+GYV ++   +A  AL+ 
Sbjct: 11  SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALEN 61

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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 40.8 bits (95), Expect = 9e-05
 Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 142 KALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
           + L + FS +G I    +  D   + SRG+ FV F+N + AK A ++ NGM L+ +++ V
Sbjct: 24  RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

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

 Score = 40.5 bits (95), Expect = 9e-05
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           ++I NL   I    + + F     I S ++ATD   G+ +G+G V F +EES  +A+ KL
Sbjct: 2   VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL-KL 59

Query: 189 NGMLLNDKQVFVG 201
           +G +L  + + + 
Sbjct: 60  DGTVLCGRPIRIA 72

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

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 40.8 bits (95), Expect = 9e-05
 Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKAL 379
           G  ++V  +   + +D+L  LF + G I   ++M DP  G++RG  FV F T E A +A+
Sbjct: 1   GTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV 60

Query: 380 TEMN 383
              N
Sbjct: 61  KLYN 64

This subgroup corresponds to the RRM1 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, 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 = 79

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 40.3 bits (95), Expect = 9e-05
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L V NL  S+++D + ELFS  G +   +++R       G   V +   ++A  A+ + N
Sbjct: 3   LVVSNLHPSVTEDDIVELFSAIGALKRARLVR------PGVAEVVYVRKDDALTAIDKYN 56

Query: 384 GKMVVSKPLYVAL 396
            + +  +P+   L
Sbjct: 57  NRELDGQPMKCKL 69

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. 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. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 40.5 bits (95), Expect = 9e-05
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +FI NL+K+     L + F  FG I+   +       +  Y F+Q+ +  S   A+ K++
Sbjct: 5   LFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPA--YAFIQYADIASVVKAMRKMD 62

Query: 190 GMLLNDKQVFVG 201
           G  L + +V +G
Sbjct: 63  GEYLGNNRVKLG 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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 221 VYVKNLSETTTEDDLKKIF-GEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           ++V +L+   T+  L++ F   +  +    V+ D   G+SK +GFV F D D+  R++  
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 279 LNGK 282
           +NG 
Sbjct: 64  MNGV 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|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLG-QSRGYGFVQFDNEESAKSAIDKL 188
           +++ NL  S+ N  LH  FS +G ++   +  D    +S+G  F+ F + E A   +  L
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 189 NGMLLN 194
           N   L 
Sbjct: 64  NNKELF 69

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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAI 185
           +F+  L+    +  L   F+ +G +  C V  D +  +SRG+GF+ F + + A  A+
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

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|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 40.4 bits (94), Expect = 1e-04
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 8/74 (10%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLS-TRRSLGYGYVNYNAAHEATRAL 98
           T+LY+ +L LS+++ +L  +    GQV+S R+ RD S T R +G+      A  E+T   
Sbjct: 1   TNLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGF------ARMESTEKC 54

Query: 99  DELNFTPLNGKPIR 112
           + +  T  NGK I+
Sbjct: 55  EAI-ITHFNGKYIK 67

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|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 8/78 (10%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSR-------GYGFVQFDNEESAK 182
           ++I NL  S   + L +    F   +S  + + ++   R       G  + +F + E A+
Sbjct: 2   VYISNLSYSSSEEDLEEFLKDF-EPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60

Query: 183 SAIDKLNGMLLNDKQVFV 200
             +  LNG +  ++++FV
Sbjct: 61  KVVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

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

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
           ++V  + E   E+D+   F EFG I +  +  D   G  K +  + ++   +A  ++E L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 280 NGKKFDDKEWYV 291
           NGK+   +   V
Sbjct: 69  NGKELLGQTISV 80

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE-- 277
           +++  LS  TT+ DLK  F +FG ++  T  +    G+S+ FGFV F + +   + ++  
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 278 --ALNGKKFDDKE 288
              LNGK  D K 
Sbjct: 61  EHKLNGKVIDPKR 73

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 40.4 bits (94), Expect = 1e-04
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 9/77 (11%)

Query: 324 LYVKNLDDSISDDKLKELFSEF--GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
           LYV+NL    S+D +K+ F +F  G +   K +RD         FV F++ E+A  A+  
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD-------YAFVHFTSREDAVHAMNN 56

Query: 382 MNGKMVVSKPLYVALAQ 398
           +NG  +    + V LA+
Sbjct: 57  LNGTELEGSCIEVTLAK 73

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 41.1 bits (96), Expect = 1e-04
 Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAI 185
           +F++NL      ++L   FS FG++       D S G+++G GFV F ++ +  + +
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

This subgroup corresponds to the RRM3 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 = 107

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 325 YVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNG 384
           YV NLD + + D+L E FS+ G +   ++  D    +R   FV F+       AL  +NG
Sbjct: 8   YVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTR-YAFVEFAEQTSVINALK-LNG 65

Query: 385 KMVVSKPLYV 394
            M   +PL V
Sbjct: 66  AMFGGRPLKV 75

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

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

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 18/63 (28%), Positives = 31/63 (49%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
             I +KNL      K +   FS++G + S +V       +RG+ FV+F   + A +A++ 
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNA 60

Query: 188 LNG 190
           L  
Sbjct: 61  LKD 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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 20/73 (27%), Positives = 35/73 (47%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           N+FI NLD ++    L   F  +G I    +   + GQ   Y F++F N + A  A   +
Sbjct: 10  NLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAM 69

Query: 189 NGMLLNDKQVFVG 201
           +G ++    + +G
Sbjct: 70  SGRVIGRNPIKIG 82

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B 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. RBM15B belongs 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 = 85

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

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 13/47 (27%), Positives = 31/47 (65%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFS 370
           ++V  +D  + + +++  F+++G++   K++ D  G+S+G GFV+F 
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFY 54

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

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
           VYV ++S    ED +++ F  FG I S  +  D    K K F FV ++ P+ A  ++E +
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 280 NG 281
           NG
Sbjct: 63  NG 64

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|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 1/69 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIF-GEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
            V V NL +  TE  +++ F  + G I    +  +  GKS     + F    DA ++ + 
Sbjct: 1   KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60

Query: 279 LNGKKFDDK 287
            NG+  D  
Sbjct: 61  FNGRIDDGN 69

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

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

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 18/56 (32%), Positives = 32/56 (57%)

Query: 132 IKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
           ++NL   + N+ L + FS FG +    V  D  G+S G G V+F ++ +A+ A ++
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|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTF-STFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +FI N+   +  + L D F    G +   ++  D  G+SRG G V+F ++ES + A++ +
Sbjct: 2   VFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETM 61

Query: 189 NGMLLNDKQVFV 200
           N   L  +++ V
Sbjct: 62  NRYELKGRKLVV 73

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

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

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VG +   V + +L  +F  +G++  +R+  D   +   GY +V Y   HEA RA+ EL
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNR-GYAFVMYTQKHEAKRAVREL 62

Query: 102 N 102
           N
Sbjct: 63  N 63

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

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

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 12/73 (16%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTI----TSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           L+V+N++ ++ D++L+ LF +FG I    T+CK         RG   V++     A +A 
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRTLYTACK--------HRGFIMVSYYDIRAARRAK 55

Query: 380 TEMNGKMVVSKPL 392
             + G  +  + L
Sbjct: 56  RALQGTELGGRKL 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|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1-beta) and similar proteins

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           EG  +Y++NL  S+S  +LK+ F  FG I  CKV+    G     GF+ +  +E A+ +L
Sbjct: 1   EGRVIYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRG--EKYGFITYRHSEHAALSL 58

Query: 380 TEMNGKMVVSKP 391
            +       ++P
Sbjct: 59  GKGASLRKRNEP 70

This subfamily corresponds to the RRM of PGC-1beta, also termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or PGC-1-related estrogen receptor alpha coactivator, which is one of the members of PGC-1 transcriptional coactivators family, including PGC-1alpha and PGC-1-related coactivator (PRC). PGC-1beta plays a nonredundant role in controlling mitochondrial oxidative energy metabolism and affects both, insulin sensitivity and mitochondrial biogenesis, and functions in a number of oxidative tissues. It is involved in maintaining baseline mitochondrial function and cardiac contractile function following pressure overload hypertrophy by preserving glucose metabolism and preventing oxidative stress. PGC-1beta induces hypertriglyceridemia in response to dietary fats through activating hepatic lipogenesis and lipoprotein secretion. It can stimulate apolipoprotein C3 (APOC3) expression, further mediating hypolipidemic effect of nicotinic acid. PGC-1beta also drives nuclear respiratory factor 1 (NRF-1) target gene expression and NRF-1 and estrogen related receptor alpha (ERRalpha)-dependent mitochondrial biogenesis. The modulation of the expression of PGC-1beta can trigger ERRalpha-induced adipogenesis. PGC-1beta is also a potent regulator inducing angiogenesis in skeletal muscle. The transcriptional activity of PGC-1beta can be increased through binding to host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. PGC-1beta is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, two glutamic/aspartic acid-rich acidic domains, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha, PGC-1beta lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 79

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 132 IKNLDKSIDNKALHDTFSTFGNILSC-KVATDSLGQSRGYGFVQFDNEESAKSAIDKLNG 190
           + NL  S   +   +    +GNI  C  V ++  G S+GYGFV++  ++SA  A  +L G
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63

Query: 191 MLLNDKQVFV 200
             L +  +F 
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|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 40.4 bits (94), Expect = 1e-04
 Identities = 26/65 (40%), Positives = 39/65 (60%), Gaps = 5/65 (7%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV+NL  +TTE+ ++K   EF  I   AV R    K + + FV+F + +DA  ++ ALN
Sbjct: 11  LYVRNLMLSTTEETIEK---EFNSIKPGAVERVK--KIRDYAFVHFSNREDAVDAMNALN 65

Query: 281 GKKFD 285
           GK  D
Sbjct: 66  GKVID 70

This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 83

>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 231 TEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGK 282
           +ED+L+KIF ++G + S  V+     K K    V F     A  +VE   G 
Sbjct: 17  SEDELRKIFSKYGDV-SDVVVSS---KKKGSAIVEFASKKAAEAAVENECGL 64

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|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 9/68 (13%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSK---CFGFVNFDDPDDAARSVE 277
           +YV NL       D++ +F ++G I      RD D K++    F FV F+DP DA  +V 
Sbjct: 2   IYVGNLPPDIRTKDIEDLFYKYGAI------RDIDLKNRRGPPFAFVEFEDPRDAEDAVY 55

Query: 278 ALNGKKFD 285
             +G  +D
Sbjct: 56  GRDGYDYD 63

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 5/58 (8%)

Query: 143 ALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
            L D F  FG ++   +        + YG+ ++ + ESA+ AI  L+G  +N  ++ V
Sbjct: 15  ILEDVFCRFGGLIDVYLVPG-----KNYGYAKYADRESAERAITTLHGKEVNGVKLKV 67

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|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 24/64 (37%), Positives = 33/64 (51%), Gaps = 7/64 (10%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           VY+  LS    E D+++ F  +G I       + D K+  +GFV FDD  DA  +V  LN
Sbjct: 2   VYIGRLSYQARERDVERFFKGYGKIL------EVDLKNG-YGFVEFDDLRDADDAVYELN 54

Query: 281 GKKF 284
           GK  
Sbjct: 55  GKDL 58

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 2/65 (3%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV NL     E D++ +F ++G I +  +     G    F FV F+DP DA  +V   +
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPP--FAFVEFEDPRDAEDAVRGRD 59

Query: 281 GKKFD 285
           G  FD
Sbjct: 60  GYDFD 64

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           +YV  +    ++D+++  FS  G I    +M  P+ G  RG  F+ F T E A +AL  +
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL-AL 59

Query: 383 NGKMVVSKPLYV 394
           +G+ +  + L V
Sbjct: 60  DGEDMGGRFLKV 71

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 1/64 (1%)

Query: 222 YVKNLSETTTEDD-LKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +V  L +T  +   L+K+F + G  T   +    +G+ + F FV +   +DA  + +ALN
Sbjct: 6   FVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALN 65

Query: 281 GKKF 284
           G   
Sbjct: 66  GHSL 69

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 8/81 (9%)

Query: 39  STSLYVGDLDLS-VNDSQLYDLFNQMGQVVSVRVCRDLSTRR---SLGYGYVNYNAAHEA 94
           S  L+V  L  +  + S L  LF+Q   V     C+ L+        G+ +V Y  A +A
Sbjct: 2   SRCLFVDRLPKTFRDVSILRKLFSQ---VGKPTFCQ-LAIAPNGQPRGFAFVEYATAEDA 57

Query: 95  TRALDELNFTPLNGKPIRIMY 115
             A   LN   L G PIR+ +
Sbjct: 58  EEAQQALNGHSLQGSPIRVSF 78

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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 40.1 bits (93), Expect = 2e-04
 Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 8/83 (9%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLS-TRRSLGYGYVNYNAAHEATRAL 98
           T+LY+ +L LS+++ +L ++    GQV+S R+ RD S T R +G+  +      EA    
Sbjct: 1   TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAV--- 57

Query: 99  DELNFTPLNGKPIRIMYSYRDPT 121
                +  NGK I+       P 
Sbjct: 58  ----ISHFNGKFIKTPPGVSAPA 76

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 325 YVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEMN 383
           +V  L   + +  L E FS+ G +   +++RD N   S+G  +V F   E    AL  + 
Sbjct: 3   FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GLT 61

Query: 384 GKMVVSKPLYV 394
           G+ ++ +P+ V
Sbjct: 62  GQRLLGQPIMV 72

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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 16/47 (34%), Positives = 27/47 (57%)

Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNY 88
          +++G L+    D  L + F Q G+V    V RD +T RS G+G++ +
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTF 47

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|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 = 39.4 bits (92), Expect = 2e-04
 Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
           ++V N+    ++++LK++FSE G + S +++ D   G  +G GF  +   E A  A+  +
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 383 NGKMVVSKPLYVALA 397
           NG  +  + L V  A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 2/78 (2%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +LYV  L  ++   +L  LF+Q G++++ R+  D  T  S G G++ ++   EA  A+  
Sbjct: 4   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63

Query: 101 LNFTPLNG--KPIRIMYS 116
           LN    +G  +PI + ++
Sbjct: 64  LNGQKPSGAAEPITVKFA 81

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 16/68 (23%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V NL    TE++ K++F ++G ++   + ++     K FGF+  D   +A ++   L+
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAELD 58

Query: 281 GKKFDDKE 288
           G     ++
Sbjct: 59  GIMRKGRQ 66

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPD 270
           ++V NL  T    +LK+ F +FG + S  V  D + G SK +GFV+F   D
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRD 52

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|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 7/76 (9%)

Query: 43  YVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRD--LSTRRSLGYGYVNYNAAHEATRALDE 100
           +VG +D S+++  L + F+  G+V  VR+C D   S R    + +V +  A  A  AL  
Sbjct: 4   HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR----FAFVEFADAESALSAL-N 58

Query: 101 LNFTPLNGKPIRIMYS 116
           L+ T L G P+R+  S
Sbjct: 59  LSGTLLGGHPLRVSPS 74

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|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 = 18/61 (29%), Positives = 31/61 (50%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           + VKNL    T+ D++ +F  +G + S  V +  D  ++ F FV F    +A  ++ AL 
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 281 G 281
            
Sbjct: 63  D 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|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 142 KALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
           + L + FS +G +    V  D   G+SRG+ FV F+  + +K A++  NGM L+ +++ V
Sbjct: 14  RDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRV 73

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD--SLGQSRGYGFVQFDNEESAKSAIDK 187
           I ++N+      K L + FSTFG + + ++       G  RG+GFV F  ++ AK A   
Sbjct: 3   ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62

Query: 188 L 188
           L
Sbjct: 63  L 63

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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 22/75 (29%), Positives = 39/75 (52%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L V  L L   +  L ++F++ G +  V +  D  +RRS G+ +V +    +A  A +  
Sbjct: 12  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 71

Query: 102 NFTPLNGKPIRIMYS 116
           N   L+G+ IR+ +S
Sbjct: 72  NGMELDGRRIRVDFS 86

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            +YV  +    +  +L++ F  FG I    +    +G +   GFV +  A +A +A+   
Sbjct: 4   VIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN--YGFVTYRYACDAFRAIEHG 61

Query: 383 N 383
           N
Sbjct: 62  N 62

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

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 20/60 (33%), Positives = 31/60 (51%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           V+V  +     ED+L  +F   G I    +M D DGK++ + FV +    +A R+V  LN
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63

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

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDA----ARS 275
           +++  LS  TT++ L++ FG+FG +    VMRD   K S+ FGFV F D        A+S
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 276 VEALNGKKFDDK 287
              L+ K  D K
Sbjct: 63  RHELDSKTIDPK 74

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSC-KVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           L V NL  S + ++ +EL   +G I  C  V  +  G S+G GFV +   + ASKA  E+
Sbjct: 2   LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLEL 61

Query: 383 NGKMVVSKPLYV 394
            GK +    L+ 
Sbjct: 62  LGKQLGESTLFA 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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMR-DADGKSKCFGFVNFDDPDDAARSVEAL 279
           VYV  +   +TED+++  F   G I    +M     G+ +   F+ F   ++AA+   AL
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKT-EEAAKRALAL 59

Query: 280 NGKKFDDK 287
           +G+    +
Sbjct: 60  DGEDMGGR 67

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 5/67 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKAL--- 379
           L+V NL    + + L   F   G   S +++ D   G S+G  FV F TAE  +KAL   
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 380 -TEMNGK 385
            T + G+
Sbjct: 63  HTLLKGR 69

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

>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 21/64 (32%), Positives = 28/64 (43%), Gaps = 5/64 (7%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           VYV N+   TT+ DL  +F  FG I       D     + F FV  D  + AA ++  L 
Sbjct: 3   VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD-----RGFAFVKLDTHEQAAMAIVQLQ 57

Query: 281 GKKF 284
           G   
Sbjct: 58  GFPV 61

This subfamily corresponds to the RRM3 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. 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 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|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 5/68 (7%)

Query: 325 YVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNG 384
           YV N+    +   L  LF  FG I   +   D     RG  FV   T E+A+ A+ ++ G
Sbjct: 4   YVGNIPPYTTQADLIPLFQNFGYILEFRHQPD-----RGFAFVKLDTHEQAAMAIVQLQG 58

Query: 385 KMVVSKPL 392
             V  +PL
Sbjct: 59  FPVHGRPL 66

This subfamily corresponds to the RRM3 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. 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 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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKL 188
           IF+ N+D     + L + F + G I    +  D   GQ +G+ +++F ++ S ++A+  L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-L 60

Query: 189 NGMLLNDKQVFV 200
           N      +Q+ V
Sbjct: 61  NESEFRGRQIKV 72

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

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 8/68 (11%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVE-- 277
           ++V N+   TT ++L++ F   G I    ++ D   G+ K F ++ F D      SVE  
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKS----SVENA 57

Query: 278 -ALNGKKF 284
             LN  +F
Sbjct: 58  LLLNESEF 65

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

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

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 11/68 (16%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAF---STAEEASKAL 379
           L V NLD S+S+D L ++F  +G I   K +R+ PN   R   F+ F    +AE A KAL
Sbjct: 4   LVVFNLDPSVSNDDLHQIFGAYGEI---KEIRETPN--KRHHKFIEFYDVRSAEAALKAL 58

Query: 380 --TEMNGK 385
             +E+ GK
Sbjct: 59  NRSEIAGK 66

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

>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 5/70 (7%)

Query: 220 NVYVKNLSETTTEDD----LKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAAR 274
            +YV  +S   TE++    L   F +FG++ S  V  +A       + FV F     A+R
Sbjct: 2   TLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASR 61

Query: 275 SVEALNGKKF 284
           + +A NGK  
Sbjct: 62  AQKACNGKWL 71

This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA. . Length = 81

>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 6/65 (9%)

Query: 225 NLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKK 283
           N+S+T  E+ +K  F + G  +    +  D +G       V F+ P DA ++  +LNG +
Sbjct: 7   NVSDTVNEEQIKAFFEKIGPDVRKIELFPDHEG-----ALVEFESPSDAGKASLSLNGSQ 61

Query: 284 FDDKE 288
           F  K 
Sbjct: 62  FGGKT 66

This subfamily corresponds to the RRM4 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 21/71 (29%), Positives = 40/71 (56%), Gaps = 7/71 (9%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQV-VSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           L++GDL+  ++++ +  ++  +G   V+V+V R  ++  + GY +V + + H A  AL  
Sbjct: 2   LWMGDLEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNALS- 60

Query: 101 LNFTPLNGKPI 111
                LNG PI
Sbjct: 61  -----LNGTPI 66

This subgroup corresponds to the RRM1 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), 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 carboxyl terminus which also harbors a methionine-rich region. The subgroup also includes NAM8, 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 = 81

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           IF+  L      + + + F  FGNI+  ++  D    + RG+ F+ FD+EE  K  ++ 
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 5/61 (8%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           ++   +   +  + +  TFS FG I+  +V  +     +GY F++F   ESA  AI  +N
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE-----KGYSFIRFSTHESAAHAIVSVN 57

Query: 190 G 190
           G
Sbjct: 58  G 58

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

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP---NGISRGSGFVAFSTAEEASKA 378
           + ++V  +  S S+  L+ELF ++G +    V+RD       S+G  FV F T + A +A
Sbjct: 2   IKMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 61

Query: 379 LTEM 382
              +
Sbjct: 62  QNAL 65

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. 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) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The 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 binds specifically 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 contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also 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. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. 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 = 84

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 7/65 (10%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+ NL      + +   F  +G +L C +        + YGFV  D++ +A  AI  L+
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDII-------KNYGFVHMDDKTAADEAIRNLH 55

Query: 190 GMLLN 194
              L+
Sbjct: 56  HYKLH 60

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSE-FGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           L++ N+  S++++ LKELF++  GT+ + K         R    +   + EEA +AL  +
Sbjct: 2   LHLSNIPPSVTEEDLKELFTQTGGTVKAFKFFPK----DRKMALIQMGSVEEAIEALIAL 57

Query: 383 NGKM 386
           +   
Sbjct: 58  HNYQ 61

This subfamily corresponds to the RRM4 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 9/77 (11%)

Query: 324 LYVKNLDDSISDDKLKELFSEF--GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
           LYV+NL  S +++ +K  F++F  G +   K +RD         FV F   E+A  A++ 
Sbjct: 4   LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD-------YAFVHFFNREDAVAAMSV 56

Query: 382 MNGKMVVSKPLYVALAQ 398
           MNGK +    + V LA+
Sbjct: 57  MNGKCIDGASIEVTLAK 73

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is 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 = 74

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 43.1 bits (101), Expect = 3e-04
 Identities = 19/81 (23%), Positives = 43/81 (53%), Gaps = 2/81 (2%)

Query: 33  DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAH 92
           +A++F    +YV  +   ++++ +  +F   G++V  ++ R  + R   GYG++ YN   
Sbjct: 200 EAKKF--NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQ 257

Query: 93  EATRALDELNFTPLNGKPIRI 113
             + A+  +N   L G+ +R+
Sbjct: 258 SQSEAIASMNLFDLGGQYLRV 278

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

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

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 231 TEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKK 283
            E  +   F E G +TS  ++R+   GKS  +GFV F   + A +++++LNGK 
Sbjct: 12  DEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKP 65

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 19/72 (26%), Positives = 37/72 (51%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG L  +VN   L ++F+  G V  V +  D       GY YV + +  +A +A+  +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 102 NFTPLNGKPIRI 113
           +   ++G+ + +
Sbjct: 61  DGGQIDGQEVTV 72

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 8/63 (12%)

Query: 221 VYVKNL-SETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           V+V NL ++  +++DL++IF ++G I   ++        K +GFV FD+ +DA  +V   
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISL-------HKGYGFVQFDNEEDARAAVAGE 55

Query: 280 NGK 282
           NG+
Sbjct: 56  NGR 58

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

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 23/61 (37%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 142 KALHDTFSTFGNILSCKV--ATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVF 199
           K L   FS FG      +    D  G+++GY FV+F   E AK A+  LNG  L+ K  F
Sbjct: 22  KVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKLDKKHTF 81

Query: 200 V 200
            
Sbjct: 82  A 82

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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 21/72 (29%), Positives = 36/72 (50%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+ NLD ++    L   F  FG I    +     GQ+  YGF++F+N + A  A   ++
Sbjct: 10  LFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMS 69

Query: 190 GMLLNDKQVFVG 201
           G +L    + +G
Sbjct: 70  GKVLRRNPIKIG 81

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 7/80 (8%)

Query: 126 GAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQS-RGYGFVQFDNEESAKSA 184
            +G +FI+NL  +   + L   FS +G +    +  D L +  +G+ FV +   E A  A
Sbjct: 1   ESGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKA 60

Query: 185 IDKLNGMLLNDKQVFVGPFL 204
             +L+G       VF G  L
Sbjct: 61  FAELDG------TVFQGRLL 74

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

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 7/69 (10%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F++NL  ++  + L   F  FG +   K   D       Y F+ FD  + A  A++++N
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 56

Query: 190 GMLLNDKQV 198
           G  L  + +
Sbjct: 57  GKELEGENI 65

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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 39.0 bits (91), Expect = 3e-04
 Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 3/58 (5%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVAT--DSLGQSRGYGFVQFDNEESAKSAI 185
           +F+ NL        L   F   G I   ++ T  DS G+ +G+ FV F+  E A +A+
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDS-GKCKGFAFVDFEEIEFATNAL 57

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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 39.4 bits (92), Expect = 3e-04
 Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQF 175
           +F+  L      + L   FS +G ++ C +  D +  +SRG+GFV+F
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKF 48

This subfamily corresponds to the RRM1 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 form is predominantly nuclear and the nonacetylated form is in cytoplasm. It 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 = 82

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 8/63 (12%)

Query: 324 LYVKNLDD-SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           L+V   D  +  ++ +++LF  FG +  C        I +   FV F  +E+A+KAL  +
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCD-------IRKTFAFVEFEDSEDATKALEAL 54

Query: 383 NGK 385
           +G 
Sbjct: 55  HGS 57

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 21/70 (30%), Positives = 37/70 (52%)

Query: 47  LDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL 106
           L L   +  L ++F++ G +  V V  D  T RS G+ +V +    ++  A++  N   L
Sbjct: 7   LSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMEL 66

Query: 107 NGKPIRIMYS 116
           +G+ IR+ YS
Sbjct: 67  DGRRIRVDYS 76

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           ++Y+G+L   + +  + + F    ++ SVR+  D  T    G+G+V++ A  E+  A  +
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDF-ADEESLDAALK 58

Query: 101 LNFTPLNGKPIRI 113
           L+ T L G+PIRI
Sbjct: 59  LDGTVLCGRPIRI 71

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

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 3/78 (3%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG +  ++ + ++  +F + G V+ V + +D  T    G  +V Y+   EA RA+  L
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 102 N---FTPLNGKPIRIMYS 116
           +     P    P+++ Y+
Sbjct: 62  HNQRTLPGGASPVQVRYA 79

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. 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|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 39.3 bits (91), Expect = 3e-04
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 9/77 (11%)

Query: 324 LYVKNLDDSISDDKLKELFSEF--GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
           LYV+NL  S +++ +++ F+    G +   K +RD         FV FS  E+A  A+  
Sbjct: 11  LYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRD-------YAFVHFSNREDAVDAMNA 63

Query: 382 MNGKMVVSKPLYVALAQ 398
           +NGK++   P+ V LA+
Sbjct: 64  LNGKVIDGSPIEVTLAK 80

This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 83

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

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           S++VG++D      +L + F   G +  + +  D  T +  G+ Y+ +        AL  
Sbjct: 1   SIFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL- 59

Query: 101 LNFTPLNGKPIRI 113
           LN +   G+ I++
Sbjct: 60  LNESEFRGRQIKV 72

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

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 14/60 (23%), Positives = 32/60 (53%), Gaps = 7/60 (11%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V NL    TE +++ +F ++G +    ++++       +GFV+ DD   A  ++  L+
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN-------YGFVHMDDKTAADEAIRNLH 55

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 38.9 bits (90), Expect = 3e-04
 Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 9/67 (13%)

Query: 221 VYVKNLSETTTEDDLKKIFGEF--GIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           +YV+NL  +TTE+ +K  F +F  G++     +RD       + FV+F + +DA  ++  
Sbjct: 4   LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD-------YAFVHFFNREDAVAAMSV 56

Query: 279 LNGKKFD 285
           +NGK  D
Sbjct: 57  MNGKCID 63

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is 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 = 74

>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 39.0 bits (91), Expect = 3e-04
 Identities = 15/56 (26%), Positives = 30/56 (53%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKA 378
           +L+V NL +++ ++++ E F  +G + S K++         + FV F   + A KA
Sbjct: 1   HLWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKA 56

This subfamily corresponds to the RRM1 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 = 75

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 39.1 bits (91), Expect = 3e-04
 Identities = 24/60 (40%), Positives = 36/60 (60%), Gaps = 4/60 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L V NL  S S+D L+E+F +    TS ++ ++ NG  +G  FV F +AE+A +AL   N
Sbjct: 4   LVVNNLSYSASEDSLQEVFEK---ATSIRIPQN-NGRPKGYAFVEFESAEDAKEALNSCN 59

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis thaliana zinc finger CCCH domain-containing protein 46 (AtC3H46) and similar proteins

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 146 DTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
           + F  FG +L  ++      Q R +GFV F+N E+ K  + K N   +   +V V
Sbjct: 18  EYFGQFGPVLDVRI---PYQQKRMFGFVTFENAETVKRILSKGNPHFICGSRVRV 69

This subfamily corresponds to the RRM domain in AtC3H46, a putative RNA-binding protein that contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCCH class of zinc finger, typically C-X8-C-X5-C-X3-H. It may possess ribonuclease activity. . Length = 70

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 39.1 bits (91), Expect = 3e-04
 Identities = 20/63 (31%), Positives = 35/63 (55%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
           G  ++V  +   + +D+L  LF   G I   ++M + +G +RG  FV ++T EEA  A+ 
Sbjct: 1   GCEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIR 60

Query: 381 EMN 383
            +N
Sbjct: 61  ILN 63

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|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           +++  LD+S+++  L   FS +G +    + R      RG   V F   E A  A+ EM 
Sbjct: 10  VWLDGLDESVTEQYLTRHFSRYGPVVHVVIDR-----QRGQALVFFDKVEAAQAAVNEMK 64

Query: 384 GKMVVSKPLYV 394
           G+ +  + L V
Sbjct: 65  GRKLGGRKLQV 75

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is 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 = 77

>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARS 275
           +   +++  LS  TT++ L+  F ++G +T   VMRD + K S+ FGFV +   ++   +
Sbjct: 1   QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA 60

Query: 276 VEA 278
           + A
Sbjct: 61  MNA 63

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

>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 = 38.9 bits (91), Expect = 4e-04
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           ST+L++G L   V +  L +LF + G++ S+ +   +  R   G  YV      +A RAL
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDM---IPPR---GCAYVCMETRQDAHRAL 55

Query: 99  DELNFTPLNGKPIRI 113
            +L    L GK I++
Sbjct: 56  QKLRNVKLAGKKIKV 70

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

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

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+V ++     D  L  +F Q G ++ V +    + R S G+G+V +  + +A RA ++L
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEII--FNERGSKGFGFVTFANSADADRAREKL 60

Query: 102 NFTPLNGKPIRIMYS 116
           + T + G+ I +  +
Sbjct: 61  HGTVVEGRKIEVNNA 75

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 19/62 (30%), Positives = 36/62 (58%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +LYV  L  +++  ++  LF+Q G++++ R+  D  T  S G G++ ++   EA  A+  
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62

Query: 101 LN 102
           LN
Sbjct: 63  LN 64

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|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 = 38.7 bits (91), Expect = 4e-04
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T L V ++       +L +LF+  GQV SVR+ +        G+ +V +    EA  A++
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKF-DGSHRGFAFVEFVTKQEAQNAME 59

Query: 100 ELNFTPLNGKPIRIMYS 116
            L  T L G+ + + Y+
Sbjct: 60  ALKSTHLYGRHLVLEYA 76

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

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 39.0 bits (90), Expect = 4e-04
 Identities = 20/66 (30%), Positives = 35/66 (53%)

Query: 36  QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEAT 95
           Q   T+LY+  L  +  D  L  L    G++VS +   D +T +  GYG+V++++   A 
Sbjct: 4   QLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQ 63

Query: 96  RALDEL 101
           +A+  L
Sbjct: 64  KAVSAL 69

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|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITS--------CKVMRDPNGISRGSGFVAFSTAEEA 375
           +Y+  L D +++D L ELF   G I           K+  D     +G   V +     A
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 376 SKALTEMNGKMVVSKPLYVAL 396
             A+   NG       + V+L
Sbjct: 61  QAAIEWFNGYEFRGNKIKVSL 81

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 38.9 bits (90), Expect = 4e-04
 Identities = 16/57 (28%), Positives = 32/57 (56%)

Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
          L++G L     +  L + + Q G++    V RD +++RS G+G+V ++  +E   A+
Sbjct: 5  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which 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 A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 38.4 bits (89), Expect = 4e-04
 Identities = 21/56 (37%), Positives = 35/56 (62%), Gaps = 4/56 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSA 184
           +F+K L +    + L ++F   G+I + ++ TD   G S+G+GFV F +EE AK+A
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAA 55

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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG+L     + +L   F ++G++  VR+     + +  G+ +V++     AT AL   
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKG- 59

Query: 102 NFTPLNGKPIRIMY 115
               LNG+ +R+ Y
Sbjct: 60  --KHLNGRALRVEY 71

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG L   V +  L + F+Q G V    V  D  T +  G+G+V +     A +A   +
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA-VV 60

Query: 102 NFTPLNGKPIRI 113
            F P+NG  + +
Sbjct: 61  KFHPINGHRVEV 72

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

 Score = 38.3 bits (90), Expect = 4e-04
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 4/71 (5%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
           G + + NLD  I ++ L   FS FG +   +  T      +   FV+F +  +A++A+D 
Sbjct: 2   GTLLVFNLDSPISDQELRSLFSQFGEVKDIR-ETPLRPSQK---FVEFYDIRAAEAALDA 57

Query: 188 LNGMLLNDKQV 198
           LNG      ++
Sbjct: 58  LNGRPFLGGRL 68

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

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 17/60 (28%), Positives = 31/60 (51%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+  + + +    L   F + G I   ++  D  G++RGY FV +  +  AK A+ +LN
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63

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

>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 10/70 (14%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSK----CFGFVNFDDPDDAARSV 276
           +YV NL     E DL+ +F ++G I      RD + K++     F FV F+DP DA  +V
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGRI------RDIELKNRRGLVPFAFVRFEDPRDAEDAV 55

Query: 277 EALNGKKFDD 286
              NG  F  
Sbjct: 56  FGRNGYDFGQ 65

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

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

 Score = 38.3 bits (90), Expect = 4e-04
 Identities = 14/64 (21%), Positives = 23/64 (35%), Gaps = 5/64 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V  L    S  +L+  F  FG I             R   ++ + + E A  A   + 
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPG-----RNYAYIEYESIEAAQAAKEALR 55

Query: 384 GKMV 387
           G  +
Sbjct: 56  GFPL 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|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 38.9 bits (90), Expect = 4e-04
 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSV 276
           ++V  + E T E  L+  F E+G I +  ++ D   GK + FGFV FDD D   + V
Sbjct: 3   LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIV 59

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

>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESA 181
           R   +  +F+ NL   ID   L + F +FGN++  ++ T  + G+   +GFV FD+ E  
Sbjct: 1   RYPDSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPV 60

Query: 182 K 182
           +
Sbjct: 61  Q 61

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 38.5 bits (89), Expect = 5e-04
 Identities = 19/51 (37%), Positives = 31/51 (60%), Gaps = 1/51 (1%)

Query: 217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNF 266
           +   +++  LS  TT+D L++ F ++G +T   VMRD   K S+ FGFV +
Sbjct: 1   QLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTY 51

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>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 = 38.5 bits (90), Expect = 5e-04
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 9/77 (11%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +++ +LS+  TE+DLK +F E+G I S     D      C  +V  +   DA R+++ L 
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSI----DMIPPRGC-AYVCMETRQDAHRALQKLR 59

Query: 281 GKKFDDKE----WYVGK 293
             K   K+    W   K
Sbjct: 60  NVKLAGKKIKVAWAPNK 76

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 5/71 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           ++I NL   ++   L   F      +     +  L +  GY FV   ++  A  AI+KLN
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHK--IPV---SSVLVKKGGYAFVDCPDQSWADKAIEKLN 55

Query: 190 GMLLNDKQVFV 200
           G +L  K + V
Sbjct: 56  GKILQGKVIEV 66

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

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYV +L   ++  +LYDLF + G +  +R+     TR   G  +V Y   ++A  A D L
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETR---GTAFVVYEDIYDAKNACDHL 61

Query: 102 NFTPLNGKPIRIMY 115
           +   +  + + ++Y
Sbjct: 62  SGFNVANRYLVVLY 75

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

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 38.3 bits (90), Expect = 5e-04
 Identities = 17/63 (26%), Positives = 33/63 (52%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           V+V  +     ED+L  +F + G I    +M D  G ++ + FV + + + A R+V+ L+
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 281 GKK 283
             +
Sbjct: 64  NYE 66

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 38.2 bits (88), Expect = 5e-04
 Identities = 19/63 (30%), Positives = 33/63 (52%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
            T+LY+  L     D  L  L    G++VS +   D +T +  GYG+V++++   A +A+
Sbjct: 1   KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60

Query: 99  DEL 101
             L
Sbjct: 61  TAL 63

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|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 38.6 bits (90), Expect = 5e-04
 Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 5/60 (8%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           NVY+ NL E+ +E++L++   +FG I    ++++     K   FV+F    +A + V  L
Sbjct: 5   NVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFLSIANAIKVVTTL 59

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 38.8 bits (91), Expect = 5e-04
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           I+I  L   +    +   FS +G I+   +  D   G+S+G+ F+ ++++ S   A+D L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 189 NGMLLNDKQVFV 200
           NG+ L  + + V
Sbjct: 72  NGIKLLGRTIRV 83

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|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 29/89 (32%), Positives = 39/89 (43%), Gaps = 21/89 (23%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTI------TSCKVMRDPNGISRGSGFVAFSTAEEASK 377
           L+V NL   I++D+LKE F EFG +      +     R PN      GFV F   E   K
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPN-----FGFVVFDDPEAVQK 60

Query: 378 ALTEMNGKMVVSKPLYVALAQR--KEERR 404
            L         +KP+Y     R   EE++
Sbjct: 61  IL--------ANKPIYFRGDHRLNVEEKK 81

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate RNA-binding Raly-like protein (RALYL)

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 8/65 (12%)

Query: 130 IFIKNLDKSIDNKA-LHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +FI NL+ +I  KA +   F+ +G I+ C V        +GY FVQ+ +E  A++A+   
Sbjct: 4   VFIGNLNTAIVKKADIEAIFAKYGKIVGCSV-------HKGYAFVQYISERHARAAVAGE 56

Query: 189 NGMLL 193
           N  ++
Sbjct: 57  NARII 61

This subgroup corresponds to the RRM of RALYL, also termed heterogeneous nuclear ribonucleoprotein C-like 3, or hnRNP core protein C-like 3, a putative RNA-binding protein that shows high sequence homology with Raly, an RNA-binding protein playing a critical role in embryonic development. The biological role of RALYL remains unclear. Like Raly, RALYL contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. . Length = 69

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 41.9 bits (98), Expect = 6e-04
 Identities = 21/63 (33%), Positives = 35/63 (55%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
           G  ++V  +   + +D+L  LF + G I   ++M D +G +RG  FV F   EEA +A+ 
Sbjct: 58  GCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVK 117

Query: 381 EMN 383
            +N
Sbjct: 118 LLN 120

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

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

 Score = 38.1 bits (89), Expect = 6e-04
 Identities = 22/73 (30%), Positives = 38/73 (52%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+V +L  S  +  L  LF++ G++  V V  D  + +S G+ YV +    +A +A  EL
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 102 NFTPLNGKPIRIM 114
           +     G+ I I+
Sbjct: 65  DGKVFQGRLIHIL 77

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

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 132 IKNLDKSIDNKALHDTFSTFGNILSCKVATDSLG-QSRGYGFVQFDNEESAKSAIDKLNG 190
           + NL        L   F  +G +    +  D    +SRG+ FV+F ++  A+ A+D ++G
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 191 MLLNDKQVFV 200
             L+ +++ V
Sbjct: 63  KELDGRELRV 72

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1 small nuclear ribonucleoprotein A (U1A)

 Score = 38.5 bits (89), Expect = 6e-04
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
           + +Y+ NL+E   +D+LKK    IF  FG I    V R    + +   FV F +   A  
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATN 61

Query: 275 SVEALNGKKFDDK 287
           ++ ++ G  F DK
Sbjct: 62  ALRSMQGFPFYDK 74

This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. . Length = 89

>gnl|CDD|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 = 20/65 (30%), Positives = 35/65 (53%), Gaps = 6/65 (9%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN---GISRGSGFVAFSTAEEASKALT 380
           L+V N   S     +++LF ++G I S   +R P+     +R   +V F++ E A+ A+ 
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILS---IRFPSLRFNKTRRFCYVQFTSPESAAAAVA 59

Query: 381 EMNGK 385
            +NGK
Sbjct: 60  LLNGK 64

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|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 38.3 bits (89), Expect = 6e-04
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 130 IFIKNLDKSI-DNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           + I+NL  SI     L   F  +G +    +     G+  G+ FV     ++A+ A++  
Sbjct: 3   LIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENT 62

Query: 189 NGMLLNDKQVFVGPFLRKQ 207
           NG+ ++ + V V   ++K 
Sbjct: 63  NGLEIDGRPVAVDWAVQKN 81

This subgroup corresponds to the RRM2 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 = 83

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

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+LYVG L   V +  L D F Q G++ S+ V      R+     +V +     A +A +
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVV----PRQ--QCAFVTFTTREAAEKAAE 55

Query: 100 EL-NFTPLNGKPIRIMY 115
            L N   +NG+ +++ +
Sbjct: 56  RLFNKLIINGRRLKLKW 72

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

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 38.3 bits (90), Expect = 6e-04
 Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 4/59 (6%)

Query: 144 LHDTFSTFGNILSCKV--ATDSLGQSRGYG--FVQFDNEESAKSAIDKLNGMLLNDKQV 198
           + +    +G +LS  +           G G  FV+F + E A+ A   L G   + + V
Sbjct: 28  VKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRTV 86

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

>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 38.8 bits (91), Expect = 6e-04
 Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 328 NLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKM 386
           NL+D+I +  LK++  ++G +   K+   P      G   V F + + A + + ++N   
Sbjct: 9   NLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTS 68

Query: 387 VVSKPLYVAL 396
           V+ K + V L
Sbjct: 69  VMGKIIKVFL 78

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma Protein (EWS)

 Score = 38.3 bits (89), Expect = 6e-04
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 9/82 (10%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIIT--------STAVMRDAD-GKSKCFGFVNFDDP 269
           + +YV+ L++  T ++L   F   G++            +  D + GK K    V+++DP
Sbjct: 1   STIYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDP 60

Query: 270 DDAARSVEALNGKKFDDKEWYV 291
             A  +VE  +GK F   +  V
Sbjct: 61  PSAKAAVEWFDGKDFQGSKLKV 82

This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene. . Length = 84

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 38.4 bits (89), Expect = 6e-04
 Identities = 24/80 (30%), Positives = 38/80 (47%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           +SL+V ++        L   F + G +V V V  D  TRR  G+ YV +    +A  AL 
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 100 ELNFTPLNGKPIRIMYSYRD 119
            L+   + G+ I I ++  D
Sbjct: 61  NLDRKWICGRQIEIQFAQGD 80

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEF-GIITSTAVMRDADGKSKC-FGFVNFDDPDDAARSV 276
             ++V  L     E +L  +F  F G   S  V ++  G  K   GFV+F     AA ++
Sbjct: 1   RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAM 60

Query: 277 EALNGKKFDD 286
           +AL G +FD 
Sbjct: 61  DALQGYRFDP 70

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

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

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 10/72 (13%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFG-------IITSTAVMRDADGKSKCFGFVNFDDPDDA 272
            +++ NL    TE  L K+F ++G       +   +  ++   G+ + + FV F+  ++A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLK---GQPRGYCFVTFETKEEA 57

Query: 273 ARSVEALNGKKF 284
            +++++LNGK  
Sbjct: 58  EKALKSLNGKTA 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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 38.1 bits (89), Expect = 7e-04
 Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+LY+ +L L +++  L  +    GQV+S R+ RD    +S G G+    +  +    + 
Sbjct: 1   TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKG-QSRGVGFARMESREKCEDIIS 59

Query: 100 ELNFTPLNG 108
           + N   L G
Sbjct: 60  KFNGKYLKG 68

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

 Score = 38.1 bits (89), Expect = 7e-04
 Identities = 16/57 (28%), Positives = 29/57 (50%)

Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
          L V  L     +  L D F+  G+++ V+V +D  T +S G+G+V +    +  + L
Sbjct: 2  LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58

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

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 41.4 bits (97), Expect = 7e-04
 Identities = 47/242 (19%), Positives = 87/242 (35%), Gaps = 30/242 (12%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-------GKSKCFGFVNFDDPDDAA 273
           +YV  +     E+ +   F +  I T      D          K K F F+ F   ++A 
Sbjct: 178 LYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEAT 237

Query: 274 RSVEALNGKKFDDKEWYVGKAQK-----------KYEREMELKGKFEQSLKETADKFEGL 322
            ++ AL+   + +    + +                +   +     E+ +  T       
Sbjct: 238 FAM-ALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKD 296

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            +Y+ NL   + +D++KEL   FG + +  +++D   G+S+G  F  +        A+  
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAA 356

Query: 382 MNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPRMPMYPPVAPGLGQQLFYGQG 441
           +NGK      L+V        +RA + A   Q        M     +A  L Q +    G
Sbjct: 357 LNGKDTGDNKLHV--------QRACVGAN--QATIDTSNGMAPVTLLAKALSQSILQIGG 406

Query: 442 PP 443
            P
Sbjct: 407 KP 408

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>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 = 7e-04
 Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           L+V  L+   ++ KL+  F E+G I   +++RD   G  RG  F+ F    +   A    
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 383 NGKMV 387
           +GK +
Sbjct: 64  DGKKI 68

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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 37.9 bits (88), Expect = 7e-04
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVE-- 277
           ++V  LS  TT+ DLK+ F +FG +    +  D   G+S+ FGFV F D     + ++  
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 278 --ALNGKKFDDK 287
              L+G+  D K
Sbjct: 61  EHKLDGRVIDPK 72

This subfamily corresponds to the RRM1 in 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 family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 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 = 7e-04
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTIT--SCKVMRD-PNGISRGSGFVAFSTAEEASKALT 380
           LYV NL    +D+ L+   +E G +   S K      NG S+G  +V F++   A+    
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 381 EMNGKMVVSKPLYVAL 396
           ++ G+    K   V  
Sbjct: 61  KLEGREFNGKKCVVTY 76

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

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 38.0 bits (88), Expect = 7e-04
 Identities = 21/76 (27%), Positives = 42/76 (55%), Gaps = 7/76 (9%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVE 277
           ++++V+N+++ T  +DL++ FG +G I    V  D    + + F +V F+D  DA  ++ 
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 278 ALNGKKFDDKEWYVGK 293
            L      D++W  G+
Sbjct: 61  NL------DRKWICGR 70

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 7/71 (9%)

Query: 129 NIFIKN--LDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID 186
           ++ + N  L   +  + L   F  +G +    +        + Y FV + + E A +A D
Sbjct: 3   HLVVANGGLGNGVSREELLRVFEKYGTVEDLVMPPG-----KPYCFVSYSSIEDAAAAYD 57

Query: 187 KLNGMLLNDKQ 197
            LNG  L   Q
Sbjct: 58  ALNGKELELPQ 68

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

 Score = 37.6 bits (88), Expect = 8e-04
 Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 2/65 (3%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           V+V  LS    E DL + F + G +    ++RD +  +SK   +V F D +    ++  L
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GL 60

Query: 280 NGKKF 284
            G++ 
Sbjct: 61  TGQRL 65

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

 Score = 38.2 bits (88), Expect = 8e-04
 Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +LYV  L  ++   +L  LF+Q G++++ R+  D  T  S G G++ ++   EA  A+  
Sbjct: 7   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 66

Query: 101 LNFT--PLNGKPIRIMYS 116
           LN    P   +PI + ++
Sbjct: 67  LNGQKPPGATEPITVKFA 84

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

 Score = 37.8 bits (88), Expect = 8e-04
 Identities = 14/64 (21%), Positives = 23/64 (35%), Gaps = 3/64 (4%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           +Y      S     +K LF   G +    +    +   +   F+ F   E A  A+  +N
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTM---LSRTVQPHAFITFENLEAAQLAIETLN 58

Query: 384 GKMV 387
           G  V
Sbjct: 59  GASV 62

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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 37.7 bits (88), Expect = 8e-04
 Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 43  YVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN 102
           +VG+L  +     L  +F  +  V SVR+ RD  T +  G+ YV +        AL E +
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEAL-EYD 62

Query: 103 FTPLNGKPIRI 113
               + + +R+
Sbjct: 63  GALFDDRSLRV 73

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 37.7 bits (88), Expect = 8e-04
 Identities = 13/38 (34%), Positives = 20/38 (52%)

Query: 161 TDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQV 198
            D+  Q    G V+F      K AI+KL+G  LN +++
Sbjct: 30  ADAHKQRPNEGVVEFATYSDMKRAIEKLDGTELNGRKI 67

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

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 38.0 bits (88), Expect = 8e-04
 Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSV 276
           ++V  + E T E  L+  F ++G I +  VM D   GK + F FV FDD D   + V
Sbjct: 3   IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIV 59

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 37.6 bits (87), Expect = 8e-04
 Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 7/64 (10%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           VY+  LS    E D+++ FG +G       + + D K+  +GFV F+D  DA  +V  LN
Sbjct: 2   VYIGRLSYHVREKDIQRFFGGYG------KLLEIDLKNG-YGFVEFEDSRDADDAVYELN 54

Query: 281 GKKF 284
           GK  
Sbjct: 55  GKDL 58

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 37.9 bits (89), Expect = 9e-04
 Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 10/85 (11%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQ-------MGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
           S  LYV +L   V +  L  +F +          +  +R+   ++  R  G  +V + + 
Sbjct: 1   SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRL---MTEGRMKGQAFVTFPSE 57

Query: 92  HEATRALDELNFTPLNGKPIRIMYS 116
             AT+AL+ +N   L GKP+ I + 
Sbjct: 58  EIATKALNLVNGYVLKGKPMVIQFG 82

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|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 37.9 bits (88), Expect = 9e-04
 Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 5/83 (6%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRR-----SLGYGYVNYNAAHEAT 95
           +L+V +L+ S  +  L D F  +   V  RV      +R     S+G+G+V +    +A 
Sbjct: 2   TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQ 61

Query: 96  RALDELNFTPLNGKPIRIMYSYR 118
            AL  ++   L+G  + + +S+R
Sbjct: 62  AALKAMDGFVLDGHTLVVKFSHR 84

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

 Score = 38.0 bits (89), Expect = 9e-04
 Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 7/78 (8%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRD--LSTRRSLGYGYVNYNAAHEATRAL 98
           ++YVG+LD +    QL + F+Q G+V  VR+  D    TR    Y +V +        AL
Sbjct: 6   TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTR----YAFVEFAEQTSVINAL 61

Query: 99  DELNFTPLNGKPIRIMYS 116
            +LN     G+P+++ +S
Sbjct: 62  -KLNGAMFGGRPLKVNHS 78

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

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

 Score = 37.7 bits (88), Expect = 9e-04
 Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 4/81 (4%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMG-QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
           + ++ +  L LSV +  + +     G +   VR+ R  +T  S G+ +V + +  EATR 
Sbjct: 2   NNTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRW 61

Query: 98  LDELN--FTPLNGKPIRIMYS 116
           + ELN     L    I + YS
Sbjct: 62  M-ELNQGKLQLQDYKITLHYS 81

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

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 37.9 bits (87), Expect = 9e-04
 Identities = 20/66 (30%), Positives = 34/66 (51%)

Query: 36  QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEAT 95
           Q   T+LY+  L     D  L  L    G++VS +   D +T +  GYG+V++++   A 
Sbjct: 1   QLSKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQ 60

Query: 96  RALDEL 101
           +A+  L
Sbjct: 61  KAVASL 66

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|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal EAR1-like proteins

 Score = 37.5 bits (87), Expect = 9e-04
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L + NLD ++S + L+ +F  +G +   K +R+     R   FV F    +A+KAL  MN
Sbjct: 4   LVIFNLDPTVSSETLRSIFQVYGDV---KELRE-TPCKREQRFVEFFDVRDAAKALRAMN 59

Query: 384 GKMVVSKPLYV 394
           GK +  KP+ +
Sbjct: 60  GKEISGKPVVI 70

This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. . Length = 71

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 7/66 (10%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           ++++NL  S   + L + FS +G +   K   D       Y FV F+  + A  A++++N
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEEMN 56

Query: 190 GMLLND 195
           G  L  
Sbjct: 57  GKELEG 62

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           IF+ +L   + ++ L   FS + +    KV  D   G+S+GYGFV F +      A+ ++
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 189 NG 190
           NG
Sbjct: 69  NG 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|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 222 YVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
           Y+ NL+E   +D+LK+    +F +FG +      +    K +   FV F D + A  ++ 
Sbjct: 3   YINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTL--KMRGQAFVVFKDVESATNALR 60

Query: 278 ALNGKKFDDK 287
           AL G  F DK
Sbjct: 61  ALQGFPFYDK 70

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

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

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 7/75 (9%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAID 186
           G +F++NL  S     L   FS FG +    VA D   G+S+G+ +V F + E A  A  
Sbjct: 3   GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62

Query: 187 KLNGMLLNDKQVFVG 201
           +L      D +VF G
Sbjct: 63  EL------DGKVFQG 71

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|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 7/68 (10%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N +YV       TE+ LKK F  FG I + ++ ++     K  GFV F+  + A R++  
Sbjct: 5   NTLYVHGYG--LTEEILKKAFSPFGNIINISMEKE-----KNCGFVTFEKMESADRAIAE 57

Query: 279 LNGKKFDD 286
           LNG     
Sbjct: 58  LNGTTVQG 65

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 16/56 (28%), Positives = 27/56 (48%)

Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
          L+V  L+    D  L  +F++ G++ S  V RD  T  SL Y ++ +    +   A
Sbjct: 6  LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDKL 188
           IF+  L  ++    L   FS FG +    V  D   +  RG+GF+ F++E+S    +++ 
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE- 63

Query: 189 NGMLLNDKQV 198
           +   +N K+V
Sbjct: 64  HFHDINGKKV 73

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 18/62 (29%), Positives = 30/62 (48%)

Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGK 282
           VKNLS   + + L++ F +FG +    V+ D  G+S   G V F     A  +++  +  
Sbjct: 4   VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRCSEG 63

Query: 283 KF 284
            F
Sbjct: 64  CF 65

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+VK L +  +++ LKE F   G+I +  V     G S+G GFV FS+ E+A  A   M 
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAME 60

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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 15/47 (31%), Positives = 28/47 (59%)

Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNY 88
          +++G L    +   L D F++ G++    V RD +T+RS G+G+V +
Sbjct: 2  MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTF 48

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 37.4 bits (86), Expect = 0.001
 Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +FI  L       +L D FS FG I  C V  D +  +SRG+GFV F +  S    +DK+
Sbjct: 2   MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPAS----VDKV 57

Query: 189 NG 190
             
Sbjct: 58  LA 59

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMR-DPNGISRGSGFVAFSTAEEASKAL 379
           L+V NL    ++D+L+  F   G I   ++M  + +G  +G  FV F   E A+ AL
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 17/47 (36%), Positives = 26/47 (55%)

Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNY 88
          L+VG L        L   F+Q G+VV   + +D +T RS G+G+V +
Sbjct: 2  LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKF 48

This subfamily corresponds to the RRM1 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 form is predominantly nuclear and the nonacetylated form is in cytoplasm. It 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 = 82

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

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 2/67 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV NL  TTT D L + F + G +     M   + +   + FV F +      ++  LN
Sbjct: 7   IYVGNLDPTTTADQLLEFFSQAGEV-KYVRMAGDETQPTRYAFVEFAEQTSVINAL-KLN 64

Query: 281 GKKFDDK 287
           G  F  +
Sbjct: 65  GAMFGGR 71

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 20/73 (27%), Positives = 40/73 (54%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L+V  L  +   + L +LF + G+V+S +V  +  +  +  YG V  +++ E  R +  
Sbjct: 1   NLWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISH 60

Query: 101 LNFTPLNGKPIRI 113
           L+ T L+G+ I +
Sbjct: 61  LHRTELHGQQISV 73

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains 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. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 4/69 (5%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           + V NL    ++ +L+ +F +FG +    +       S+   FV F D   A  +++ALN
Sbjct: 4   LLVFNLDSPISDQELRSLFSQFGEVKD--IRETPLRPSQK--FVEFYDIRAAEAALDALN 59

Query: 281 GKKFDDKEW 289
           G+ F     
Sbjct: 60  GRPFLGGRL 68

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|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIIT-STAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           V ++ L  + TE+D++  F    I      ++ D DG+     +V F  P+DA R++   
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61

Query: 280 NGK 282
           N K
Sbjct: 62  NNK 64

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 5/61 (8%)

Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNG 281
           YV  L E  TE DL+  F +FG I S  V+     + +C  FV F   + A ++ E L  
Sbjct: 5   YVGGLGERVTEKDLRDHFYQFGEIRSITVVP----RQQC-AFVTFTTREAAEKAAERLFN 59

Query: 282 K 282
           K
Sbjct: 60  K 60

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

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 7/80 (8%)

Query: 41  SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
           ++Y+ +L+  V   +L    Y +F+Q GQ++ +   + L  R   G  +V +     AT 
Sbjct: 1   TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMR---GQAFVVFKDISSATN 57

Query: 97  ALDELNFTPLNGKPIRIMYS 116
           AL  +   P   KP+RI YS
Sbjct: 58  ALRSMQGFPFYDKPMRIAYS 77

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 5/60 (8%)

Query: 331 DSISDDKLKELFSEFGTITSCKVMRDP--NGISRGSG--FVAFSTAEEASKALTEMNGKM 386
           + I +D +KE   ++G + S  + R         G G  FV F+  E+A KA   + G+ 
Sbjct: 22  EEILED-VKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRK 80

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

>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1-beta) and similar proteins

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 2/58 (3%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
           I+I+NL  S+ +  L   F  FG I  CKV   S G+   YGF+ + + E A  ++ K
Sbjct: 5   IYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRGEK--YGFITYRHSEHAALSLGK 60

This subfamily corresponds to the RRM of PGC-1beta, also termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or PGC-1-related estrogen receptor alpha coactivator, which is one of the members of PGC-1 transcriptional coactivators family, including PGC-1alpha and PGC-1-related coactivator (PRC). PGC-1beta plays a nonredundant role in controlling mitochondrial oxidative energy metabolism and affects both, insulin sensitivity and mitochondrial biogenesis, and functions in a number of oxidative tissues. It is involved in maintaining baseline mitochondrial function and cardiac contractile function following pressure overload hypertrophy by preserving glucose metabolism and preventing oxidative stress. PGC-1beta induces hypertriglyceridemia in response to dietary fats through activating hepatic lipogenesis and lipoprotein secretion. It can stimulate apolipoprotein C3 (APOC3) expression, further mediating hypolipidemic effect of nicotinic acid. PGC-1beta also drives nuclear respiratory factor 1 (NRF-1) target gene expression and NRF-1 and estrogen related receptor alpha (ERRalpha)-dependent mitochondrial biogenesis. The modulation of the expression of PGC-1beta can trigger ERRalpha-induced adipogenesis. PGC-1beta is also a potent regulator inducing angiogenesis in skeletal muscle. The transcriptional activity of PGC-1beta can be increased through binding to host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. PGC-1beta is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, two glutamic/aspartic acid-rich acidic domains, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha, PGC-1beta lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 79

>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 17/66 (25%), Positives = 38/66 (57%), Gaps = 3/66 (4%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTIT-SCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
           L++ +L+  + ++ +K++++  G    + KV+R   +G++ G  FV F +   A  AL+ 
Sbjct: 2   LWMGDLEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNALS- 60

Query: 382 MNGKMV 387
           +NG  +
Sbjct: 61  LNGTPI 66

This subgroup corresponds to the RRM1 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), 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 carboxyl terminus which also harbors a methionine-rich region. The subgroup also includes NAM8, 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 = 81

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

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           +Y   +   +++  +++ FS FG I   +V  +     +G  F+ FST E A+ A+  +N
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE-----KGYSFIRFSTHESAAHAIVSVN 57

Query: 384 GKMV 387
           G  +
Sbjct: 58  GTTI 61

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 8/77 (10%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG L    + ++L   F++ G +      R +       Y Y+ Y +   A  A + L
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAI------RRIDYDPGRNYAYIEYESIEAAQAAKEAL 54

Query: 102 NFTPLN--GKPIRIMYS 116
              PL   G+ +R+ ++
Sbjct: 55  RGFPLGGPGRRLRVDFA 71

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 9/76 (11%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +++  L        L   F  FG I             R Y ++++++ E+A++A + L 
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYD-----PGRNYAYIEYESIEAAQAAKEALR 55

Query: 190 GMLLNDKQVFVGPFLR 205
           G  L       G  LR
Sbjct: 56  GFPLGGP----GRRLR 67

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|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator-related protein 1 (PRC) and similar proteins

 Score = 37.9 bits (88), Expect = 0.001
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           ++I  +   +    L D FS FG I  C +   S G +  YGFV +   E A +AI+  +
Sbjct: 5   VYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSEGDN--YGFVTYRYTEEAFAAIENGH 62

Query: 190 GMLLNDKQVF 199
            +   D+  F
Sbjct: 63  KLRRPDELPF 72

This subgroup corresponds to the RRM of PRC, also termed PGC-1-related coactivator, one of the members of PGC-1 transcriptional coactivators family, including peroxisome proliferator-activated receptor gamma coactivators PGC-1alpha and PGC-1beta. Unlike PGC-1alpha and PGC-1beta, PRC is ubiquitous and more abundantly expressed in proliferating cells than in growth-arrested cells. PRC has been implicated in the regulation of several metabolic pathways, mitochondrial biogenesis, and cell growth. It functions as a growth-regulated transcriptional cofactor activating many nuclear genes specifying mitochondrial respiratory function. PRC directly interacts with nuclear transcriptional factors implicated in respiratory chain expression including nuclear respiratory factors 1 and 2 (NRF-1 and NRF-2), CREB (cAMP-response element-binding protein), and estrogen-related receptor alpha (ERRalpha). It interacts indirectly with the NRF-2beta subunit through host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. Furthermore, like PGC-1alpha and PGC-1beta, PRC can transactivate a number of NRF-dependent nuclear genes required for mitochondrial respiratory function, including those encoding cytochrome c, 5-aminolevulinate synthase, Tfam, and TFB1M, and TFB2M. Further research indicates that PRC may also act as a sensor of metabolic stress that orchestrates a redox-sensitive program of inflammatory gene expression. PRC is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a central proline-rich region, a tetrapeptide motif (DHDY) responsible for HCF binding, a C-terminal arginine/serine-rich (SR) domain, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 91

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 10/75 (13%)

Query: 324 LYVKNLDDSISDDKLKELFSEF-GTITSCKVMRDPNGIS-RGSGFVAFSTAEEASKALTE 381
           L+++NL +  + + L+ LF++F G        ++   +  RG  FV F T E+A+ AL  
Sbjct: 5   LFLQNLPEETTKEMLEMLFNQFPG-------FKEVRLVPRRGIAFVEFETEEQATVALQA 57

Query: 382 MNG-KMVVSKPLYVA 395
           + G K+     + ++
Sbjct: 58  LQGFKITPGHAMKIS 72

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 8/62 (12%)

Query: 130 IFIKNL-DKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +FI NL  K +  + L   FST+G +    +          YGFVQFD+ ES  +AI+  
Sbjct: 2   LFIGNLPTKRVSKEDLFRIFSTYGELAQIVL-------KNAYGFVQFDSPESCANAINCE 54

Query: 189 NG 190
            G
Sbjct: 55  QG 56

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 326 VKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
           VKNL    +++K+++ F + G I   K++    G+      + F T +EA  ALT
Sbjct: 5   VKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGL---VAVIEFETEDEALAALT 56

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

>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 27/76 (35%), Positives = 37/76 (48%), Gaps = 13/76 (17%)

Query: 326 VKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGK 385
           VKNL       +L+ELFS+FG++   +V+  P GI   +  V F    EA  A      K
Sbjct: 5   VKNLPAGTLTAELRELFSKFGSLG--RVLLPPAGI---TAIVEFLEPSEAKLAFR----K 55

Query: 386 MVVSK----PLYVALA 397
           +  SK    PLY+  A
Sbjct: 56  LAYSKFKHVPLYLEWA 71

This subgroup corresponds to the RRM4 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 = 72

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 40.1 bits (93), Expect = 0.002
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           +YV ++   + +D ++  F  FG I S  +  DP  G  +G  FV +   E A  AL +M
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 383 NGKMVVSKPLYVALAQ 398
           NG+M+  + + V    
Sbjct: 170 NGQMLGGRNIKVGRPS 185

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           +YVG+L       +L D F + G + SV V      R   G+ +V +    +A  A+  L
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWV-----ARNPPGFAFVEFEDPRDAEDAVRAL 56

Query: 102 NFTPLNGKPIRI 113
           +   + G  +R+
Sbjct: 57  DGRRICGNRVRV 68

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|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 16/60 (26%), Positives = 33/60 (55%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +++  +S+   E+D++ +F  FG I    ++R  DG S+   FV F     A  +++A++
Sbjct: 4   LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), 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 binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 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 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 preferentially binds 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 contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also 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 = 81

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

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG L+    + ++ ++F+  G+V  + + RD   ++S G  +V Y++   A  A+  L
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKAL 60

Query: 102 N 102
           N
Sbjct: 61  N 61

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

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG+L   + + +  +LF++ G+V  V + ++       G+G++  +    A +A  EL
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEK------GFGFIRLDTRTNAEKAKAEL 57

Query: 102 NFTPLNGKPIRI 113
           +     G+ +R+
Sbjct: 58  DGIMRKGRQLRV 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|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 18/71 (25%), Positives = 34/71 (47%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           +Y+G L     + +L   F+Q G V  +R+ R   T +S GY +V + +   A    + +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 102 NFTPLNGKPIR 112
           N   L  + ++
Sbjct: 62  NNYLLFERLLK 72

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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 19/66 (28%), Positives = 37/66 (56%), Gaps = 2/66 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFG-TITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           L++ +L+  + ++ +K  F+  G T+ S K++R+   G   G  FV F+    A + L +
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 382 MNGKMV 387
           +NGK +
Sbjct: 62  LNGKPI 67

This subgroup corresponds to the RRM1 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 = 84

>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 8/69 (11%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNI--------LSCKVATDSLGQSRGYGFVQFDNEESA 181
           I+I  L   +   +L + F   G I           K+ TD   + +G   V +D+  +A
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 182 KSAIDKLNG 190
           ++AI+  NG
Sbjct: 61  QAAIEWFNG 69

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +++ NL + +    +   FS  G   SCK+  D+ G    Y FV+F     A +++  +N
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDP-YCFVEFFEHRHAAASLAAMN 60

Query: 190 GMLLNDKQVFV 200
           G  +  K+V V
Sbjct: 61  GRKIMGKEVKV 71

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKAL 379
           L+V  L  S+++  L+E FS FGT++  ++++    G  RG  ++   T+E   K  
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKC 58

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 5/63 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +++  L + +  K L D F  FG I S  V        +   FV F   E+A+ A ++L 
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITVV-----PRQQCAFVTFTTREAAEKAAERLF 58

Query: 190 GML 192
             L
Sbjct: 59  NKL 61

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

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 17/63 (26%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           L+V  +  ++ +  L+ LF +FG I    V++D   G+ +G  F+ +   E A KA + +
Sbjct: 8   LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSAL 67

Query: 383 NGK 385
           + +
Sbjct: 68  HEQ 70

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 36.8 bits (85), Expect = 0.002
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 221 VYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSV 276
           +Y+ NL+E   +++LKK    IF +FG I     ++    K +   FV F D   A  ++
Sbjct: 2   IYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTL--KMRGQAFVVFKDISSATNAL 59

Query: 277 EALNGKKFDDK 287
            ++ G  F DK
Sbjct: 60  RSMQGFPFYDK 70

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila melanogaster sex determination protein SNF and similar proteins

 Score = 36.8 bits (85), Expect = 0.002
 Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 6/71 (8%)

Query: 130 IFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
           I+I NL++ +      K+L+  FS FG IL   VA  +L + RG  FV F +  SA +A+
Sbjct: 2   IYINNLNEKVKKEELKKSLYAIFSQFGQILDI-VALKTL-KMRGQAFVVFKDISSATNAL 59

Query: 186 DKLNGMLLNDK 196
             + G    DK
Sbjct: 60  RSMQGFPFYDK 70

This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. . Length = 78

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

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV NLS   TE  + ++F + G   S  ++ +       + FV F +  DAA ++ A+N
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAAMN 60

Query: 281 GKKFDDKE 288
           G+K   KE
Sbjct: 61  GRKILGKE 68

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 16/63 (25%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           L+V ++  +I++ +++ +F E G +    +++D   G  +G  FV +ST +EA +A+  +
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 383 NGK 385
           + +
Sbjct: 62  HNQ 64

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. 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|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 = 16/61 (26%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 334 SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY 393
            D  L+++F  FG +    ++   N      G+  ++  E A +A+T ++GK V    L 
Sbjct: 12  PDYILEDVFCRFGGLIDVYLVPGKN-----YGYAKYADRESAERAITTLHGKEVNGVKLK 66

Query: 394 V 394
           V
Sbjct: 67  V 67

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|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T++YVG++      + L  LF   G ++  R   D       G+ +V  +   +A  A+ 
Sbjct: 1   TTVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDR------GFAFVKLDTHEQAAMAIV 54

Query: 100 ELNFTPLNGKPIR 112
           +L   P++G+P+R
Sbjct: 55  QLQGFPVHGRPLR 67

This subfamily corresponds to the RRM3 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. 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 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|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 8/64 (12%)

Query: 222 YVKNL-SETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++ NL ++  +++DL +IF  +G +    +          +GFV FD P+  A ++    
Sbjct: 3   FIGNLPTKRVSKEDLFRIFSTYGELAQIVL-------KNAYGFVQFDSPESCANAINCEQ 55

Query: 281 GKKF 284
           GK  
Sbjct: 56  GKMI 59

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 8/70 (11%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL- 279
           V VKNL + TTE+ +++ F + G I    ++    G       + F+  D+A     AL 
Sbjct: 3   VKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGG---LVAVIEFETEDEAL---AALT 56

Query: 280 -NGKKFDDKE 288
            + K+    E
Sbjct: 57  KDHKRLGGNE 66

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

>gnl|CDD|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 = 37.6 bits (88), Expect = 0.002
 Identities = 21/62 (33%), Positives = 28/62 (45%), Gaps = 5/62 (8%)

Query: 335 DDKLKELFSEFGTITSCKVMRDPNGIS--RGSGFVAFSTAEEASKALTEMNGKMVVSKPL 392
           DD L E F +FG +   KV    N     RG+ +V + + EEA  A    NG+    K L
Sbjct: 43  DDVLPE-FEKFGEVVQFKVCC--NYEPHLRGNVYVQYQSEEEALAAFKMFNGRWYAGKQL 99

Query: 393 YV 394
             
Sbjct: 100 TC 101

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|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 37.1 bits (87), Expect = 0.002
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 17/80 (21%)

Query: 324 LYVKNLDDSISDDKLKELFSEF-----------GTITSCKVMRDPNGISRGSGFVAFSTA 372
           LYV NL   I++++L + F++              + S ++  + N       FV F T 
Sbjct: 4   LYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKN-----FAFVEFRTV 58

Query: 373 EEASKALTEMNGKMVVSKPL 392
           EEA+ AL  ++G +   +PL
Sbjct: 59  EEATAALA-LDGIIFKGQPL 77

The subfamily corresponds to the RRM1 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 = 82

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

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTF-STFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            FI N+   +  ++L D      G +   ++  D+ G+SRG   V+F  EES K A++ L
Sbjct: 2   AFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEVL 61

Query: 189 NGMLLNDKQVFV 200
           N  +LN + + V
Sbjct: 62  NKHVLNGRPLKV 73

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

>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 5/72 (6%)

Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGK 282
           VKN    TT ++L+ +F   G +T   +       +     V F +P  A  + +AL  +
Sbjct: 5   VKNFPYGTTAEELRDLFEPHGKLTRVLM-----PPAGTIAIVEFANPQQARLAFKALAYR 59

Query: 283 KFDDKEWYVGKA 294
           +F D   Y+ K 
Sbjct: 60  RFKDSILYLEKG 71

This subgroup corresponds to the RRM3 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 = 72

>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVE 277
           ++V  LS  TT +D+K+ F +FG +    +M D    + + FGFV F+  D   +  E
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240834 cd12388, RRM1_RAVER, RNA recognition motif 1 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 6/71 (8%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           I I+NL   +  + +HD  S +       V    + +S+    V   N + A  AI KL+
Sbjct: 2   IVIRNLPADVTKQEVHDLLSDYQ------VKYCDVDKSKRTAQVTLLNGDQASRAIAKLH 55

Query: 190 GMLLNDKQVFV 200
                ++++ V
Sbjct: 56  QSSYKERKISV 66

This subfamily corresponds to the RRM1 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 = 70

>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 5/64 (7%)

Query: 131 FIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNG 190
           F+  ++  +    + D F  FG   S  V   +       GFV+F+  E+A+     ++ 
Sbjct: 6   FLFGVEDDLPEYKIRDYFEQFGKSKSVIVNHRA-----KCGFVRFETREAAEKFAAAISE 60

Query: 191 MLLN 194
             LN
Sbjct: 61  NGLN 64

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|241069 cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1)

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 9/66 (13%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD--AARSV 276
           N +Y+ NL+E+ T  DL+K+F +  I  S   +  +       G+   D PD+  A +++
Sbjct: 2   NKLYIGNLNESVTPADLEKVFEDHKISYSGQFLVKS-------GYAFVDCPDEQWAMKAI 54

Query: 277 EALNGK 282
           E  +GK
Sbjct: 55  ETFSGK 60

This subgroup corresponds to the RRM1 of IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also termed coding region determinant-binding protein (CRD-BP), or VICKZ family member 1, or zipcode-binding protein 1 (ZBP-1). IGF2BP1 is a multi-functional regulator of RNA metabolism that has been implicated in the control of aspects of localization, stability, and translation for many mRNAs. It is predominantly located in cytoplasm and was initially identified as a trans-acting factor that interacts with the zipcode in the 3'- untranslated region (UTR) of the beta-actin mRNA, which is important for its localization and translational regulation. It inhibits IGF-II mRNA translation through binding to the 5'-UTR of the transcript. IGF2BP1 also acts as human immunodeficiency virus type 1 (HIV-1) Gag-binding factor that interacts with HIV-1 Gag protein and blocks the formation of infectious HIV-1 particles. IGF2BP1 promotes mRNA stabilization; it functions as a coding region determinant (CRD)-binding protein that binds to the coding region of betaTrCP1 mRNA and prevents miR-183-mediated degradation of betaTrCP1 mRNA. It also promotes c-myc mRNA stability by associating with the CRD and stabilizes CD44 mRNA via interaction with the 3'-UTR of the transcript. In addition, IGF2BP1 specifically interacts with both Hepatitis C virus (HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing HCV internal ribosome entry site (IRES)-mediated translation initiation via the 3'-UTR. IGF2BP1 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. It also contains two putative nuclear export signals (NESs) and a putative nuclear localization signal (NLS). . Length = 77

>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 9/76 (11%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTA--------VMRDAD-GKSKCFGFVNFDDP 269
           N ++V+ L E  T + +   F + GII +          +  D + GK K    V+FDDP
Sbjct: 3   NTIFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 62

Query: 270 DDAARSVEALNGKKFD 285
             A  +++  +GK+F 
Sbjct: 63  PSAKAAIDWFDGKEFS 78

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. . Length = 86

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

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 17/81 (20%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           ++++ +L     + +L +LF+Q G+V   R+ +D  T  S G  +V +     A + L+ 
Sbjct: 2   TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61

Query: 101 LNFTP-----LNGKPIRIMYS 116
            +        L+G+ + +  +
Sbjct: 62  ADNAEDSGLSLDGRRLIVTLA 82

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

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 19/60 (31%), Positives = 29/60 (48%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +FI  + K  +   +   FS FG I  C++     G SRG  FV F     A++AI  ++
Sbjct: 4   LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), 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 binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 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 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 preferentially binds 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 contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also 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 = 81

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 21/72 (29%), Positives = 37/72 (51%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L V +L        L  +F + G+V  V + RD  TR S G+ +V +    +A  A+D +
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 102 NFTPLNGKPIRI 113
           +   L+G+ +R+
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|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.8 bits (85), Expect = 0.003
 Identities = 22/82 (26%), Positives = 34/82 (41%), Gaps = 6/82 (7%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK------SKCFGFVNFDDPDDAAR 274
           ++VKNL+ +TT   L   F          V    D K      S  FGFV F   + A  
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 275 SVEALNGKKFDDKEWYVGKAQK 296
           +++A++G   D     V  + +
Sbjct: 63  ALKAMDGFVLDGHTLVVKFSHR 84

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

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 22/74 (29%), Positives = 35/74 (47%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           +Y+G L     + +L   F+Q G V +VRV R   T  S  YG++ +     A  A   +
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 102 NFTPLNGKPIRIMY 115
           N   L GK +++  
Sbjct: 62  NNYLLMGKVLQVHV 75

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

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 19/48 (39%), Positives = 30/48 (62%)

Query: 42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYN 89
          L+VG+L  +V   +L + F+Q G+V S  V  D  T  S GYG+V+++
Sbjct: 2  LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFS 49

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

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++V+NL    +   LK+ F+E G +    +  + NG S+G G V F + E A +A   MN
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVRFESPEVAERACRMMN 60

Query: 384 G 384
           G
Sbjct: 61  G 61

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

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 36.3 bits (83), Expect = 0.003
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           NLY++ L    +D  L +L   +G I S K + D      +G GFV F +   A KA+T 
Sbjct: 3   NLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 62

Query: 382 MNGKMVVSK 390
           +    V ++
Sbjct: 63  LKASGVQAQ 71

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|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 5/71 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           + VKNL    ++++L+ELF +FG++   +++  P   SR    V F    +A KA   + 
Sbjct: 3   ILVKNLPFGTTEEELRELFEKFGSLG--RLLLPP---SRTIALVEFLEPSDARKAFKSLA 57

Query: 384 GKMVVSKPLYV 394
            K     PLY+
Sbjct: 58  YKRFKHVPLYL 68

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 7/83 (8%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRV--CRDLSTRRSLGYGYVNYNAAHEATRA 97
           ++L+V +   S + S + DLF Q G+++S+R    R   TRR   + YV + +   A  A
Sbjct: 1   STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRR---FCYVQFTSPESAAAA 57

Query: 98  LDELNFTPLNGKPIRIMYSYRDP 120
           +  LN     G  + +  S  DP
Sbjct: 58  VALLNGKLGEGYKLVVKIS--DP 78

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           +Y+  L   +++  +  +FS++G I    ++RD   G S+G  F+A+        A+  +
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 383 NGKMVVSKPLYV 394
           NG  ++ + + V
Sbjct: 72  NGIKLLGRTIRV 83

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

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 3/69 (4%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N V+V  +     E +++  F ++G +    ++ D  G SK +GFV+F D  D  + VE+
Sbjct: 6   NTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQKIVES 65

Query: 279 ---LNGKKF 284
               +GKK 
Sbjct: 66  QINFHGKKL 74

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

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFG-TITSCKVMRDPN-GISRGSGFVAFSTAEEASKALT 380
            + ++ L  S++++ ++      G      ++MR    G SRG  FV F + EEA++ + 
Sbjct: 4   TIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWME 63

Query: 381 EMNGKMVV 388
              GK+ +
Sbjct: 64  LNQGKLQL 71

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

>gnl|CDD|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 = 22/69 (31%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           NLY++ L    +D  L +L   +G I S K + D N    +G GFV F +   A KA+  
Sbjct: 6   NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVAS 65

Query: 382 MNGKMVVSK 390
           +    V ++
Sbjct: 66  LKANGVQAQ 74

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|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 = 20/61 (32%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           N++I+ L     ++ L      +G I+S K   D +  Q +GYGFV FD+  +A+ A+  
Sbjct: 6   NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVAS 65

Query: 188 L 188
           L
Sbjct: 66  L 66

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|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           +++V NL+     D+LK    EF    + AV     G SK FG+V+F+  +D  +++E L
Sbjct: 2   SLFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKALE-L 60

Query: 280 NGKK 283
            GKK
Sbjct: 61  TGKK 64

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin 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. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 12/69 (17%), Positives = 31/69 (44%), Gaps = 4/69 (5%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITST-AVMRDADGKSKCFGFVNFDDPDDAARSVE 277
             + + N+      +DL  +   +G + +   V   ++  +     V ++ P+ A ++V 
Sbjct: 1   RKIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATV---NVTYESPEQAQQAVN 57

Query: 278 ALNGKKFDD 286
            LNG +++ 
Sbjct: 58  KLNGHEYEG 66

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|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 6/61 (9%)

Query: 334 SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY 393
           S+D+L+++FS++G ++   V+       +GS  V F++ + A  A+    G    S PL 
Sbjct: 17  SEDELRKIFSKYGDVSDV-VVSSK---KKGSAIVEFASKKAAEAAVENECGL--PSNPLL 70

Query: 394 V 394
           V
Sbjct: 71  V 71

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

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG+L        L   F   G   SVR+  D  T +S G  +V ++ A   T+AL +L
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL-KL 61

Query: 102 NFTPLNGKPIRI 113
           + T L G+ I +
Sbjct: 62  HHTLLKGRKINV 73

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

>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 5/49 (10%)

Query: 148 FSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDK 196
           F  FG IL  +   D     RG+ FV+ D  E A  AI +L G  ++ +
Sbjct: 21  FQNFGYILEFRHQPD-----RGFAFVKLDTHEQAAMAIVQLQGFPVHGR 64

This subfamily corresponds to the RRM3 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. 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 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|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 36.2 bits (83), Expect = 0.003
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 325 YVKNLDDSISDDKLKELFSE-FGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++ N+   +    LK+L  E  G +T  +++ D  G SRG   V F   E   KA+  +N
Sbjct: 3   FISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEVLN 62

Query: 384 GKMVVSKPLYV 394
             ++  +PL V
Sbjct: 63  KHVLNGRPLKV 73

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

>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 22/57 (38%), Positives = 29/57 (50%), Gaps = 4/57 (7%)

Query: 328 NLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNG 384
             DD I +D L+E  S+FG +   KV  D N    G  +V F T E A K +  +NG
Sbjct: 19  EWDDEIKEDVLEEC-SKFGPVEHIKV--DKNS-PEGVVYVKFKTVEAAQKCIQALNG 71

This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia 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. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 7/58 (12%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSK-----CFGFVNFDDPDDAA 273
           V V N+S   TE+ ++ +FG  G I    +    D  +      C  FV ++DP+D  
Sbjct: 2   VQVTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSKVC--FVKYEDPEDVG 57

This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable. . Length = 76

>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1)

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 15/64 (23%), Positives = 33/64 (51%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
           G  +++  +   + +D+L  LF   GT+   ++M   +G++RG  +  +S    AS A+ 
Sbjct: 1   GSEVFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIA 60

Query: 381 EMNG 384
            ++ 
Sbjct: 61  TLHN 64

This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast asparagine-rich protein (ARP) and similar proteins

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 14/82 (17%)

Query: 324 LYVKNLDDSISDDKLKELFSEFG----------TITSCKVMRDPNGISRGSGFVAFSTAE 373
           LY+ NL    +  +L+  F+++G          T      +   + IS   GF  F + E
Sbjct: 3   LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSIS---GFAVFQSHE 59

Query: 374 EASKALTEMNGKMVVSKPLYVA 395
           EA +AL  +NG+ +  + + V 
Sbjct: 60  EAMEALA-LNGRCLGERAIEVQ 80

This subfamily corresponds to the RRM of ARP, also termed NRP1, encoded by Saccharomyces cerevisiae YDL167C. Although its exact biological function remains unclear, ARP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), two Ran-binding protein zinc fingers (zf-RanBP), and an asparagine-rich region. It may possess RNA-binding and zinc ion binding activities. Additional research had indicated that ARP may function as a factor involved in the stress response. . Length = 88

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 2/50 (4%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEE 179
           +F+ NL   +D   L + F  +GN++  ++  +S G+   +GFV FD+ E
Sbjct: 6   LFVGNLPHDVDKSELKEFFQQYGNVVELRI--NSGGKLPNFGFVVFDDSE 53

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

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

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 22/72 (30%), Positives = 39/72 (54%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+++VG++   V+D  +  L  + G+V+S +  +D ST +   +G+  +     A RAL 
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 100 ELNFTPLNGKPI 111
            LN   L GK +
Sbjct: 61  LLNGLELGGKKL 72

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|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 1/85 (1%)

Query: 36  QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEAT 95
           Q  + +L++G+LD++V ++ L   F++ G +  V + R    + S  YG++ +     A 
Sbjct: 4   QRANRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTST-YGFLKFENLDMAH 62

Query: 96  RALDELNFTPLNGKPIRIMYSYRDP 120
           RA   ++   L   PI+I Y    P
Sbjct: 63  RAKLAMSGKVLRRNPIKIGYGKATP 87

This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. . Length = 87

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 35.9 bits (82), Expect = 0.004
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDK 187
           N+++  L  +     L + FS +G ++  KV T++    +R YGFV     E A   I+ 
Sbjct: 3   NLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINH 62

Query: 188 LNGMLLNDKQVFV 200
           L+   L+ + + V
Sbjct: 63  LHRTELHGRMISV 75

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|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 35.9 bits (82), Expect = 0.004
 Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           N++I+ L     ++ L      +G I+S K   D +  + +GYGFV FD+  +A+ A+  
Sbjct: 3   NLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 62

Query: 188 L 188
           L
Sbjct: 63  L 63

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

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 132 IKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGM 191
           +  L +    + L D     G++    V  D      G G V+F ++E  + A+ KL+G 
Sbjct: 5   VSGLPEGASWQDLKDFGRQAGDVTYADVDRDQ----EGEGVVEFTSQEDMERALRKLDGT 60

Query: 192 LLNDKQVFV 200
               ++V V
Sbjct: 61  EFRGRRVRV 69

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 5/74 (6%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L V +LD  ++D +L  LF+Q G+V  +R      +++ + +    Y+    A  ALD 
Sbjct: 3   TLLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEF----YDIRA-AEAALDA 57

Query: 101 LNFTPLNGKPIRIM 114
           LN  P  G  +++ 
Sbjct: 58  LNGRPFLGGRLKVK 71

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

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 8/65 (12%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKAL 379
           GL+LY    D       L+E+FS +G +    V+ D   G SRG  FV F   +++ +A+
Sbjct: 6   GLSLYTTERD-------LREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAM 58

Query: 380 TEMNG 384
              NG
Sbjct: 59  EHANG 63

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

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

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 5/61 (8%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           +Y   +   +++  +++ FS FG I   +V  D     +G  FV F++ E A+ A+  +N
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD-----KGYSFVRFNSHESAAHAIVSVN 57

Query: 384 G 384
           G
Sbjct: 58  G 58

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 35.6 bits (82), Expect = 0.004
 Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 2/69 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEAL 279
           V+V NL     E+ L ++FG+ G I    ++RD      K F +V F D ++A      L
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKD-ENAVEKALLL 60

Query: 280 NGKKFDDKE 288
           N KKF    
Sbjct: 61  NEKKFPPML 69

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 5/60 (8%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDKL 188
           +FI  L      + L + F  FG +  C V  D L + SRG+GFV F ++    + +DK+
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ----AGVDKV 58

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 4/64 (6%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F++N++ +++++ L   F  FG+I +   A     + RG+  V + +  +A+ A   L 
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIRTLYTAC----KHRGFIMVSYYDIRAARRAKRALQ 59

Query: 190 GMLL 193
           G  L
Sbjct: 60  GTEL 63

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

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

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 4/58 (6%)

Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           V NL  + + DDL +IFG +G I     +R+   K +   F+ F D   A  +++ALN
Sbjct: 6   VFNLDPSVSNDDLHQIFGAYGEIKE---IRETPNK-RHHKFIEFYDVRSAEAALKALN 59

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

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTA-VMRDADGKSKCFGFVNFDDPDDAARSVEA- 278
           ++V  LS  TTE+ +++ FG+FG I      M     K + F F+ FD  +   + +E  
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILETQ 61

Query: 279 ---LNGKKFDDK 287
              + GKK + K
Sbjct: 62  FHVIGGKKVEVK 73

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 35.6 bits (82), Expect = 0.004
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S  L V +L  S ++  L ++F +     S+R+ ++    R  GY +V + +A +A  AL
Sbjct: 1   SKVLVVNNLSYSASEDSLQEVFEK---ATSIRIPQN--NGRPKGYAFVEFESAEDAKEAL 55

Query: 99  DELNFTPLNGKPIRIMY 115
           +  N T + G+ IR+ +
Sbjct: 56  NSCNNTEIEGRSIRLEF 72

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

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

 Score = 35.6 bits (83), Expect = 0.004
 Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 5/68 (7%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V  L   T+  +L++ F  FG I         +     + ++ ++  + A  + EAL 
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRN-----YAYIEYESIEAAQAAKEALR 55

Query: 281 GKKFDDKE 288
           G       
Sbjct: 56  GFPLGGPG 63

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

 Score = 39.4 bits (92), Expect = 0.004
 Identities = 37/166 (22%), Positives = 64/166 (38%), Gaps = 16/166 (9%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           V+V+NL +   E DL +    FG ++   ++       K    V F+D + A      +N
Sbjct: 5   VHVRNLPQDVVEADLVEALIPFGPVSYVMML-----PGKRQALVEFEDEESAK---ACVN 56

Query: 281 GKKFDDKEWYVG--KAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
                    Y+    A   Y    E+K +   S  ++A   + L + V+N    I+ D L
Sbjct: 57  F--ATSVPIYIRGQPAFFNYSTSQEIK-RDGNSDFDSAGPNKVLRVIVENPMYPITLDVL 113

Query: 339 KELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNG 384
            ++F+ +G +         N        V F +   A  A   +NG
Sbjct: 114 YQIFNPYGKVLRIVTFTKNNVF---QALVEFESVNSAQHAKAALNG 156

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067). Length = 481

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKAL 379
           G  ++V  +   + +D+L  LF + G I   ++M DP +G +RG  F+ F   E A +A+
Sbjct: 1   GTEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV 60

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds 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. It 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, and 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; it binds RNA through its RRM domains. . Length = 79

>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 5/74 (6%)

Query: 324 LYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           L V NL+ + ++ D L  LF  +G +   K++ +     + +  +  +  ++A  ALT +
Sbjct: 2   LLVSNLNEEMVTPDALFTLFGVYGDVVRVKILFN----KKDTALIQMADPQQAQTALTHL 57

Query: 383 NGKMVVSKPLYVAL 396
           NG  +  K L V L
Sbjct: 58  NGIRLHGKKLRVTL 71

This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAAR 274
           TR   ++V  LS  T  +D+K+ F +FG +    +M D    + + FGFV F++ D   +
Sbjct: 1   TRTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEK 60

Query: 275 SVE 277
             E
Sbjct: 61  VCE 63

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 3/59 (5%)

Query: 330 DDSISDDKLKELFSEFGTITSCKVMRDPNGISRGS--GFVAFSTAEEASKALTEMNGKM 386
           D+ + D+ ++E   ++G + +  V    +  +  +   FV FS A+EA KA+  +NG+ 
Sbjct: 16  DEDLKDE-IEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRF 73

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

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

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSE-FGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           +++ N+   +    +K+L  E  G +T  ++ +D  G SRG G V F   E   KAL  M
Sbjct: 2   VFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEVM 61

Query: 383 NGKMVVSKPLYV 394
           N   +  +PL +
Sbjct: 62  NKYDLNGRPLNI 73

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	467
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	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
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	100.0
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.98
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.97
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.97
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.96
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.96
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.96
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.96
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.95
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.95
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.95
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.93
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.93
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.93
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.93
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.92
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.9
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.9
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.9
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.9
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.86
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.84
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.84
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.83
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.81
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.81
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.8
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.79
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.78
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.77
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.77
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.77
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.77
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.76
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.74
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.73
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.73
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.72
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.66
KOG0122	270	consensus Translation initiation factor 3, subunit	99.65
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.65
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.63
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.63
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.62
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.61
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.61
KOG0122	270	consensus Translation initiation factor 3, subunit	99.6
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.6
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.6
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.58
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.58
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.57
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.55
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.55
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.55
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.55
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.54
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.54
PLN03120	260	nucleic acid binding protein; Provisional	99.54
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.53
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.53
PLN03120	260	nucleic acid binding protein; Provisional	99.51
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.49
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.48
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.48
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.48
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.48
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.47
PLN03213	759	repressor of silencing 3; Provisional	99.47
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.46
smart00362	72	RRM_2 RNA recognition motif.	99.46
PLN03121	243	nucleic acid binding protein; Provisional	99.45
smart00362	72	RRM_2 RNA recognition motif.	99.44
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.44
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.43
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.43
PLN03121	243	nucleic acid binding protein; Provisional	99.42
PLN03213	759	repressor of silencing 3; Provisional	99.41
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.41
smart00360	71	RRM RNA recognition motif.	99.41
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.4
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.4
smart00360	71	RRM RNA recognition motif.	99.39
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.39
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.37
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.34
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.34
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.33
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.32
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.31
smart00361	70	RRM_1 RNA recognition motif.	99.31
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.3
smart00361	70	RRM_1 RNA recognition motif.	99.27
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.23
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.22
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.17
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.15
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.1
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.09
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.05
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.05
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.04
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.04
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.04
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.03
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.98
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.96
KOG0226	290	consensus RNA-binding proteins [General function p	98.94
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.89
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.88
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.86
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.84
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.81
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.78
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.78
KOG0226	290	consensus RNA-binding proteins [General function p	98.73
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.73
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.71
KOG4210	285	consensus Nuclear localization sequence binding pr	98.7
KOG0151	877	consensus Predicted splicing regulator, contains R	98.69
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.64
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.64
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.63
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.6
KOG4210	285	consensus Nuclear localization sequence binding pr	98.6
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.59
KOG0151	877	consensus Predicted splicing regulator, contains R	98.56
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.44
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.44
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.43
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.38
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.34
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.33
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.12
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.99
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.98
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.91
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.9
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.87
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.8
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.79
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.78
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.76
KOG3152	278	consensus TBP-binding protein, activator of basal	97.72
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.71
KOG2314	698	consensus Translation initiation factor 3, subunit	97.67
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.63
KOG3152	278	consensus TBP-binding protein, activator of basal	97.61
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.54
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.52
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.48
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.43
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.35
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.32
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.23
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.16
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.03
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.96
KOG2314	698	consensus Translation initiation factor 3, subunit	96.95
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.93
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.75
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.68
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.55
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.49
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.48
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.34
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.3
KOG2135	526	consensus Proteins containing the RNA recognition	96.18
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.86
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.85
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.78
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.75
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.49
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.06
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.02
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	94.88
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.77
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.68
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.67
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.62
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	94.56
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	94.55
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.35
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.13
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	93.7
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.68
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	93.62
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	93.56
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	93.54
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	93.37
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	93.3
KOG2135	526	consensus Proteins containing the RNA recognition	92.55
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	92.11
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	91.91
KOG2318	650	consensus Uncharacterized conserved protein [Funct	90.42
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	90.18
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	87.66
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	85.88
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	85.31
KOG2318	650	consensus Uncharacterized conserved protein [Funct	84.82

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

Probab=100.00  E-value=6.1e-66  Score=514.46  Aligned_cols=370  Identities=64%  Similarity=1.026  Sum_probs=335.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecccC
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRD  119 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~  119 (467)
                      .+|||+|||++++|++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++|++.+++..+.|+.|+|.|+...
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            37999999999999999999999999999999999999999999999999999999999999999999999999999888


Q ss_pred             cccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeE
Q 012257          120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVF  199 (467)
Q Consensus       120 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~  199 (467)
                      +..+....++|||+|||.++++++|+++|+.||.|.+|++..+.+|.++|||||+|.+.++|.+|++.++|..+.++.+.
T Consensus        81 ~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~  160 (562)
T TIGR01628        81 PSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVY  160 (562)
T ss_pred             ccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEE
Confidence            88777888899999999999999999999999999999999998899999999999999999999999999999999999


Q ss_pred             ecccccccccccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHh
Q 012257          200 VGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL  279 (467)
Q Consensus       200 v~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l  279 (467)
                      +.......... .......++|||+||+.++++++|+++|+.||.|.++.+..+.++.++|||||+|.+.++|.+|+..+
T Consensus       161 v~~~~~~~~~~-~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l  239 (562)
T TIGR01628       161 VGRFIKKHERE-AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEM  239 (562)
T ss_pred             Eeccccccccc-cccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHh
Confidence            97766554443 22344567899999999999999999999999999999999988999999999999999999999999


Q ss_pred             CCCccC----CceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEee
Q 012257          280 NGKKFD----DKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMR  355 (467)
Q Consensus       280 ~~~~~~----~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~  355 (467)
                      ++..+.    +..+.+.++..+..+......................+|||+||+..+++++|+++|++||.|++|+++.
T Consensus       240 ~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~  319 (562)
T TIGR01628       240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVML  319 (562)
T ss_pred             CCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEE
Confidence            999999    9999999998877765555444444333334455677899999999999999999999999999999999


Q ss_pred             CCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhhHHHHHHHHhh
Q 012257          356 DPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQ  410 (467)
Q Consensus       356 ~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~  410 (467)
                      +.+|.++|||||+|.+.++|.+|+..|||..++|++|.|.++..+..+....+.+
T Consensus       320 d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~~~~~~~~~  374 (562)
T TIGR01628       320 DEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQ  374 (562)
T ss_pred             CCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999887766554443

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

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

Probab=100.00  E-value=5.5e-51  Score=395.83  Aligned_cols=349  Identities=20%  Similarity=0.254  Sum_probs=279.2

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHh--CCcccCCceeeeee
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL--NFTPLNGKPIRIMY  115 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l--~~~~~~g~~~~v~~  115 (467)
                      +|++|||+|||++++|++|+++|+.||.|.+|.+++++      +||||+|.+.++|++|++.+  ++..+.|+.|+|.|
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k------~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGK------RQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCC------CEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            58999999999999999999999999999999998643      69999999999999999864  67889999999999


Q ss_pred             cccCccccc----------CCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHH
Q 012257          116 SYRDPTIRK----------SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI  185 (467)
Q Consensus       116 ~~~~~~~~~----------~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~  185 (467)
                      +........          ....+|+|.||+..+++++|+++|+.||.|.+|.+.++.   ..++|||+|.+.++|.+|+
T Consensus        75 s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~---~~~~afVef~~~~~A~~A~  151 (481)
T TIGR01649        75 STSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN---NVFQALVEFESVNSAQHAK  151 (481)
T ss_pred             cCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC---CceEEEEEECCHHHHHHHH
Confidence            864431111          122368999999999999999999999999999988753   2468999999999999999


Q ss_pred             HHhcCCccCCe--eeEecccccccc--------------------cc-----------cc--------------------
Q 012257          186 DKLNGMLLNDK--QVFVGPFLRKQE--------------------RE-----------ST--------------------  212 (467)
Q Consensus       186 ~~l~~~~~~g~--~~~v~~~~~~~~--------------------~~-----------~~--------------------  212 (467)
                      +.|||..+.+.  .|.+.++.....                    +.           ..                    
T Consensus       152 ~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  231 (481)
T TIGR01649       152 AALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGP  231 (481)
T ss_pred             HHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCC
Confidence            99999998653  555544321100                    00           00                    


Q ss_pred             --------------------------------------cccccccceeecCCCc-cCCHHHHHHhhcccCCeeEEEEEEC
Q 012257          213 --------------------------------------ADKTRFNNVYVKNLSE-TTTEDDLKKIFGEFGIITSTAVMRD  253 (467)
Q Consensus       213 --------------------------------------~~~~~~~~l~v~nlp~-~~~~~~l~~~f~~~g~v~~~~~~~~  253 (467)
                                                            .......+|+|+||+. .+++++|+++|+.||.|.+++++.+
T Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~  311 (481)
T TIGR01649       232 LAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN  311 (481)
T ss_pred             CCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC
Confidence                                                  0011345899999997 6999999999999999999999876


Q ss_pred             CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccchHHHHHh---h-h------hhhhhhhc---------
Q 012257          254 ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMEL---K-G------KFEQSLKE---------  314 (467)
Q Consensus       254 ~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~~---~-~------~~~~~~~~---------  314 (467)
                          .+|+|||+|.+.++|..|+..|++..+.|+.|.+.++..........   . .      ........         
T Consensus       312 ----~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~  387 (481)
T TIGR01649       312 ----KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANK  387 (481)
T ss_pred             ----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccc
Confidence                35899999999999999999999999999999998875532110000   0 0      00000000         


Q ss_pred             cccCCCCceEEEecCCCCCCHHHHHHhhccCCc--eeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccc-
Q 012257          315 TADKFEGLNLYVKNLDDSISDDKLKELFSEFGT--ITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP-  391 (467)
Q Consensus       315 ~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~--v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-  391 (467)
                      .....++.+|||+|||..+++++|+++|+.||.  |..+++....++ .+++|||+|.+.++|.+|+..|||+.|.++. 
T Consensus       388 ~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~-~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~  466 (481)
T TIGR01649       388 NNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNE-RSKMGLLEWESVEDAVEALIALNHHQLNEPNG  466 (481)
T ss_pred             cccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCCC-cceeEEEEcCCHHHHHHHHHHhcCCccCCCCC
Confidence            001245678999999999999999999999998  888988765544 5789999999999999999999999999885 


Q ss_pred             -----eEEehhhhh
Q 012257          392 -----LYVALAQRK  400 (467)
Q Consensus       392 -----l~v~~~~~~  400 (467)
                           |+|+|+++.
T Consensus       467 ~~~~~lkv~fs~~~  480 (481)
T TIGR01649       467 SAPYHLKVSFSTSR  480 (481)
T ss_pred             CccceEEEEeccCC
Confidence                 999999753

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=100.00  E-value=4.4e-50  Score=368.02  Aligned_cols=359  Identities=64%  Similarity=1.014  Sum_probs=329.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecccC
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRD  119 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~  119 (467)
                      ..|||+   ++++|..|+++|+.+|+|++|++++|. |  +.|||||.|.+++||.+|+.+++...+.|+.++|.|+..+
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            468999   899999999999999999999999998 6  9999999999999999999999999999999999999988


Q ss_pred             cccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeE
Q 012257          120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVF  199 (467)
Q Consensus       120 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~  199 (467)
                      ++.       |||.||+++++..+|.++|+.||.|++|++..+..| ++|| ||+|.+++.|.+|++.+||..+.++.+.
T Consensus        76 ~~~-------~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~  146 (369)
T KOG0123|consen   76 PSL-------VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIY  146 (369)
T ss_pred             Cce-------eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeE
Confidence            776       999999999999999999999999999999999888 8999 9999999999999999999999999999


Q ss_pred             eccccccccccccc--ccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHH
Q 012257          200 VGPFLRKQERESTA--DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE  277 (467)
Q Consensus       200 v~~~~~~~~~~~~~--~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~  277 (467)
                      +.....+.++....  .....+++++.+++.+.+++.|.++|..+|.|.++.++.+..+++++|+||.|.+.++|..|+.
T Consensus       147 vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~  226 (369)
T KOG0123|consen  147 VGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVE  226 (369)
T ss_pred             EeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHH
Confidence            98888776654333  3355678999999999999999999999999999999999988899999999999999999999


Q ss_pred             HhCCCccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC
Q 012257          278 ALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP  357 (467)
Q Consensus       278 ~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~  357 (467)
                      .+++..+.+..+.+..++.+.+.......................+|||.|++..++++.|++.|+.||+|.++++..+.
T Consensus       227 ~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~  306 (369)
T KOG0123|consen  227 TLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDE  306 (369)
T ss_pred             hccCCcCCccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccceeeEEEEecc
Confidence            99999999999999999998888777777666666666666778899999999999999999999999999999999999


Q ss_pred             CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhhHHHHHHHHhhccC
Q 012257          358 NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQ  413 (467)
Q Consensus       358 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~  413 (467)
                      .|.++||+||.|.+.++|.+|+..+||..+.++.|.|.++...+.+..+.+.+...
T Consensus       307 ~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~~r~~~~~~~~~~  362 (369)
T KOG0123|consen  307 NGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKEDRRARLQAVFGA  362 (369)
T ss_pred             CCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhccchhhhhhhcce
Confidence            99999999999999999999999999999999999999999766665555544443

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=1.3e-46  Score=355.67  Aligned_cols=338  Identities=25%  Similarity=0.414  Sum_probs=233.6

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      +.++|||+|||.+++|++|+++|+.||+|.+|+|++|+.+|+++|||||+|.+.++|++|++.|++..+.|+.|+|.++.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             cCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCccCC-
Q 012257          118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLND-  195 (467)
Q Consensus       118 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g-  195 (467)
                      ....  .....+|||+|||..+++++|+.+|+.||.|..+.+..+ .++.++|+|||+|.+.++|..|++.|+|..+.| 
T Consensus        82 ~~~~--~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~  159 (352)
T TIGR01661        82 PSSD--SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGC  159 (352)
T ss_pred             cccc--ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCC
Confidence            4432  234568999999999999999999999999999999887 577899999999999999999999999998877 


Q ss_pred             -eeeEecccccccccccccccccccce-----eecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCC-
Q 012257          196 -KQVFVGPFLRKQERESTADKTRFNNV-----YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDD-  268 (467)
Q Consensus       196 -~~~~v~~~~~~~~~~~~~~~~~~~~l-----~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~-  268 (467)
                       ..+.+.+...................     ....++..+..       ...+.+...            .  ..+.. 
T Consensus       160 ~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~------------~--~~~~~~  218 (352)
T TIGR01661       160 TEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTA-------AGIGPMHHA------------A--ARFRPS  218 (352)
T ss_pred             ceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccc-------cCCCCccCc------------c--cccccC
Confidence             45566554333211100000000000     00000000000       000000000            0  00000 


Q ss_pred             HHHHHHHH-HHhCCCccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCc
Q 012257          269 PDDAARSV-EALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGT  347 (467)
Q Consensus       269 ~~~a~~a~-~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~  347 (467)
                      ........ ..................... . . ..................+.+|||+|||+.+++++|+++|++||.
T Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~-~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~  295 (352)
T TIGR01661       219 AGDFTAVLAHQQQQHAVAQQHAAQRASPPA-T-D-GQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGA  295 (352)
T ss_pred             cchhhhhhhhhhhhcccccccccccCCCcc-c-c-ccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCC
Confidence            00000000 000000000000000000000 0 0 000000000001111234557999999999999999999999999


Q ss_pred             eeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhhH
Q 012257          348 ITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKE  401 (467)
Q Consensus       348 v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  401 (467)
                      |.+|+|+.+. +|.++|||||+|.+.++|.+|+..|||..|+|+.|+|+|+..+.
T Consensus       296 v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       296 VQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             eEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCC
Confidence            9999999998 89999999999999999999999999999999999999987653

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

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

Probab=100.00  E-value=2.8e-43  Score=310.31  Aligned_cols=286  Identities=26%  Similarity=0.378  Sum_probs=238.0

Q ss_pred             cChHHHHHHHHHhCCcccCCceeeeeecccC--------cccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEe
Q 012257           89 NAAHEATRALDELNFTPLNGKPIRIMYSYRD--------PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVA  160 (467)
Q Consensus        89 ~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~--------~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~  160 (467)
                      .+.++|.+||.+-.     |-.+.+.....+        +.......+.|||+.||.++.+++|..+|++.|.|.+++++
T Consensus        42 ~~~eaal~al~E~t-----gy~l~ve~gqrk~ggPpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLM  116 (506)
T KOG0117|consen   42 QSEEAALKALLERT-----GYTLVVENGQRKYGGPPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLM  116 (506)
T ss_pred             ccHHHHHHHHHHhc-----CceEEEeccccccCCCCCcccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEe
Confidence            34677788876532     334444332211        11122446789999999999999999999999999999999


Q ss_pred             eC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCcc-CCeeeEecccccccccccccccccccceeecCCCccCCHHHHHHh
Q 012257          161 TD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLL-NDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKI  238 (467)
Q Consensus       161 ~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~-~g~~~~v~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~  238 (467)
                      ++ .+|.++|||||.|.+.++|++|++.||+.+| .|+.|.|+.+..+            ++|||+|+|+..+.++|++.
T Consensus       117 mD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan------------~RLFiG~IPK~k~keeIlee  184 (506)
T KOG0117|consen  117 MDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVAN------------CRLFIGNIPKTKKKEEILEE  184 (506)
T ss_pred             ecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeec------------ceeEeccCCccccHHHHHHH
Confidence            99 8999999999999999999999999999987 5888888776665            77999999999999999999


Q ss_pred             hcccCC-eeEEEEEECC--CCCceeEEEEEeCCHHHHHHHHHHhCC--CccCCceEEEcccccchHHHHHhhhhhhhhhh
Q 012257          239 FGEFGI-ITSTAVMRDA--DGKSKCFGFVNFDDPDDAARSVEALNG--KKFDDKEWYVGKAQKKYEREMELKGKFEQSLK  313 (467)
Q Consensus       239 f~~~g~-v~~~~~~~~~--~~~~~g~afv~f~~~~~a~~a~~~l~~--~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  313 (467)
                      +++.+. |.++.+..+.  ..++||||||+|.++..|..|...|-.  ..+.|..+.|.|+.+..+.......       
T Consensus       185 ~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms-------  257 (506)
T KOG0117|consen  185 MKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMS-------  257 (506)
T ss_pred             HHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChhhhh-------
Confidence            999875 7777777764  467999999999999999999988755  4467899999999876554332111       


Q ss_pred             ccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceE
Q 012257          314 ETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY  393 (467)
Q Consensus       314 ~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  393 (467)
                            .-..|||+||+..+|++.|+++|++||.|++|+.++|       ||||+|.++++|.+|++.+||+.|+|..|.
T Consensus       258 ------~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~davkAm~~~ngkeldG~~iE  324 (506)
T KOG0117|consen  258 ------KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDAVKAMKETNGKELDGSPIE  324 (506)
T ss_pred             ------heeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHHHHHHHHhcCceecCceEE
Confidence                  2236999999999999999999999999999999988       999999999999999999999999999999


Q ss_pred             EehhhhhHHHHHHHHhhc
Q 012257          394 VALAQRKEERRARLQAQF  411 (467)
Q Consensus       394 v~~~~~~~~~~~~~~~~~  411 (467)
                      |.+|++..+++..+...+
T Consensus       325 vtLAKP~~k~k~~r~~~~  342 (506)
T KOG0117|consen  325 VTLAKPVDKKKKERKAMR  342 (506)
T ss_pred             EEecCChhhhccchhhhh
Confidence            999999888776654333

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

Probab=100.00  E-value=3.1e-42  Score=282.29  Aligned_cols=316  Identities=28%  Similarity=0.454  Sum_probs=236.7

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      .......+.|.|..||.+++++||+.+|...|+|+++++++|+.+|++.||+||.|.+++||++|+..|++..+..++|+
T Consensus        35 ~~t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIK  114 (360)
T KOG0145|consen   35 NDTDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIK  114 (360)
T ss_pred             CCcCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEE
Confidence            33445578899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCC
Q 012257          113 IMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGM  191 (467)
Q Consensus       113 v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~  191 (467)
                      |.++.+...  .-...+|||.+||+..|..||..+|+.||.|..-+|+.| .+|.++|.+||+|...++|++|++.|||.
T Consensus       115 VSyARPSs~--~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~  192 (360)
T KOG0145|consen  115 VSYARPSSD--SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQ  192 (360)
T ss_pred             EEeccCChh--hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCC
Confidence            988865433  334568999999999999999999999999988888888 78999999999999999999999999998


Q ss_pred             ccCCe--eeEecccccccccccccccccccceeecCCCccCCHHHHHHhhc----ccCCeeEEEEEECCCCCceeEEEEE
Q 012257          192 LLNDK--QVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG----EFGIITSTAVMRDADGKSKCFGFVN  265 (467)
Q Consensus       192 ~~~g~--~~~v~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~----~~g~v~~~~~~~~~~~~~~g~afv~  265 (467)
                      .-.|.  .|.|..+...                    ....+..-+..++.    .|+.-......+        +   .
T Consensus       193 ~P~g~tepItVKFannP--------------------sq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r--------~---r  241 (360)
T KOG0145|consen  193 KPSGCTEPITVKFANNP--------------------SQKTNQALLSQLYQSPARRYGGPMHHQAQR--------F---R  241 (360)
T ss_pred             CCCCCCCCeEEEecCCc--------------------ccccchhhhHHhhcCccccCCCcccchhhh--------h---c
Confidence            65553  3444332221                    11112222222321    111100000000        0   0


Q ss_pred             eCCHHHHHHHHHHhCCCccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccC
Q 012257          266 FDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEF  345 (467)
Q Consensus       266 f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~  345 (467)
                      +...-....++.......+++..-.+..                   .-......+++|||.||.++.+|.-|.++|.+|
T Consensus       242 ~~~~~~~~~~~~rfsP~~~d~m~~l~~~-------------------~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpF  302 (360)
T KOG0145|consen  242 LDNLLNPHAAQARFSPMTIDGMSGLAGV-------------------NLPGGPGGGWCIFVYNLSPDADESILWQLFGPF  302 (360)
T ss_pred             cccccchhhhhccCCCccccccceeeee-------------------ccCCCCCCeeEEEEEecCCCchHhHHHHHhCcc
Confidence            0000011111111111111111111000                   001122346799999999999999999999999


Q ss_pred             CceeEEEEeeCCC-CCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          346 GTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       346 G~v~~v~i~~~~~-~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      |.|..|++++|.+ .+.+||+||.+.+-++|.-||..|||..+++|.|.|+|...+
T Consensus       303 GAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  303 GAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             cceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            9999999999984 889999999999999999999999999999999999997654

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

Probab=100.00  E-value=4.3e-41  Score=322.31  Aligned_cols=296  Identities=21%  Similarity=0.329  Sum_probs=242.0

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccC-Cceeeeeec
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLN-GKPIRIMYS  116 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~-g~~~~v~~~  116 (467)
                      ..++|||+|||++++|++|+++|++||.|.+++|++| .+++++|||||+|.+.++|++|++.|++..+. |+.+.|.++
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            4699999999999999999999999999999999999 78999999999999999999999999998885 788877665


Q ss_pred             ccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCC-eEEEEEeeC--CCCCceeEEEEEeCCHHHHHHHHHHhcC--C
Q 012257          117 YRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN-ILSCKVATD--SLGQSRGYGFVQFDNEESAKSAIDKLNG--M  191 (467)
Q Consensus       117 ~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~-v~~~~~~~~--~~g~~~~~afV~f~~~~~A~~a~~~l~~--~  191 (467)
                      .        ..++|||+|||.++++++|.+.|+.++. +.++.+...  ..+++++||||+|.+.++|..|++.|+.  .
T Consensus       136 ~--------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki  207 (578)
T TIGR01648       136 V--------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRI  207 (578)
T ss_pred             c--------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccce
Confidence            3        3468999999999999999999999874 444444333  4467899999999999999999988864  3


Q ss_pred             ccCCeeeEecccccccccccccccccccceeecCCCccCCHHHHHHhhccc--CCeeEEEEEECCCCCceeEEEEEeCCH
Q 012257          192 LLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEF--GIITSTAVMRDADGKSKCFGFVNFDDP  269 (467)
Q Consensus       192 ~~~g~~~~v~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~--g~v~~~~~~~~~~~~~~g~afv~f~~~  269 (467)
                      .+.|+.|.|.++....... .......++|||+||+..+++++|+++|+.|  |.|+++.++       ++||||+|.+.
T Consensus       208 ~l~Gr~I~VdwA~p~~~~d-~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~-------rgfAFVeF~s~  279 (578)
T TIGR01648       208 QLWGHVIAVDWAEPEEEVD-EDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-------RDYAFVHFEDR  279 (578)
T ss_pred             EecCceEEEEeeccccccc-ccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee-------cCeEEEEeCCH
Confidence            5789999998876543322 1222345789999999999999999999999  999999876       45999999999


Q ss_pred             HHHHHHHHHhCCCccCCceEEEcccccchHHHHHhh----------hhhhhhhhccccCCCCceEEEecCCCCCCHHHHH
Q 012257          270 DDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELK----------GKFEQSLKETADKFEGLNLYVKNLDDSISDDKLK  339 (467)
Q Consensus       270 ~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~  339 (467)
                      ++|.+|+..+++..+.|+.|.+.|+...........          ...........-.+...+++++|+++..+++.+.
T Consensus       280 e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~~~~~~~~rg~gg~~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~~~~~~~  359 (578)
T TIGR01648       280 EDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAPSL  359 (578)
T ss_pred             HHHHHHHHHhCCCEECCEEEEEEEccCCCcccccccccccCCCcccccccccccCcccCccccccccccccccccccchh
Confidence            999999999999999999999999976543211000          0000111112234467789999999999999999


Q ss_pred             HhhccCCceeE
Q 012257          340 ELFSEFGTITS  350 (467)
Q Consensus       340 ~~F~~~G~v~~  350 (467)
                      ++|..+|.|..
T Consensus       360 ~~f~~~g~~~~  370 (578)
T TIGR01648       360 HFPRMPGPIRG  370 (578)
T ss_pred             hccccCccccC
Confidence            99999998753

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

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

Probab=100.00  E-value=3.7e-40  Score=315.91  Aligned_cols=281  Identities=24%  Similarity=0.337  Sum_probs=228.7

Q ss_pred             ChHHHHHHHHHhCCcccCCceeeeeecccCc---ccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCC
Q 012257           90 AAHEATRALDELNFTPLNGKPIRIMYSYRDP---TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ  166 (467)
Q Consensus        90 ~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~~---~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~  166 (467)
                      -.++|.+|+.++++..+........+..+.+   .......++|||+|||.++++++|+++|++||.|.+++++++.+|.
T Consensus        18 ~~~~a~~a~~~~~gy~~~~~~g~r~~g~Pp~~~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~   97 (578)
T TIGR01648        18 PDEAALKALLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQ   97 (578)
T ss_pred             ccHHHHHHHHHhhCccccccCCcccCCCCCCcccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCC
Confidence            3678899998888776655544444432221   1223345799999999999999999999999999999999998899


Q ss_pred             ceeEEEEEeCCHHHHHHHHHHhcCCccC-CeeeEecccccccccccccccccccceeecCCCccCCHHHHHHhhcccCC-
Q 012257          167 SRGYGFVQFDNEESAKSAIDKLNGMLLN-DKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGI-  244 (467)
Q Consensus       167 ~~~~afV~f~~~~~A~~a~~~l~~~~~~-g~~~~v~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~-  244 (467)
                      ++|||||+|.+.++|++|++.|++..+. ++.+.+..+.            ..++|||+|||.++++++|.+.|++++. 
T Consensus        98 sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~------------~~~rLFVgNLP~~~TeeeL~eeFskv~eg  165 (578)
T TIGR01648        98 NRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV------------DNCRLFVGGIPKNKKREEILEEFSKVTEG  165 (578)
T ss_pred             ccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc------------cCceeEeecCCcchhhHHHHHHhhcccCC
Confidence            9999999999999999999999998875 6666664432            2368999999999999999999999864 


Q ss_pred             eeEEEEEEC--CCCCceeEEEEEeCCHHHHHHHHHHhCC--CccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCC
Q 012257          245 ITSTAVMRD--ADGKSKCFGFVNFDDPDDAARSVEALNG--KKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFE  320 (467)
Q Consensus       245 v~~~~~~~~--~~~~~~g~afv~f~~~~~a~~a~~~l~~--~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  320 (467)
                      +.++.+...  ..++++|||||+|.+.++|..|+..++.  ..+.++.+.+.|+........             .....
T Consensus       166 vv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~-------------~~~~~  232 (578)
T TIGR01648       166 VVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDE-------------DVMAK  232 (578)
T ss_pred             ceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccccccc-------------ccccc
Confidence            444444333  3457899999999999999999988864  357899999999876432110             11123


Q ss_pred             CceEEEecCCCCCCHHHHHHhhccC--CceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEF--GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~--G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      .++|||+||+..+++++|+++|+.|  |.|++|+++++       ||||+|++.++|.+|++.|||..|+|+.|+|+|++
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~rg-------fAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Ak  305 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD-------YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAK  305 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeecC-------eEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            4589999999999999999999999  99999988754       99999999999999999999999999999999998


Q ss_pred             hhHH
Q 012257          399 RKEE  402 (467)
Q Consensus       399 ~~~~  402 (467)
                      +...
T Consensus       306 p~~~  309 (578)
T TIGR01648       306 PVDK  309 (578)
T ss_pred             CCCc
Confidence            7543

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.

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

Probab=100.00  E-value=6.5e-40  Score=327.43  Aligned_cols=258  Identities=41%  Similarity=0.652  Sum_probs=230.3

Q ss_pred             cEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEeccccccc
Q 012257          129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQ  207 (467)
Q Consensus       129 ~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~~  207 (467)
                      +|||+|||.++|+++|+++|+.||.|.+|++.++ .+++++|||||+|.+.++|.+|++.+++..+.|+.|++.++....
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            6999999999999999999999999999999998 568999999999999999999999999999999999998875432


Q ss_pred             ccccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCc
Q 012257          208 ERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDK  287 (467)
Q Consensus       208 ~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~  287 (467)
                      ..    ......+|||+||+.++++++|+++|+.||.|.++.+..+.+++++|||||+|.+.++|..|+..+++..+.++
T Consensus        82 ~~----~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~  157 (562)
T TIGR01628        82 SL----RRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDK  157 (562)
T ss_pred             cc----cccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCc
Confidence            22    22234679999999999999999999999999999999998899999999999999999999999999999999


Q ss_pred             eEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEE
Q 012257          288 EWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFV  367 (467)
Q Consensus       288 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV  367 (467)
                      .+.+........+.             .......++|||+||+..+++++|+++|+.||.|.++++..+.+|.++|||||
T Consensus       158 ~i~v~~~~~~~~~~-------------~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV  224 (562)
T TIGR01628       158 EVYVGRFIKKHERE-------------AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFV  224 (562)
T ss_pred             eEEEeccccccccc-------------cccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEE
Confidence            99987665443321             01122345799999999999999999999999999999999999999999999


Q ss_pred             EcCCHHHHHHHHHHhCCcEec----ccceEEehhhhhHHH
Q 012257          368 AFSTAEEASKALTEMNGKMVV----SKPLYVALAQRKEER  403 (467)
Q Consensus       368 ~f~~~~~A~~A~~~l~g~~~~----g~~l~v~~~~~~~~~  403 (467)
                      +|.+.++|.+|++.|||..+.    |+.|.|.+++.+.++
T Consensus       225 ~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er  264 (562)
T TIGR01628       225 NFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAER  264 (562)
T ss_pred             EECCHHHHHHHHHHhCCcEecccccceeeEeecccChhhh
Confidence            999999999999999999999    999999998766554

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

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

Probab=100.00  E-value=5.9e-40  Score=287.89  Aligned_cols=363  Identities=24%  Similarity=0.362  Sum_probs=240.1

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCc-ccCC--ceeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFT-PLNG--KPIRI  113 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~-~~~g--~~~~v  113 (467)
                      .+.-++||+-||...+|.||+++|++||.|.+|.|++|+.|+.++|||||.|.+.++|.+|+..|++. .+.|  .+|+|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            56789999999999999999999999999999999999999999999999999999999999999764 4555  56777


Q ss_pred             eecccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCc-
Q 012257          114 MYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGML-  192 (467)
Q Consensus       114 ~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~-  192 (467)
                      .++..... +-.+.++|||+-|++.++|.|++++|++||.|++|.|.++.++.++|||||.|.+.+.|..|++.|||.. 
T Consensus       112 k~Ad~E~e-r~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~t  190 (510)
T KOG0144|consen  112 KYADGERE-RIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQT  190 (510)
T ss_pred             cccchhhh-ccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhcccee
Confidence            77654322 2355789999999999999999999999999999999999999999999999999999999999999975 


Q ss_pred             cCCe--eeEeccccccccccccccc--c-----------cc------------------------cceeecCCCcc--CC
Q 012257          193 LNDK--QVFVGPFLRKQERESTADK--T-----------RF------------------------NNVYVKNLSET--TT  231 (467)
Q Consensus       193 ~~g~--~~~v~~~~~~~~~~~~~~~--~-----------~~------------------------~~l~v~nlp~~--~~  231 (467)
                      +.|.  .|.|.++..+.++......  .           .+                        +-.-+++++.-  ..
T Consensus       191 meGcs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~  270 (510)
T KOG0144|consen  191 MEGCSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLN  270 (510)
T ss_pred             eccCCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcc
Confidence            6664  5777776555444322110  0           00                        00111122211  11


Q ss_pred             HHHHHHh--hcccC-----CeeEEE--EEECCC---CC----ceeEEEEEe--CCHHHH--HHHHHHhCCCccC------
Q 012257          232 EDDLKKI--FGEFG-----IITSTA--VMRDAD---GK----SKCFGFVNF--DDPDDA--ARSVEALNGKKFD------  285 (467)
Q Consensus       232 ~~~l~~~--f~~~g-----~v~~~~--~~~~~~---~~----~~g~afv~f--~~~~~a--~~a~~~l~~~~~~------  285 (467)
                      ...+...  .....     ...+..  -.+..+   +.    ...+++-.-  .+....  .-++..+-+...+      
T Consensus       271 a~~~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~  350 (510)
T KOG0144|consen  271 ATQLQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGG  350 (510)
T ss_pred             hhHHHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccc
Confidence            1111110  00000     000000  000000   00    000000000  000000  0011111111000      


Q ss_pred             --CceEEEcc----------cccchHH-HHHhh-------------------------hhhhhhhhccccCCCCceEEEe
Q 012257          286 --DKEWYVGK----------AQKKYER-EMELK-------------------------GKFEQSLKETADKFEGLNLYVK  327 (467)
Q Consensus       286 --~~~l~~~~----------~~~~~~~-~~~~~-------------------------~~~~~~~~~~~~~~~~~~l~V~  327 (467)
                        +.......          ....... .....                         .............+.+..|||.
T Consensus       351 ~a~a~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiy  430 (510)
T KOG0144|consen  351 MAGAGTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIY  430 (510)
T ss_pred             cccccccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeee
Confidence              00000000          0000000 00000                         0000111123445677889999


Q ss_pred             cCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          328 NLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       328 nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      +||.+.-+.+|-..|..||.|.+.++..|+ ++.+++|+||.|++..+|.+||..|||..+++++|+|..++++
T Consensus       431 hlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~  504 (510)
T KOG0144|consen  431 HLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDR  504 (510)
T ss_pred             eCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeecc
Confidence            999999999999999999999999998887 8999999999999999999999999999999999999988765

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

Probab=100.00  E-value=2.7e-39  Score=285.13  Aligned_cols=249  Identities=27%  Similarity=0.456  Sum_probs=222.8

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc-CCceeeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL-NGKPIRIMY  115 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~-~g~~~~v~~  115 (467)
                      ...|.|||+.||.++.|+||.-+|++.|+|.+++++.|+.+|.++|||||+|.++++|++|++.||+..| .|+.|.|+.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            4579999999999999999999999999999999999999999999999999999999999999999887 789999987


Q ss_pred             cccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCC-eEEEEEeeC--CCCCceeEEEEEeCCHHHHHHHHHHhc-C-
Q 012257          116 SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN-ILSCKVATD--SLGQSRGYGFVQFDNEESAKSAIDKLN-G-  190 (467)
Q Consensus       116 ~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~-v~~~~~~~~--~~g~~~~~afV~f~~~~~A~~a~~~l~-~-  190 (467)
                      +..        .++|||+|||++.++++|.+.+++.++ |+.|.+..+  +..+++|||||+|.+...|.-|...|- + 
T Consensus       161 Sva--------n~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~  232 (506)
T KOG0117|consen  161 SVA--------NCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGK  232 (506)
T ss_pred             eee--------cceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCc
Confidence            754        378999999999999999999999984 667777766  456789999999999999999998774 3 


Q ss_pred             CccCCeeeEecccccccccccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHH
Q 012257          191 MLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPD  270 (467)
Q Consensus       191 ~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~  270 (467)
                      ..++|..+.|.|+-+..+.... .......|||+||+.++|+|.|..+|++||.|++++.+++       ||||.|.+.+
T Consensus       233 ~klwgn~~tVdWAep~~e~ded-~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~  304 (506)
T KOG0117|consen  233 IKLWGNAITVDWAEPEEEPDED-TMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAERE  304 (506)
T ss_pred             eeecCCcceeeccCcccCCChh-hhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchH
Confidence            3589999999998776555444 5556678999999999999999999999999999998765       9999999999


Q ss_pred             HHHHHHHHhCCCccCCceEEEcccccchHHH
Q 012257          271 DAARSVEALNGKKFDDKEWYVGKAQKKYERE  301 (467)
Q Consensus       271 ~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~  301 (467)
                      +|.+|++.+++..++|..|.+..+++.....
T Consensus       305 davkAm~~~ngkeldG~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  305 DAVKAMKETNGKELDGSPIEVTLAKPVDKKK  335 (506)
T ss_pred             HHHHHHHHhcCceecCceEEEEecCChhhhc
Confidence            9999999999999999999999998865543

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

Probab=100.00  E-value=1.1e-39  Score=269.26  Aligned_cols=235  Identities=24%  Similarity=0.447  Sum_probs=196.1

Q ss_pred             CCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEecccc
Q 012257          125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFL  204 (467)
Q Consensus       125 ~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~  204 (467)
                      +..++|||+||...+|++-|..+|+..|.|.+|+++.+                                  .+.+.+..
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            45679999999999999999999999999999998875                                  22333333


Q ss_pred             cccccccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCc
Q 012257          205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKK  283 (467)
Q Consensus       205 ~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~  283 (467)
                      .. ...+.......-.++|+.|...++.++|++.|.+||+|.+++++++ .+++++||+||.|...++|+.|+..|+|.+
T Consensus        50 ~p-~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqW  128 (321)
T KOG0148|consen   50 AP-GNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQW  128 (321)
T ss_pred             Cc-ccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCee
Confidence            32 1111222222456899999999999999999999999999999999 679999999999999999999999999999


Q ss_pred             cCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccc
Q 012257          284 FDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRG  363 (467)
Q Consensus       284 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g  363 (467)
                      ++++.++..|+.++...........+.  .-....++.++|||+|++..++|++|++.|++||.|.+||+.++     +|
T Consensus       129 lG~R~IRTNWATRKp~e~n~~~ltfde--V~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-----qG  201 (321)
T KOG0148|consen  129 LGRRTIRTNWATRKPSEMNGKPLTFDE--VYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-----QG  201 (321)
T ss_pred             eccceeeccccccCccccCCCCccHHH--HhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-----cc
Confidence            999999999999877322211111111  11234567889999999999999999999999999999999998     67


Q ss_pred             eEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhhH
Q 012257          364 SGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKE  401 (467)
Q Consensus       364 ~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  401 (467)
                      |+||.|++.|+|.+||..+||..++|..+++.|-+...
T Consensus       202 YaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~  239 (321)
T KOG0148|consen  202 YAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGD  239 (321)
T ss_pred             eEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCC
Confidence            99999999999999999999999999999999987544

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

Probab=100.00  E-value=7.7e-39  Score=288.74  Aligned_cols=343  Identities=26%  Similarity=0.410  Sum_probs=275.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecccC
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRD  119 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~  119 (467)
                      .||||++||+.++.++|.++|+..|+|..+.++.++.++.++||+||+|+=.||+++|++...+..|.|+.|+|..+...
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            89999999999999999999999999999999999999999999999999999999999999999999999999776432


Q ss_pred             cccc------------------------cCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEe
Q 012257          120 PTIR------------------------KSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQF  175 (467)
Q Consensus       120 ~~~~------------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f  175 (467)
                      ....                        .....+|.|+|||..+.+.+|..+|+.||.|.+|.|.+..+|.-.|||||+|
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            2111                        1114579999999999999999999999999999999888888889999999


Q ss_pred             CCHHHHHHHHHHhcCCccCCeeeEecccccccccccccc-----------------------------------------
Q 012257          176 DNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTAD-----------------------------------------  214 (467)
Q Consensus       176 ~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~~~~~~~~~-----------------------------------------  214 (467)
                      ....+|..|++.+|+..|.|+.|.|.|+..+........                                         
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            999999999999999999999999988876543332100                                         


Q ss_pred             -------------------------------------------cccccceeecCCCccCCHHHHHHhhcccCCeeEEEEE
Q 012257          215 -------------------------------------------KTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVM  251 (467)
Q Consensus       215 -------------------------------------------~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~  251 (467)
                                                                 .....++||.|||+++++++|.+.|++||.|..+.+.
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                                                       0000459999999999999999999999999999988


Q ss_pred             EC-CCCCceeEEEEEeCCHHHHHHHHHHhC-----C-CccCCceEEEcccccchHHHHHhhhh-----------------
Q 012257          252 RD-ADGKSKCFGFVNFDDPDDAARSVEALN-----G-KKFDDKEWYVGKAQKKYEREMELKGK-----------------  307 (467)
Q Consensus       252 ~~-~~~~~~g~afv~f~~~~~a~~a~~~l~-----~-~~~~~~~l~~~~~~~~~~~~~~~~~~-----------------  307 (467)
                      .+ .++.+.|.|||.|.+..+|..|+....     + ..++|+.|.+..+-.+..........                 
T Consensus       326 ~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~RkeA~dmeqkk~~Kk~~gkrNLyLa~EG  405 (678)
T KOG0127|consen  326 KDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRKEAADMEQKKKRKKPKGKRNLYLAREG  405 (678)
T ss_pred             eccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchHHHHHHHHHhhhhccCCccceeeeccC
Confidence            88 568999999999999999999998762     2 56889999998876543332210000                 


Q ss_pred             ----------------------hh----hhhhccccCCCCceEEEecCCCCCCHHHHHHhhcc----C-CceeE-EEEee
Q 012257          308 ----------------------FE----QSLKETADKFEGLNLYVKNLDDSISDDKLKELFSE----F-GTITS-CKVMR  355 (467)
Q Consensus       308 ----------------------~~----~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~----~-G~v~~-v~i~~  355 (467)
                                            ..    ....++.--...+.|.|.|||..+++..|..+...    | +.+.. ++.+.
T Consensus       406 ~I~~gt~aAeglS~~Dm~kRer~~~~k~k~lknpnlhlSrtRL~i~Nlpramn~KqL~~Ll~~Av~~~at~~kk~~R~~~  485 (678)
T KOG0127|consen  406 LIRDGTPAAEGLSATDMAKRERIAERKRKKLKNPNLHLSRTRLVIRNLPRAMNPKQLNRLLRDAVTGFATKVKKCIRQIK  485 (678)
T ss_pred             ccccCChhhcccchhhHHHHHHHHHHHHHhhcCCceeeehhhhhhhcCccccCHHHHHHHHHHHHhhhhhhcchhhhhhh
Confidence                                  00    00001111123446889999999999999988743    2 33322 44444


Q ss_pred             CC----CCCccceEEEEcCCHHHHHHHHHHh
Q 012257          356 DP----NGISRGSGFVAFSTAEEASKALTEM  382 (467)
Q Consensus       356 ~~----~~~~~g~afV~f~~~~~A~~A~~~l  382 (467)
                      ..    .+.+.||+|+.|..++.|.+|+..+
T Consensus       486 ~le~~~k~~s~g~aF~~f~EhEhalkalk~~  516 (678)
T KOG0127|consen  486 FLEEEKKNYSEGYAFVGFTEHEHALKALKVL  516 (678)
T ss_pred             hHHhhhhcccccccccCccHHHHHHHhhhcc
Confidence            32    4667899999999999999999865

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

Probab=100.00  E-value=4.5e-38  Score=301.68  Aligned_cols=170  Identities=22%  Similarity=0.487  Sum_probs=154.4

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ..++|||+|||++++|++|+++|+.||+|.+|++.+|+.+++++|||||+|.+.++|++|++.+|+..+.|+.|+|.+..
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            46899999999999999999999999999999999999999999999999999999999999999999999999998654


Q ss_pred             cCccc---------ccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHH
Q 012257          118 RDPTI---------RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK  187 (467)
Q Consensus       118 ~~~~~---------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~  187 (467)
                      ..+..         .....++|||+||+.++++++|+++|+.||.|.++++.++ .+|.++|||||+|.+.++|..|++.
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            32211         1123468999999999999999999999999999999998 5678999999999999999999999


Q ss_pred             hcCCccCCeeeEeccccccc
Q 012257          188 LNGMLLNDKQVFVGPFLRKQ  207 (467)
Q Consensus       188 l~~~~~~g~~~~v~~~~~~~  207 (467)
                      ||+..+.|+.|+|.++..+.
T Consensus       266 mNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       266 MNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             hCCCeeCCeEEEEEecCCCc
Confidence            99999999999998877543

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.

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

Probab=100.00  E-value=3.3e-37  Score=301.45  Aligned_cols=342  Identities=22%  Similarity=0.307  Sum_probs=230.1

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ..++.++|||+|||.++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|.+|+. |++..+.|+.|.|.
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~  163 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQ  163 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEe
Confidence            45568899999999999999999999999999999999999999999999999999999999997 89999999999998


Q ss_pred             ecccCccc----------ccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHH
Q 012257          115 YSYRDPTI----------RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKS  183 (467)
Q Consensus       115 ~~~~~~~~----------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~  183 (467)
                      ++......          ......+|||+|||..+++++|+++|+.||.|..|.+..+ .+|.++|||||+|.+.++|..
T Consensus       164 ~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~  243 (457)
T TIGR01622       164 SSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKE  243 (457)
T ss_pred             ecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHH
Confidence            75432111          0112478999999999999999999999999999999988 567899999999999999999


Q ss_pred             HHHHhcCCccCCeeeEecccccccccccccccc-cccce-eecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeE
Q 012257          184 AIDKLNGMLLNDKQVFVGPFLRKQERESTADKT-RFNNV-YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCF  261 (467)
Q Consensus       184 a~~~l~~~~~~g~~~~v~~~~~~~~~~~~~~~~-~~~~l-~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~  261 (467)
                      |++.|+|..+.|+.|.|.++............. ..... ..+..........+...+...+..-...+ .         
T Consensus       244 A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~---------  313 (457)
T TIGR01622       244 ALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLI-P---------  313 (457)
T ss_pred             HHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccC-C---------
Confidence            999999999999999998865322211110000 00000 00000001112222222221111000000 0         


Q ss_pred             EEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCC-------
Q 012257          262 GFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSIS-------  334 (467)
Q Consensus       262 afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~-------  334 (467)
                            ........+..+.................     .....................+|+|.||....+       
T Consensus       314 ------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~  382 (457)
T TIGR01622       314 ------GTGSKIALMQKLQRDGIIDPNIPSRYATG-----ALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFD  382 (457)
T ss_pred             ------Cccchhhhhcccccccccccccccccccc-----ccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHH
Confidence                  00000000000000000000000000000     000000000000001224567899999954433       


Q ss_pred             ---HHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhhH
Q 012257          335 ---DDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKE  401 (467)
Q Consensus       335 ---~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  401 (467)
                         .++|++.|++||.|++|.+...   ...|++||+|.+.++|.+|++.|||+.|+|+.|.+.|.....
T Consensus       383 ~~~~~dv~~e~~k~G~v~~v~v~~~---~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~~  449 (457)
T TIGR01622       383 NEILDDVKEECSKYGGVVHIYVDTK---NSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDV  449 (457)
T ss_pred             HHHHHHHHHHHHhcCCeeEEEEeCC---CCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHHH
Confidence               3689999999999999998743   346899999999999999999999999999999999987654

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.

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

Probab=100.00  E-value=3.2e-36  Score=292.64  Aligned_cols=262  Identities=21%  Similarity=0.318  Sum_probs=209.0

Q ss_pred             CccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHh--cCCccCCeeeEecccc
Q 012257          127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL--NGMLLNDKQVFVGPFL  204 (467)
Q Consensus       127 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l--~~~~~~g~~~~v~~~~  204 (467)
                      ++.|||+|||.++++++|+++|+.||.|.+|.+++     ++++|||+|.+.++|..|++.+  ++..+.|+.|.+.++.
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            45799999999999999999999999999999886     4689999999999999999875  6788999999998876


Q ss_pred             cccccccc------cccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHH
Q 012257          205 RKQEREST------ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA  278 (467)
Q Consensus       205 ~~~~~~~~------~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~  278 (467)
                      ........      .......+|+|.||+..+++++|+++|+.||.|.++.+.++.   .+++|||+|.+.++|.+|+..
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~---~~~~afVef~~~~~A~~A~~~  153 (481)
T TIGR01649        77 SQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN---NVFQALVEFESVNSAQHAKAA  153 (481)
T ss_pred             CcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC---CceEEEEEECCHHHHHHHHHH
Confidence            54322211      112233478999999999999999999999999999987753   246899999999999999999


Q ss_pred             hCCCccCC--ceEEEcccccchH-------H-------------HHHhh----hhhhh----------------------
Q 012257          279 LNGKKFDD--KEWYVGKAQKKYE-------R-------------EMELK----GKFEQ----------------------  310 (467)
Q Consensus       279 l~~~~~~~--~~l~~~~~~~~~~-------~-------------~~~~~----~~~~~----------------------  310 (467)
                      |||..+.+  ..+.+.|++....       +             .....    .....                      
T Consensus       154 Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  233 (481)
T TIGR01649       154 LNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLA  233 (481)
T ss_pred             hcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCC
Confidence            99999965  3677766653110       0             00000    00000                      


Q ss_pred             ---------------hh--------h--------ccccCCCCceEEEecCCC-CCCHHHHHHhhccCCceeEEEEeeCCC
Q 012257          311 ---------------SL--------K--------ETADKFEGLNLYVKNLDD-SISDDKLKELFSEFGTITSCKVMRDPN  358 (467)
Q Consensus       311 ---------------~~--------~--------~~~~~~~~~~l~V~nlp~-~~~~~~l~~~F~~~G~v~~v~i~~~~~  358 (467)
                                     ..        .        .......+++|||+||+. .+++++|+++|+.||.|.+|+++++  
T Consensus       234 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~--  311 (481)
T TIGR01649       234 PLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN--  311 (481)
T ss_pred             cccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC--
Confidence                           00        0        000123567999999997 6999999999999999999999987  


Q ss_pred             CCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          359 GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       359 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                        .+|+|||+|.+.++|.+|+..|||..|.|+.|+|++++..
T Consensus       312 --~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       312 --KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             --CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence              3579999999999999999999999999999999998654

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).

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

Probab=100.00  E-value=1.7e-34  Score=286.47  Aligned_cols=258  Identities=21%  Similarity=0.341  Sum_probs=207.9

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcC------------CCeEEEEEEecCCCCccccEEEEEecChHHHHHHHH
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQM------------GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD   99 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~------------G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~   99 (467)
                      .+...+..++|||+|||+++++++|+++|+.+            +.|.++.+.+      .+|||||+|.+.++|.+||+
T Consensus       168 ~~~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~------~kg~afVeF~~~e~A~~Al~  241 (509)
T TIGR01642       168 QQQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINK------EKNFAFLEFRTVEEATFAMA  241 (509)
T ss_pred             CccCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECC------CCCEEEEEeCCHHHHhhhhc
Confidence            44567778999999999999999999999975            3455555543      45799999999999999995


Q ss_pred             HhCCcccCCceeeeeecccCc---------------------------ccccCCCccEEEcCCCCcCCHHHHHHHHhhcC
Q 012257          100 ELNFTPLNGKPIRIMYSYRDP---------------------------TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFG  152 (467)
Q Consensus       100 ~l~~~~~~g~~~~v~~~~~~~---------------------------~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g  152 (467)
                       |++..|.|+.|+|.......                           .......++|||+|||..+++++|+++|+.||
T Consensus       242 -l~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G  320 (509)
T TIGR01642       242 -LDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFG  320 (509)
T ss_pred             -CCCeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC
Confidence             99999999999996532211                           00112346899999999999999999999999


Q ss_pred             CeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEecccccccccccc-------------------
Q 012257          153 NILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST-------------------  212 (467)
Q Consensus       153 ~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~~~~~~~-------------------  212 (467)
                      .|..+.++.+ .+|.++|||||+|.+.++|..|++.|+|..+.|+.|.|.++.........                   
T Consensus       321 ~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~  400 (509)
T TIGR01642       321 DLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQS  400 (509)
T ss_pred             CeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhh
Confidence            9999999988 68999999999999999999999999999999999998765432111000                   


Q ss_pred             ---cccccccceeecCCCccC----------CHHHHHHhhcccCCeeEEEEEECC----CCCceeEEEEEeCCHHHHHHH
Q 012257          213 ---ADKTRFNNVYVKNLSETT----------TEDDLKKIFGEFGIITSTAVMRDA----DGKSKCFGFVNFDDPDDAARS  275 (467)
Q Consensus       213 ---~~~~~~~~l~v~nlp~~~----------~~~~l~~~f~~~g~v~~~~~~~~~----~~~~~g~afv~f~~~~~a~~a  275 (467)
                         ........|++.|+....          ..++|+++|++||.|..+.+....    .+...|++||+|.+.++|..|
T Consensus       401 ~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A  480 (509)
T TIGR01642       401 ILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKA  480 (509)
T ss_pred             hccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHH
Confidence               001234567888885321          236799999999999999998652    234578999999999999999


Q ss_pred             HHHhCCCccCCceEEEccccc
Q 012257          276 VEALNGKKFDDKEWYVGKAQK  296 (467)
Q Consensus       276 ~~~l~~~~~~~~~l~~~~~~~  296 (467)
                      +..|+|..|+|+.+.+.+...
T Consensus       481 ~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       481 MEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             HHHcCCCEECCeEEEEEEeCH
Confidence            999999999999999988654

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

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

Probab=100.00  E-value=1.8e-34  Score=260.66  Aligned_cols=277  Identities=29%  Similarity=0.454  Sum_probs=228.3

Q ss_pred             ccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEecccccc
Q 012257          128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRK  206 (467)
Q Consensus       128 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~  206 (467)
                      .+|||++||+.++.++|.++|+.+|+|..+.++.+ ..+.++||+||.|.-.+++++|++..++..+.|+.+.+..+...
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            68999999999999999999999999999999988 66789999999999999999999999999999999999776544


Q ss_pred             cccccccc--------------------cccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEe
Q 012257          207 QERESTAD--------------------KTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNF  266 (467)
Q Consensus       207 ~~~~~~~~--------------------~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f  266 (467)
                      ........                    ......|+|.|||+.+..++|..+|+.||.|..+.|.+..+++..|||||+|
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            33321100                    1113579999999999999999999999999999999888888889999999


Q ss_pred             CCHHHHHHHHHHhCCCccCCceEEEcccccchHHHH----------------Hh--------------------------
Q 012257          267 DDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREM----------------EL--------------------------  304 (467)
Q Consensus       267 ~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~----------------~~--------------------------  304 (467)
                      ....+|..|+..+|+..++|+++-+.|+-.+..-..                +.                          
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            999999999999999999999999999854321100                00                          


Q ss_pred             hhhhh---------hh--hhc-------------------cccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEe
Q 012257          305 KGKFE---------QS--LKE-------------------TADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVM  354 (467)
Q Consensus       305 ~~~~~---------~~--~~~-------------------~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~  354 (467)
                      ....+         ..  ...                   ......+.+|||+|||+++++++|.+.|++||.|.++.++
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            00000         00  000                   0011124689999999999999999999999999999999


Q ss_pred             eCC-CCCccceEEEEcCCHHHHHHHHHHh-----CC-cEecccceEEehhhhhHHHH
Q 012257          355 RDP-NGISRGSGFVAFSTAEEASKALTEM-----NG-KMVVSKPLYVALAQRKEERR  404 (467)
Q Consensus       355 ~~~-~~~~~g~afV~f~~~~~A~~A~~~l-----~g-~~~~g~~l~v~~~~~~~~~~  404 (467)
                      .++ ++.++|.|||.|.+..+|.+||+..     .| ..+.|+.|.|..+-++....
T Consensus       326 ~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~RkeA~  382 (678)
T KOG0127|consen  326 KDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRKEAA  382 (678)
T ss_pred             eccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchHHHH
Confidence            988 8999999999999999999999976     34 67789999999987766544

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

Probab=100.00  E-value=2.4e-34  Score=237.63  Aligned_cols=222  Identities=29%  Similarity=0.508  Sum_probs=194.1

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      +.+.|+|||+||..+++|+-|..+|+..|.|+..+|+.|                                   .++|.|
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~-----------------------------------e~~v~w   47 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD-----------------------------------ELKVNW   47 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceeehh-----------------------------------hhcccc
Confidence            456899999999999999999999999999999888765                                   344444


Q ss_pred             cccCccccc---CCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCC
Q 012257          116 SYRDPTIRK---SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGM  191 (467)
Q Consensus       116 ~~~~~~~~~---~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~  191 (467)
                      +.......+   .....+||+.|...++.++|++.|..||+|.++++++| .+++++||+||.|-+.++|++||..|+|.
T Consensus        48 a~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGq  127 (321)
T KOG0148|consen   48 ATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQ  127 (321)
T ss_pred             ccCcccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCe
Confidence            433211111   11446999999999999999999999999999999999 89999999999999999999999999999


Q ss_pred             ccCCeeeEeccccccccccccc----------ccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeE
Q 012257          192 LLNDKQVFVGPFLRKQERESTA----------DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCF  261 (467)
Q Consensus       192 ~~~g~~~~v~~~~~~~~~~~~~----------~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~  261 (467)
                      -|.+|.|+..|+.++.......          .....+++|++|++.-+++++|++.|+.||.|.+|++.++     +||
T Consensus       128 WlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-----qGY  202 (321)
T KOG0148|consen  128 WLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-----QGY  202 (321)
T ss_pred             eeccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-----cce
Confidence            9999999999998887443222          2445678999999999999999999999999999999987     789


Q ss_pred             EEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccc
Q 012257          262 GFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKK  297 (467)
Q Consensus       262 afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~  297 (467)
                      +||.|++.+.|..|+-.+|+..+.|..+++.|.+..
T Consensus       203 aFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~  238 (321)
T KOG0148|consen  203 AFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEG  238 (321)
T ss_pred             EEEEecchhhHHHHHHHhcCceeCceEEEEeccccC
Confidence            999999999999999999999999999999999763

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

Probab=100.00  E-value=7.7e-34  Score=281.74  Aligned_cols=271  Identities=20%  Similarity=0.313  Sum_probs=208.7

Q ss_pred             CCCccEEEcCCCCcCCHHHHHHHHhhc------------CCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCc
Q 012257          125 SGAGNIFIKNLDKSIDNKALHDTFSTF------------GNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGML  192 (467)
Q Consensus       125 ~~~~~l~v~nlp~~~t~~~l~~~f~~~------------g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~  192 (467)
                      ...++|||+|||..+++++|+++|..+            +.|..+.+.     ..++||||+|.+.++|..|++ |+|..
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~-----~~kg~afVeF~~~e~A~~Al~-l~g~~  246 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN-----KEKNFAFLEFRTVEEATFAMA-LDSII  246 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEEC-----CCCCEEEEEeCCHHHHhhhhc-CCCeE
Confidence            346789999999999999999999975            234444332     367999999999999999995 99999


Q ss_pred             cCCeeeEecccccccccc-----------------------cccccccccceeecCCCccCCHHHHHHhhcccCCeeEEE
Q 012257          193 LNDKQVFVGPFLRKQERE-----------------------STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTA  249 (467)
Q Consensus       193 ~~g~~~~v~~~~~~~~~~-----------------------~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~  249 (467)
                      +.|+.|.+..........                       ........++|||+|||..+++++|.++|+.||.|..+.
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            999999986432211000                       000122346899999999999999999999999999999


Q ss_pred             EEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccchHHHHHhhhh-------hhhhh---hccccC
Q 012257          250 VMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGK-------FEQSL---KETADK  318 (467)
Q Consensus       250 ~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~-------~~~~~---~~~~~~  318 (467)
                      ++.+ .+|.++|||||+|.+.++|..|+..|+|..+.|+.|.+.++.............       .....   ......
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            9887 568899999999999999999999999999999999998875432110000000       00000   001123


Q ss_pred             CCCceEEEecCCCC--C--------CHHHHHHhhccCCceeEEEEeeCC----CCCccceEEEEcCCHHHHHHHHHHhCC
Q 012257          319 FEGLNLYVKNLDDS--I--------SDDKLKELFSEFGTITSCKVMRDP----NGISRGSGFVAFSTAEEASKALTEMNG  384 (467)
Q Consensus       319 ~~~~~l~V~nlp~~--~--------~~~~l~~~F~~~G~v~~v~i~~~~----~~~~~g~afV~f~~~~~A~~A~~~l~g  384 (467)
                      .++.+|+|.|+...  +        ..++|+++|++||.|++|+|+++.    .+.+.|+|||+|.+.++|.+|+..|||
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            35678999999632  1        136899999999999999998763    345679999999999999999999999


Q ss_pred             cEecccceEEehhhhhH
Q 012257          385 KMVVSKPLYVALAQRKE  401 (467)
Q Consensus       385 ~~~~g~~l~v~~~~~~~  401 (467)
                      ..|+|+.|.|.|.....
T Consensus       487 r~~~gr~v~~~~~~~~~  503 (509)
T TIGR01642       487 RKFNDRVVVAAFYGEDC  503 (509)
T ss_pred             CEECCeEEEEEEeCHHH
Confidence            99999999999987543

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

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

Probab=100.00  E-value=1.6e-34  Score=269.69  Aligned_cols=328  Identities=25%  Similarity=0.399  Sum_probs=264.2

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ++.+|||+|||+.++|+|++.+|                       |||.|...+.|.+|-..+++..+.|+.++|....
T Consensus       226 etgrlf~RNLpyt~~eed~~~lf-----------------------a~v~~~~~~~avka~~~~D~k~fqgrmlhvlp~~  282 (725)
T KOG0110|consen  226 ETGRLFVRNLPYTSTEEDLLKLF-----------------------AFVTFMFPEHAVKAYSELDGKVFQGRMLHVLPSK  282 (725)
T ss_pred             hhhhhhhccCCccccHHHHHHhh-----------------------HHHhhhhhHHHHhhhhhccccccccceeeecCcc
Confidence            57889999999999999999999                       7999999999999999999999999999875543


Q ss_pred             cCccc---------------------------------------------------------------------------
Q 012257          118 RDPTI---------------------------------------------------------------------------  122 (467)
Q Consensus       118 ~~~~~---------------------------------------------------------------------------  122 (467)
                      ...+.                                                                           
T Consensus       283 ~k~~~~~~~~~~~~~~k~~ke~~rk~~~~~~~~wn~l~~~~~ava~~~a~k~~v~k~~i~d~~~~gsavr~al~etr~~~  362 (725)
T KOG0110|consen  283 EKSTAKEDASELGSDYKKEKELKRKAASASFHSWNTLFMGANAVAGILAQKLGVEKSRILDGSLSGSAVRLALGETRVVQ  362 (725)
T ss_pred             hhhhhhhhHhhcCCcHHHHHHhccccchhcceecccccccccHHHHHHHHHhCCeeeeeechhhcchHHHHHHHHhhhch
Confidence            21100                                                                           


Q ss_pred             ------------------ccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHH
Q 012257          123 ------------------RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA  184 (467)
Q Consensus       123 ------------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a  184 (467)
                                        .......++++|||..+..++|...|..||.|..+.+.  +   ..-.|+|+|.++.+|..|
T Consensus       363 e~~~~~ee~gV~l~~F~~~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp--~---~G~~aiv~fl~p~eAr~A  437 (725)
T KOG0110|consen  363 EVRRFFEENGVKLDAFSQAERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP--P---GGTGAIVEFLNPLEARKA  437 (725)
T ss_pred             hhhhhHHhhCcccccchhhhhhcceeeeccCccccccHHHHHHhhcccccceeecC--c---ccceeeeeecCccchHHH
Confidence                              00011358999999999999999999999999988544  2   223589999999999999


Q ss_pred             HHHhcCCccCCeeeEecccccccccc------------cc--------------------------------cccccccc
Q 012257          185 IDKLNGMLLNDKQVFVGPFLRKQERE------------ST--------------------------------ADKTRFNN  220 (467)
Q Consensus       185 ~~~l~~~~~~g~~~~v~~~~~~~~~~------------~~--------------------------------~~~~~~~~  220 (467)
                      +..|....+....+.+.++....-..            ..                                ......+.
T Consensus       438 frklaysr~k~~plyle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~  517 (725)
T KOG0110|consen  438 FRKLAYSRFKSAPLYLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETK  517 (725)
T ss_pred             HHHhchhhhccCccccccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchh
Confidence            99998887777776665443221110            00                                00011133


Q ss_pred             eeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCC----ceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccccc
Q 012257          221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK----SKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQK  296 (467)
Q Consensus       221 l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~----~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~  296 (467)
                      ||+.|+....+.+++...|...|.|.++.|...++..    +.|||||+|.+.++|..|+..|+|..++|+.+.+.++..
T Consensus       518 lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~  597 (725)
T KOG0110|consen  518 LFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISEN  597 (725)
T ss_pred             hhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccC
Confidence            9999999999999999999999999999998876553    569999999999999999999999999999999998872


Q ss_pred             chHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHH
Q 012257          297 KYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEA  375 (467)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A  375 (467)
                      .......         ........+..|.|.|||+..+-.+++++|..||.|.+|+|+... .+.++|||||+|-+..+|
T Consensus       598 k~~~~~g---------K~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea  668 (725)
T KOG0110|consen  598 KPASTVG---------KKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREA  668 (725)
T ss_pred             ccccccc---------cccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHH
Confidence            2111111         111122236689999999999999999999999999999999883 556799999999999999


Q ss_pred             HHHHHHhCCcEecccceEEehhhhhHH
Q 012257          376 SKALTEMNGKMVVSKPLYVALAQRKEE  402 (467)
Q Consensus       376 ~~A~~~l~g~~~~g~~l~v~~~~~~~~  402 (467)
                      .+|+.+|.+..+.||+|.++|++....
T Consensus       669 ~nA~~al~STHlyGRrLVLEwA~~d~~  695 (725)
T KOG0110|consen  669 KNAFDALGSTHLYGRRLVLEWAKSDNT  695 (725)
T ss_pred             HHHHHhhcccceechhhheehhccchH
Confidence            999999999999999999999985543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=7.5e-32  Score=246.83  Aligned_cols=170  Identities=27%  Similarity=0.503  Sum_probs=153.1

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ......++|||+|||++++|++|+++|+.||+|++|+|++|+.+++++|||||+|.+.++|++|++.|++..+.++.|+|
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            34446799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCc
Q 012257          114 MYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGML  192 (467)
Q Consensus       114 ~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~  192 (467)
                      .++....  .....++|||+|||..+++++|+++|++||.|..++++.+ .++.++++|||+|.+.++|++|++.|++..
T Consensus       182 ~~a~p~~--~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~  259 (346)
T TIGR01659       182 SYARPGG--ESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVI  259 (346)
T ss_pred             ecccccc--cccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCc
Confidence            9876432  2234568999999999999999999999999999999988 689999999999999999999999999998


Q ss_pred             cCC--eeeEeccccc
Q 012257          193 LND--KQVFVGPFLR  205 (467)
Q Consensus       193 ~~g--~~~~v~~~~~  205 (467)
                      +.+  +.|.|.++..
T Consensus       260 ~~g~~~~l~V~~a~~  274 (346)
T TIGR01659       260 PEGGSQPLTVRLAEE  274 (346)
T ss_pred             cCCCceeEEEEECCc
Confidence            876  5677765543

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).

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

Probab=99.98  E-value=1.3e-30  Score=239.72  Aligned_cols=249  Identities=40%  Similarity=0.636  Sum_probs=225.4

Q ss_pred             cEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEecccccccc
Q 012257          129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQE  208 (467)
Q Consensus       129 ~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~~~  208 (467)
                      .|+|+   +++|+..|.++|+.+|+|+++++.++. + +-|||||.|.++++|.+|++.+|...+.|+.+++.|+.....
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~   77 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDPS   77 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCCc
Confidence            57888   899999999999999999999999998 6 999999999999999999999999999999999998866644


Q ss_pred             cccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCce
Q 012257          209 RESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKE  288 (467)
Q Consensus       209 ~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~  288 (467)
                      .           ++|.||++.++..+|.+.|+.||.|.++++..+.+| ++|| ||+|++.+.|.+|+..+||..+.++.
T Consensus        78 ~-----------~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kk  144 (369)
T KOG0123|consen   78 L-----------VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKK  144 (369)
T ss_pred             e-----------eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCe
Confidence            3           999999999999999999999999999999999888 7899 99999999999999999999999999


Q ss_pred             EEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEE
Q 012257          289 WYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVA  368 (467)
Q Consensus       289 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~  368 (467)
                      +.+.....+.++...... ..         ..-..++|.+++.+.+++.|.++|+.||.|.++.++.+..|.+++|+||.
T Consensus       145 i~vg~~~~~~er~~~~~~-~~---------~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~  214 (369)
T KOG0123|consen  145 IYVGLFERKEEREAPLGE-YK---------KRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVN  214 (369)
T ss_pred             eEEeeccchhhhcccccc-hh---------hhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCcccee
Confidence            999888876665433322 11         12236999999999999999999999999999999999999999999999


Q ss_pred             cCCHHHHHHHHHHhCCcEecccceEEehhhhhHHHHH
Q 012257          369 FSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRA  405 (467)
Q Consensus       369 f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~~  405 (467)
                      |.+.++|..|+..|++..+.++.+.|.-+..+.++..
T Consensus       215 f~~~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~  251 (369)
T KOG0123|consen  215 FENPEDAKKAVETLNGKIFGDKELYVGRAQKKSEREA  251 (369)
T ss_pred             ecChhHHHHHHHhccCCcCCccceeecccccchhhHH
Confidence            9999999999999999999999999998877554443

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.97  E-value=2.7e-30  Score=236.55  Aligned_cols=170  Identities=33%  Similarity=0.558  Sum_probs=152.5

Q ss_pred             cccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcc
Q 012257          215 KTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGK  293 (467)
Q Consensus       215 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~  293 (467)
                      ....++|||++||.++++++|+++|+.||.|.++.++.+ .+++++|||||+|.+.++|..|+..|++..+.++.+.+.+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            345578999999999999999999999999999999988 5788999999999999999999999999999999999988


Q ss_pred             cccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCH
Q 012257          294 AQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTA  372 (467)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~  372 (467)
                      +.....                  .....+|||+|||..+++++|+++|++||.|++++|+++. +++++|||||+|.+.
T Consensus       184 a~p~~~------------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~  245 (346)
T TIGR01659       184 ARPGGE------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKR  245 (346)
T ss_pred             cccccc------------------ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCH
Confidence            754211                  1134579999999999999999999999999999999987 789999999999999


Q ss_pred             HHHHHHHHHhCCcEecc--cceEEehhhhhHH
Q 012257          373 EEASKALTEMNGKMVVS--KPLYVALAQRKEE  402 (467)
Q Consensus       373 ~~A~~A~~~l~g~~~~g--~~l~v~~~~~~~~  402 (467)
                      ++|.+|++.||+..+.+  ++|+|++++....
T Consensus       246 e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       246 EEAQEAISALNNVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             HHHHHHHHHhCCCccCCCceeEEEEECCcccc
Confidence            99999999999999876  6899999886543

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).

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

Probab=99.97  E-value=1.5e-28  Score=214.91  Aligned_cols=350  Identities=21%  Similarity=0.238  Sum_probs=256.7

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCc--ccCCcee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFT--PLNGKPI  111 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~--~~~g~~~  111 (467)
                      ....+++.|.+||||++++|+||.+++.+||.|+.+.+.+.+.      .||++|.+.+.|..-+......  .+.|+++
T Consensus        23 ~~~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn------QAflem~d~~sAvtmv~~y~~~~p~lr~~~~   96 (492)
T KOG1190|consen   23 SMAEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN------QAFLEMADEESAVTMVNYYTSVTPVLRGQPI   96 (492)
T ss_pred             cccCCcceeEeccCCccccHHHHHHhcccccceeeeeeeccch------hhhhhhcchhhhhheeecccccCccccCcce
Confidence            3445789999999999999999999999999999999988764      7999999999998855433222  2567777


Q ss_pred             eeeecccCc-------c---------------------cc--cC--------CCccEEEcCCCCcCCHHHHHHHHhhcCC
Q 012257          112 RIMYSYRDP-------T---------------------IR--KS--------GAGNIFIKNLDKSIDNKALHDTFSTFGN  153 (467)
Q Consensus       112 ~v~~~~~~~-------~---------------------~~--~~--------~~~~l~v~nlp~~~t~~~l~~~f~~~g~  153 (467)
                      .|.++.-..       .                     ..  ..        .--+++|.|+-+.++-|-|..+|++||.
T Consensus        97 yiq~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~  176 (492)
T KOG1190|consen   97 YIQYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGF  176 (492)
T ss_pred             eehhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcce
Confidence            776643210       0                     00  00        0114778999999999999999999999


Q ss_pred             eEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEeccccccc-----------ccc--------c---
Q 012257          154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQ-----------ERE--------S---  211 (467)
Q Consensus       154 v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~~-----------~~~--------~---  211 (467)
                      |..|....+..   .-.|.|+|.+...|..|...|+|..|.+..+.+.....+.           .+.        .   
T Consensus       177 VlKIiTF~Knn---~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~  253 (492)
T KOG1190|consen  177 VLKIITFTKNN---GFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQ  253 (492)
T ss_pred             eEEEEEEeccc---chhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCccc
Confidence            98887666532   2359999999999999999999998766544331111000           000        0   


Q ss_pred             -----------------------------------ccccc--cccceeecCCCc-cCCHHHHHHhhcccCCeeEEEEEEC
Q 012257          212 -----------------------------------TADKT--RFNNVYVKNLSE-TTTEDDLKKIFGEFGIITSTAVMRD  253 (467)
Q Consensus       212 -----------------------------------~~~~~--~~~~l~v~nlp~-~~~~~~l~~~f~~~g~v~~~~~~~~  253 (467)
                                                         ..-..  ....|.+.|+.. .+|.+.|..+|.-||+|.++++...
T Consensus       254 p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~n  333 (492)
T KOG1190|consen  254 PSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYN  333 (492)
T ss_pred             cccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhcceEEEEeeec
Confidence                                               00000  124567778754 5899999999999999999999987


Q ss_pred             CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccchHHHHH-------hh---------hhhhhhhhc-cc
Q 012257          254 ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREME-------LK---------GKFEQSLKE-TA  316 (467)
Q Consensus       254 ~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~-------~~---------~~~~~~~~~-~~  316 (467)
                      +.    ..|.|++.+...|.-|+..|+|..+.|+.+++.++++..-....       ..         ........+ ..
T Consensus       334 kk----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~n  409 (492)
T KOG1190|consen  334 KK----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQN  409 (492)
T ss_pred             CC----cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccCCCCCCccccccccCCCCchhhccCcccccccc
Confidence            43    47999999999999999999999999999999998764321100       00         000000001 11


Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEeccc-ceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSK-PLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~-~l~v~  395 (467)
                      -.+++.+|+..|+|..++||+|+..|..-|...+....-.   +.+.+|++.+.+.|+|..|+-.++++.+++. .|+|+
T Consensus       410 i~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~---kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvS  486 (492)
T KOG1190|consen  410 IFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ---KDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVS  486 (492)
T ss_pred             cCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC---CCcceeecccCChhHhhhhccccccccCCCCceEEEE
Confidence            2256678999999999999999999988876655433322   2345999999999999999999999999765 89999


Q ss_pred             hhhh
Q 012257          396 LAQR  399 (467)
Q Consensus       396 ~~~~  399 (467)
                      |++.
T Consensus       487 FSks  490 (492)
T KOG1190|consen  487 FSKS  490 (492)
T ss_pred             eecc
Confidence            9874

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

Probab=99.96  E-value=1.1e-28  Score=212.44  Aligned_cols=169  Identities=22%  Similarity=0.484  Sum_probs=151.7

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      .|+|||+.|.+++.|+.|+..|..||+|++|.+..|..|++++|||||+|+-+|.|+.|++.+|+..+.||.|+|.....
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999975432


Q ss_pred             Cccc---------ccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHh
Q 012257          119 DPTI---------RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL  188 (467)
Q Consensus       119 ~~~~---------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l  188 (467)
                      -+.-         ....-++|||..+-++++++||+..|+.||+|..|.+-++ ..+.++||+|++|.+...-..|+..+
T Consensus       193 mpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasM  272 (544)
T KOG0124|consen  193 MPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM  272 (544)
T ss_pred             CcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhc
Confidence            2111         1122358999999999999999999999999999999999 45668999999999999999999999


Q ss_pred             cCCccCCeeeEeccccccc
Q 012257          189 NGMLLNDKQVFVGPFLRKQ  207 (467)
Q Consensus       189 ~~~~~~g~~~~v~~~~~~~  207 (467)
                      |-..+.|..++|..+....
T Consensus       273 NlFDLGGQyLRVGk~vTPP  291 (544)
T KOG0124|consen  273 NLFDLGGQYLRVGKCVTPP  291 (544)
T ss_pred             chhhcccceEecccccCCC
Confidence            9999999999997776543

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

Probab=99.96  E-value=4.1e-28  Score=213.70  Aligned_cols=239  Identities=19%  Similarity=0.240  Sum_probs=199.6

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhc-CCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQ-MGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~-~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      .|.+||.|||+++..++|+++|++ -|+|+.|.++.|. .|+++|||.|+|+++|.++||++.|+...+.|++|.|....
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            456999999999999999999975 5899999999996 78999999999999999999999999999999999997654


Q ss_pred             cCccc----ccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCcc
Q 012257          118 RDPTI----RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLL  193 (467)
Q Consensus       118 ~~~~~----~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~  193 (467)
                      .....    ........|++++....-..-|...|+.-|.+..-.+.+|.++.+++..++.|.+.-++..++..+.....
T Consensus       123 d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~  202 (608)
T KOG4212|consen  123 DEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSAS  202 (608)
T ss_pred             chhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhh
Confidence            32211    11234578999999999889999999888888888888889999999999999999888888876665544


Q ss_pred             CCeeeEecccccccccccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHH
Q 012257          194 NDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAA  273 (467)
Q Consensus       194 ~g~~~~v~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~  273 (467)
                      .-+.+..            ...+....+||.||...+....|.+.|.-.|.|..+.+..++.+.++|++.++|...-.|.
T Consensus       203 Flr~~h~------------f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveav  270 (608)
T KOG4212|consen  203 FLRSLHI------------FSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAV  270 (608)
T ss_pred             hhhhccC------------CCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHH
Confidence            4444432            1223346789999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhCCCccCCceEE
Q 012257          274 RSVEALNGKKFDDKEWY  290 (467)
Q Consensus       274 ~a~~~l~~~~~~~~~l~  290 (467)
                      .|+..+++..+..++..
T Consensus       271 qaIsml~~~g~~~~~~~  287 (608)
T KOG4212|consen  271 QAISMLDRQGLFDRRMT  287 (608)
T ss_pred             HHHHhhccCCCccccce
Confidence            99998886554444433

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

Probab=99.96  E-value=1.9e-28  Score=215.82  Aligned_cols=175  Identities=30%  Similarity=0.569  Sum_probs=150.6

Q ss_pred             cccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCc-cCC--ceEEEc
Q 012257          217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKK-FDD--KEWYVG  292 (467)
Q Consensus       217 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~-~~~--~~l~~~  292 (467)
                      ..-.+||+.+|+.++|.||+++|++||.|.+|.+++| .++.++|||||.|.+.++|.+|+.+|+... +.|  ..+.++
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            3457999999999999999999999999999999999 568899999999999999999999998865 334  356666


Q ss_pred             ccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCH
Q 012257          293 KAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTA  372 (467)
Q Consensus       293 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~  372 (467)
                      ++....++.                 ...++|||+.|+..+||.+|+++|++||.|++|+|+++..+.+||||||.|.+.
T Consensus       113 ~Ad~E~er~-----------------~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstk  175 (510)
T KOG0144|consen  113 YADGERERI-----------------VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTK  175 (510)
T ss_pred             ccchhhhcc-----------------ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehH
Confidence            665433221                 345579999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCcEe-cc--cceEEehhhhhHHHHHHHH
Q 012257          373 EEASKALTEMNGKMV-VS--KPLYVALAQRKEERRARLQ  408 (467)
Q Consensus       373 ~~A~~A~~~l~g~~~-~g--~~l~v~~~~~~~~~~~~~~  408 (467)
                      +.|..||+.|||..- .|  .+|.|+||++++.+..++.
T Consensus       176 e~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~~~l  214 (510)
T KOG0144|consen  176 EMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDGKRL  214 (510)
T ss_pred             HHHHHHHHhhccceeeccCCCceEEEecccCCCchHHHH
Confidence            999999999999844 44  5899999998776654443

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

Probab=99.96  E-value=7.3e-28  Score=231.62  Aligned_cols=176  Identities=26%  Similarity=0.443  Sum_probs=150.8

Q ss_pred             cccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccc
Q 012257          217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQ  295 (467)
Q Consensus       217 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~  295 (467)
                      ..++|||+||+..+++++|+++|+.||.|.++.+..+ .+++++|||||+|.+.++|..|+..++|..+.|+.+.+.+..
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            3467999999999999999999999999999999988 578899999999999999999999999999999999998654


Q ss_pred             cchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHH
Q 012257          296 KKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEE  374 (467)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~  374 (467)
                      .........       ..........++|||+||+..+++++|+++|+.||.|+++++.++. +|+++|||||+|.+.++
T Consensus       186 ~~p~a~~~~-------~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~  258 (612)
T TIGR01645       186 NMPQAQPII-------DMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQS  258 (612)
T ss_pred             ccccccccc-------ccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHH
Confidence            321110000       0000111234689999999999999999999999999999999987 57799999999999999


Q ss_pred             HHHHHHHhCCcEecccceEEehhhh
Q 012257          375 ASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       375 A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      |.+|++.|||..++|+.|+|.++.+
T Consensus       259 A~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       259 QSEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             HHHHHHHhCCCeeCCeEEEEEecCC
Confidence            9999999999999999999999875

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.95  E-value=4.2e-27  Score=222.60  Aligned_cols=170  Identities=31%  Similarity=0.509  Sum_probs=149.1

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC--ceeeeee
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG--KPIRIMY  115 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g--~~~~v~~  115 (467)
                      ..++|||+|||.++++++|+++|+.||.|..+.+..+..++.++|||||+|.+.++|++|++.|++..+.|  ..+.+.+
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            35789999999999999999999999999999999999899999999999999999999999999998877  5567766


Q ss_pred             cccCccc------------------c------------------------------------------------------
Q 012257          116 SYRDPTI------------------R------------------------------------------------------  123 (467)
Q Consensus       116 ~~~~~~~------------------~------------------------------------------------------  123 (467)
                      +......                  .                                                      
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            5322100                  0                                                      


Q ss_pred             ------------------cCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHH
Q 012257          124 ------------------KSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSA  184 (467)
Q Consensus       124 ------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a  184 (467)
                                        .....+|||+|||.++++++|+++|+.||.|.+++++.+ .+|.++|||||+|.+.++|..|
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~A  327 (352)
T TIGR01661       248 ATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMA  327 (352)
T ss_pred             cccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHH
Confidence                              001125999999999999999999999999999999999 5899999999999999999999


Q ss_pred             HHHhcCCccCCeeeEeccccccc
Q 012257          185 IDKLNGMLLNDKQVFVGPFLRKQ  207 (467)
Q Consensus       185 ~~~l~~~~~~g~~~~v~~~~~~~  207 (467)
                      ++.|+|..+.|+.|.|.+...+.
T Consensus       328 i~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       328 ILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             HHHhCCCEECCeEEEEEEccCCC
Confidence            99999999999999998876553

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

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

Probab=99.95  E-value=3.8e-27  Score=220.63  Aligned_cols=259  Identities=23%  Similarity=0.390  Sum_probs=215.5

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ..+..+.|+|+|||..+..++|..+|.+||.|..|.+.+...      -|+|.|.++.+|.+|++.|.+..+..-++.+.
T Consensus       381 ~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~G~------~aiv~fl~p~eAr~Afrklaysr~k~~plyle  454 (725)
T KOG0110|consen  381 AERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPGGT------GAIVEFLNPLEARKAFRKLAYSRFKSAPLYLE  454 (725)
T ss_pred             hhhhcceeeeccCccccccHHHHHHhhcccccceeecCcccc------eeeeeecCccchHHHHHHhchhhhccCccccc
Confidence            566789999999999999999999999999999996653322      49999999999999999999888888888776


Q ss_pred             ecccCc----------------------cc----------c----------------cCCCccEEEcCCCCcCCHHHHHH
Q 012257          115 YSYRDP----------------------TI----------R----------------KSGAGNIFIKNLDKSIDNKALHD  146 (467)
Q Consensus       115 ~~~~~~----------------------~~----------~----------------~~~~~~l~v~nlp~~~t~~~l~~  146 (467)
                      |+...-                      ..          .                ....++|||.||+.+.+.+++..
T Consensus       455 ~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~  534 (725)
T KOG0110|consen  455 WAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLED  534 (725)
T ss_pred             cChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHH
Confidence            643210                      00          0                00113499999999999999999


Q ss_pred             HHhhcCCeEEEEEeeCCCCC----ceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEecccccccccc---ccccccccc
Q 012257          147 TFSTFGNILSCKVATDSLGQ----SRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERE---STADKTRFN  219 (467)
Q Consensus       147 ~f~~~g~v~~~~~~~~~~g~----~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~~~~~---~~~~~~~~~  219 (467)
                      +|...|.|.++.|.+..++.    +.|||||+|.+.++|+.|++.|+|+.++|+.|.+..+-.+....   ........+
T Consensus       535 ~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~t  614 (725)
T KOG0110|consen  535 LFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGT  614 (725)
T ss_pred             HHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccccccccccccc
Confidence            99999999999888775543    55999999999999999999999999999999997765221111   111122246


Q ss_pred             ceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccch
Q 012257          220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKY  298 (467)
Q Consensus       220 ~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~  298 (467)
                      .|+|.|+|...+..+++.+|..||.+.++.+... ..+..+|||||+|.+..+|..|+.+|.+.++.|++|...|+....
T Consensus       615 KIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  615 KILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             eeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            8999999999999999999999999999999887 445579999999999999999999999999999999999998765


Q ss_pred             H
Q 012257          299 E  299 (467)
Q Consensus       299 ~  299 (467)
                      .
T Consensus       695 ~  695 (725)
T KOG0110|consen  695 T  695 (725)
T ss_pred             H
Confidence            5

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

Probab=99.95  E-value=6.7e-28  Score=219.65  Aligned_cols=329  Identities=21%  Similarity=0.292  Sum_probs=227.6

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      .++..+++|+--|.-.+++.+|+++|+.+|.|-+|.++.|+.+++++|.|||+|.+.++...|+. |.|..+.|.+|.|.
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq  253 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQ  253 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEec
Confidence            44567899999999999999999999999999999999999999999999999999999999996 89999999999997


Q ss_pred             ecccCccc--------c----cCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCC-CCCceeEEEEEeCCHHHH
Q 012257          115 YSYRDPTI--------R----KSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESA  181 (467)
Q Consensus       115 ~~~~~~~~--------~----~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~-~g~~~~~afV~f~~~~~A  181 (467)
                      .+......        .    ...-.+|+|+||-.++++++|+.+|+.||.|..|.+.++. +|.++||+||+|.+.++|
T Consensus       254 ~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~a  333 (549)
T KOG0147|consen  254 LSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDA  333 (549)
T ss_pred             ccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHH
Confidence            75432111        1    1111238999999999999999999999999999999994 999999999999999999


Q ss_pred             HHHHHHhcCCccCCeeeEecccccccccccccccc-cccceeecCCCccC-CHHHHHHhhcccCCeeEEEEEECCCCCce
Q 012257          182 KSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKT-RFNNVYVKNLSETT-TEDDLKKIFGEFGIITSTAVMRDADGKSK  259 (467)
Q Consensus       182 ~~a~~~l~~~~~~g~~~~v~~~~~~~~~~~~~~~~-~~~~l~v~nlp~~~-~~~~l~~~f~~~g~v~~~~~~~~~~~~~~  259 (467)
                      .+|+..|||.++-|+.|+|................ ...-.--.+|+.-. ...++...|.+.-.+   .+         
T Consensus       334 r~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~---~~---------  401 (549)
T KOG0147|consen  334 RKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGR---SL---------  401 (549)
T ss_pred             HHHHHHhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCc---cc---------
Confidence            99999999999999999986554443322110000 00000001111110 112222222211000   00         


Q ss_pred             eEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCC--C---
Q 012257          260 CFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSI--S---  334 (467)
Q Consensus       260 g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~--~---  334 (467)
                            ..+...+..++..+......+....+.-..+              ....+.-..++.++.+.|+-...  |   
T Consensus       402 ------~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p--------------~~~~p~~~i~t~C~lL~nMFdpstete~n  461 (549)
T KOG0147|consen  402 ------PSTAISALLLLAKLASAAQFNGVVRVRSVDP--------------ADASPAFDIPTQCLLLSNMFDPSTETEPN  461 (549)
T ss_pred             ------cchhhhHHHhccccchHHhhcCCcCccccCc--------------cccccccCCccHHHHHhhcCCcccccCcc
Confidence                  0111222222222222211111111100000              00011112566678888883222  2   


Q ss_pred             -----HHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          335 -----DDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       335 -----~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                           .++|.+-+++||+|..|.+-++    +-|+.||.|.+.++|..|+++|||.+|.|+.|..+|-...
T Consensus       462 ~d~eI~edV~Eec~k~g~v~hi~vd~n----s~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~~~  528 (549)
T KOG0147|consen  462 WDQEIREDVIEECGKHGKVCHIFVDKN----SAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLPLE  528 (549)
T ss_pred             hhhHHHHHHHHHHHhcCCeeEEEEccC----CCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEeehh
Confidence                 2688889999999998887665    3479999999999999999999999999999999987644

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

Probab=99.93  E-value=3.7e-25  Score=216.53  Aligned_cols=176  Identities=31%  Similarity=0.507  Sum_probs=150.8

Q ss_pred             cccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccc
Q 012257          217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQ  295 (467)
Q Consensus       217 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~  295 (467)
                      ..++|||+|||..+++++|+++|++||.|.++.++.+ .+++++|||||+|.+.++|..|+. +++..+.|+.+.+....
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            3478999999999999999999999999999999988 468899999999999999999997 99999999999998765


Q ss_pred             cchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHH
Q 012257          296 KKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEE  374 (467)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~  374 (467)
                      ...........      ..........+|||+|||..+++++|+++|++||.|.+|++..+. +|.++|||||+|.+.++
T Consensus       167 ~~~~~~~~~~~------~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~  240 (457)
T TIGR01622       167 AEKNRAAKAAT------HQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEE  240 (457)
T ss_pred             hhhhhhhhccc------ccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHH
Confidence            43222111000      001112236789999999999999999999999999999999887 46899999999999999


Q ss_pred             HHHHHHHhCCcEecccceEEehhhh
Q 012257          375 ASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       375 A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      |.+|+..|||..|.|+.|.|.|+..
T Consensus       241 A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       241 AKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             HHHHHHhcCCcEECCEEEEEEEccC
Confidence            9999999999999999999999763

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=99.93  E-value=9.8e-26  Score=175.92  Aligned_cols=170  Identities=34%  Similarity=0.635  Sum_probs=153.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      ..+|||+||+..++++-|+++|-+.|+|.++.+.+|+.+..++||||++|.+.|||+-|++-|+...+.|++|+|..+. 
T Consensus         9 d~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas-   87 (203)
T KOG0131|consen    9 DATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS-   87 (203)
T ss_pred             CceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc-
Confidence            5899999999999999999999999999999999999999999999999999999999999999999999999999877 


Q ss_pred             CcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEE-EEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCe
Q 012257          119 DPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILS-CKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDK  196 (467)
Q Consensus       119 ~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~-~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~  196 (467)
                      ....+.....++||+||.+.+++..|.+.|+.||.+.. -+++++ .+|.+++++||-|.+.+.+..|+..++|..+.++
T Consensus        88 ~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr  167 (203)
T KOG0131|consen   88 AHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNR  167 (203)
T ss_pred             cccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCC
Confidence            33333444579999999999999999999999998754 356666 6789999999999999999999999999999999


Q ss_pred             eeEeccccccccc
Q 012257          197 QVFVGPFLRKQER  209 (467)
Q Consensus       197 ~~~v~~~~~~~~~  209 (467)
                      .+.+..+..+...
T Consensus       168 ~itv~ya~k~~~k  180 (203)
T KOG0131|consen  168 PITVSYAFKKDTK  180 (203)
T ss_pred             ceEEEEEEecCCC
Confidence            9999887665443

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

Probab=99.93  E-value=1.7e-25  Score=184.20  Aligned_cols=167  Identities=33%  Similarity=0.619  Sum_probs=151.8

Q ss_pred             cccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccc
Q 012257          217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQ  295 (467)
Q Consensus       217 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~  295 (467)
                      ..++|+|..||..++.||++.+|...|+|++++++++ .+|.+-||+||.|-+.++|.+|+..+||..+..+.++|.++.
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyAR  119 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYAR  119 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEecc
Confidence            3468999999999999999999999999999999999 579999999999999999999999999999999999999997


Q ss_pred             cchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHH
Q 012257          296 KKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEE  374 (467)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~  374 (467)
                      +....                  .....|||++||..+|..||.++|++||.|.--+|+.|. +|.++|.+||.|+.+.+
T Consensus       120 PSs~~------------------Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~E  181 (360)
T KOG0145|consen  120 PSSDS------------------IKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIE  181 (360)
T ss_pred             CChhh------------------hcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhH
Confidence            75332                  234479999999999999999999999999999999888 89999999999999999


Q ss_pred             HHHHHHHhCCcEeccc--ceEEehhhhhH
Q 012257          375 ASKALTEMNGKMVVSK--PLYVALAQRKE  401 (467)
Q Consensus       375 A~~A~~~l~g~~~~g~--~l~v~~~~~~~  401 (467)
                      |.+||..|||..=.|+  +|.|+|+....
T Consensus       182 Ae~AIk~lNG~~P~g~tepItVKFannPs  210 (360)
T KOG0145|consen  182 AEEAIKGLNGQKPSGCTEPITVKFANNPS  210 (360)
T ss_pred             HHHHHHhccCCCCCCCCCCeEEEecCCcc
Confidence            9999999999977654  79999987543

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

Probab=99.93  E-value=9.2e-23  Score=176.63  Aligned_cols=350  Identities=17%  Similarity=0.162  Sum_probs=259.7

Q ss_pred             CCCCCCCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHh--CC
Q 012257           26 ANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL--NF  103 (467)
Q Consensus        26 ~~~~~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l--~~  103 (467)
                      ..+...++-...++-.|.|++|-..++|.+|.+.++.||+|..|..+..++      .|.|+|++.+.|+.++...  +.
T Consensus        18 ~~e~~~dphk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r------~alvefedi~~akn~Vnfaa~n~   91 (494)
T KOG1456|consen   18 RREDNADPHKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKR------QALVEFEDIEGAKNCVNFAADNQ   91 (494)
T ss_pred             CcccCCCCCCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccccc------eeeeeeccccchhhheehhccCc
Confidence            355566777778899999999999999999999999999999998887765      7999999999999998742  44


Q ss_pred             cccCCceeeeeecccCccccc----CCCcc---EEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeC
Q 012257          104 TPLNGKPIRIMYSYRDPTIRK----SGAGN---IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFD  176 (467)
Q Consensus       104 ~~~~g~~~~v~~~~~~~~~~~----~~~~~---l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~  176 (467)
                      ..+.|...-++++......+.    ...++   +.|-|--+.+|.+.|..++...|.|..|.|.+.    ..-.|.|+|.
T Consensus        92 i~i~gq~Al~NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk----ngVQAmVEFd  167 (494)
T KOG1456|consen   92 IYIAGQQALFNYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK----NGVQAMVEFD  167 (494)
T ss_pred             ccccCchhhcccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec----cceeeEEeec
Confidence            567787777777643322221    11222   336676788999999999999999999999885    3457999999


Q ss_pred             CHHHHHHHHHHhcCCccCCe--eeEecccccccccccccc----------------------------------------
Q 012257          177 NEESAKSAIDKLNGMLLNDK--QVFVGPFLRKQERESTAD----------------------------------------  214 (467)
Q Consensus       177 ~~~~A~~a~~~l~~~~~~g~--~~~v~~~~~~~~~~~~~~----------------------------------------  214 (467)
                      +.+.|++|.+.|||..|...  .|++.++.+.........                                        
T Consensus       168 sv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G  247 (494)
T KOG1456|consen  168 SVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGG  247 (494)
T ss_pred             hhHHHHHHHhhcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCC
Confidence            99999999999999876443  334433222111000000                                        


Q ss_pred             ------------------------------------cccccceeecCCCcc-CCHHHHHHhhcccCCeeEEEEEECCCCC
Q 012257          215 ------------------------------------KTRFNNVYVKNLSET-TTEDDLKKIFGEFGIITSTAVMRDADGK  257 (467)
Q Consensus       215 ------------------------------------~~~~~~l~v~nlp~~-~~~~~l~~~f~~~g~v~~~~~~~~~~~~  257 (467)
                                                          ......++|.+|... ++-+.|.++|..||+|.++++++.+   
T Consensus       248 ~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk---  324 (494)
T KOG1456|consen  248 GHSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK---  324 (494)
T ss_pred             CCCCCcccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc---
Confidence                                                000123677777654 5678899999999999999999875   


Q ss_pred             ceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccchHHHHH-------------------hhhhhhhhhhccccC
Q 012257          258 SKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREME-------------------LKGKFEQSLKETADK  318 (467)
Q Consensus       258 ~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~  318 (467)
                       .|.|+|++.+..+.++|+..|++..+.|.+|.+..++...-....                   .............-.
T Consensus       325 -~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq  403 (494)
T KOG1456|consen  325 -PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQ  403 (494)
T ss_pred             -cceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccccccCCceecCCCCcchhhcccccccccCChhHhhccccc
Confidence             458999999999999999999999999999998777543211110                   000011111112234


Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCc-eeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEeccc
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGT-ITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSK  390 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~-v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  390 (467)
                      ++++.|+..|.|..+||+.|.++|...+. -.+++++..++-++ ..++++|++.++|..|+..+|...+.+.
T Consensus       404 ~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp~kserS-ssGllEfe~~s~Aveal~~~NH~pi~~p  475 (494)
T KOG1456|consen  404 PPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPLKSERS-SSGLLEFENKSDAVEALMKLNHYPIEGP  475 (494)
T ss_pred             CCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeeccccccc-ccceeeeehHHHHHHHHHHhccccccCC
Confidence            67889999999999999999999976643 46778877664443 4799999999999999999999999653

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

Probab=99.92  E-value=4.2e-23  Score=185.91  Aligned_cols=336  Identities=15%  Similarity=0.210  Sum_probs=240.2

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ..-.|.+++|||.+|++||+++|+.+ .|+++.+.+.  +|+..|-|||+|.+.||+++|++ .+...+..+.|.|-.+.
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRR--NGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAG   84 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcC-ceeEEEEecc--CCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccC
Confidence            35678999999999999999999998 6688777653  68889999999999999999998 57778888889886654


Q ss_pred             cCccc-------cc--CCCccEEEcCCCCcCCHHHHHHHHhhcCCeEE-EEEeeCCCCCceeEEEEEeCCHHHHHHHHHH
Q 012257          118 RDPTI-------RK--SGAGNIFIKNLDKSIDNKALHDTFSTFGNILS-CKVATDSLGQSRGYGFVQFDNEESAKSAIDK  187 (467)
Q Consensus       118 ~~~~~-------~~--~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~-~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~  187 (467)
                      ..+..       ..  .....|.+++||..||++||.++|+..-.|.. +.+..+..+++.+-|||+|++.+.|+.|+..
T Consensus        85 ~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r  164 (510)
T KOG4211|consen   85 GAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR  164 (510)
T ss_pred             CccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH
Confidence            33211       11  24567999999999999999999997755544 5667778888999999999999999999975


Q ss_pred             hcCCccCCeeeEecccccccccccc------------------------------------------------------c
Q 012257          188 LNGMLLNDKQVFVGPFLRKQEREST------------------------------------------------------A  213 (467)
Q Consensus       188 l~~~~~~g~~~~v~~~~~~~~~~~~------------------------------------------------------~  213 (467)
                       +...|..+.|.|-.+.....+...                                                      .
T Consensus       165 -hre~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~  243 (510)
T KOG4211|consen  165 -HRENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQ  243 (510)
T ss_pred             -HHHhhccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccc
Confidence             555666777666322111110000                                                      0


Q ss_pred             ----------------cc-----------------ccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCcee
Q 012257          214 ----------------DK-----------------TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKC  260 (467)
Q Consensus       214 ----------------~~-----------------~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g  260 (467)
                                      ..                 .....+....||...+..+|.++|+....+ .+.+-...+++.+|
T Consensus       244 d~~~~gs~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~dGr~TG  322 (510)
T KOG4211|consen  244 DYGNFGSYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGPDGRATG  322 (510)
T ss_pred             ccccccccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCCCCccCC
Confidence                            00                 000236788899999999999999986554 78888889999999


Q ss_pred             EEEEEeCCHHHHHHHHHHhCCCccCCceEEEccc-----ccchHHH----------H---------H-------hhhhh-
Q 012257          261 FGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA-----QKKYERE----------M---------E-------LKGKF-  308 (467)
Q Consensus       261 ~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~-----~~~~~~~----------~---------~-------~~~~~-  308 (467)
                      -|.|+|.+.++|..|+.. ++..+..+-+..-..     .......          .         .       +.... 
T Consensus       323 EAdveF~t~edav~Amsk-d~anm~hrYVElFln~~~ga~g~~~~s~~~g~~~~~~~~~~Gg~a~g~~~gG~~g~~~~~~  401 (510)
T KOG4211|consen  323 EADVEFATGEDAVGAMGK-DGANMGHRYVELFLNGAPGASGGGGPSGPGGVGSSGDRNGGGGYASGSYGGGGNGGGGRGS  401 (510)
T ss_pred             cceeecccchhhHhhhcc-CCcccCcceeeecccCCcccccCccCCCCCCccccccccCCCCccccccccCCCCCccccC
Confidence            999999999999999863 333333222221110     0000000          0         0       00000 


Q ss_pred             ------------------hhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcC
Q 012257          309 ------------------EQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFS  370 (467)
Q Consensus       309 ------------------~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~  370 (467)
                                        ....-..........|..+++|...++.++.++|.+++.- .|.+..++.+...+-|-|.|.
T Consensus       402 ~~G~~~~~~~~~~~~Gy~g~~~~~~~~~~e~~~~~~rgap~~a~eadv~d~~~~~~~a-~~~~~yd~~~~~~~~a~~~~~  480 (510)
T KOG4211|consen  402 PYGRPSDGYSSPGGGGYSGPRGYGRGPQNEHFVIRMRGAPFRASEADVYDFFHPIRPA-QVELLYDHQFQRSGDARVIFY  480 (510)
T ss_pred             CCCCCcccccCCCCCCCcCcccCCCCccccccccCcCCCCccccccchhhcccccCcc-cccccccccccccCceeEEEe
Confidence                              0000001122234468888999999999999999998654 788888887777889999999


Q ss_pred             CHHHHHHHHHH
Q 012257          371 TAEEASKALTE  381 (467)
Q Consensus       371 ~~~~A~~A~~~  381 (467)
                      +.++++.|+.+
T Consensus       481 ~~~~~q~a~~~  491 (510)
T KOG4211|consen  481 NRKDYQDALMK  491 (510)
T ss_pred             chhhhHHHHHh
Confidence            99999999874

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

Probab=99.90  E-value=7.1e-24  Score=177.69  Aligned_cols=150  Identities=25%  Similarity=0.494  Sum_probs=138.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecccC
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRD  119 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~  119 (467)
                      -+|||+|||..+++.+|+.+|++||+|+++.|+++        |+||-.++...|..|+..|++..|+|..|+|+.++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            47999999999999999999999999999999864        8999999999999999999999999999999988765


Q ss_pred             cccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeE
Q 012257          120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVF  199 (467)
Q Consensus       120 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~  199 (467)
                          ....++|+|+||.+.++.+||++.|++||+|.+|.|++       +|+||.|.-.++|..|++.|++.++.|+++.
T Consensus        75 ----sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk-------dy~fvh~d~~eda~~air~l~~~~~~gk~m~  143 (346)
T KOG0109|consen   75 ----SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK-------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMH  143 (346)
T ss_pred             ----CCCccccccCCCCccccCHHHhhhhcccCCceeeeeec-------ceeEEEEeeccchHHHHhcccccccccceee
Confidence                33467899999999999999999999999999999975       5999999999999999999999999999999


Q ss_pred             ecccccccc
Q 012257          200 VGPFLRKQE  208 (467)
Q Consensus       200 v~~~~~~~~  208 (467)
                      |..+.....
T Consensus       144 vq~stsrlr  152 (346)
T KOG0109|consen  144 VQLSTSRLR  152 (346)
T ss_pred             eeeeccccc
Confidence            977665433

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

Probab=99.90  E-value=1.5e-23  Score=173.46  Aligned_cols=292  Identities=24%  Similarity=0.330  Sum_probs=176.6

Q ss_pred             CceeeeeecccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHH
Q 012257          108 GKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK  187 (467)
Q Consensus       108 g~~~~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~  187 (467)
                      .|.+.|..+..  +.+..+.++|||+-|.+.-+|+|++.+|+.||.+.+|.+.+..+|.++|+|||+|.+..+|..||..
T Consensus         2 nrpiqvkpads--esrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~a   79 (371)
T KOG0146|consen    2 NRPIQVKPADS--ESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINA   79 (371)
T ss_pred             CCCcccccccc--ccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHH
Confidence            35566655432  2233467899999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCc-cCC--eeeEecccccccccccccc----------cccc-----------------ccee----ecCCCccCCH-
Q 012257          188 LNGML-LND--KQVFVGPFLRKQERESTAD----------KTRF-----------------NNVY----VKNLSETTTE-  232 (467)
Q Consensus       188 l~~~~-~~g--~~~~v~~~~~~~~~~~~~~----------~~~~-----------------~~l~----v~nlp~~~~~-  232 (467)
                      |+|.. +.|  ..+.|.......++....-          ..-.                 ..+.    ...|...++. 
T Consensus        80 LHgSqTmpGASSSLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~  159 (371)
T KOG0146|consen   80 LHGSQTMPGASSSLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFA  159 (371)
T ss_pred             hcccccCCCCccceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhH
Confidence            99874 444  3455544433333221100          0000                 0000    0111111111 


Q ss_pred             ---HHHHHhhcccCCeeEEEEEECCCCCc-----------------eeE-EEEEeCCHHHHHHHHHHhCCCccCC-ceEE
Q 012257          233 ---DDLKKIFGEFGIITSTAVMRDADGKS-----------------KCF-GFVNFDDPDDAARSVEALNGKKFDD-KEWY  290 (467)
Q Consensus       233 ---~~l~~~f~~~g~v~~~~~~~~~~~~~-----------------~g~-afv~f~~~~~a~~a~~~l~~~~~~~-~~l~  290 (467)
                         -.....+.--|.+..-..........                 .|| +...+..-..|..++. -++..... ..-.
T Consensus       160 ~~~mQ~~aA~~angl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy-~ng~~pypaQsp~  238 (371)
T KOG0146|consen  160 AAQMQQMAALNANGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVY-ANGLHPYPAQSPT  238 (371)
T ss_pred             HHHHHHHHHHhhcccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHh-hcCCccCCCCCcc
Confidence               01111122222211111111100000                 001 1222223233333333 12221111 0000


Q ss_pred             E-cccccchHHH-----------HHhhhhhh----hhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEe
Q 012257          291 V-GKAQKKYERE-----------MELKGKFE----QSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVM  354 (467)
Q Consensus       291 ~-~~~~~~~~~~-----------~~~~~~~~----~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~  354 (467)
                      + ...+......           ........    .-.......+++|+|||..||.+..+.||.+.|-+||.|.+.+++
T Consensus       239 va~~lq~a~~g~~~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVF  318 (371)
T KOG0146|consen  239 VADPLQQAYAGVQQYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVF  318 (371)
T ss_pred             ccchhhhhhhhHHHHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeee
Confidence            0 0000000000           00000000    001123456789999999999999999999999999999999999


Q ss_pred             eCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhhHH
Q 012257          355 RDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEE  402 (467)
Q Consensus       355 ~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~  402 (467)
                      .|. ++.+++|+||.|++..+|+.||.+|||..|+-|+|+|.+.+++..
T Consensus       319 vDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkda  367 (371)
T KOG0146|consen  319 VDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDA  367 (371)
T ss_pred             ehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCcccc
Confidence            987 888999999999999999999999999999999999999988764

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

Probab=99.90  E-value=1e-23  Score=164.71  Aligned_cols=168  Identities=32%  Similarity=0.533  Sum_probs=147.1

Q ss_pred             cccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccc
Q 012257          217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQ  295 (467)
Q Consensus       217 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~  295 (467)
                      ...+||++||+..++++-|.++|-+.|.|.++.+.++ .+...+||||++|.+.++|..|++-++...+.|+++++..+.
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            3468999999999999999999999999999999988 456689999999999999999999999999999999998876


Q ss_pred             cchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEE-EEeeCC-CCCccceEEEEcCCHH
Q 012257          296 KKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSC-KVMRDP-NGISRGSGFVAFSTAE  373 (467)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v-~i~~~~-~~~~~g~afV~f~~~~  373 (467)
                      .....                 ...+..|||+||.+.++|..|.+.|+.||.+.+. +++++. +|.++|||||.|++.+
T Consensus        88 ~~~~n-----------------l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfe  150 (203)
T KOG0131|consen   88 AHQKN-----------------LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFE  150 (203)
T ss_pred             ccccc-----------------ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHH
Confidence            21110                 1122479999999999999999999999998663 667776 5889999999999999


Q ss_pred             HHHHHHHHhCCcEecccceEEehhhhhH
Q 012257          374 EASKALTEMNGKMVVSKPLYVALAQRKE  401 (467)
Q Consensus       374 ~A~~A~~~l~g~~~~g~~l~v~~~~~~~  401 (467)
                      .+.+|+..+||..++.++++|+|+..+.
T Consensus       151 asd~ai~s~ngq~l~nr~itv~ya~k~~  178 (203)
T KOG0131|consen  151 ASDAAIGSMNGQYLCNRPITVSYAFKKD  178 (203)
T ss_pred             HHHHHHHHhccchhcCCceEEEEEEecC
Confidence            9999999999999999999999986443

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

Probab=99.90  E-value=1.1e-23  Score=176.63  Aligned_cols=148  Identities=23%  Similarity=0.514  Sum_probs=137.1

Q ss_pred             cceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccch
Q 012257          219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKY  298 (467)
Q Consensus       219 ~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~  298 (467)
                      ..|||+|||.+.++.+|+.+|++||.|.++.|+++       |+||..++...+..|+.+|++..++|..++|..++.+.
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            35899999999999999999999999999999965       99999999999999999999999999999998776541


Q ss_pred             HHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHH
Q 012257          299 EREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKA  378 (467)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A  378 (467)
                                          -.+.+|+|+||.+.++-++|+..|++||.|.+|+|.++       ++||.|+-.++|..|
T Consensus        76 --------------------k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd-------y~fvh~d~~eda~~a  128 (346)
T KOG0109|consen   76 --------------------KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD-------YAFVHFDRAEDAVEA  128 (346)
T ss_pred             --------------------CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc-------eeEEEEeeccchHHH
Confidence                                14457999999999999999999999999999999998       999999999999999


Q ss_pred             HHHhCCcEecccceEEehhhhh
Q 012257          379 LTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       379 ~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      ++.|+|..|.|++|+|+++..+
T Consensus       129 ir~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen  129 IRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             Hhcccccccccceeeeeeeccc
Confidence            9999999999999999987543

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

Probab=99.86  E-value=6e-21  Score=168.80  Aligned_cols=247  Identities=19%  Similarity=0.210  Sum_probs=204.2

Q ss_pred             CccEEEcCCCCcCCHHHHHHHHh-hcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEeccccc
Q 012257          127 AGNIFIKNLDKSIDNKALHDTFS-TFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLR  205 (467)
Q Consensus       127 ~~~l~v~nlp~~~t~~~l~~~f~-~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~  205 (467)
                      .+.+||+|||++....+|+++|. +.|+|..|.++.|..|+++++|.|+|+++|.+++|++.|+.+.+.|+.|.+.....
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            35699999999999999999997 78999999999999999999999999999999999999999999999999966544


Q ss_pred             ccccccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccC
Q 012257          206 KQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFD  285 (467)
Q Consensus       206 ~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~  285 (467)
                      ............-...|+.++....-...+...|.--|.+.+..+.++.+..+++..+++|+..-.+..++.-++.....
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            33333333333445788999988888888888888888888888888888889999999999877777666644433333


Q ss_pred             CceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceE
Q 012257          286 DKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSG  365 (467)
Q Consensus       286 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~a  365 (467)
                      .+.+.. +                       ..+....+||.||.+.+..+.|++.|.--|.|..+.+..++.|.++|+|
T Consensus       204 lr~~h~-f-----------------------~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~  259 (608)
T KOG4212|consen  204 LRSLHI-F-----------------------SPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFA  259 (608)
T ss_pred             hhhccC-C-----------------------CCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCee
Confidence            333332 1                       1123346999999999999999999999999999999999999999999


Q ss_pred             EEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          366 FVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       366 fV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      .++|+..-+|..||..|++..+.+++..+.+.
T Consensus       260 vi~y~hpveavqaIsml~~~g~~~~~~~~Rl~  291 (608)
T KOG4212|consen  260 VIEYDHPVEAVQAISMLDRQGLFDRRMTVRLD  291 (608)
T ss_pred             EEEecchHHHHHHHHhhccCCCccccceeecc
Confidence            99999999999999999987777777777763

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

Probab=99.84  E-value=1e-20  Score=167.59  Aligned_cols=170  Identities=27%  Similarity=0.452  Sum_probs=152.0

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      +.++|||++|+++++++.|+++|.+||+|.++.+.+|+.+++++||+||+|++.+...+++. .....|+|+.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            78999999999999999999999999999999999999999999999999999999999997 45567999999998877


Q ss_pred             cCcccccCC----CccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCc
Q 012257          118 RDPTIRKSG----AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGML  192 (467)
Q Consensus       118 ~~~~~~~~~----~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~  192 (467)
                      +........    ..+|||++||.+++++++++.|.+||.|..+.++.+ .+..+++|+||.|.+++.+.+++. ...+.
T Consensus        84 ~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~  162 (311)
T KOG4205|consen   84 SREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHD  162 (311)
T ss_pred             CcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceee
Confidence            665544444    348999999999999999999999999999988888 778899999999999999999986 47788


Q ss_pred             cCCeeeEeccccccccc
Q 012257          193 LNDKQVFVGPFLRKQER  209 (467)
Q Consensus       193 ~~g~~~~v~~~~~~~~~  209 (467)
                      +.++.+.|..+.++...
T Consensus       163 ~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  163 FNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             ecCceeeEeeccchhhc
Confidence            99999999887766553

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

Probab=99.84  E-value=2.2e-20  Score=161.58  Aligned_cols=172  Identities=27%  Similarity=0.468  Sum_probs=146.1

Q ss_pred             cceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccc
Q 012257          219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKK  297 (467)
Q Consensus       219 ~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~  297 (467)
                      .++||+.+..++.++.|+..|..||.|+++.+.-+ .+++.+|||||+|+-.+.|..|++.+||..++|+.+++.....-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            56999999999999999999999999999999887 57889999999999999999999999999999999999866543


Q ss_pred             hHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCC-CCccceEEEEcCCHHHHH
Q 012257          298 YEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEAS  376 (467)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~-~~~~g~afV~f~~~~~A~  376 (467)
                      .....-.+.-.+...       .-..|||..+.++++|+||+.+|+.||+|.+|.+-+.++ +.++||+|++|.+..+-.
T Consensus       194 pQAQpiID~vqeeAk-------~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~  266 (544)
T KOG0124|consen  194 PQAQPIIDMVQEEAK-------KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS  266 (544)
T ss_pred             cccchHHHHHHHHHH-------hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchH
Confidence            222111111111000       112699999999999999999999999999999999985 457999999999999999


Q ss_pred             HHHHHhCCcEecccceEEehh
Q 012257          377 KALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       377 ~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      .|+..||-+.++|.-|+|--+
T Consensus       267 eAiasMNlFDLGGQyLRVGk~  287 (544)
T KOG0124|consen  267 EAIASMNLFDLGGQYLRVGKC  287 (544)
T ss_pred             HHhhhcchhhcccceEecccc
Confidence            999999999999999998754

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.83  E-value=2.8e-19  Score=155.74  Aligned_cols=288  Identities=15%  Similarity=0.157  Sum_probs=201.2

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ..+..|..++|||..++.+|..+|+..........+.....|+..|.|.|.|.+.|.-..|++ .+...+.++.+.|..+
T Consensus        58 ~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~Rdlalk-Rhkhh~g~ryievYka  136 (508)
T KOG1365|consen   58 DDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALK-RHKHHMGTRYIEVYKA  136 (508)
T ss_pred             CcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhH-hhhhhccCCceeeecc
Confidence            346778999999999999999999877544444445555677788999999999999999998 4566678888988765


Q ss_pred             ccCccc--------------ccCCCccEEEcCCCCcCCHHHHHHHHhh----cCCeEEEEEeeCCCCCceeEEEEEeCCH
Q 012257          117 YRDPTI--------------RKSGAGNIFIKNLDKSIDNKALHDTFST----FGNILSCKVATDSLGQSRGYGFVQFDNE  178 (467)
Q Consensus       117 ~~~~~~--------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~----~g~v~~~~~~~~~~g~~~~~afV~f~~~  178 (467)
                      ...+-.              .+.+.--|.+++||+++++.++.++|..    -|..+.+.++..++|+..|-|||.|..+
T Consensus       137 ~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~e  216 (508)
T KOG1365|consen  137 TGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACE  216 (508)
T ss_pred             CchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCH
Confidence            543221              1122334778999999999999999963    2356678888889999999999999999


Q ss_pred             HHHHHHHHHhcCCccCCeeeEecccccccccccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCc
Q 012257          179 ESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKS  258 (467)
Q Consensus       179 ~~A~~a~~~l~~~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~  258 (467)
                      ++|+.|+.. +...+.-|.|.+-                           ..|..++......+-.-   -++..     
T Consensus       217 e~aq~aL~k-hrq~iGqRYIElF---------------------------RSTaaEvqqvlnr~~s~---pLi~~-----  260 (508)
T KOG1365|consen  217 EDAQFALRK-HRQNIGQRYIELF---------------------------RSTAAEVQQVLNREVSE---PLIPG-----  260 (508)
T ss_pred             HHHHHHHHH-HHHHHhHHHHHHH---------------------------HHhHHHHHHHHHhhccc---cccCC-----
Confidence            999999975 3333333333331                           12334444444332100   00000     


Q ss_pred             eeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHH
Q 012257          259 KCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL  338 (467)
Q Consensus       259 ~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l  338 (467)
                                          +....+.+..  .....                     ......+|.+++||+..+.++|
T Consensus       261 --------------------~~sp~~p~~p--~~~~p---------------------~~~~kdcvRLRGLPy~AtvEdI  297 (508)
T KOG1365|consen  261 --------------------LTSPLLPGGP--ARLVP---------------------PTRSKDCVRLRGLPYEATVEDI  297 (508)
T ss_pred             --------------------CCCCCCCCCc--cccCC---------------------CCCCCCeeEecCCChhhhHHHH
Confidence                                0000000000  00000                     0011347999999999999999


Q ss_pred             HHhhccCCc-eeE--EEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhhHHHH
Q 012257          339 KELFSEFGT-ITS--CKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERR  404 (467)
Q Consensus       339 ~~~F~~~G~-v~~--v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  404 (467)
                      .+||..|.. |+.  |++..+..|++.|.|||+|.+.++|..|....+++...++-|.|=-+...+..+
T Consensus       298 L~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~eeln~  366 (508)
T KOG1365|consen  298 LDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVEELNE  366 (508)
T ss_pred             HHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHHHHHH
Confidence            999999864 444  899999999999999999999999999999888887778888776665555443

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

Probab=99.81  E-value=3.6e-18  Score=150.23  Aligned_cols=246  Identities=17%  Similarity=0.245  Sum_probs=190.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC--ceeeeeecc
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG--KPIRIMYSY  117 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g--~~~~v~~~~  117 (467)
                      -+++|.|+-+.++-+-|+++|++||.|+.|.-+.+..+    -.|+|+|.+.+.|+.|...|++..|..  ..++|.++.
T Consensus       151 Lr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn~----FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sk  226 (492)
T KOG1190|consen  151 LRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNNG----FQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSK  226 (492)
T ss_pred             EEEEeccceeeeEHHHHHHHHhhcceeEEEEEEecccc----hhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhh
Confidence            56789999999999999999999999999988876543    369999999999999999999987743  446665442


Q ss_pred             cC----------------cccccC---------------------------------------------CCccEEEcCC-
Q 012257          118 RD----------------PTIRKS---------------------------------------------GAGNIFIKNL-  135 (467)
Q Consensus       118 ~~----------------~~~~~~---------------------------------------------~~~~l~v~nl-  135 (467)
                      -.                +.....                                             ....|.|.|| 
T Consensus       227 lt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln  306 (492)
T KOG1190|consen  227 LTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLN  306 (492)
T ss_pred             cccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCc
Confidence            10                000000                                             0234677887 


Q ss_pred             CCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEeccccccccccccc--
Q 012257          136 DKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTA--  213 (467)
Q Consensus       136 p~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~~~~~~~~--  213 (467)
                      +..+|.+.|..+|..||+|..|+|...    .+-.|.|+|.+...|..|++.|+|..+.|+.|++..+.-........  
T Consensus       307 ~~~VT~d~LftlFgvYGdVqRVkil~n----kkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~egq  382 (492)
T KOG1190|consen  307 EEAVTPDVLFTLFGVYGDVQRVKILYN----KKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREGQ  382 (492)
T ss_pred             hhccchhHHHHHHhhhcceEEEEeeec----CCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccCCCCCC
Confidence            466799999999999999999999986    23579999999999999999999999999999996553322111100  


Q ss_pred             ---------------------------ccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEe
Q 012257          214 ---------------------------DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNF  266 (467)
Q Consensus       214 ---------------------------~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f  266 (467)
                                                 .-+.+.++++.|+|.++++|++++.|...|...+......   +.+.++++.+
T Consensus       383 ~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~---kd~kmal~q~  459 (492)
T KOG1190|consen  383 EDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ---KDRKMALPQL  459 (492)
T ss_pred             ccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC---CCcceeeccc
Confidence                                       0123346889999999999999999999888755554433   2345999999


Q ss_pred             CCHHHHHHHHHHhCCCccCCc-eEEEccccc
Q 012257          267 DDPDDAARSVEALNGKKFDDK-EWYVGKAQK  296 (467)
Q Consensus       267 ~~~~~a~~a~~~l~~~~~~~~-~l~~~~~~~  296 (467)
                      .+.++|..|+-.++...++.. .+++.+++.
T Consensus       460 ~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  460 ESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             CChhHhhhhccccccccCCCCceEEEEeecc
Confidence            999999999999988888765 788887764

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

Probab=99.81  E-value=5.7e-18  Score=153.10  Aligned_cols=264  Identities=17%  Similarity=0.249  Sum_probs=189.4

Q ss_pred             CCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEeccccc
Q 012257          126 GAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLR  205 (467)
Q Consensus       126 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~  205 (467)
                      ...-|.+++||.++|++||+++|+.. .|..+.+.+ .+|+..|-|||+|++++++.+|++ .+...+..+.|.|-....
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r-~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPR-RNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGG   85 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcC-ceeEEEEec-cCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCC
Confidence            34568899999999999999999988 566655544 468889999999999999999998 477788899999866533


Q ss_pred             cccccccc-----ccccccceeecCCCccCCHHHHHHhhcccCCeeE-EEEEECCCCCceeEEEEEeCCHHHHHHHHHHh
Q 012257          206 KQERESTA-----DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITS-TAVMRDADGKSKCFGFVNFDDPDDAARSVEAL  279 (467)
Q Consensus       206 ~~~~~~~~-----~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~-~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l  279 (467)
                      ........     .......|.+.+||..++++||.++|+..-.+.. +.+..+..+++.|-|||+|++.+.|+.|+.. 
T Consensus        86 ~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-  164 (510)
T KOG4211|consen   86 AEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-  164 (510)
T ss_pred             ccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-
Confidence            32211111     1123456889999999999999999998877776 5566677888999999999999999999973 


Q ss_pred             CCCccCCceEEEcccccchHHHHHhh------------------h-----------------------------------
Q 012257          280 NGKKFDDKEWYVGKAQKKYEREMELK------------------G-----------------------------------  306 (467)
Q Consensus       280 ~~~~~~~~~l~~~~~~~~~~~~~~~~------------------~-----------------------------------  306 (467)
                      +...++-+-+.+-.+...........                  .                                   
T Consensus       165 hre~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d  244 (510)
T KOG4211|consen  165 HRENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQD  244 (510)
T ss_pred             HHHhhccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCccccc
Confidence            34444444444433322211111100                  0                                   


Q ss_pred             -----hhh--h--hhhcc-------------ccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccce
Q 012257          307 -----KFE--Q--SLKET-------------ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGS  364 (467)
Q Consensus       307 -----~~~--~--~~~~~-------------~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~  364 (467)
                           ...  .  .....             .-......++.++||+..++.++..+|+..-.+ .|+|-..++|+.+|-
T Consensus       245 ~~~~gs~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~dGr~TGE  323 (510)
T KOG4211|consen  245 YGNFGSYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGPDGRATGE  323 (510)
T ss_pred             cccccccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCCCCccCCc
Confidence                 000  0  00000             000112458889999999999999999987555 899999999999999


Q ss_pred             EEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          365 GFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       365 afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      |+|+|.|.++|..|+.. ++..+..+-+.+-
T Consensus       324 AdveF~t~edav~Amsk-d~anm~hrYVElF  353 (510)
T KOG4211|consen  324 ADVEFATGEDAVGAMGK-DGANMGHRYVELF  353 (510)
T ss_pred             ceeecccchhhHhhhcc-CCcccCcceeeec
Confidence            99999999999999974 5555555544443

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

Probab=99.80  E-value=1.3e-18  Score=136.23  Aligned_cols=149  Identities=19%  Similarity=0.334  Sum_probs=126.0

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ++.+++|||+|||.++-|.||.++|-+||.|..|.+..-.   ...+||||+|++..||+.|+...++..++|..|+|++
T Consensus         3 gr~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEf   79 (241)
T KOG0105|consen    3 GRNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEF   79 (241)
T ss_pred             CcccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEe
Confidence            4678999999999999999999999999999999885322   2347999999999999999999999999999999999


Q ss_pred             cccCccc------------------------ccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEE
Q 012257          116 SYRDPTI------------------------RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYG  171 (467)
Q Consensus       116 ~~~~~~~------------------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~a  171 (467)
                      .......                        ......+|.|.+||...+.++|+++..+.|.|-...+.++      +.+
T Consensus        80 prggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------g~G  153 (241)
T KOG0105|consen   80 PRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------GVG  153 (241)
T ss_pred             ccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------cce
Confidence            7654211                        1112347999999999999999999999999966666654      478


Q ss_pred             EEEeCCHHHHHHHHHHhcCCcc
Q 012257          172 FVQFDNEESAKSAIDKLNGMLL  193 (467)
Q Consensus       172 fV~f~~~~~A~~a~~~l~~~~~  193 (467)
                      .|+|...++.+-|+..|+...+
T Consensus       154 vV~~~r~eDMkYAvr~ld~~~~  175 (241)
T KOG0105|consen  154 VVEYLRKEDMKYAVRKLDDQKF  175 (241)
T ss_pred             eeeeeehhhHHHHHHhhccccc
Confidence            8999999999999999987654

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

Probab=99.79  E-value=5.7e-18  Score=157.57  Aligned_cols=263  Identities=22%  Similarity=0.411  Sum_probs=202.1

Q ss_pred             CCCCCCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcC-----------C-CeEEEEEEecCCCCccccEEEEEecChHHH
Q 012257           27 NNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQM-----------G-QVVSVRVCRDLSTRRSLGYGYVNYNAAHEA   94 (467)
Q Consensus        27 ~~~~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~-----------G-~v~~v~i~~~~~~~~~~g~afV~f~~~~~A   94 (467)
                      .....+....+..+.++|+++|..+.|+....+|..-           | .+..+.+-..+      ++||++|.+.++|
T Consensus       163 ~~~~~~~~~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~------nfa~ie~~s~~~a  236 (500)
T KOG0120|consen  163 PTPPMDSQATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEK------NFAFIEFRSISEA  236 (500)
T ss_pred             CCCccCcchhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccc------cceeEEecCCCch
Confidence            3344556667788999999999999999999988653           3 47778776665      4999999999999


Q ss_pred             HHHHHHhCCcccCCceeeeeecccCc---------------------ccccCCCccEEEcCCCCcCCHHHHHHHHhhcCC
Q 012257           95 TRALDELNFTPLNGKPIRIMYSYRDP---------------------TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN  153 (467)
Q Consensus        95 ~~A~~~l~~~~~~g~~~~v~~~~~~~---------------------~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~  153 (467)
                      ..|+. +++..+.|..+++......-                     +.......+++|++||..++++++++++..||.
T Consensus       237 t~~~~-~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~  315 (500)
T KOG0120|consen  237 TEAMA-LDGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGP  315 (500)
T ss_pred             hhhhc-ccchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhccc
Confidence            99997 78888999988875432210                     001123457999999999999999999999999


Q ss_pred             eEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEeccccccccccccccc-----------------
Q 012257          154 ILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADK-----------------  215 (467)
Q Consensus       154 v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~~~~~~~~~~-----------------  215 (467)
                      +....++.+ .+|.++||||.+|.++.....|+..|+|..+.++.+.+..+............                 
T Consensus       316 lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~  395 (500)
T KOG0120|consen  316 LKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMA  395 (500)
T ss_pred             chhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCccccccccchhhhcccC
Confidence            999999999 67999999999999999999999999999999999998766544332222111                 


Q ss_pred             -ccccceeecCC--CccC-C-------HHHHHHhhcccCCeeEEEEEEC-CC---CCceeEEEEEeCCHHHHHHHHHHhC
Q 012257          216 -TRFNNVYVKNL--SETT-T-------EDDLKKIFGEFGIITSTAVMRD-AD---GKSKCFGFVNFDDPDDAARSVEALN  280 (467)
Q Consensus       216 -~~~~~l~v~nl--p~~~-~-------~~~l~~~f~~~g~v~~~~~~~~-~~---~~~~g~afv~f~~~~~a~~a~~~l~  280 (467)
                       .....+.+.|+  +.+. +       .|+++..+.+||.|..|.+... ..   ....|-.||+|.+.++++.|+.+|+
T Consensus       396 g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~  475 (500)
T KOG0120|consen  396 GIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELT  475 (500)
T ss_pred             CCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHcc
Confidence             11122233332  1111 1       2445667889999999998877 33   2356778999999999999999999


Q ss_pred             CCccCCceEEEccccc
Q 012257          281 GKKFDDKEWYVGKAQK  296 (467)
Q Consensus       281 ~~~~~~~~l~~~~~~~  296 (467)
                      |.+|.++.+...+...
T Consensus       476 GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  476 GRKFANRTVVASYYDE  491 (500)
T ss_pred             CceeCCcEEEEEecCH
Confidence            9999999998877654

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

Probab=99.78  E-value=1.8e-18  Score=143.50  Aligned_cols=169  Identities=28%  Similarity=0.457  Sum_probs=142.6

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcc-cCC--ceeeee
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTP-LNG--KPIRIM  114 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~-~~g--~~~~v~  114 (467)
                      +.++|||+-|...-.|+|++++|..||.|.++.+++.. .|.++|||||.|.+-.+|+.||..|++.. .-|  ..+-|.
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            57999999999999999999999999999999999985 78999999999999999999999998642 322  334443


Q ss_pred             ecccCccc------------------------------------------------------------------------
Q 012257          115 YSYRDPTI------------------------------------------------------------------------  122 (467)
Q Consensus       115 ~~~~~~~~------------------------------------------------------------------------  122 (467)
                      ++....+.                                                                        
T Consensus        97 ~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A  176 (371)
T KOG0146|consen   97 FADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAA  176 (371)
T ss_pred             eccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhccccc
Confidence            33221000                                                                        


Q ss_pred             --------------------------------------------------------------------------------
Q 012257          123 --------------------------------------------------------------------------------  122 (467)
Q Consensus       123 --------------------------------------------------------------------------------  122 (467)
                                                                                                      
T Consensus       177 ~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aa  256 (371)
T KOG0146|consen  177 APVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAA  256 (371)
T ss_pred             CCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhh
Confidence                                                                                            


Q ss_pred             ------------------------ccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCC
Q 012257          123 ------------------------RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDN  177 (467)
Q Consensus       123 ------------------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~  177 (467)
                                              ...+.++|||..||....+.||-..|-.||.|.+.++..| -+..++-|+||.|.+
T Consensus       257 ypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDN  336 (371)
T KOG0146|consen  257 YPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDN  336 (371)
T ss_pred             cchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCC
Confidence                                    1123357999999999999999999999999999999888 788899999999999


Q ss_pred             HHHHHHHHHHhcCCccCCeeeEeccccccc
Q 012257          178 EESAKSAIDKLNGMLLNDKQVFVGPFLRKQ  207 (467)
Q Consensus       178 ~~~A~~a~~~l~~~~~~g~~~~v~~~~~~~  207 (467)
                      +..|+.||..+||..|.-++++|....++.
T Consensus       337 p~SaQaAIqAMNGFQIGMKRLKVQLKRPkd  366 (371)
T KOG0146|consen  337 PASAQAAIQAMNGFQIGMKRLKVQLKRPKD  366 (371)
T ss_pred             chhHHHHHHHhcchhhhhhhhhhhhcCccc
Confidence            999999999999999999999987655543

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

Probab=99.77  E-value=4.6e-18  Score=136.12  Aligned_cols=88  Identities=36%  Similarity=0.615  Sum_probs=81.1

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      ......+++|||+|||++++|++|+++|++||.|.++.+..|+.+++++|||||+|.+.++|++|++.|++..|.|+.|+
T Consensus        28 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~  107 (144)
T PLN03134         28 GSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIR  107 (144)
T ss_pred             ccccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            33345578999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecccCc
Q 012257          113 IMYSYRDP  120 (467)
Q Consensus       113 v~~~~~~~  120 (467)
                      |.++...+
T Consensus       108 V~~a~~~~  115 (144)
T PLN03134        108 VNPANDRP  115 (144)
T ss_pred             EEeCCcCC
Confidence            99986543

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

Probab=99.77  E-value=1e-18  Score=160.15  Aligned_cols=178  Identities=24%  Similarity=0.416  Sum_probs=148.1

Q ss_pred             ccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccc
Q 012257          216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA  294 (467)
Q Consensus       216 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~  294 (467)
                      ...+++|+.-+....+.-+|.++|+.+|.|.++.++.+ ..+.++|.+||+|.+.+....|+. |.|..+.|.++.+...
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            34477888888888999999999999999999999998 457799999999999999888885 9999999999999877


Q ss_pred             ccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHH
Q 012257          295 QKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAE  373 (467)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~  373 (467)
                      ........+......    ...-..+...|||+||-+++++++|+.+|++||.|+.|.+.++. +|.++||+||+|.+.+
T Consensus       256 Eaeknr~a~~s~a~~----~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~  331 (549)
T KOG0147|consen  256 EAEKNRAANASPALQ----GKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKE  331 (549)
T ss_pred             HHHHHHHHhcccccc----ccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHH
Confidence            654443221111111    01111122239999999999999999999999999999999998 9999999999999999


Q ss_pred             HHHHHHHHhCCcEecccceEEehhh
Q 012257          374 EASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       374 ~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      +|.+|++.|||..+-|+.|+|....
T Consensus       332 ~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  332 DARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             HHHHHHHHhccceecCceEEEEEee
Confidence            9999999999999999999998654

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

Probab=99.77  E-value=7.3e-18  Score=156.86  Aligned_cols=270  Identities=21%  Similarity=0.388  Sum_probs=200.2

Q ss_pred             CccEEEcCCCCcCCHHHHHHHHhhc-----------C-CeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccC
Q 012257          127 AGNIFIKNLDKSIDNKALHDTFSTF-----------G-NILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLN  194 (467)
Q Consensus       127 ~~~l~v~nlp~~~t~~~l~~~f~~~-----------g-~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~  194 (467)
                      ...++|+++|..+++++...+|..-           | .+..+.+..     .+++||++|.+.++|..|+. +++..+.
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            4579999999999999999988643           2 355555543     57899999999999999996 6788888


Q ss_pred             CeeeEecccccccccc-----------------cccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCC
Q 012257          195 DKQVFVGPFLRKQERE-----------------STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADG  256 (467)
Q Consensus       195 g~~~~v~~~~~~~~~~-----------------~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~  256 (467)
                      |..+.+..........                 ..........+++++||...++++++++...||.+....+..+ .+|
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            8777663322221111                 1111223357999999999999999999999999999999888 558


Q ss_pred             CceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccchHHHHHhhhhhh---hhhh---ccccCCCCceEEEecC-
Q 012257          257 KSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFE---QSLK---ETADKFEGLNLYVKNL-  329 (467)
Q Consensus       257 ~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~---~~~~---~~~~~~~~~~l~V~nl-  329 (467)
                      .++||||.+|.+......|++.|||..++++.+.+..+...............   ....   ......+...|...|+ 
T Consensus       329 ~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~V  408 (500)
T KOG0120|consen  329 NSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVV  408 (500)
T ss_pred             cccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcC
Confidence            89999999999999999999999999999999999888665433322222000   0000   0112223333444443 


Q ss_pred             -CCCC-CH-------HHHHHhhccCCceeEEEEeeC-CC---CCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          330 -DDSI-SD-------DKLKELFSEFGTITSCKVMRD-PN---GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       330 -p~~~-~~-------~~l~~~F~~~G~v~~v~i~~~-~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                       |.++ .+       ++++.-+++||.|.+|.+.++ .+   ..+.|..||+|++.+++++|+++|+|..|.|+.+..+|
T Consensus       409 t~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsY  488 (500)
T KOG0120|consen  409 TPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASY  488 (500)
T ss_pred             CHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEe
Confidence             1111 11       567777889999999999988 33   34578999999999999999999999999999999999


Q ss_pred             hhhhHH
Q 012257          397 AQRKEE  402 (467)
Q Consensus       397 ~~~~~~  402 (467)
                      ....+-
T Consensus       489 ydeDkY  494 (500)
T KOG0120|consen  489 YDEDKY  494 (500)
T ss_pred             cCHHHh
Confidence            876543

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

Probab=99.77  E-value=2.2e-17  Score=135.17  Aligned_cols=156  Identities=24%  Similarity=0.480  Sum_probs=132.8

Q ss_pred             ccCeEEEcCCCCCCCHHHHHH----HHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           38 VSTSLYVGDLDLSVNDSQLYD----LFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~----~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      +..||||.||+..+..++|++    +|+.||.|.+|...+   +.+.+|.|||.|.+.+.|..|+..|+|.+|.|+.++|
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            345999999999999999887    999999999999884   5668899999999999999999999999999999999


Q ss_pred             eecccCcccc------------------------------------------------cCCCccEEEcCCCCcCCHHHHH
Q 012257          114 MYSYRDPTIR------------------------------------------------KSGAGNIFIKNLDKSIDNKALH  145 (467)
Q Consensus       114 ~~~~~~~~~~------------------------------------------------~~~~~~l~v~nlp~~~t~~~l~  145 (467)
                      .++..+...-                                                ......+++.|||..++.+.+.
T Consensus        85 qyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~  164 (221)
T KOG4206|consen   85 QYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLS  164 (221)
T ss_pred             ecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHH
Confidence            9876542110                                                1112458999999999999999


Q ss_pred             HHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccC-CeeeEe
Q 012257          146 DTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLN-DKQVFV  200 (467)
Q Consensus       146 ~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~-g~~~~v  200 (467)
                      .+|..|....+++++..    .++.|||+|.+...|..|...+++..+. ...+.+
T Consensus       165 ~lf~qf~g~keir~i~~----~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i  216 (221)
T KOG4206|consen  165 DLFEQFPGFKEIRLIPP----RSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQI  216 (221)
T ss_pred             HHHhhCcccceeEeccC----CCceeEEecchhhhhHHHhhhhccceeccCceEEe
Confidence            99999999999998874    5679999999999999999999887765 445544

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

Probab=99.76  E-value=5.4e-17  Score=131.29  Aligned_cols=153  Identities=19%  Similarity=0.324  Sum_probs=118.8

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEE-EecCCCCccccEEEEEecChHHHHHHHHHhCCccc---CCceeee
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRV-CRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL---NGKPIRI  113 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i-~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~---~g~~~~v  113 (467)
                      .-|+|||++||.++...||+.+|++|--.+...+ ..++...-.+.+|||+|.+.++|..|++.|||..|   .+..++|
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhi  112 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHI  112 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEe
Confidence            3699999999999999999999999833333333 33444344568999999999999999999999987   5788888


Q ss_pred             eecccCcccccC--------------------------------------------------------------------
Q 012257          114 MYSYRDPTIRKS--------------------------------------------------------------------  125 (467)
Q Consensus       114 ~~~~~~~~~~~~--------------------------------------------------------------------  125 (467)
                      ..++.+....+.                                                                    
T Consensus       113 ElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~  192 (284)
T KOG1457|consen  113 ELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPS  192 (284)
T ss_pred             eehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCc
Confidence            876654211000                                                                    


Q ss_pred             ----------------CCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhc
Q 012257          126 ----------------GAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN  189 (467)
Q Consensus       126 ----------------~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~  189 (467)
                                      ...+|||.||..++++++|+.+|++|......+|... .  ....||++|++.+.|..|+..|+
T Consensus       193 a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~-~--g~~vaf~~~~~~~~at~am~~lq  269 (284)
T KOG1457|consen  193 ANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR-G--GMPVAFADFEEIEQATDAMNHLQ  269 (284)
T ss_pred             ccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC-C--CcceEeecHHHHHHHHHHHHHhh
Confidence                            0125999999999999999999999986655555432 2  34579999999999999999999


Q ss_pred             CCcc
Q 012257          190 GMLL  193 (467)
Q Consensus       190 ~~~~  193 (467)
                      |..+
T Consensus       270 g~~~  273 (284)
T KOG1457|consen  270 GNLL  273 (284)
T ss_pred             ccee
Confidence            8765

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

Probab=99.74  E-value=5e-17  Score=133.17  Aligned_cols=174  Identities=22%  Similarity=0.397  Sum_probs=142.7

Q ss_pred             cceeecCCCccCCHHHHHH----hhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccc
Q 012257          219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA  294 (467)
Q Consensus       219 ~~l~v~nlp~~~~~~~l~~----~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~  294 (467)
                      .+|||.||...+..++|+.    +|++||.|.+|....  +.+.+|.|||.|.+.+.|..|+.+|+|..+.|+.+++.++
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k--t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA   87 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK--TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYA   87 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC--CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecc
Confidence            4899999999999999888    999999998887664  5567999999999999999999999999999999999999


Q ss_pred             ccchHHHHHhhhhhhh------------------hhh--------------ccccCCCCceEEEecCCCCCCHHHHHHhh
Q 012257          295 QKKYEREMELKGKFEQ------------------SLK--------------ETADKFEGLNLYVKNLDDSISDDKLKELF  342 (467)
Q Consensus       295 ~~~~~~~~~~~~~~~~------------------~~~--------------~~~~~~~~~~l~V~nlp~~~~~~~l~~~F  342 (467)
                      +.+........+....                  ...              ......+...||+.|||..++.+.+..+|
T Consensus        88 ~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~lf  167 (221)
T KOG4206|consen   88 KSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDLF  167 (221)
T ss_pred             cCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHHH
Confidence            8664332221100000                  000              01224566789999999999999999999


Q ss_pred             ccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEec-ccceEEehhh
Q 012257          343 SEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVV-SKPLYVALAQ  398 (467)
Q Consensus       343 ~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~v~~~~  398 (467)
                      .+|..-++++++...    ++.|||+|.+...|..|...|+|..+- ...+.|.|++
T Consensus       168 ~qf~g~keir~i~~~----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  168 EQFPGFKEIRLIPPR----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             hhCcccceeEeccCC----CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            999999999998863    469999999999999999999999996 7788888874

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

Probab=99.73  E-value=1.3e-17  Score=147.94  Aligned_cols=244  Identities=25%  Similarity=0.402  Sum_probs=182.4

Q ss_pred             CCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEecccc
Q 012257          126 GAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFL  204 (467)
Q Consensus       126 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~  204 (467)
                      +.+++||++|+.+++++.|++.|..||+|.+|.++++ .++.+++|+||+|++++....++. ...+.+.|+.|....+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            5679999999999999999999999999999999999 779999999999999999999986 35678999999998888


Q ss_pred             cccccccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCc
Q 012257          205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKK  283 (467)
Q Consensus       205 ~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~  283 (467)
                      ................++|++||..++++++++.|++||.|..+.++.+ ...+.+||+||.|.+.++...++. ..-+.
T Consensus        84 ~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~  162 (311)
T KOG4205|consen   84 SREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHD  162 (311)
T ss_pred             CcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceee
Confidence            8777666666667789999999999999999999999999999988888 557899999999999998888876 67888


Q ss_pred             cCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEe------eCC
Q 012257          284 FDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVM------RDP  357 (467)
Q Consensus       284 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~------~~~  357 (467)
                      +.++.+.+..+.++............             .....++....+--.|..+|.-||.+-...--      +-.
T Consensus       163 ~~gk~vevkrA~pk~~~~~~~~~~~~-------------~~~~~~~g~~~~~~~l~~~~~g~~~~~~~~~~~~~~~~~~~  229 (311)
T KOG4205|consen  163 FNGKKVEVKRAIPKEVMQSTKSSVST-------------RGKGNNLGNGRTGFFLKKYFKGYGPVGMSDYGGRPVGRRYG  229 (311)
T ss_pred             ecCceeeEeeccchhhcccccccccc-------------ccccccccccccccccchhccccCccccccccccccccccc
Confidence            99999999998876443221111000             01111333333333444555555444210000      000


Q ss_pred             CCCccceEEEEcCCHHHHHHHHHHhCC
Q 012257          358 NGISRGSGFVAFSTAEEASKALTEMNG  384 (467)
Q Consensus       358 ~~~~~g~afV~f~~~~~A~~A~~~l~g  384 (467)
                      ...+.+.+|..|........+...+++
T Consensus       230 ~~~~~g~g~~~~~~~~~~~~~~~~~~~  256 (311)
T KOG4205|consen  230 PLFNGGSGYPEFGNSGLGFGYGNKLNR  256 (311)
T ss_pred             cccCCCccccccCccccccccccccCC
Confidence            012456888888877766665555444

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

Probab=99.73  E-value=3.9e-16  Score=135.87  Aligned_cols=260  Identities=19%  Similarity=0.283  Sum_probs=198.0

Q ss_pred             CccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhc--CCccCCeeeEecccc
Q 012257          127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN--GMLLNDKQVFVGPFL  204 (467)
Q Consensus       127 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~--~~~~~g~~~~v~~~~  204 (467)
                      +--|.|++|-..+++.+|.+.++.||.|..+..+.     .++.|.|+|++.+.|..++....  ...+.|....+.++.
T Consensus        31 spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P-----~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NySt  105 (494)
T KOG1456|consen   31 SPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMP-----HKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYST  105 (494)
T ss_pred             CceEEEeccccccchhHHHHHHhcCCceEEEEecc-----ccceeeeeeccccchhhheehhccCcccccCchhhcccch
Confidence            34689999999999999999999999998777664     56789999999999999997543  335778877777776


Q ss_pred             ccccccccccccccccee---ecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCC
Q 012257          205 RKQERESTADKTRFNNVY---VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNG  281 (467)
Q Consensus       205 ~~~~~~~~~~~~~~~~l~---v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  281 (467)
                      .+...+........+.+.   |-|--..++.+-|..++...|.|.+|.+...    +.-.|+|+|++.+.|++|..+|||
T Consensus       106 sq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk----ngVQAmVEFdsv~~AqrAk~alNG  181 (494)
T KOG1456|consen  106 SQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK----NGVQAMVEFDSVEVAQRAKAALNG  181 (494)
T ss_pred             hhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec----cceeeEEeechhHHHHHHHhhccc
Confidence            655554444433334333   3455567899999999999999999999875    334899999999999999999999


Q ss_pred             CccCC--ceEEEcccccchHH-------HHH--------------------------------hhhhh----h-------
Q 012257          282 KKFDD--KEWYVGKAQKKYER-------EME--------------------------------LKGKF----E-------  309 (467)
Q Consensus       282 ~~~~~--~~l~~~~~~~~~~~-------~~~--------------------------------~~~~~----~-------  309 (467)
                      ..+..  ..|++.++++...+       .+.                                +.+..    .       
T Consensus       182 ADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~  261 (494)
T KOG1456|consen  182 ADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPP  261 (494)
T ss_pred             ccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCC
Confidence            98764  35666666532100       000                                00000    0       


Q ss_pred             --------------hhhhccccCCCCceEEEecCC-CCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHH
Q 012257          310 --------------QSLKETADKFEGLNLYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEE  374 (467)
Q Consensus       310 --------------~~~~~~~~~~~~~~l~V~nlp-~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~  374 (467)
                                    ..........+++.+.|.+|. ..++.+.|..+|..||.|++|++++.+.    |.|.|++.|..+
T Consensus       262 ~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~----gtamVemgd~~a  337 (494)
T KOG1456|consen  262 HPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKP----GTAMVEMGDAYA  337 (494)
T ss_pred             CCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeeccc----ceeEEEcCcHHH
Confidence                          000001223456789999998 5679999999999999999999999865    489999999999


Q ss_pred             HHHHHHHhCCcEecccceEEehhhh
Q 012257          375 ASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       375 A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      .++|+..||+..+-|.+|.|.+++.
T Consensus       338 ver~v~hLnn~~lfG~kl~v~~SkQ  362 (494)
T KOG1456|consen  338 VERAVTHLNNIPLFGGKLNVCVSKQ  362 (494)
T ss_pred             HHHHHHHhccCccccceEEEeeccc
Confidence            9999999999999999999988763

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

Probab=99.72  E-value=3.1e-17  Score=131.35  Aligned_cols=82  Identities=32%  Similarity=0.558  Sum_probs=76.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ...++|||+|||..+++++|+++|++||.|.+++++.+. +++++|||||+|.+.++|++|++.||+..|+|+.|+|+++
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            356689999999999999999999999999999999887 7889999999999999999999999999999999999998


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ..+
T Consensus       112 ~~~  114 (144)
T PLN03134        112 NDR  114 (144)
T ss_pred             CcC
Confidence            754

>PF00076 RRM_1: RNA recognition motif

Probab=99.66  E-value=5.7e-16  Score=109.40  Aligned_cols=70  Identities=44%  Similarity=0.797  Sum_probs=67.5

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceE
Q 012257          324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY  393 (467)
Q Consensus       324 l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  393 (467)
                      |||+|||..+++++|+++|++||.|..+++..+..+..+++|||+|.+.++|.+|++.|+|..++|+.|+
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            7999999999999999999999999999999988888999999999999999999999999999999885

(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 ....

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

Probab=99.65  E-value=1.3e-15  Score=125.48  Aligned_cols=82  Identities=24%  Similarity=0.426  Sum_probs=79.0

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ++++|.|.||+.+++|++|+++|.+||.|..|.+.+|+.||.++|||||.|.+.+||++|++.|++.-++.--|+|+|+.
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             cC
Q 012257          118 RD  119 (467)
Q Consensus       118 ~~  119 (467)
                      +.
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            54

>PF00076 RRM_1: RNA recognition motif

Probab=99.65  E-value=1.1e-15  Score=107.99  Aligned_cols=70  Identities=41%  Similarity=0.788  Sum_probs=67.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        42 l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      |||+|||+++++++|+++|+.||.|..+.+..+ .+++++++|||+|.+.++|++|++.+++..+.|+.|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999998 6788999999999999999999999999999999885

(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 ....

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

Probab=99.63  E-value=3.5e-15  Score=117.24  Aligned_cols=164  Identities=21%  Similarity=0.315  Sum_probs=130.6

Q ss_pred             cccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccccc
Q 012257          217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQK  296 (467)
Q Consensus       217 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~  296 (467)
                      ....|+|+|||.++.+.+|.++|-+||.|..|.+.....  .-.||||+|++..+|..|+..-+|..++|..|.|.++..
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g--~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPG--PPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCC--CCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            347899999999999999999999999999999865432  245999999999999999999999999999999998865


Q ss_pred             chHHHHHhhhhh--------hhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEE
Q 012257          297 KYEREMELKGKF--------EQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVA  368 (467)
Q Consensus       297 ~~~~~~~~~~~~--------~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~  368 (467)
                      ............        .....-....-....|.|.+||..-++++|+++..+-|.|....+.++      |.+.|+
T Consensus        83 gr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------g~GvV~  156 (241)
T KOG0105|consen   83 GRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------GVGVVE  156 (241)
T ss_pred             CCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------cceeee
Confidence            421110000000        000011122234457999999999999999999999999999998887      489999


Q ss_pred             cCCHHHHHHHHHHhCCcEec
Q 012257          369 FSTAEEASKALTEMNGKMVV  388 (467)
Q Consensus       369 f~~~~~A~~A~~~l~g~~~~  388 (467)
                      |...++-.-|+..|+...+.
T Consensus       157 ~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  157 YLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             eeehhhHHHHHHhhcccccc
Confidence            99999999999999988774

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

Probab=99.63  E-value=5.4e-15  Score=138.72  Aligned_cols=165  Identities=10%  Similarity=0.028  Sum_probs=129.7

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .+.+.+-+.+.+.++++.+++++|... .|.++.|..+...+...|-++|.|....++++|++ .+...+-.+.+.+...
T Consensus       309 ~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~-rn~~~~~~R~~q~~P~  386 (944)
T KOG4307|consen  309 SDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFT-RNPSDDVNRPFQTGPP  386 (944)
T ss_pred             chhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHh-cCchhhhhcceeecCC
Confidence            456778889999999999999999765 56677777776555557899999999999999997 5666677777777443


Q ss_pred             ccCc-------------------------------------ccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEE-EE
Q 012257          117 YRDP-------------------------------------TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILS-CK  158 (467)
Q Consensus       117 ~~~~-------------------------------------~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~-~~  158 (467)
                      ....                                     ........+|+|..||..+++.++.++|...-.|++ |.
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            2110                                     011122357999999999999999999998878877 66


Q ss_pred             EeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEeccc
Q 012257          159 VATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPF  203 (467)
Q Consensus       159 ~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~  203 (467)
                      +-..++++.++.|||.|.+++++..|...-+.+.+..+.|.|...
T Consensus       467 lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  467 LTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             eccCCcccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence            666688889999999999999999998766677777888887443

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

Probab=99.62  E-value=9.9e-16  Score=131.38  Aligned_cols=82  Identities=27%  Similarity=0.471  Sum_probs=76.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....+.|+|+|||+...|-||+..|.+||.|.+|.|+.+..| +|||+||+|++.+||.+|.++|||..+.||+|.|..+
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            345568999999999999999999999999999999999877 6999999999999999999999999999999999987


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ..+
T Consensus       172 Tar  174 (376)
T KOG0125|consen  172 TAR  174 (376)
T ss_pred             chh
Confidence            644

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

Probab=99.61  E-value=1.4e-15  Score=111.90  Aligned_cols=85  Identities=27%  Similarity=0.471  Sum_probs=80.4

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ..+.|++|||+||..-++||.|+++|+++|+|..|.+-.|+.+....|||||+|-+.+||..|++-++++.++.+.|++-
T Consensus        32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ecccC
Q 012257          115 YSYRD  119 (467)
Q Consensus       115 ~~~~~  119 (467)
                      |....
T Consensus       112 ~D~GF  116 (153)
T KOG0121|consen  112 WDAGF  116 (153)
T ss_pred             ccccc
Confidence            87543

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

Probab=99.61  E-value=1.5e-15  Score=124.74  Aligned_cols=79  Identities=32%  Similarity=0.505  Sum_probs=72.5

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      -++|||+||+|++..++|+++|++||+|++..|+.|+.+|+|+||+||+|++.++|.+|++.-+ -.|+||+..++.+..
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccccchhhh
Confidence            5899999999999999999999999999999999999999999999999999999999998543 358999998877654

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

Probab=99.60  E-value=2e-15  Score=124.29  Aligned_cols=81  Identities=32%  Similarity=0.569  Sum_probs=77.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      +..+|.|.||+.+++|++|+++|.+||.|.++.|.+++ +|.++|||||.|.++++|.+||+.|||+-++.=-|+|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            66689999999999999999999999999999999998 89999999999999999999999999999999999999998


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ++
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            75

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.60  E-value=5.9e-15  Score=103.90  Aligned_cols=70  Identities=29%  Similarity=0.617  Sum_probs=64.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        42 l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      |+|+|||+++++++|+++|+.||.|..+.+..++. +.++++|||+|.+.++|.+|++.+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999977 89999999999999999999999888999999875

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 ....

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.60  E-value=6.8e-15  Score=103.56  Aligned_cols=70  Identities=36%  Similarity=0.710  Sum_probs=65.3

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceE
Q 012257          324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY  393 (467)
Q Consensus       324 l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  393 (467)
                      |+|+|||..+++++|+++|+.||.|..+++..++++.++++|||+|.+.++|.+|+..++|..++|+.|+
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            7999999999999999999999999999999998888999999999999999999999999999999874

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 ....

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

Probab=99.58  E-value=2.1e-13  Score=118.20  Aligned_cols=165  Identities=21%  Similarity=0.354  Sum_probs=133.4

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeE--------EEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVV--------SVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK  109 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~--------~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  109 (467)
                      -++.|||+|||.++|.+++.++|++||.|.        .|++.++.. |.-+|=|++.|-..++...|++.|++..+.|+
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            367799999999999999999999999553        478888875 88999999999999999999999999999999


Q ss_pred             eeeeeecccC------------------------------------cccccCCCccEEEcCC--CCc--CC-------HH
Q 012257          110 PIRIMYSYRD------------------------------------PTIRKSGAGNIFIKNL--DKS--ID-------NK  142 (467)
Q Consensus       110 ~~~v~~~~~~------------------------------------~~~~~~~~~~l~v~nl--p~~--~t-------~~  142 (467)
                      .++|..+.-.                                    ...+....++|.+.|+  |..  .+       .+
T Consensus       212 ~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlke  291 (382)
T KOG1548|consen  212 KLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKE  291 (382)
T ss_pred             EEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHH
Confidence            9999765210                                    0011223457888887  222  22       45


Q ss_pred             HHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEecccccc
Q 012257          143 ALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRK  206 (467)
Q Consensus       143 ~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~  206 (467)
                      +|++-.++||.|.++.+...   .+.|.+-|.|.+.++|..|++.|+|+.+.|+.|.....-..
T Consensus       292 dl~eec~K~G~v~~vvv~d~---hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  292 DLTEECEKFGQVRKVVVYDR---HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHhCCcceEEEecc---CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            66777899999999988754   35678999999999999999999999999999988655443

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

Probab=99.58  E-value=5.9e-15  Score=115.24  Aligned_cols=78  Identities=28%  Similarity=0.494  Sum_probs=72.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      .++|||+||+..+++.||+..|..||+|.+|||-+.+.     |||||+|+++.||++|+..|++..|+|..++|+.+..
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPP-----GfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPP-----GFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCC-----CceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            68999999999999999999999999999999987554     7999999999999999999999999999999998865


Q ss_pred             Ccc
Q 012257          119 DPT  121 (467)
Q Consensus       119 ~~~  121 (467)
                      .+.
T Consensus        85 ~~r   87 (195)
T KOG0107|consen   85 RPR   87 (195)
T ss_pred             Ccc
Confidence            543

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

Probab=99.57  E-value=3.3e-14  Score=115.32  Aligned_cols=170  Identities=21%  Similarity=0.336  Sum_probs=122.7

Q ss_pred             ccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCC--CceeEEEEEeCCHHHHHHHHHHhCCCccCC---ceEE
Q 012257          216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG--KSKCFGFVNFDDPDDAARSVEALNGKKFDD---KEWY  290 (467)
Q Consensus       216 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~--~~~g~afv~f~~~~~a~~a~~~l~~~~~~~---~~l~  290 (467)
                      ...++|||.+||.++...+|..+|..|-.-+...+.....+  ..+.+||++|.+..+|..|++.|||..|+.   ..|+
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            34589999999999999999999999877666666554222  245699999999999999999999999874   4666


Q ss_pred             EcccccchHHHHHhhhh--------------hhhh------------------------------------------h--
Q 012257          291 VGKAQKKYEREMELKGK--------------FEQS------------------------------------------L--  312 (467)
Q Consensus       291 ~~~~~~~~~~~~~~~~~--------------~~~~------------------------------------------~--  312 (467)
                      +..++............              ..+.                                          +  
T Consensus       112 iElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P  191 (284)
T KOG1457|consen  112 IELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAP  191 (284)
T ss_pred             eeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCC
Confidence            66654321110000000              0000                                          0  


Q ss_pred             ----------hccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHh
Q 012257          313 ----------KETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM  382 (467)
Q Consensus       313 ----------~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l  382 (467)
                                ........+.+|||.||..+++|++|+.+|+.|-....++|.. .+|  ...||++|++.+.|..||..|
T Consensus       192 ~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~-~~g--~~vaf~~~~~~~~at~am~~l  268 (284)
T KOG1457|consen  192 SANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA-RGG--MPVAFADFEEIEQATDAMNHL  268 (284)
T ss_pred             cccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec-CCC--cceEeecHHHHHHHHHHHHHh
Confidence                      0000111244799999999999999999999998777666643 333  459999999999999999999


Q ss_pred             CCcEec
Q 012257          383 NGKMVV  388 (467)
Q Consensus       383 ~g~~~~  388 (467)
                      +|..+.
T Consensus       269 qg~~~s  274 (284)
T KOG1457|consen  269 QGNLLS  274 (284)
T ss_pred             hcceec
Confidence            999884

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

Probab=99.55  E-value=2e-13  Score=118.27  Aligned_cols=177  Identities=21%  Similarity=0.309  Sum_probs=138.0

Q ss_pred             ccceeecCCCccCCHHHHHHhhcccCCeeE--------EEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceE
Q 012257          218 FNNVYVKNLSETTTEDDLKKIFGEFGIITS--------TAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEW  289 (467)
Q Consensus       218 ~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~--------~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l  289 (467)
                      ...|||+|||.++|.+++.++|+++|-|..        +++.++..|..+|-|.+.|...++...|+..|++..+.|+.+
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            356999999999999999999999998765        788888899999999999999999999999999999999999


Q ss_pred             EEcccccchHHHHHhhhh-----------hhh---------hhhccccCCCCceEEEecCC----CCCC-------HHHH
Q 012257          290 YVGKAQKKYEREMELKGK-----------FEQ---------SLKETADKFEGLNLYVKNLD----DSIS-------DDKL  338 (467)
Q Consensus       290 ~~~~~~~~~~~~~~~~~~-----------~~~---------~~~~~~~~~~~~~l~V~nlp----~~~~-------~~~l  338 (467)
                      +|..|+-...........           ...         ........-..++|.+.|+-    ...+       .++|
T Consensus       214 rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl  293 (382)
T KOG1548|consen  214 RVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDL  293 (382)
T ss_pred             EEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHH
Confidence            998886322111110000           000         00112223345689999983    2233       3677


Q ss_pred             HHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          339 KELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       339 ~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ++-+++||.|.+|.|.-..   +.|.+-|.|.+.++|..||..|+|++|+|+.|..+..
T Consensus       294 ~eec~K~G~v~~vvv~d~h---PdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~  349 (382)
T KOG1548|consen  294 TEECEKFGQVRKVVVYDRH---PDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIW  349 (382)
T ss_pred             HHHHHHhCCcceEEEeccC---CCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEe
Confidence            7789999999999887542   4679999999999999999999999999999988764

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

Probab=99.55  E-value=9.8e-15  Score=121.35  Aligned_cols=148  Identities=23%  Similarity=0.472  Sum_probs=126.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecccC
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRD  119 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~  119 (467)
                      .++||++||+.+.+.+|.++|..||.+.++.+..        ||+||+|.+..||..|+..+++..+.|-.+-+.++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            5799999999999999999999999999988742        58999999999999999999999999988888776631


Q ss_pred             ------cc------------cccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHH
Q 012257          120 ------PT------------IRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESA  181 (467)
Q Consensus       120 ------~~------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A  181 (467)
                            +.            ........+.+.+++..+...+|...|..+|.+....+       ..+++||+|++.++|
T Consensus        74 ~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-------~~~~~~v~Fs~~~da  146 (216)
T KOG0106|consen   74 RRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-------RRNFAFVEFSEQEDA  146 (216)
T ss_pred             ccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh-------hccccceeehhhhhh
Confidence                  00            01223457999999999999999999999999954443       467899999999999


Q ss_pred             HHHHHHhcCCccCCeeeEecc
Q 012257          182 KSAIDKLNGMLLNDKQVFVGP  202 (467)
Q Consensus       182 ~~a~~~l~~~~~~g~~~~v~~  202 (467)
                      .+|+..|++..+.++.|.+..
T Consensus       147 ~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  147 KRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             hhcchhccchhhcCceeeecc
Confidence            999999999999999999843

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

Probab=99.55  E-value=5.4e-15  Score=122.87  Aligned_cols=165  Identities=29%  Similarity=0.453  Sum_probs=130.8

Q ss_pred             ceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccchH
Q 012257          220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYE  299 (467)
Q Consensus       220 ~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~  299 (467)
                      .+||+++++...+.++..+|..||.+.++.+.       .||+||+|.+..+|..|+..+++..+.+..+.+.++.....
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk-------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~   75 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK-------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRR   75 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee-------cccceeccCchhhhhcccchhcCceecceeeeeeccccccc
Confidence            58999999999999999999999999999886       45999999999999999999999999999888877764211


Q ss_pred             HHHHhh-hhhh-hhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHH
Q 012257          300 REMELK-GKFE-QSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASK  377 (467)
Q Consensus       300 ~~~~~~-~~~~-~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~  377 (467)
                      ...... +.-. .........-..+.+.|.++...+.+.+|.+.|+++|.+......       ++++||+|.+.++|.+
T Consensus        76 ~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~-------~~~~~v~Fs~~~da~r  148 (216)
T KOG0106|consen   76 GRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR-------RNFAFVEFSEQEDAKR  148 (216)
T ss_pred             ccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhhh-------ccccceeehhhhhhhh
Confidence            110000 0000 011111223355679999999999999999999999999655552       4599999999999999


Q ss_pred             HHHHhCCcEecccceEEehhh
Q 012257          378 ALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       378 A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      |++.|+|..+.|+.|.+...-
T Consensus       149 a~~~l~~~~~~~~~l~~~~~~  169 (216)
T KOG0106|consen  149 ALEKLDGKKLNGRRISVEKNS  169 (216)
T ss_pred             cchhccchhhcCceeeecccC
Confidence            999999999999999995543

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

Probab=99.55  E-value=1.5e-14  Score=118.79  Aligned_cols=78  Identities=28%  Similarity=0.467  Sum_probs=71.0

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      -.+|||+||++++..++|+++|++||+|+++.|+.|+ +|+++||+||+|.|.++|.+|++. -+-.|+||+-.|.+|.-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhhh
Confidence            3479999999999999999999999999999999987 899999999999999999999984 45788999999988764

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

Probab=99.54  E-value=8.4e-15  Score=117.29  Aligned_cols=80  Identities=31%  Similarity=0.476  Sum_probs=75.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ...+|.|.||.+.++.++|+.+|++||.|-+|.|+.+. ++.++|||||.|.+..+|+.|+++|+|..++|+.|+|++|+
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            44579999999999999999999999999999999998 88899999999999999999999999999999999999987


Q ss_pred             h
Q 012257          399 R  399 (467)
Q Consensus       399 ~  399 (467)
                      -
T Consensus        92 y   92 (256)
T KOG4207|consen   92 Y   92 (256)
T ss_pred             c
Confidence            3

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

Probab=99.54  E-value=3.7e-14  Score=121.85  Aligned_cols=78  Identities=27%  Similarity=0.466  Sum_probs=72.5

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      .++|+|+|||....|.||+..|.+||.|++|.|+-..  ..||||+||+|++.+||++|.++|++..+.||.|.|+.+..
T Consensus        96 pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125|consen   96 PKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             CceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence            5789999999999999999999999999999999864  35899999999999999999999999999999999987653

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.54  E-value=3.1e-14  Score=121.65  Aligned_cols=77  Identities=21%  Similarity=0.325  Sum_probs=70.6

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      .++|||+||++.+++++|+++|+.||.|++|+|+.+..  .+|||||+|.+.++|..|+. |+|..|+|+.|+|.++...
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCC
Confidence            46899999999999999999999999999999998753  46899999999999999995 9999999999999987643

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

Probab=99.53  E-value=1.6e-14  Score=112.82  Aligned_cols=77  Identities=27%  Similarity=0.493  Sum_probs=71.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ..+.|||+||+..+++.||..+|..||.+.+|.|-.+    +.|||||+|++..||..|+..|+|..|+|..|+|+++..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            4568999999999999999999999999999999886    457999999999999999999999999999999999864


Q ss_pred             h
Q 012257          400 K  400 (467)
Q Consensus       400 ~  400 (467)
                      .
T Consensus        85 ~   85 (195)
T KOG0107|consen   85 R   85 (195)
T ss_pred             C
Confidence            4

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

Probab=99.53  E-value=1.9e-14  Score=115.24  Aligned_cols=84  Identities=29%  Similarity=0.438  Sum_probs=79.0

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ..-...++|.|-||-+.++.++|+.+|++||.|-+|.|.+|+.|+.++|||||.|.+..||++|++.|++..++|+.|+|
T Consensus         8 Pdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrV   87 (256)
T KOG4207|consen    8 PDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRV   87 (256)
T ss_pred             CCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeee
Confidence            33445899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecc
Q 012257          114 MYSY  117 (467)
Q Consensus       114 ~~~~  117 (467)
                      ..+.
T Consensus        88 q~ar   91 (256)
T KOG4207|consen   88 QMAR   91 (256)
T ss_pred             hhhh
Confidence            7764

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.51  E-value=8.2e-14  Score=119.11  Aligned_cols=76  Identities=16%  Similarity=0.258  Sum_probs=70.5

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      .++|||+|||+.++|++|+++|+.||.|.+|.|.+++.   ++|||||+|.+.++|+.|+. |++..|.|+.|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            68999999999999999999999999999999998864   45899999999999999996 999999999999998753

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

Probab=99.49  E-value=6.7e-14  Score=103.16  Aligned_cols=84  Identities=24%  Similarity=0.356  Sum_probs=75.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      .+++|||+||.+.++|+.|.++|+++|.|+.|.+-.+. +..+-|||||+|-+.++|..|+.-++|..++.+.|++.|..
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            45689999999999999999999999999999887776 44567999999999999999999999999999999999987


Q ss_pred             hhHHH
Q 012257          399 RKEER  403 (467)
Q Consensus       399 ~~~~~  403 (467)
                      .-.+.
T Consensus       115 GF~eG  119 (153)
T KOG0121|consen  115 GFVEG  119 (153)
T ss_pred             cchhh
Confidence            66543

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

Probab=99.48  E-value=1.8e-13  Score=116.25  Aligned_cols=86  Identities=22%  Similarity=0.395  Sum_probs=79.2

Q ss_pred             CCCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCc
Q 012257           30 GVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK  109 (467)
Q Consensus        30 ~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  109 (467)
                      ....+...+=+||||+-|+++++|.+|+..|+.||+|+.|.|++|+.||+++|||||+|.+..+-..|.+..++..|+|+
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            34444556789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeeee
Q 012257          110 PIRIMY  115 (467)
Q Consensus       110 ~~~v~~  115 (467)
                      .|-|-.
T Consensus       172 ri~VDv  177 (335)
T KOG0113|consen  172 RILVDV  177 (335)
T ss_pred             EEEEEe
Confidence            998743

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

Probab=99.48  E-value=1.1e-13  Score=102.98  Aligned_cols=90  Identities=22%  Similarity=0.379  Sum_probs=84.2

Q ss_pred             CCCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCc
Q 012257           30 GVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK  109 (467)
Q Consensus        30 ~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  109 (467)
                      .++|.++-+.=.|||.++...++|++|.+.|..||+|++|.+-.|++||..+|||+|+|++.++|+.|+..+|+..+.|.
T Consensus        63 ~pgPqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q  142 (170)
T KOG0130|consen   63 RPGPQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQ  142 (170)
T ss_pred             CCCCccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCC
Confidence            45566777788899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeeeecccC
Q 012257          110 PIRIMYSYRD  119 (467)
Q Consensus       110 ~~~v~~~~~~  119 (467)
                      .+.|-|+...
T Consensus       143 ~v~VDw~Fv~  152 (170)
T KOG0130|consen  143 NVSVDWCFVK  152 (170)
T ss_pred             ceeEEEEEec
Confidence            9999998654

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

Probab=99.48  E-value=6.6e-13  Score=122.66  Aligned_cols=124  Identities=28%  Similarity=0.563  Sum_probs=108.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc-
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY-  117 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~-  117 (467)
                      .++|||+|||.++++++|+++|..||.|..+.+..++.+++++|+|||.|.+.++|..|+..+++..|.|+.++|.+.. 
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            6999999999999999999999999999999999999899999999999999999999999999999999999999853 


Q ss_pred             ---cCccc------------------ccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC
Q 012257          118 ---RDPTI------------------RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD  162 (467)
Q Consensus       118 ---~~~~~------------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~  162 (467)
                         .....                  .......+++.+++..++..++...|..+|.+....+...
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPS  260 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCC
Confidence               11111                  1122356899999999999999999999999966665544

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

Probab=99.48  E-value=3.9e-13  Score=95.20  Aligned_cols=82  Identities=23%  Similarity=0.468  Sum_probs=73.7

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ....++-|||+|||.+++.++.+++|.+||+|..|+|-..+.|   +|.|||.|++..||.+|+..|++..+.++.+.|.
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vl   90 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVL   90 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEE
Confidence            3455899999999999999999999999999999999876654   5899999999999999999999999999999998


Q ss_pred             ecccC
Q 012257          115 YSYRD  119 (467)
Q Consensus       115 ~~~~~  119 (467)
                      +....
T Consensus        91 yyq~~   95 (124)
T KOG0114|consen   91 YYQPE   95 (124)
T ss_pred             ecCHH
Confidence            76544

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

Probab=99.47  E-value=2.9e-13  Score=95.84  Aligned_cols=82  Identities=27%  Similarity=0.436  Sum_probs=73.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ...+.|||.|||+.+|.++..++|.+||.|..++|-..+.  .+|.|||.|++..+|.+|+..|+|..++++.|.|-|-.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~--TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE--TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC--cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            3456799999999999999999999999999999876543  47899999999999999999999999999999999877


Q ss_pred             hhHH
Q 012257          399 RKEE  402 (467)
Q Consensus       399 ~~~~  402 (467)
                      +...
T Consensus        94 ~~~~   97 (124)
T KOG0114|consen   94 PEDA   97 (124)
T ss_pred             HHHH
Confidence            6554

>PLN03213 repressor of silencing 3; Provisional

Probab=99.47  E-value=2.8e-13  Score=122.63  Aligned_cols=81  Identities=26%  Similarity=0.418  Sum_probs=73.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCH--HHHHHHHHHhCCcEecccceEEeh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTA--EEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~--~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ..+.+|||+||.+.+++++|+.+|+.||.|.+|.|++. +|  ||||||+|.+.  .++.+||..|||..+.|+.|+|.-
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            34568999999999999999999999999999999943 55  89999999987  789999999999999999999999


Q ss_pred             hhhhHH
Q 012257          397 AQRKEE  402 (467)
Q Consensus       397 ~~~~~~  402 (467)
                      |++.--
T Consensus        85 AKP~YL   90 (759)
T PLN03213         85 AKEHYL   90 (759)
T ss_pred             ccHHHH
Confidence            986543

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

Probab=99.46  E-value=9.1e-15  Score=114.68  Aligned_cols=78  Identities=27%  Similarity=0.523  Sum_probs=75.2

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ++.-|||+|||++.+|.+|.-.|++||+|.+|.+++|+.||+|+||||+-|++..+...|+..++++.|.||.|+|-.
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeee
Confidence            578899999999999999999999999999999999999999999999999999999999999999999999999943

>smart00362 RRM_2 RNA recognition motif

Probab=99.46  E-value=3.9e-13  Score=95.28  Aligned_cols=72  Identities=43%  Similarity=0.752  Sum_probs=67.6

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      +|+|+|||..+++++|+++|++||.|.++++..+. +.++|+|||+|.+.++|.+|+..++|..+.|+.|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            48999999999999999999999999999999877 7788999999999999999999999999999998874

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.45  E-value=4.6e-13  Score=112.45  Aligned_cols=77  Identities=21%  Similarity=0.384  Sum_probs=70.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      .+.+|+|+||++.+|+++|+++|+.||.|.+|+|+++  +..+++|||+|.+.++|..|+ .|+|..|.++.|.|.-...
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D--~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS--GEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC--CCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCcc
Confidence            4578999999999999999999999999999999988  445689999999999999999 5999999999999986543

>smart00362 RRM_2 RNA recognition motif

Probab=99.44  E-value=6.6e-13  Score=94.09  Aligned_cols=71  Identities=34%  Similarity=0.735  Sum_probs=66.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        41 ~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      +|+|+|||.++++++|+++|+.||.|..+.+..++  +.++|+|||+|.+.++|++|++.+++..+.|+.++|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            58999999999999999999999999999999876  678899999999999999999999999999988876

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

Probab=99.44  E-value=1.8e-13  Score=101.73  Aligned_cols=85  Identities=21%  Similarity=0.457  Sum_probs=78.5

Q ss_pred             ccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       316 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      .....++.|||.++....+|++|.+.|..||+|+.+++..+. +|..+|||+|+|++.++|++|+..+||..+.|..|.|
T Consensus        67 qrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~V  146 (170)
T KOG0130|consen   67 QRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSV  146 (170)
T ss_pred             ccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeE
Confidence            345577889999999999999999999999999999998886 8999999999999999999999999999999999999


Q ss_pred             ehhhhh
Q 012257          395 ALAQRK  400 (467)
Q Consensus       395 ~~~~~~  400 (467)
                      .|+-.+
T Consensus       147 Dw~Fv~  152 (170)
T KOG0130|consen  147 DWCFVK  152 (170)
T ss_pred             EEEEec
Confidence            997543

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

Probab=99.43  E-value=1.8e-14  Score=113.00  Aligned_cols=77  Identities=21%  Similarity=0.475  Sum_probs=73.3

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      +.-|||+|||+.+||.||..+|++||+|.+|.+++|. +|+++||||+.|++..+..-|+..|||..|.||.|+|...
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            3469999999999999999999999999999999998 8999999999999999999999999999999999999853

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

Probab=99.43  E-value=5.8e-14  Score=113.53  Aligned_cols=85  Identities=31%  Similarity=0.500  Sum_probs=79.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ..++|||++|..+++|.-|...|-+||.|.+|.++.|. ++++||||||+|.-.+||..||..||+..+.||.|+|.||+
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            45689999999999999999999999999999999997 78899999999999999999999999999999999999998


Q ss_pred             hhHHHH
Q 012257          399 RKEERR  404 (467)
Q Consensus       399 ~~~~~~  404 (467)
                      +.+-..
T Consensus        89 P~kike   94 (298)
T KOG0111|consen   89 PEKIKE   94 (298)
T ss_pred             CccccC
Confidence            776433

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.42  E-value=1e-12  Score=110.39  Aligned_cols=76  Identities=18%  Similarity=0.218  Sum_probs=69.2

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ...+|+|+||++.++|++|+++|+.||.|.+|.|.+|..   .+++|||+|.+.++|+.|+. |++..|.++.|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~e---t~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGE---YACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCC---cceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            457999999999999999999999999999999998854   44799999999999999995 99999999999997654

>PLN03213 repressor of silencing 3; Provisional

Probab=99.41  E-value=8e-13  Score=119.71  Aligned_cols=78  Identities=23%  Similarity=0.363  Sum_probs=71.2

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecCh--HHHHHHHHHhCCcccCCceeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA--HEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~--~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ....+||||||++++++++|+.+|..||.|.+|.|+++  +|  +|||||+|.+.  .++.+|++.|++..+.|+.|+|+
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            34689999999999999999999999999999999954  55  79999999987  78999999999999999999998


Q ss_pred             eccc
Q 012257          115 YSYR  118 (467)
Q Consensus       115 ~~~~  118 (467)
                      .+..
T Consensus        84 KAKP   87 (759)
T PLN03213         84 KAKE   87 (759)
T ss_pred             eccH
Confidence            8755

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.41  E-value=9.1e-13  Score=115.54  Aligned_cols=163  Identities=17%  Similarity=0.261  Sum_probs=124.4

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcC----CCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQM----GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~----G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      .--.|.+++||+++++.++.++|-.-    |-.+.|..++. ..|+..|-|||.|...++|+.|+.+ +...+..|.|.+
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIEl  237 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIEL  237 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHH
Confidence            34668899999999999999999633    23345544443 4788889999999999999999985 444555555655


Q ss_pred             eecccCc-----------------------------ccccCCCccEEEcCCCCcCCHHHHHHHHhhcC-Ce--EEEEEee
Q 012257          114 MYSYRDP-----------------------------TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFG-NI--LSCKVAT  161 (467)
Q Consensus       114 ~~~~~~~-----------------------------~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g-~v--~~~~~~~  161 (467)
                      -.+...+                             ........+|.+++||+..+.++|..+|..|. .|  ..+.++.
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            3322100                             00112256899999999999999999999886 33  3377888


Q ss_pred             CCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEecc
Q 012257          162 DSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGP  202 (467)
Q Consensus       162 ~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~  202 (467)
                      +..|...|-|||+|.+.+.|..|....+++....+.|.+-.
T Consensus       318 N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  318 NGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFP  358 (508)
T ss_pred             cCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEee
Confidence            88899999999999999999999999888888888888743

>smart00360 RRM RNA recognition motif

Probab=99.41  E-value=1.1e-12  Score=92.54  Aligned_cols=70  Identities=36%  Similarity=0.740  Sum_probs=66.3

Q ss_pred             EcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           44 VGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        44 v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      |+|||.++++++|+++|+.||.|..+.+..++.++.++|+|||+|.+.++|.+|++.+++..+.|+.++|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            5899999999999999999999999999998888899999999999999999999999988999998876

>PF13893 RRM_5: RNA recognition motif

Probab=99.40  E-value=8.7e-13  Score=87.85  Aligned_cols=56  Identities=39%  Similarity=0.738  Sum_probs=51.3

Q ss_pred             HHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          338 LKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       338 l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      |+++|++||+|+++.+..+.    +++|||+|.+.++|.+|++.|||..+.|++|+|+|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68899999999999998764    479999999999999999999999999999999985

(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 ....

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

Probab=99.40  E-value=1.2e-12  Score=111.23  Aligned_cols=81  Identities=22%  Similarity=0.447  Sum_probs=76.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ..+-++|||.-|+.+++|.+|+..|+.||.|+.|+|+.+. +|+++|||||+|++..+-..|.+..+|..|+|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            3466799999999999999999999999999999999996 999999999999999999999999999999999999998


Q ss_pred             hh
Q 012257          397 AQ  398 (467)
Q Consensus       397 ~~  398 (467)
                      -.
T Consensus       178 ER  179 (335)
T KOG0113|consen  178 ER  179 (335)
T ss_pred             cc
Confidence            65

>smart00360 RRM RNA recognition motif

Probab=99.39  E-value=1.6e-12  Score=91.78  Aligned_cols=70  Identities=44%  Similarity=0.764  Sum_probs=65.4

Q ss_pred             EecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          326 VKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       326 V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      |+|||..+++++|+++|++||.|.++++..+. ++.++|+|||+|.+.++|.+|++.+++..+.|+.|.|+
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            57899999999999999999999999999877 47889999999999999999999999999999998874

>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=99.39  E-value=3.3e-12  Score=90.98  Aligned_cols=74  Identities=41%  Similarity=0.741  Sum_probs=69.7

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      +|+|+|||..+++++|+++|+.||.|..+.+..+..+.++++|||+|.+.++|..|++.+++..+.|+.+.|++
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            38999999999999999999999999999999988777789999999999999999999999999999999875

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).

>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=99.37  E-value=5.3e-12  Score=89.89  Aligned_cols=74  Identities=38%  Similarity=0.764  Sum_probs=68.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        41 ~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      +|+|+|||+++++++|+++|+.+|.|..+.+..+..+ ..+|+|||+|.+.++|..|++.+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            5899999999999999999999999999999987654 6678999999999999999999999999999998753

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

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

Probab=99.34  E-value=1.4e-12  Score=105.72  Aligned_cols=83  Identities=27%  Similarity=0.519  Sum_probs=79.1

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ..|+|||++|-.+++|.-|...|=.||.|.+|.+..|..+++++||+||+|.-.|||..|+..+|...+.||.|+|+++.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCc
Q 012257          118 RDP  120 (467)
Q Consensus       118 ~~~  120 (467)
                      +..
T Consensus        89 P~k   91 (298)
T KOG0111|consen   89 PEK   91 (298)
T ss_pred             Ccc
Confidence            543

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=99.34  E-value=1.4e-14  Score=139.71  Aligned_cols=321  Identities=16%  Similarity=0.145  Sum_probs=230.7

Q ss_pred             CeEEEcCCCCCCCHHHHH-HHHhcCCCeEE-EEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           40 TSLYVGDLDLSVNDSQLY-DLFNQMGQVVS-VRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~-~~f~~~G~v~~-v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ++.+|-|-+...+...|. .+++-++-+.. +...   .......+|+++..+.+++..++..+.......-++.+--..
T Consensus       480 ~~R~iWn~imty~~~~iag~Wle~~~lE~~~g~~~---~~R~~~R~ay~~~~~~~~~~ev~~~~~r~Ere~gtl~~~~~~  556 (881)
T KOG0128|consen  480 KAREIWNFIMTYGGGSIAGKWLEAINLEREYGDGP---SARKVLRKAYSQVVDPEDALEVLEFFRRFEREYGTLESFDLC  556 (881)
T ss_pred             hhhHhhhccccCCcchHHHHHHHHHhHHHHhCCch---hHHHHHHHHHhcCcCchhHHHHHHHHHHHHhccccHHHHhhh
Confidence            455677777778888887 66665532111 1111   111244589999999999999998765544333232221111


Q ss_pred             cCc-----ccccCCCccEEEcCCCCcCCHH-HHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcC
Q 012257          118 RDP-----TIRKSGAGNIFIKNLDKSIDNK-ALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNG  190 (467)
Q Consensus       118 ~~~-----~~~~~~~~~l~v~nlp~~~t~~-~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~  190 (467)
                      ...     ...........+.++.+...+. ..+..|..+|.|..+.+... ..-....++++.+.....++.|.. ..+
T Consensus       557 ~~~~~pr~~~~~~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~  635 (881)
T KOG0128|consen  557 PEKVLPRVYEAPLERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAG  635 (881)
T ss_pred             HHhhcchhhhhhhhhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhccc-ccc
Confidence            100     0111223456677776665444 56788999999999988774 222233478899999999988886 466


Q ss_pred             CccCCeeeEeccccccccccccccc----ccccceeecCCCccCCHHHHHHhhcccCCeeEEEEE-ECCCCCceeEEEEE
Q 012257          191 MLLNDKQVFVGPFLRKQERESTADK----TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVM-RDADGKSKCFGFVN  265 (467)
Q Consensus       191 ~~~~g~~~~v~~~~~~~~~~~~~~~----~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~-~~~~~~~~g~afv~  265 (467)
                      ..+.++...+....+..........    ....++|++|++..+.++++...|..+|.+..+.+. ....++.+|+||+.
T Consensus       636 ~~~a~~~~av~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~  715 (881)
T KOG0128|consen  636 GALANRSAAVGLADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVE  715 (881)
T ss_pred             cccCCccccCCCCCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeE
Confidence            6777777777666554433322222    223468999999999999999999999988877766 33567789999999


Q ss_pred             eCCHHHHHHHHHHhCCCccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccC
Q 012257          266 FDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEF  345 (467)
Q Consensus       266 f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~  345 (467)
                      |...+++.+|+....+..++                                   ...|+|.|.|+..|.++++.+++.+
T Consensus       716 F~~~~~~~aaV~f~d~~~~g-----------------------------------K~~v~i~g~pf~gt~e~~k~l~~~~  760 (881)
T KOG0128|consen  716 FLKPEHAGAAVAFRDSCFFG-----------------------------------KISVAISGPPFQGTKEELKSLASKT  760 (881)
T ss_pred             eecCCchhhhhhhhhhhhhh-----------------------------------hhhhheeCCCCCCchHHHHhhcccc
Confidence            99999999999854433332                                   1159999999999999999999999


Q ss_pred             CceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          346 GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       346 G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      |++.+++++....|+++|.|+|.|.+..+|.++....+...+.-+.+.|..+.+
T Consensus       761 gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  761 GNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             CCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            999999999999999999999999999999999999888888888888887655

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

Probab=99.33  E-value=6.2e-12  Score=117.20  Aligned_cols=85  Identities=26%  Similarity=0.468  Sum_probs=79.1

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      +.|||+|+|+++++++|.++|+..|.|.++++..|. +|+++||||++|.+.++|.+|++.|||..+.|++|+|.|+...
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            689999999999999999999999999999999997 8999999999999999999999999999999999999999766


Q ss_pred             HHHHHH
Q 012257          401 EERRAR  406 (467)
Q Consensus       401 ~~~~~~  406 (467)
                      ..+...
T Consensus        99 ~~~~~~  104 (435)
T KOG0108|consen   99 KNAERS  104 (435)
T ss_pred             chhHHH
Confidence            554433

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

Probab=99.32  E-value=9e-12  Score=115.34  Aligned_cols=156  Identities=22%  Similarity=0.292  Sum_probs=105.9

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      ...+-+.++|+|-|||..+++++|+++|+.||+|..|+..+.+     +|.+||+|-|..+|+.|++.|+...+.|++++
T Consensus        69 ~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~-----~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   69 SEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNK-----RGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccccc-----CceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            3445668999999999999999999999999999997765544     37999999999999999999999999999988


Q ss_pred             eeecccCcc------------------cccCC--CccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEE
Q 012257          113 IMYSYRDPT------------------IRKSG--AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGF  172 (467)
Q Consensus       113 v~~~~~~~~------------------~~~~~--~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~af  172 (467)
                      -........                  ....+  ...++ +.|++..+..-++..++.+|.+.. ..    ++.-...-+
T Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~-g~l~P~~s~~~~~~~~~~~~~~~~-~~----~~~~~hq~~  217 (549)
T KOG4660|consen  144 RPGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLF-GMLSPTRSSILLEHISSVDGSSPG-RE----TPLLNHQRF  217 (549)
T ss_pred             CCCcccccchhcccchhhhhccchhhcCCCCCCcCCcce-eeeccchhhhhhhcchhccCcccc-cc----ccchhhhhh
Confidence            222111000                  00011  11233 338887777666667777887754 21    111222566


Q ss_pred             EEeCCHHHHHHHHHHhcCCccCCeeeEe
Q 012257          173 VQFDNEESAKSAIDKLNGMLLNDKQVFV  200 (467)
Q Consensus       173 V~f~~~~~A~~a~~~l~~~~~~g~~~~v  200 (467)
                      +.|.+..++..+.... |..+.+.....
T Consensus       218 ~~~~~~~s~a~~~~~~-G~~~s~~~~v~  244 (549)
T KOG4660|consen  218 VEFADNRSYAFSEPRG-GFLISNSSGVI  244 (549)
T ss_pred             hhhccccchhhcccCC-ceecCCCCceE
Confidence            7777777775555432 55555555333

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

Probab=99.31  E-value=7.2e-12  Score=116.80  Aligned_cols=80  Identities=29%  Similarity=0.597  Sum_probs=77.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecccC
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRD  119 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~  119 (467)
                      +.|||||||++.+|++|.++|+..|.|.++++..|+.+|+.+||||++|.+.++|++|++.|++..+.|++|+|.|....
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            99999999999999999999999999999999999999999999999999999999999999999999999999987543

>smart00361 RRM_1 RNA recognition motif

Probab=99.31  E-value=7.8e-12  Score=87.26  Aligned_cols=61  Identities=23%  Similarity=0.523  Sum_probs=54.1

Q ss_pred             HHHHHHhhc----cCCceeEEE-EeeCC-C--CCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          335 DDKLKELFS----EFGTITSCK-VMRDP-N--GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       335 ~~~l~~~F~----~~G~v~~v~-i~~~~-~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      +++|+++|+    .||.|.++. +..+. +  +.++|+|||+|.+.++|.+|++.|||+.+.|+.|+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            578889998    999999995 55544 4  8899999999999999999999999999999999874

>PF13893 RRM_5: RNA recognition motif

Probab=99.30  E-value=1.2e-11  Score=82.40  Aligned_cols=56  Identities=29%  Similarity=0.778  Sum_probs=51.0

Q ss_pred             HHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           56 LYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        56 l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      |+++|++||+|.+|.+.+++     +++|||+|.+.++|++|++.|++..+.|+.|+|.|+
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            68999999999999998776     369999999999999999999999999999999875

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>smart00361 RRM_1 RNA recognition motif

Probab=99.27  E-value=2.1e-11  Score=85.06  Aligned_cols=61  Identities=21%  Similarity=0.404  Sum_probs=55.2

Q ss_pred             HHHHHHHHh----cCCCeEEEE-EEecCCC--CccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           53 DSQLYDLFN----QMGQVVSVR-VCRDLST--RRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        53 e~~l~~~f~----~~G~v~~v~-i~~~~~~--~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      +++|+++|+    .||.|.+|. +..++.+  +.++|+|||+|.+.++|.+|++.|++..+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            678899998    999999995 7666666  889999999999999999999999999999999876

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.23  E-value=3.3e-10  Score=104.26  Aligned_cols=151  Identities=21%  Similarity=0.311  Sum_probs=115.6

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCC--cccc---EEEEEecChHHHHHHHHHhCC----c---
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTR--RSLG---YGYVNYNAAHEATRALDELNF----T---  104 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~--~~~g---~afV~f~~~~~A~~A~~~l~~----~---  104 (467)
                      +-+++|||++||++++|++|...|..||.+.-=+-.+....+  ..+|   |+|+.|++....+..+..+..    .   
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~yf~  336 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYYFK  336 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccceEEE
Confidence            448999999999999999999999999986544432222222  2456   999999999999988887632    1   


Q ss_pred             ----ccCCceeeeeeccc-------CcccccCCCccEEEcCCCCcCCHHHHHHHHh-hcCCeEEEEEeeC-CCCCceeEE
Q 012257          105 ----PLNGKPIRIMYSYR-------DPTIRKSGAGNIFIKNLDKSIDNKALHDTFS-TFGNILSCKVATD-SLGQSRGYG  171 (467)
Q Consensus       105 ----~~~g~~~~v~~~~~-------~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~-~~g~v~~~~~~~~-~~g~~~~~a  171 (467)
                          .+..+.++|.....       .....-+..++|||++||..++-++|..+|. -||.|..+-|-.| .-+..+|-|
T Consensus       337 vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaG  416 (520)
T KOG0129|consen  337 VSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAG  416 (520)
T ss_pred             EecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcc
Confidence                12333344433211       1233345567999999999999999999999 8999999988888 678899999


Q ss_pred             EEEeCCHHHHHHHHHH
Q 012257          172 FVQFDNEESAKSAIDK  187 (467)
Q Consensus       172 fV~f~~~~~A~~a~~~  187 (467)
                      -|.|.+...-.+||..
T Consensus       417 RVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  417 RVTFSNQQAYIKAISA  432 (520)
T ss_pred             eeeecccHHHHHHHhh
Confidence            9999999999999973

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

Probab=99.22  E-value=1.1e-10  Score=107.68  Aligned_cols=169  Identities=29%  Similarity=0.439  Sum_probs=124.8

Q ss_pred             ccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccccc
Q 012257          218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQK  296 (467)
Q Consensus       218 ~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~  296 (467)
                      ..+|||+||+..+++++|.++|..||.+..+.+..+ .++..+|+|||+|.+.+++..|+..+++..+.|+.+.+.+...
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            589999999999999999999999999999999998 4799999999999999999999999999999999999999652


Q ss_pred             ----chHHHH--HhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCC-ccceEEEEc
Q 012257          297 ----KYEREM--ELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAF  369 (467)
Q Consensus       297 ----~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~-~~g~afV~f  369 (467)
                          ......  .....................+++.+++..++..++...|..+|.+....+.....+. .....++.+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  274 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGN  274 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccch
Confidence                111110  0000001111222334456689999999999999999999999999777766654332 333444555


Q ss_pred             CCHHHHHHHHHHhCCcE
Q 012257          370 STAEEASKALTEMNGKM  386 (467)
Q Consensus       370 ~~~~~A~~A~~~l~g~~  386 (467)
                      .....+...........
T Consensus       275 ~~~~~~~~~~~~~~~~~  291 (306)
T COG0724         275 EASKDALESNSRGNKKK  291 (306)
T ss_pred             hHHHhhhhhhcccccee
Confidence            55555555544433333

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

Probab=99.17  E-value=1.2e-10  Score=111.68  Aligned_cols=80  Identities=28%  Similarity=0.455  Sum_probs=73.5

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ..+.+++|||++|+..+++.||..+|+.||.|.+|.++..     +|||||.+..+.+|.+|+.+|++..+.++.|+|.|
T Consensus       417 isV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~W  491 (894)
T KOG0132|consen  417 ISVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAW  491 (894)
T ss_pred             eeEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHhcccccceeeEEee
Confidence            3456789999999999999999999999999999999875     88999999999999999999999999999999999


Q ss_pred             hhhhH
Q 012257          397 AQRKE  401 (467)
Q Consensus       397 ~~~~~  401 (467)
                      +..+.
T Consensus       492 a~g~G  496 (894)
T KOG0132|consen  492 AVGKG  496 (894)
T ss_pred             eccCC
Confidence            86443

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=99.15  E-value=4.8e-12  Score=122.54  Aligned_cols=233  Identities=17%  Similarity=0.140  Sum_probs=184.3

Q ss_pred             CccCeEEEcCCCCCCCHH-HHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           37 FVSTSLYVGDLDLSVNDS-QLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~-~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ...+...+.++-+..... ..++.|..+|.|+.|.+......-....+.++.+....+++.|.. ..+..+.++...+..
T Consensus       569 ~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~~av~~  647 (881)
T KOG0128|consen  569 LERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAGGALANRSAAVGL  647 (881)
T ss_pred             hhhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhccc-ccccccCCccccCCC
Confidence            345677888887776665 568899999999999987633222232388999999999999987 566677788877766


Q ss_pred             cccCccccc--------CCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEe-eCCCCCceeEEEEEeCCHHHHHHHHH
Q 012257          116 SYRDPTIRK--------SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVA-TDSLGQSRGYGFVQFDNEESAKSAID  186 (467)
Q Consensus       116 ~~~~~~~~~--------~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~-~~~~g~~~~~afV~f~~~~~A~~a~~  186 (467)
                      +...+....        ....++|+.||+..+.+.+|...|..+|.+..+.+. ....+..+|+||+.|..++++.+|+.
T Consensus       648 ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~  727 (881)
T KOG0128|consen  648 ADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVA  727 (881)
T ss_pred             CCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhh
Confidence            654432211        123479999999999999999999999988777666 33677889999999999999999998


Q ss_pred             HhcCCccCCeeeEecccccccccccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEe
Q 012257          187 KLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNF  266 (467)
Q Consensus       187 ~l~~~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f  266 (467)
                      ..+++.+.                       ...++|.|.|...|.++++.++..+|.+.+..++..+.|+.+|.++|.|
T Consensus       728 f~d~~~~g-----------------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y  784 (881)
T KOG0128|consen  728 FRDSCFFG-----------------------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDY  784 (881)
T ss_pred             hhhhhhhh-----------------------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccC
Confidence            65554443                       1458899999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHhCCCccCCceEEEcc
Q 012257          267 DDPDDAARSVEALNGKKFDDKEWYVGK  293 (467)
Q Consensus       267 ~~~~~a~~a~~~l~~~~~~~~~l~~~~  293 (467)
                      .+..++..++...+...+.-..+.+..
T Consensus       785 ~~ea~~s~~~~s~d~~~~rE~~~~v~v  811 (881)
T KOG0128|consen  785 NTEADASRKVASVDVAGKRENNGEVQV  811 (881)
T ss_pred             CCcchhhhhcccchhhhhhhcCccccc
Confidence            999999998877766666555555444

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

Probab=99.10  E-value=1.9e-10  Score=100.17  Aligned_cols=87  Identities=29%  Similarity=0.463  Sum_probs=80.9

Q ss_pred             ccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       316 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      ...++...|||..|.+.+++++|.-+|+.||.|.+|.++++. +|-+-.||||+|++.+++.+|.-.|++..|.+++|.|
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV  313 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV  313 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe
Confidence            445677899999999999999999999999999999999997 8888999999999999999999999999999999999


Q ss_pred             ehhhhhHH
Q 012257          395 ALAQRKEE  402 (467)
Q Consensus       395 ~~~~~~~~  402 (467)
                      .|++....
T Consensus       314 DFSQSVsk  321 (479)
T KOG0415|consen  314 DFSQSVSK  321 (479)
T ss_pred             ehhhhhhh
Confidence            99986654

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

Probab=99.09  E-value=2.9e-11  Score=98.20  Aligned_cols=147  Identities=24%  Similarity=0.326  Sum_probs=121.4

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ....++|||.|+-..++|+-|.++|=..|+|..|.|..++ .+..+ ||||.|.+.-+..-|++.+|+..+.+..+++.+
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhccc
Confidence            3457999999999999999999999999999999998776 45555 999999999999999999999999999998854


Q ss_pred             cccCcccccCCCccEEEcC----CCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCC
Q 012257          116 SYRDPTIRKSGAGNIFIKN----LDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGM  191 (467)
Q Consensus       116 ~~~~~~~~~~~~~~l~v~n----lp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~  191 (467)
                                     +-++    |...++++.+.+.|+..|.+..+++..+.+|..+.++++.+--.-..-.++...++.
T Consensus        84 ---------------r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l  148 (267)
T KOG4454|consen   84 ---------------RCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGL  148 (267)
T ss_pred             ---------------ccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhccc
Confidence                           3333    555678888899999999999999999988889999999887766666667665555


Q ss_pred             ccCCeeeE
Q 012257          192 LLNDKQVF  199 (467)
Q Consensus       192 ~~~g~~~~  199 (467)
                      ...-+++.
T Consensus       149 ~~~~~~~~  156 (267)
T KOG4454|consen  149 ELFQKKVT  156 (267)
T ss_pred             CcCCCCcc
Confidence            44444433

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

Probab=99.05  E-value=7.4e-10  Score=89.74  Aligned_cols=84  Identities=21%  Similarity=0.353  Sum_probs=76.0

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcC-CCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQM-GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~-G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      .........++|..+|...-|.+|..+|.++ |.|..+++-+.+.||.|+|||||+|++.+.|.-|.+.||+..+.|+.|
T Consensus        43 ~p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL  122 (214)
T KOG4208|consen   43 KPEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLL  122 (214)
T ss_pred             CCccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhhee
Confidence            3344456789999999999999999999999 799999999999999999999999999999999999999999999999


Q ss_pred             eeeec
Q 012257          112 RIMYS  116 (467)
Q Consensus       112 ~v~~~  116 (467)
                      .+.+-
T Consensus       123 ~c~vm  127 (214)
T KOG4208|consen  123 ECHVM  127 (214)
T ss_pred             eeEEe
Confidence            88654

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

Probab=99.05  E-value=4.5e-10  Score=90.99  Aligned_cols=81  Identities=25%  Similarity=0.409  Sum_probs=74.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccC-CceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEF-GTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~-G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|..+|.-+.+.+|..+|.+| |.|..+++.++. +|.++|||||+|++.+.|.-|-+.||+..|+++-|.|.+-
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vm  127 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVM  127 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEe
Confidence            34469999999999999999999999 788888886766 9999999999999999999999999999999999999998


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      .+.
T Consensus       128 ppe  130 (214)
T KOG4208|consen  128 PPE  130 (214)
T ss_pred             Cch
Confidence            777

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

Probab=99.04  E-value=4.8e-10  Score=107.64  Aligned_cols=76  Identities=24%  Similarity=0.476  Sum_probs=70.3

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      -||||||++|+..++|++|.++|+.||.|.+|+++..+      |||||.+.+.+||.+|+.+|+...+.++.|+|.|+.
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R------~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~  493 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPR------GCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAV  493 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeeccCC------ceeEEEEeehhHHHHHHHHHhcccccceeeEEeeec
Confidence            37899999999999999999999999999999997654      699999999999999999999999999999999985


Q ss_pred             cC
Q 012257          118 RD  119 (467)
Q Consensus       118 ~~  119 (467)
                      .+
T Consensus       494 g~  495 (894)
T KOG0132|consen  494 GK  495 (894)
T ss_pred             cC
Confidence            43

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

Probab=99.04  E-value=4.7e-09  Score=99.60  Aligned_cols=73  Identities=19%  Similarity=0.326  Sum_probs=64.5

Q ss_pred             ceeecCCCccCCHHHHHHhhcccCCeeE-EEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEc
Q 012257          220 NVYVKNLSETTTEDDLKKIFGEFGIITS-TAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVG  292 (467)
Q Consensus       220 ~l~v~nlp~~~~~~~l~~~f~~~g~v~~-~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~  292 (467)
                      .|-+.|+|.+++.+||.++|..|-.+.. |.+....+|..+|-|.|-|++.++|..|...+++..+..+.+++.
T Consensus       869 V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~  942 (944)
T KOG4307|consen  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLR  942 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEE
Confidence            4788999999999999999999976554 556666889999999999999999999999999999998887764

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

Probab=99.04  E-value=7.4e-11  Score=95.87  Aligned_cols=138  Identities=24%  Similarity=0.377  Sum_probs=121.3

Q ss_pred             cccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccccc
Q 012257          217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQK  296 (467)
Q Consensus       217 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~  296 (467)
                      ..++|+|.|+...++++-|.++|-+.|.|..+.|...++++.+ ||||.|.++.....|+.-+||..+.+..+.+     
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~-----   81 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQR-----   81 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhc-----
Confidence            3478999999999999999999999999999999888888777 9999999999999999999999998887776     


Q ss_pred             chHHHHHhhhhhhhhhhccccCCCCceEEEec----CCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCH
Q 012257          297 KYEREMELKGKFEQSLKETADKFEGLNLYVKN----LDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTA  372 (467)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~n----lp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~  372 (467)
                                                +++-++    |...++++.+...|+.-|.++.+++..+.+|+++.++|+.+--.
T Consensus        82 --------------------------~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~  135 (267)
T KOG4454|consen   82 --------------------------TLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRL  135 (267)
T ss_pred             --------------------------ccccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhh
Confidence                                      355555    67788999999999999999999999999999999999999888


Q ss_pred             HHHHHHHHHhCCcE
Q 012257          373 EEASKALTEMNGKM  386 (467)
Q Consensus       373 ~~A~~A~~~l~g~~  386 (467)
                      .+.-.++....+..
T Consensus       136 ~~~P~~~~~y~~l~  149 (267)
T KOG4454|consen  136 CAVPFALDLYQGLE  149 (267)
T ss_pred             hcCcHHhhhhcccC
Confidence            77777777665553

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

Probab=99.03  E-value=5.1e-10  Score=97.54  Aligned_cols=88  Identities=22%  Similarity=0.352  Sum_probs=81.2

Q ss_pred             CCCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCc
Q 012257           30 GVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK  109 (467)
Q Consensus        30 ~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  109 (467)
                      -+++.-.++...|||..|.+-++.++|.-+|++||.|.++.|++|+.||-+.-||||+|++.+++++|.=+|++..|+.+
T Consensus       230 lpdAd~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDr  309 (479)
T KOG0415|consen  230 LPDADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDR  309 (479)
T ss_pred             CcccccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccc
Confidence            34455556789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeeeecc
Q 012257          110 PIRIMYSY  117 (467)
Q Consensus       110 ~~~v~~~~  117 (467)
                      +|+|-++.
T Consensus       310 RIHVDFSQ  317 (479)
T KOG0415|consen  310 RIHVDFSQ  317 (479)
T ss_pred             eEEeehhh
Confidence            99998764

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

Probab=98.98  E-value=1.5e-09  Score=94.81  Aligned_cols=82  Identities=23%  Similarity=0.417  Sum_probs=72.4

Q ss_pred             CCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHh-CCcccCCc
Q 012257           31 VGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL-NFTPLNGK  109 (467)
Q Consensus        31 ~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l-~~~~~~g~  109 (467)
                      -.+......++|||++|-..++|.+|+++|-+||+|.+|.+...+      ++|||+|.+.+.|++|..+. +...|.|+
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~  293 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGF  293 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecce
Confidence            345566678999999999999999999999999999999998765      49999999999999998874 56678999


Q ss_pred             eeeeeeccc
Q 012257          110 PIRIMYSYR  118 (467)
Q Consensus       110 ~~~v~~~~~  118 (467)
                      +|.|.|...
T Consensus       294 Rl~i~Wg~~  302 (377)
T KOG0153|consen  294 RLKIKWGRP  302 (377)
T ss_pred             EEEEEeCCC
Confidence            999999876

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

Probab=98.96  E-value=1.6e-09  Score=94.57  Aligned_cols=78  Identities=23%  Similarity=0.435  Sum_probs=68.6

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhC-CcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN-GKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~v~  395 (467)
                      .+....+|||++|...++|.+|+++|.+||+|+++++...     +++|||+|.++++|+.|.+++- ...|.|.+|.|.
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~  298 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIK  298 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeeecceEEEEE
Confidence            3345568999999999999999999999999999999886     5699999999999999988654 446689999999


Q ss_pred             hhhh
Q 012257          396 LAQR  399 (467)
Q Consensus       396 ~~~~  399 (467)
                      |.++
T Consensus       299 Wg~~  302 (377)
T KOG0153|consen  299 WGRP  302 (377)
T ss_pred             eCCC
Confidence            9988

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

Probab=98.94  E-value=2.8e-09  Score=88.96  Aligned_cols=163  Identities=20%  Similarity=0.329  Sum_probs=126.7

Q ss_pred             CeEEEcCCCCCCCHHH-H--HHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee-
Q 012257           40 TSLYVGDLDLSVNDSQ-L--YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY-  115 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~-l--~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~-  115 (467)
                      -.++++++-.++..+- |  ...|+.+=.+..-+++++. .+.-++++|+.|.....-.++-..-++..+....+++.. 
T Consensus        97 f~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~-p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~g  175 (290)
T KOG0226|consen   97 FRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDR-PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAG  175 (290)
T ss_pred             ccccccccccccCCCCCCcchhhhccchhhhhhhhhhcC-CCccCcccccCcchhhhhhhhccccccccccCcceeeccc
Confidence            4456666666555543 3  6677766555555555553 455668999999988888888876667777667677743 


Q ss_pred             ---cccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCC
Q 012257          116 ---SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGM  191 (467)
Q Consensus       116 ---~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~  191 (467)
                         ...+...-+.+..+||.+.|-.+++++-|...|.+|-.....+++++ .+|+++||+||.|.+..++..|++.++|.
T Consensus       176 tswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gk  255 (290)
T KOG0226|consen  176 TSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGK  255 (290)
T ss_pred             cccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhccc
Confidence               33333444566789999999999999999999999998888888888 89999999999999999999999999999


Q ss_pred             ccCCeeeEeccc
Q 012257          192 LLNDKQVFVGPF  203 (467)
Q Consensus       192 ~~~g~~~~v~~~  203 (467)
                      .++.+.|.+...
T Consensus       256 yVgsrpiklRkS  267 (290)
T KOG0226|consen  256 YVGSRPIKLRKS  267 (290)
T ss_pred             ccccchhHhhhh
Confidence            999998887543

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

Probab=98.89  E-value=2.5e-09  Score=104.60  Aligned_cols=157  Identities=18%  Similarity=0.265  Sum_probs=132.7

Q ss_pred             cceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccch
Q 012257          219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKY  298 (467)
Q Consensus       219 ~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~  298 (467)
                      ++|+++|+...+++.+|+..|..+|.|.++.+....-+...-|+|+.|.+...+..|...+.+..+....+...+...  
T Consensus       373 rTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~~--  450 (975)
T KOG0112|consen  373 RTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQP--  450 (975)
T ss_pred             hhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccccc--
Confidence            579999999999999999999999999999998775566666999999999988888888888887766655554432  


Q ss_pred             HHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHH
Q 012257          299 EREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKA  378 (467)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A  378 (467)
                                        .....+.+++++|..++....|...|..||.|..|.+-..     .-||+|.|.+...|+.|
T Consensus       451 ------------------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-----q~yayi~yes~~~aq~a  507 (975)
T KOG0112|consen  451 ------------------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-----QPYAYIQYESPPAAQAA  507 (975)
T ss_pred             ------------------ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-----CcceeeecccCccchhh
Confidence                              1124456999999999999999999999999988776543     23999999999999999


Q ss_pred             HHHhCCcEecc--cceEEehhhhh
Q 012257          379 LTEMNGKMVVS--KPLYVALAQRK  400 (467)
Q Consensus       379 ~~~l~g~~~~g--~~l~v~~~~~~  400 (467)
                      ++.|.|..|+|  +.++|.|+.+.
T Consensus       508 ~~~~rgap~G~P~~r~rvdla~~~  531 (975)
T KOG0112|consen  508 THDMRGAPLGGPPRRLRVDLASPP  531 (975)
T ss_pred             HHHHhcCcCCCCCcccccccccCC
Confidence            99999999985  67999998755

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

Probab=98.88  E-value=1.4e-09  Score=106.19  Aligned_cols=156  Identities=18%  Similarity=0.279  Sum_probs=130.3

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ..+.+++||++||+..+++.+|+..|..+|.|.+|.|..-+ -++-.-||||.|.+...+-.|...+.+..|....+++.
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            34568999999999999999999999999999999987653 23444599999999999999998888888876677776


Q ss_pred             ecccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccC
Q 012257          115 YSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLN  194 (467)
Q Consensus       115 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~  194 (467)
                      ....    .....+.+|+++|...+....|...|..||.|..|.+-.     ...||||.|.+...++.|++.+.|..+.
T Consensus       447 lG~~----kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h-----gq~yayi~yes~~~aq~a~~~~rgap~G  517 (975)
T KOG0112|consen  447 LGQP----KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH-----GQPYAYIQYESPPAAQAATHDMRGAPLG  517 (975)
T ss_pred             cccc----ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc-----CCcceeeecccCccchhhHHHHhcCcCC
Confidence            5543    233457899999999999999999999999998877654     4679999999999999999999998886


Q ss_pred             C--eeeEe
Q 012257          195 D--KQVFV  200 (467)
Q Consensus       195 g--~~~~v  200 (467)
                      +  +.+.+
T Consensus       518 ~P~~r~rv  525 (975)
T KOG0112|consen  518 GPPRRLRV  525 (975)
T ss_pred             CCCccccc
Confidence            5  34444

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

Probab=98.86  E-value=1.6e-08  Score=93.93  Aligned_cols=83  Identities=25%  Similarity=0.466  Sum_probs=76.2

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      +--.+.|||++|...+--.+|+.+|++||.|...+|+....+-.-++|+||++.+.++|.+||+.|+.+.+.|+-|.|..
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            34468899999999999999999999999999999999888877788999999999999999999999999999999987


Q ss_pred             ccc
Q 012257          116 SYR  118 (467)
Q Consensus       116 ~~~  118 (467)
                      ++.
T Consensus       482 aKN  484 (940)
T KOG4661|consen  482 AKN  484 (940)
T ss_pred             ccc
Confidence            654

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.84  E-value=4.3e-08  Score=90.58  Aligned_cols=151  Identities=21%  Similarity=0.359  Sum_probs=108.8

Q ss_pred             CccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEe----eCCCCCcee---EEEEEeCCHHHHHHHHHHhcC---C-c---
Q 012257          127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVA----TDSLGQSRG---YGFVQFDNEESAKSAIDKLNG---M-L---  192 (467)
Q Consensus       127 ~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~----~~~~g~~~~---~afV~f~~~~~A~~a~~~l~~---~-~---  192 (467)
                      +++|||++||.++++++|...|..||.+. +.-.    ....-..+|   |+|+-|+++..+..-+..+.-   . .   
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~yf~v  337 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYYFKV  337 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccceEEEE
Confidence            56899999999999999999999999874 2222    111112455   999999999998888876532   0 0   


Q ss_pred             ----cCCeeeEeccccccc---ccccccccccccceeecCCCccCCHHHHHHhhc-ccCCeeEEEEEEC-CCCCceeEEE
Q 012257          193 ----LNDKQVFVGPFLRKQ---ERESTADKTRFNNVYVKNLSETTTEDDLKKIFG-EFGIITSTAVMRD-ADGKSKCFGF  263 (467)
Q Consensus       193 ----~~g~~~~v~~~~~~~---~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~-~~g~v~~~~~~~~-~~~~~~g~af  263 (467)
                          +..+.+.+.......   .......-...+++||++||..++.++|..+|+ .||.|..+.|-.+ +-+-.+|-|-
T Consensus       338 ss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGR  417 (520)
T KOG0129|consen  338 SSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGR  417 (520)
T ss_pred             ecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcce
Confidence                112222221111110   011222334558999999999999999999997 7999999999888 4566889999


Q ss_pred             EEeCCHHHHHHHHHH
Q 012257          264 VNFDDPDDAARSVEA  278 (467)
Q Consensus       264 v~f~~~~~a~~a~~~  278 (467)
                      |+|.+..+-.+|+.+
T Consensus       418 VtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  418 VTFSNQQAYIKAISA  432 (520)
T ss_pred             eeecccHHHHHHHhh
Confidence            999999999999874

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

Probab=98.81  E-value=2.1e-08  Score=93.31  Aligned_cols=79  Identities=14%  Similarity=0.307  Sum_probs=68.6

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ...+|||+|||.++++.+|+++|+.||+|+...|......++..+||||+|.+.++++.|+.. +...+.++++.|+.-.
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            345599999999999999999999999999999988765555558999999999999999985 5778899999997543

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

Probab=98.78  E-value=1.7e-08  Score=86.55  Aligned_cols=80  Identities=30%  Similarity=0.498  Sum_probs=75.1

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhhH
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKE  401 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  401 (467)
                      ..|.|.|||..++++||+++|..||.++.+-+..++.|.+.|.|-|.|...++|.+|++.+||..++|+.|.+....+..
T Consensus        84 ~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~~  163 (243)
T KOG0533|consen   84 TKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSPS  163 (243)
T ss_pred             ceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCcc
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999998765443

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

Probab=98.78  E-value=1.2e-08  Score=94.65  Aligned_cols=83  Identities=29%  Similarity=0.464  Sum_probs=74.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ...+++|||.+|...+...+|+.+|++||+|+-.+++.+. +.-.++|+||++.+.++|.++|+.||...|.|+.|.|.-
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            3456789999999999999999999999999999999886 333589999999999999999999999999999999998


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      ++..
T Consensus       482 aKNE  485 (940)
T KOG4661|consen  482 AKNE  485 (940)
T ss_pred             cccC
Confidence            7643

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

Probab=98.73  E-value=1.5e-08  Score=84.65  Aligned_cols=153  Identities=22%  Similarity=0.327  Sum_probs=125.3

Q ss_pred             HHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEecccccccccccccccccccceeec
Q 012257          145 HDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVK  224 (467)
Q Consensus       145 ~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~l~v~  224 (467)
                      ...|+.+..+...+++++..+.-.+++|+.|...+.-.++...-++..+.-..++..............-.....+||++
T Consensus       117 ~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedPsl~ew~~~DfRIfcg  196 (290)
T KOG0226|consen  117 PVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDPSLAEWDEDDFRIFCG  196 (290)
T ss_pred             hhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCcccccCccccceeecc
Confidence            45667777777778888877788899999999988888888766777777776776555555444444445566789999


Q ss_pred             CCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccc
Q 012257          225 NLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKK  297 (467)
Q Consensus       225 nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~  297 (467)
                      .|..+++++-+...|.+|-.-...+++++ .+++++||+||.|.+..++..|+..++|..++.+.+..+....+
T Consensus       197 dlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wk  270 (290)
T KOG0226|consen  197 DLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWK  270 (290)
T ss_pred             cccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHH
Confidence            99999999999999999998888888888 67999999999999999999999999999999998877655443

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

Probab=98.73  E-value=1.1e-07  Score=69.30  Aligned_cols=81  Identities=20%  Similarity=0.295  Sum_probs=70.6

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccC--CceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEec----ccceEE
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEF--GTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVV----SKPLYV  394 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~--G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~----g~~l~v  394 (467)
                      ++|.|+|||...+.++|.+++...  |...-+.++.|. ++.+.|||||.|.+.++|.+-.+.++|..+.    .|.+.|
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            589999999999999999998543  788888998886 6678999999999999999999999999885    578899


Q ss_pred             ehhhhhHH
Q 012257          395 ALAQRKEE  402 (467)
Q Consensus       395 ~~~~~~~~  402 (467)
                      .||+-+..
T Consensus        82 ~yAriQG~   89 (97)
T PF04059_consen   82 SYARIQGK   89 (97)
T ss_pred             ehhHhhCH
Confidence            99986543

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

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

Probab=98.71  E-value=5e-08  Score=83.68  Aligned_cols=78  Identities=35%  Similarity=0.515  Sum_probs=72.0

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      +++|+|.|||+.+.+++|.++|..||.++.+.+-.+. .|++.|.|-|.|...+||..|++.+++..++|+.+++....
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            4789999999999999999999999998888887775 78999999999999999999999999999999999887654

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.70  E-value=2.3e-08  Score=89.38  Aligned_cols=168  Identities=22%  Similarity=0.305  Sum_probs=134.2

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ...+++|++++-..+.++++..++..+|.+.............++|++++.|+..+.+..|+.......+.++.+..-..
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            46789999999999999999999999997777777766667789999999999999999999854433445544433222


Q ss_pred             ccCc--------ccccCCCccEE-EcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHH
Q 012257          117 YRDP--------TIRKSGAGNIF-IKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAID  186 (467)
Q Consensus       117 ~~~~--------~~~~~~~~~l~-v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~  186 (467)
                      +...        ........+++ |.+++..+++++|+.+|..+|.|..+++..+ .++..+++|||.|.+...+..++.
T Consensus       166 ~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~  245 (285)
T KOG4210|consen  166 TRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALN  245 (285)
T ss_pred             ccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhh
Confidence            2111        11223344566 9999999999999999999999999999888 788899999999999999999998


Q ss_pred             HhcCCccCCeeeEeccccc
Q 012257          187 KLNGMLLNDKQVFVGPFLR  205 (467)
Q Consensus       187 ~l~~~~~~g~~~~v~~~~~  205 (467)
                      . +...+.++.+.+.....
T Consensus       246 ~-~~~~~~~~~~~~~~~~~  263 (285)
T KOG4210|consen  246 D-QTRSIGGRPLRLEEDEP  263 (285)
T ss_pred             c-ccCcccCcccccccCCC
Confidence            7 78888898888855433

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

Probab=98.69  E-value=7.9e-08  Score=91.77  Aligned_cols=82  Identities=28%  Similarity=0.443  Sum_probs=72.6

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCC---CccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLST---RRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      ...++.|||+||++.++|+.|...|-+||+|.+|+|+.-+..   .+.+.|+||.|-+..||++|++.|+++.+.+..++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            456889999999999999999999999999999999853322   23456999999999999999999999999999999


Q ss_pred             eeecc
Q 012257          113 IMYSY  117 (467)
Q Consensus       113 v~~~~  117 (467)
                      +.|..
T Consensus       251 ~gWgk  255 (877)
T KOG0151|consen  251 LGWGK  255 (877)
T ss_pred             ecccc
Confidence            99984

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

Probab=98.64  E-value=6.3e-08  Score=90.19  Aligned_cols=81  Identities=26%  Similarity=0.402  Sum_probs=69.1

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ..+|||.|||.++++++|+++|..||.|+..+|.... .++..+||||+|.+.+++..|+.+ +-..+++++|.|+-.++
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            3459999999999999999999999999998887755 444449999999999999999986 46778999999998776


Q ss_pred             hHH
Q 012257          400 KEE  402 (467)
Q Consensus       400 ~~~  402 (467)
                      ...
T Consensus       367 ~~~  369 (419)
T KOG0116|consen  367 GFR  369 (419)
T ss_pred             ccc
Confidence            443

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

Probab=98.64  E-value=2.1e-08  Score=93.45  Aligned_cols=72  Identities=29%  Similarity=0.467  Sum_probs=65.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceE
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY  393 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  393 (467)
                      +....+|+|-|||..+++++|+++|+.||+|+.|+.-+.    .+|.+||+|-|..+|.+|+++|++..+.|+.|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            445668999999999999999999999999999776555    456999999999999999999999999999988

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

Probab=98.63  E-value=2.9e-07  Score=67.16  Aligned_cols=78  Identities=19%  Similarity=0.336  Sum_probs=65.0

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcC--CCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccC----Cceee
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQM--GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLN----GKPIR  112 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~--G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~----g~~~~  112 (467)
                      .+||.|+|||-..+.++|.+++...  |..--+.+.-|-.++.+.|||||.|.+.++|.+..+..++..+.    .+.+.
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~   80 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCE   80 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEE
Confidence            3799999999999999999888654  67777788888889999999999999999999999998887663    34445


Q ss_pred             eeec
Q 012257          113 IMYS  116 (467)
Q Consensus       113 v~~~  116 (467)
                      |.++
T Consensus        81 i~yA   84 (97)
T PF04059_consen   81 ISYA   84 (97)
T ss_pred             Eehh
Confidence            5544

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

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

Probab=98.60  E-value=6.6e-08  Score=83.42  Aligned_cols=83  Identities=20%  Similarity=0.359  Sum_probs=76.8

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      -...+.+.+||+|+...++.+++..+|+.||.|..|.+..|+.++.++|||||+|.+.+.+.+|+. |++..|.|+.+.+
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            445668999999999999999999999999999999999999999999999999999999999998 9999999999988


Q ss_pred             eecc
Q 012257          114 MYSY  117 (467)
Q Consensus       114 ~~~~  117 (467)
                      .+-.
T Consensus       175 t~~r  178 (231)
T KOG4209|consen  175 TLKR  178 (231)
T ss_pred             eeee
Confidence            6643

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.60  E-value=4.7e-08  Score=87.42  Aligned_cols=175  Identities=22%  Similarity=0.244  Sum_probs=131.8

Q ss_pred             ccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccccc
Q 012257          218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQK  296 (467)
Q Consensus       218 ~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~  296 (467)
                      ..+++++++...+.+.+...++..+|......+... ....+++++++.|...+.+..++.........+..+.......
T Consensus        88 ~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~~  167 (285)
T KOG4210|consen   88 SSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNTR  167 (285)
T ss_pred             cccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccccc
Confidence            467899999988888888888888887777666653 5577899999999999999999985444455444444333322


Q ss_pred             chHHHHHhhhhhhhhhhccccCCCCceEE-EecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHH
Q 012257          297 KYEREMELKGKFEQSLKETADKFEGLNLY-VKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEE  374 (467)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~  374 (467)
                      ....        ..............+++ |.++++.+++++|+.+|..+|.|..+++..+. .+..+|+|+|.|.+...
T Consensus       168 ~~~~--------~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~  239 (285)
T KOG4210|consen  168 RGLR--------PKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNS  239 (285)
T ss_pred             cccc--------ccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchh
Confidence            2100        00000011112233455 99999999999999999999999999998887 78899999999999999


Q ss_pred             HHHHHHHhCCcEecccceEEehhhhhH
Q 012257          375 ASKALTEMNGKMVVSKPLYVALAQRKE  401 (467)
Q Consensus       375 A~~A~~~l~g~~~~g~~l~v~~~~~~~  401 (467)
                      +..++.. ....+.++++.+.+..+..
T Consensus       240 ~~~~~~~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  240 KKLALND-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             HHHHhhc-ccCcccCcccccccCCCCc
Confidence            9999987 8889999999999987653

>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=98.59  E-value=2.4e-07  Score=63.76  Aligned_cols=73  Identities=23%  Similarity=0.359  Sum_probs=48.9

Q ss_pred             CeEEEcCCCCCCCHHHH----HHHHhcCC-CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           40 TSLYVGDLDLSVNDSQL----YDLFNQMG-QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l----~~~f~~~G-~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      +.|+|.|||.+.+-..|    ++++..|| .|.+|.       +   +.|+|.|.+.+.|.+|.+.|++....|+.|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~-------~---~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS-------G---GTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE---------T---T-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe-------C---CEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            57999999999998765    45666786 888772       1   479999999999999999999999999999999


Q ss_pred             ecccCccc
Q 012257          115 YSYRDPTI  122 (467)
Q Consensus       115 ~~~~~~~~  122 (467)
                      +.......
T Consensus        73 ~~~~~r~~   80 (90)
T PF11608_consen   73 FSPKNREF   80 (90)
T ss_dssp             SS--S---
T ss_pred             EcCCcccc
Confidence            88654433

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

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

Probab=98.56  E-value=2.3e-07  Score=88.67  Aligned_cols=83  Identities=31%  Similarity=0.511  Sum_probs=74.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC----CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceE
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP----NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY  393 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~----~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  393 (467)
                      ++..++|||+||++.++++.|...|..||.|.+++|+-..    ..+.+.|+||-|-++.+|.+|++.|+|..+.+..++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            4567789999999999999999999999999999987654    234567999999999999999999999999999999


Q ss_pred             Eehhhhh
Q 012257          394 VALAQRK  400 (467)
Q Consensus       394 v~~~~~~  400 (467)
                      +-|++..
T Consensus       251 ~gWgk~V  257 (877)
T KOG0151|consen  251 LGWGKAV  257 (877)
T ss_pred             ecccccc
Confidence            9998754

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

Probab=98.44  E-value=3.4e-07  Score=79.01  Aligned_cols=82  Identities=23%  Similarity=0.396  Sum_probs=75.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ..+.+.+||+|+.+.++.+++...|+.||.|..+.++.+. .|.++||+||+|.+.+.+.+|+. |+|..|.|+.+.|++
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            3456689999999999999999999999999999999998 45789999999999999999998 999999999999998


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      .+..
T Consensus       177 ~r~~  180 (231)
T KOG4209|consen  177 KRTN  180 (231)
T ss_pred             eeee
Confidence            8755

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.44  E-value=2.1e-08  Score=88.88  Aligned_cols=212  Identities=16%  Similarity=0.176  Sum_probs=126.3

Q ss_pred             ccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCC----CCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEeccc
Q 012257          128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL----GQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPF  203 (467)
Q Consensus       128 ~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~----g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~  203 (467)
                      +-|.|.||.+.++.++++.+|...|.|.++.++...+    ......|||.|.+...+..|-. |.++.+-++.+.|.++
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            4688999999999999999999999999999987522    2345789999999998888875 7777777777777443


Q ss_pred             ccccccccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCc
Q 012257          204 LRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKK  283 (467)
Q Consensus       204 ~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~  283 (467)
                      ...                       +-++..  .|..++.-..+--....+                         |..
T Consensus        87 ~~~-----------------------~~p~r~--af~~l~~~navprll~pd-------------------------g~L  116 (479)
T KOG4676|consen   87 GDE-----------------------VIPDRF--AFVELADQNAVPRLLPPD-------------------------GVL  116 (479)
T ss_pred             CCC-----------------------CCccHH--HHHhcCcccccccccCCC-------------------------Ccc
Confidence            222                       111111  232222211111111111                         111


Q ss_pred             cCCceEEEcc-cccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCcc
Q 012257          284 FDDKEWYVGK-AQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISR  362 (467)
Q Consensus       284 ~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~  362 (467)
                      +....+...- ..........+.......   .... -.++++|++|+..+...++.+.|..+|+|...++--...   .
T Consensus       117 p~~~~lt~~nh~p~ailktP~Lp~~~~A~---klee-irRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask~~---s  189 (479)
T KOG4676|consen  117 PGDRPLTKINHSPNAILKTPELPPQAAAK---KLEE-IRRTREVQSLISAAILPESGESFERKGEVSYAHTASKSR---S  189 (479)
T ss_pred             CCCCccccccCCccceecCCCCChHhhhh---hhHH-HHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhccCC---C
Confidence            1111110000 000000000000000000   0000 124799999999999999999999999999888765433   3


Q ss_pred             ceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          363 GSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       363 g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      -+|-|+|....+...|+. .+|..+.-........+
T Consensus       190 ~~c~~sf~~qts~~halr-~~gre~k~qhsr~ai~k  224 (479)
T KOG4676|consen  190 SSCSHSFRKQTSSKHALR-SHGRERKRQHSRRAIIK  224 (479)
T ss_pred             cchhhhHhhhhhHHHHHH-hcchhhhhhhhhhhhcC
Confidence            377799998888888876 57777764444444433

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.43  E-value=1.3e-06  Score=76.53  Aligned_cols=79  Identities=16%  Similarity=0.271  Sum_probs=65.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCC--ceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccc-eEEehh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFG--TITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP-LYVALA  397 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G--~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-l~v~~~  397 (467)
                      .++||+||-+++|++||.+....-|  .+.+++++.+. +|+++|||+|...+..+..+.++.|--+.|.|.. ..++|.
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~N  160 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSYN  160 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeeccc
Confidence            4799999999999999999887766  45667777665 8999999999999999999999999999998865 555555


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      +..
T Consensus       161 K~~  163 (498)
T KOG4849|consen  161 KTN  163 (498)
T ss_pred             hhh
Confidence            543

>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=98.38  E-value=1.2e-06  Score=60.42  Aligned_cols=69  Identities=26%  Similarity=0.432  Sum_probs=47.9

Q ss_pred             eEEEecCCCCCCHHH----HHHhhccCC-ceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          323 NLYVKNLDDSISDDK----LKELFSEFG-TITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~----l~~~F~~~G-~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      .|+|.|||.+.+...    |++++..+| .|.+|.         .+.|+|.|.+.+.|.+|.+.|+|..+.|++|.|+|.
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~---------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~   74 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS---------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFS   74 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe---------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEc
Confidence            599999999888754    556666774 677662         258999999999999999999999999999999998


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ...
T Consensus        75 ~~~   77 (90)
T PF11608_consen   75 PKN   77 (90)
T ss_dssp             --S
T ss_pred             CCc
Confidence            543

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

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.34  E-value=8.8e-08  Score=85.85  Aligned_cols=154  Identities=23%  Similarity=0.350  Sum_probs=121.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCc-ccCCceeeeeeccc
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFT-PLNGKPIRIMYSYR  118 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~-~~~g~~~~v~~~~~  118 (467)
                      .++|++||.+.++..+|..+|.....-.+-.++.+      .|||||++.+..-|.+|++.+++. .+.|+++.+..+..
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            57999999999999999999976521111122222      169999999999999999999875 68999999987765


Q ss_pred             CcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeee
Q 012257          119 DPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQV  198 (467)
Q Consensus       119 ~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~  198 (467)
                      +...    ++++-|+|+|+..-.+.|..++..||.+..|......+  ..-..-|+|.+.+.+..|+..++|..+.+..+
T Consensus        76 kkqr----srk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~--etavvnvty~~~~~~~~ai~kl~g~Q~en~~~  149 (584)
T KOG2193|consen   76 KKQR----SRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDS--ETAVVNVTYSAQQQHRQAIHKLNGPQLENQHL  149 (584)
T ss_pred             HHHH----hhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccch--HHHHHHHHHHHHHHHHHHHHhhcchHhhhhhh
Confidence            4332    45699999999999999999999999999887754321  12223468899999999999999999988888


Q ss_pred             Eeccccc
Q 012257          199 FVGPFLR  205 (467)
Q Consensus       199 ~v~~~~~  205 (467)
                      .+.+...
T Consensus       150 k~~YiPd  156 (584)
T KOG2193|consen  150 KVGYIPD  156 (584)
T ss_pred             hcccCch
Confidence            8866543

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.33  E-value=4.1e-07  Score=81.67  Aligned_cols=156  Identities=23%  Similarity=0.416  Sum_probs=119.8

Q ss_pred             cceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCc-cCCceEEEcccccc
Q 012257          219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKK-FDDKEWYVGKAQKK  297 (467)
Q Consensus       219 ~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~-~~~~~l~~~~~~~~  297 (467)
                      +.++++||.+.++.+++..+|...-.--+-.++.     ..||+||.+.+...|.+|+..+++.. +.|+++.+...-.+
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     36799999999999999999988754 67777777554433


Q ss_pred             hHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHH
Q 012257          298 YEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASK  377 (467)
Q Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~  377 (467)
                      ..                    .++.+-|.|+|+...++.|..+...||.|+.|.......  -....-|+|.+.+.+.-
T Consensus        77 kq--------------------rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~--etavvnvty~~~~~~~~  134 (584)
T KOG2193|consen   77 KQ--------------------RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDS--ETAVVNVTYSAQQQHRQ  134 (584)
T ss_pred             HH--------------------HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccch--HHHHHHHHHHHHHHHHH
Confidence            22                    223488999999999999999999999999987644321  12234478999999999


Q ss_pred             HHHHhCCcEecccceEEehhhhhH
Q 012257          378 ALTEMNGKMVVSKPLYVALAQRKE  401 (467)
Q Consensus       378 A~~~l~g~~~~g~~l~v~~~~~~~  401 (467)
                      ||..|+|..+....++|.|-....
T Consensus       135 ai~kl~g~Q~en~~~k~~YiPdeq  158 (584)
T KOG2193|consen  135 AIHKLNGPQLENQHLKVGYIPDEQ  158 (584)
T ss_pred             HHHhhcchHhhhhhhhcccCchhh
Confidence            999999999999999999976553

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

Probab=98.12  E-value=1.1e-05  Score=60.69  Aligned_cols=72  Identities=28%  Similarity=0.453  Sum_probs=46.0

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCc-----EecccceEEeh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGK-----MVVSKPLYVAL  396 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-----~~~g~~l~v~~  396 (467)
                      +.|+|.+++..++-++|++.|+.||.|..|.+....     ..|+|.|.+.++|.+|+..+...     .+.+..+.++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~-----~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD-----TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC-----CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            468999999999999999999999999999887753     38999999999999999877544     55677777765


Q ss_pred             hh
Q 012257          397 AQ  398 (467)
Q Consensus       397 ~~  398 (467)
                      -.
T Consensus        77 Le   78 (105)
T PF08777_consen   77 LE   78 (105)
T ss_dssp             --
T ss_pred             CC
Confidence            43

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

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.99  E-value=1.5e-05  Score=69.74  Aligned_cols=78  Identities=23%  Similarity=0.481  Sum_probs=62.3

Q ss_pred             eEEEecCCCCCCHHH----H--HHhhccCCceeEEEEeeCCCC-Cc-cce--EEEEcCCHHHHHHHHHHhCCcEecccce
Q 012257          323 NLYVKNLDDSISDDK----L--KELFSEFGTITSCKVMRDPNG-IS-RGS--GFVAFSTAEEASKALTEMNGKMVVSKPL  392 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~----l--~~~F~~~G~v~~v~i~~~~~~-~~-~g~--afV~f~~~~~A~~A~~~l~g~~~~g~~l  392 (467)
                      -+||-+|++.+-+++    |  .++|.+||.|..+.+-+.... .+ .+.  .+|+|.+.++|.+||.+.+|..++|+.|
T Consensus       116 LvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~l  195 (480)
T COG5175         116 LVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVL  195 (480)
T ss_pred             eeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceE
Confidence            489999998876665    2  378999999999888765411 11 122  3999999999999999999999999999


Q ss_pred             EEehhhhh
Q 012257          393 YVALAQRK  400 (467)
Q Consensus       393 ~v~~~~~~  400 (467)
                      +.+|...+
T Consensus       196 katYGTTK  203 (480)
T COG5175         196 KATYGTTK  203 (480)
T ss_pred             eeecCchH
Confidence            99986544

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

Probab=97.98  E-value=7.9e-06  Score=72.63  Aligned_cols=84  Identities=24%  Similarity=0.423  Sum_probs=72.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeE--------EEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEec
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITS--------CKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVV  388 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~--------v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~  388 (467)
                      .....+|||.+||..+++.+|.++|.++|.|..        +.|.++. ++.+++-|.|.|.+...|+.|+.-++++.++
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            345558999999999999999999999998854        4444444 7889999999999999999999999999999


Q ss_pred             ccceEEehhhhhH
Q 012257          389 SKPLYVALAQRKE  401 (467)
Q Consensus       389 g~~l~v~~~~~~~  401 (467)
                      +..|+|.++....
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999999987554

>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=97.91  E-value=3e-05  Score=58.24  Aligned_cols=58  Identities=26%  Similarity=0.417  Sum_probs=39.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCC
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNF  103 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~  103 (467)
                      +.|.|.++...++-++|++.|+.||.|..|.+.+...      .|||.|.+.++|++|++.+..
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~~   59 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLKE   59 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHHh
Confidence            5789999999999999999999999999998876543      699999999999999998743

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

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.90  E-value=1.7e-05  Score=69.69  Aligned_cols=86  Identities=19%  Similarity=0.320  Sum_probs=72.4

Q ss_pred             CCCCCCCCCcc--CeEEEcCCCCCCCHHHHHHHHhcCC--CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCc
Q 012257           29 GGVGDARQFVS--TSLYVGDLDLSVNDSQLYDLFNQMG--QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFT  104 (467)
Q Consensus        29 ~~~~~~~~~~~--~~l~v~nLp~~~~e~~l~~~f~~~G--~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~  104 (467)
                      -+.+++-+.+.  -++||+||-|++|+++|.+.+...|  .+.+++.+..+..|+++|||+|...+....++.++.|-.+
T Consensus        68 ~~~~~~~s~~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k  147 (498)
T KOG4849|consen   68 IGAKPATSSEGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTK  147 (498)
T ss_pred             ccCCccccccCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccc
Confidence            34444444443  4589999999999999999998887  7889999999999999999999999999999999999888


Q ss_pred             ccCCceeeee
Q 012257          105 PLNGKPIRIM  114 (467)
Q Consensus       105 ~~~g~~~~v~  114 (467)
                      .|.|..-.|.
T Consensus       148 ~iHGQ~P~V~  157 (498)
T KOG4849|consen  148 TIHGQSPTVL  157 (498)
T ss_pred             eecCCCCeee
Confidence            8988765553

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

Probab=97.87  E-value=3.4e-05  Score=49.76  Aligned_cols=53  Identities=23%  Similarity=0.453  Sum_probs=42.8

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHH
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL   98 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~   98 (467)
                      ++.|-|.|.+++.. ++|+.+|..||+|..+.+....      ..++|.|.+..+|++|+
T Consensus         1 ~~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~~~------~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    1 STWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPEST------NWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             CcEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCCCC------cEEEEEECCHHHHHhhC
Confidence            36788999887555 5566799999999998886332      38999999999999985

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.80  E-value=6.1e-06  Score=73.67  Aligned_cols=201  Identities=13%  Similarity=0.152  Sum_probs=117.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCC---CccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLST---RRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        41 ~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      .|.|.||.+.++.++++.+|...|.|.++.++.....   .-....|||.|.+...+.-|.. |-++.|-++.+-|....
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~~   87 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPYG   87 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEecC
Confidence            8999999999999999999999999999999863211   1233589999999999998886 66666666665553321


Q ss_pred             cCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCee
Q 012257          118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQ  197 (467)
Q Consensus       118 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~  197 (467)
                                         ..+-.+..  +|..++.-..+.-...++|       |-+.+.-          ...++...
T Consensus        88 -------------------~~~~p~r~--af~~l~~~navprll~pdg-------~Lp~~~~----------lt~~nh~p  129 (479)
T KOG4676|consen   88 -------------------DEVIPDRF--AFVELADQNAVPRLLPPDG-------VLPGDRP----------LTKINHSP  129 (479)
T ss_pred             -------------------CCCCccHH--HHHhcCcccccccccCCCC-------ccCCCCc----------cccccCCc
Confidence                               11111111  4443332221111111111       0000000          00000000


Q ss_pred             --eEecccccccccccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHH
Q 012257          198 --VFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARS  275 (467)
Q Consensus       198 --~~v~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a  275 (467)
                        +...+..+........... .+++++.+|+..+...++.+.|..+|.|....+...   ....+|.+.|........|
T Consensus       130 ~ailktP~Lp~~~~A~kleei-rRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask---~~s~~c~~sf~~qts~~ha  205 (479)
T KOG4676|consen  130 NAILKTPELPPQAAAKKLEEI-RRTREVQSLISAAILPESGESFERKGEVSYAHTASK---SRSSSCSHSFRKQTSSKHA  205 (479)
T ss_pred             cceecCCCCChHhhhhhhHHH-Hhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhcc---CCCcchhhhHhhhhhHHHH
Confidence              0001111111111111111 267899999999999999999999999877665443   2344777999888777777


Q ss_pred             HHHhCCCccC
Q 012257          276 VEALNGKKFD  285 (467)
Q Consensus       276 ~~~l~~~~~~  285 (467)
                      +. .+|..+.
T Consensus       206 lr-~~gre~k  214 (479)
T KOG4676|consen  206 LR-SHGRERK  214 (479)
T ss_pred             HH-hcchhhh
Confidence            76 5666654

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.79  E-value=6.6e-05  Score=63.56  Aligned_cols=92  Identities=27%  Similarity=0.316  Sum_probs=81.7

Q ss_pred             HHHHHHHHhCCCccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeE
Q 012257          271 DAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITS  350 (467)
Q Consensus       271 ~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~  350 (467)
                      -|..|...|++....++.+.+.++...                         .|+|.||...++-+.+.+.|+.||.|+.
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~a-------------------------~l~V~nl~~~~sndll~~~f~~fg~~e~   60 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMHA-------------------------ELYVVNLMQGASNDLLEQAFRRFGPIER   60 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeeccc-------------------------eEEEEecchhhhhHHHHHhhhhcCccch
Confidence            466677779999999999999998762                         5999999999999999999999999999


Q ss_pred             EEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEe
Q 012257          351 CKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV  387 (467)
Q Consensus       351 v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  387 (467)
                      ..+..|..++..+-++|+|...-.|.+|.......-|
T Consensus        61 av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~   97 (275)
T KOG0115|consen   61 AVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGF   97 (275)
T ss_pred             heeeecccccccccchhhhhcchhHHHHHHHhccCcc
Confidence            9999999999999999999999999999998754433

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

Probab=97.78  E-value=3.6e-05  Score=68.55  Aligned_cols=84  Identities=20%  Similarity=0.265  Sum_probs=75.2

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeE--------EEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccC
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVV--------SVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLN  107 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~--------~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~  107 (467)
                      .....+|||-+||..+++++|.++|..+|.|.        -|+|.+++.|+..++-|.|.|.+...|+.|+.-++...+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            45578899999999999999999999998553        5778899999999999999999999999999999999999


Q ss_pred             CceeeeeecccC
Q 012257          108 GKPIRIMYSYRD  119 (467)
Q Consensus       108 g~~~~v~~~~~~  119 (467)
                      ++.|+|..+...
T Consensus       143 gn~ikvs~a~~r  154 (351)
T KOG1995|consen  143 GNTIKVSLAERR  154 (351)
T ss_pred             CCCchhhhhhhc
Confidence            999999776544

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.76  E-value=8e-05  Score=65.33  Aligned_cols=116  Identities=18%  Similarity=0.359  Sum_probs=80.2

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHH------HHHHhcCCCeEEEEEEecCCCCccc-cEE--EEEecChHHHHHHHHHhC
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQL------YDLFNQMGQVVSVRVCRDLSTRRSL-GYG--YVNYNAAHEATRALDELN  102 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l------~~~f~~~G~v~~v~i~~~~~~~~~~-g~a--fV~f~~~~~A~~A~~~l~  102 (467)
                      ..++.....-+||-+||+.+..|++      .++|.+||.|..|.|-+....-.+. +.+  ||+|.+.|||.+|+...+
T Consensus       107 sniRVvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vD  186 (480)
T COG5175         107 SNIRVVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVD  186 (480)
T ss_pred             ccceeeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhc
Confidence            3455556677999999998888773      5799999999988887654222221 223  999999999999999999


Q ss_pred             CcccCCceeeeeecccC------cccccCCCccEEEcCCC---CcCCHHHHHHH
Q 012257          103 FTPLNGKPIRIMYSYRD------PTIRKSGAGNIFIKNLD---KSIDNKALHDT  147 (467)
Q Consensus       103 ~~~~~g~~~~v~~~~~~------~~~~~~~~~~l~v~nlp---~~~t~~~l~~~  147 (467)
                      +..++|+.|+..+...+      ....=.+..+.|+.---   ...+++||...
T Consensus       187 gs~~DGr~lkatYGTTKYCtsYLRn~~CpNp~CMyLHEpg~e~Ds~tK~el~n~  240 (480)
T COG5175         187 GSLLDGRVLKATYGTTKYCTSYLRNAVCPNPDCMYLHEPGPEKDSLTKDELCNS  240 (480)
T ss_pred             cccccCceEeeecCchHHHHHHHcCCCCCCCCeeeecCCCcccccccHHHHhhh
Confidence            99999999998664321      11111233466664432   23467777654

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

Probab=97.72  E-value=2e-05  Score=66.52  Aligned_cols=69  Identities=19%  Similarity=0.341  Sum_probs=60.1

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCC---------CC----ccceEEEEcCCHHHHHHHHHHhCCcEec
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN---------GI----SRGSGFVAFSTAEEASKALTEMNGKMVV  388 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~---------~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~  388 (467)
                      -.||+++||+.+....|+++|+.||.|-+|.+-+...         |.    ....|+|+|.+...|.++...|||..|+
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Ig  154 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIG  154 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccC
Confidence            3699999999999999999999999999999877642         12    2246789999999999999999999999


Q ss_pred             cc
Q 012257          389 SK  390 (467)
Q Consensus       389 g~  390 (467)
                      |+
T Consensus       155 gk  156 (278)
T KOG3152|consen  155 GK  156 (278)
T ss_pred             CC
Confidence            86

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.71  E-value=0.0001  Score=62.39  Aligned_cols=89  Identities=24%  Similarity=0.388  Sum_probs=80.3

Q ss_pred             HHHHHHHHHhCCcccCCceeeeeecccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEE
Q 012257           92 HEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYG  171 (467)
Q Consensus        92 ~~A~~A~~~l~~~~~~g~~~~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~a  171 (467)
                      .-|..|-..|++....|+.++|.++..         ..|+|.||...++.+.+...|+.||+|....++.|..+...+-+
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~---------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg   75 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH---------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREG   75 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc---------ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccc
Confidence            446777778999999999999998863         46999999999999999999999999999999999889999999


Q ss_pred             EEEeCCHHHHHHHHHHhc
Q 012257          172 FVQFDNEESAKSAIDKLN  189 (467)
Q Consensus       172 fV~f~~~~~A~~a~~~l~  189 (467)
                      +|+|...-.|.+|+..+.
T Consensus        76 ~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   76 IVEFAKKPNARKAARRCR   93 (275)
T ss_pred             hhhhhcchhHHHHHHHhc
Confidence            999999999999998874

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

Probab=97.67  E-value=0.00016  Score=68.13  Aligned_cols=80  Identities=24%  Similarity=0.309  Sum_probs=65.6

Q ss_pred             CCceEEEecCCCCCCH------HHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEec-ccce
Q 012257          320 EGLNLYVKNLDDSISD------DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVV-SKPL  392 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~------~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l  392 (467)
                      -...|+|.|+|.--..      .-|..+|+++|+|..+.++.++.|..+|+.|++|++..+|..|++.|||+.|+ .+..
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            3447999999853222      35667899999999999999998889999999999999999999999999997 4567


Q ss_pred             EEehhhh
Q 012257          393 YVALAQR  399 (467)
Q Consensus       393 ~v~~~~~  399 (467)
                      .|..-+.
T Consensus       137 ~v~~f~d  143 (698)
T KOG2314|consen  137 FVRLFKD  143 (698)
T ss_pred             Eeehhhh
Confidence            7765443

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

Probab=97.63  E-value=0.00013  Score=47.06  Aligned_cols=52  Identities=21%  Similarity=0.369  Sum_probs=41.9

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHH
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL  379 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~  379 (467)
                      +.|-|.+.+....+ .+..+|..||+|.++.+...     ..+.+|.|.++.+|.+|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~-----~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPES-----TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCC-----CcEEEEEECCHHHHHhhC
Confidence            35888999977664 45568889999999888732     349999999999999985

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

Probab=97.61  E-value=3.8e-05  Score=64.94  Aligned_cols=74  Identities=22%  Similarity=0.356  Sum_probs=63.2

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCC--------Cccc----cEEEEEecChHHHHHHHHHhCCcc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLST--------RRSL----GYGYVNYNAAHEATRALDELNFTP  105 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~--------~~~~----g~afV~f~~~~~A~~A~~~l~~~~  105 (467)
                      .+-.||+++||+......|+++|+.||.|-.|.+-+...+        |.+.    .-++|+|.+...|.++...||+.+
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            4578999999999999999999999999999999876555        2222    357899999999999999999999


Q ss_pred             cCCcee
Q 012257          106 LNGKPI  111 (467)
Q Consensus       106 ~~g~~~  111 (467)
                      |.|+.-
T Consensus       153 Iggkk~  158 (278)
T KOG3152|consen  153 IGGKKK  158 (278)
T ss_pred             cCCCCC
Confidence            988653

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

Probab=97.54  E-value=7.3e-05  Score=67.92  Aligned_cols=69  Identities=23%  Similarity=0.410  Sum_probs=57.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeC---C-C--CC--------ccceEEEEcCCHHHHHHHHHHhCC
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD---P-N--GI--------SRGSGFVAFSTAEEASKALTEMNG  384 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~---~-~--~~--------~~g~afV~f~~~~~A~~A~~~l~g  384 (467)
                      -++++|.+.|||.+-.-+.|.++|+.+|.|+.|+|+..   + +  +.        .+-+|+|+|+..+.|.+|.+.|+.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            36779999999998888999999999999999999887   2 1  11        146899999999999999998865


Q ss_pred             cEe
Q 012257          385 KMV  387 (467)
Q Consensus       385 ~~~  387 (467)
                      ..-
T Consensus       309 e~~  311 (484)
T KOG1855|consen  309 EQN  311 (484)
T ss_pred             hhh
Confidence            433

>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=97.52  E-value=0.0004  Score=51.24  Aligned_cols=79  Identities=22%  Similarity=0.240  Sum_probs=53.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEE-EeeC-------CCCCccceEEEEcCCHHHHHHHHHHhCCcEecccc
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCK-VMRD-------PNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP  391 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~-i~~~-------~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  391 (467)
                      ....|.|.+.|+. ....|.+.|++||.|.+.. +.++       +........-|+|++..+|.+|+. -||..+.|..
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            3446999999988 5567889999999998764 1111       111124589999999999999997 5999998864


Q ss_pred             -eEEehhhhh
Q 012257          392 -LYVALAQRK  400 (467)
Q Consensus       392 -l~v~~~~~~  400 (467)
                       +-|.+.++.
T Consensus        83 mvGV~~~~~~   92 (100)
T PF05172_consen   83 MVGVKPCDPA   92 (100)
T ss_dssp             EEEEEE-HHH
T ss_pred             EEEEEEcHHh
Confidence             557776543

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.

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

Probab=97.48  E-value=0.00029  Score=66.77  Aligned_cols=84  Identities=21%  Similarity=0.248  Sum_probs=67.3

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhc-cCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEe---cccce
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFS-EFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV---VSKPL  392 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~-~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~---~g~~l  392 (467)
                      ....+..|+|.||---+|.-.|+.++. ..|.|++. ++-.    -+..|||.|.+.++|.+.+.+|||..+   +++.|
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L  514 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHL  514 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHH-HHHH----hhcceeEecccHHHHHHHHHHHhccccCCCCCcee
Confidence            344566899999999999999999998 55677766 2221    234899999999999999999999988   57899


Q ss_pred             EEehhhhhHHHHH
Q 012257          393 YVALAQRKEERRA  405 (467)
Q Consensus       393 ~v~~~~~~~~~~~  405 (467)
                      .+.|.........
T Consensus       515 ~adf~~~deld~h  527 (718)
T KOG2416|consen  515 IADFVRADELDKH  527 (718)
T ss_pred             EeeecchhHHHHH
Confidence            9999876665543

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

Probab=97.43  E-value=5.6e-05  Score=64.17  Aligned_cols=63  Identities=21%  Similarity=0.389  Sum_probs=54.0

Q ss_pred             HHHHHhhc-cCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          336 DKLKELFS-EFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       336 ~~l~~~F~-~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ++|...|+ +||+|+++.|..+-.-.-+|-++|.|...++|++|+..|||.++.|++|...+..
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            45555555 9999999988777655568899999999999999999999999999999999864

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

Probab=97.35  E-value=0.00053  Score=53.71  Aligned_cols=57  Identities=25%  Similarity=0.475  Sum_probs=47.1

Q ss_pred             HHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          336 DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       336 ~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      .+|.+.|..||+|.-+|+..+       .-+|+|.+-++|.+|+. ++|..++|+.|+|+...+.
T Consensus        51 ~~ll~~~~~~GevvLvRfv~~-------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVGD-------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEETT-------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             HHHHHHHHhCCceEEEEEeCC-------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            377788999999998888775       78999999999999996 8999999999999987654

; PDB: 1UFW_A 2DNR_A.

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

Probab=97.32  E-value=0.00023  Score=64.78  Aligned_cols=77  Identities=19%  Similarity=0.320  Sum_probs=61.1

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEec---CCC---Cc-------cccEEEEEecChHHHHHHHHHhCC
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRD---LST---RR-------SLGYGYVNYNAAHEATRALDELNF  103 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~---~~~---~~-------~~g~afV~f~~~~~A~~A~~~l~~  103 (467)
                      -++++|.+.|||.+-.-+.|.++|..+|.|.+|+|++-   ...   ..       .+-+|+|+|...+.|.+|.+.++.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            47899999999999999999999999999999999864   111   11       246899999999999999997755


Q ss_pred             cccCCceeee
Q 012257          104 TPLNGKPIRI  113 (467)
Q Consensus       104 ~~~~g~~~~v  113 (467)
                      ..-+..-+++
T Consensus       309 e~~wr~glkv  318 (484)
T KOG1855|consen  309 EQNWRMGLKV  318 (484)
T ss_pred             hhhhhhcchh
Confidence            4433333444

>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=97.23  E-value=0.0016  Score=48.13  Aligned_cols=77  Identities=19%  Similarity=0.181  Sum_probs=50.7

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEE-ecC------CCCccccEEEEEecChHHHHHHHHHhCCcccCCce
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVC-RDL------STRRSLGYGYVNYNAAHEATRALDELNFTPLNGKP  110 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~-~~~------~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  110 (467)
                      ..+-|.|-+.|+. ....|.++|++||.|++..-. ++.      ..-...+..-|+|+++.+|.+||. .|+..+.|..
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            3567889998886 678899999999999887500 000      000112478999999999999998 6999888865


Q ss_pred             e-eeeec
Q 012257          111 I-RIMYS  116 (467)
Q Consensus       111 ~-~v~~~  116 (467)
                      + -|.+.
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            4 34443

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.

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

Probab=97.16  E-value=0.0011  Score=57.32  Aligned_cols=67  Identities=21%  Similarity=0.346  Sum_probs=55.3

Q ss_pred             HHHHHHhhccCCceeEEEEeeCCCCC--ccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhhH
Q 012257          335 DDKLKELFSEFGTITSCKVMRDPNGI--SRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKE  401 (467)
Q Consensus       335 ~~~l~~~F~~~G~v~~v~i~~~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  401 (467)
                      ++++++-+++||.|..|.|...++..  ----.||+|...++|.+|+-.|||++|+|+.+..-|.....
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~ek  368 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNLEK  368 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccHHh
Confidence            46889999999999999888775311  12358999999999999999999999999999988876443

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=97.03  E-value=0.0041  Score=41.07  Aligned_cols=54  Identities=28%  Similarity=0.419  Sum_probs=45.0

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccC---CceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEF---GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM  382 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~---G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l  382 (467)
                      ..|+|.|++ .++.++|+.+|..|   ....+|.++.|.      .|-|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC------cEEEEECCHHHHHHHHHcC
Confidence            369999996 57888999999998   234588888874      6889999999999999865

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

Probab=96.96  E-value=0.004  Score=48.91  Aligned_cols=71  Identities=28%  Similarity=0.391  Sum_probs=51.6

Q ss_pred             ccCeEEEcCCCC------CCCH---HHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC
Q 012257           38 VSTSLYVGDLDL------SVND---SQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG  108 (467)
Q Consensus        38 ~~~~l~v~nLp~------~~~e---~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g  108 (467)
                      +..||.|+=+.+      ..++   .+|.+.|+.||.|.=|++..+        .-+|+|.+.++|.+|++ +++..+.|
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g   96 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNG   96 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETT
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECC
Confidence            345666665552      1222   368889999999888887754        36999999999999997 89999999


Q ss_pred             ceeeeeecc
Q 012257          109 KPIRIMYSY  117 (467)
Q Consensus       109 ~~~~v~~~~  117 (467)
                      +.++|..-.
T Consensus        97 ~~l~i~LKt  105 (146)
T PF08952_consen   97 RTLKIRLKT  105 (146)
T ss_dssp             EEEEEEE--
T ss_pred             EEEEEEeCC
Confidence            999996543

; PDB: 1UFW_A 2DNR_A.

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

Probab=96.95  E-value=0.003  Score=59.85  Aligned_cols=76  Identities=28%  Similarity=0.423  Sum_probs=60.9

Q ss_pred             CCCccEEEcCCCCcCC------HHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccC-Cee
Q 012257          125 SGAGNIFIKNLDKSID------NKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLN-DKQ  197 (467)
Q Consensus       125 ~~~~~l~v~nlp~~~t------~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~-g~~  197 (467)
                      .-...|+|.|+|.--.      ..-|..+|+++|.+....+..+..|..+|+.|++|++..+|..|++.|||..+. +..
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            3456899999985321      234557899999999999998877779999999999999999999999998765 444


Q ss_pred             eEe
Q 012257          198 VFV  200 (467)
Q Consensus       198 ~~v  200 (467)
                      ..+
T Consensus       136 f~v  138 (698)
T KOG2314|consen  136 FFV  138 (698)
T ss_pred             EEe
Confidence            444

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.93  E-value=0.0051  Score=42.83  Aligned_cols=54  Identities=22%  Similarity=0.432  Sum_probs=43.1

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhC
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN  383 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  383 (467)
                      .||--..|..|-..||.++|++||.| .|.++.+      ..|||...+++.|..|+..+.
T Consensus        10 HVFhltFPkeWK~~DI~qlFspfG~I-~VsWi~d------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLTFPKEWKTSDIYQLFSPFGQI-YVSWIND------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE--TT--HHHHHHHCCCCCCE-EEEEECT------TEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEeCchHhhhhhHHHHhccCCcE-EEEEEcC------CcEEEEeecHHHHHHHHHHhc
Confidence            45555599999999999999999999 7777776      389999999999999999886

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.75  E-value=0.0089  Score=46.11  Aligned_cols=79  Identities=13%  Similarity=0.203  Sum_probs=60.8

Q ss_pred             CCCCCCCccCeEEEcCCCCCCCH-H---HHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc
Q 012257           31 VGDARQFVSTSLYVGDLDLSVND-S---QLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL  106 (467)
Q Consensus        31 ~~~~~~~~~~~l~v~nLp~~~~e-~---~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  106 (467)
                      .......+..+|.|+=|..++.. +   .|.+.++.||+|.+|...-..       .|.|.|.+..+|-+|+...+. ..
T Consensus        78 kk~~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGrq-------savVvF~d~~SAC~Av~Af~s-~~  149 (166)
T PF15023_consen   78 KKNTKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGRQ-------SAVVVFKDITSACKAVSAFQS-RA  149 (166)
T ss_pred             cccCCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCCc-------eEEEEehhhHHHHHHHHhhcC-CC
Confidence            34556778899999888776554 3   456677889999999885322       699999999999999998765 56


Q ss_pred             CCceeeeeecc
Q 012257          107 NGKPIRIMYSY  117 (467)
Q Consensus       107 ~g~~~~v~~~~  117 (467)
                      .|..++..|..
T Consensus       150 pgtm~qCsWqq  160 (166)
T PF15023_consen  150 PGTMFQCSWQQ  160 (166)
T ss_pred             CCceEEeeccc
Confidence            77888877754

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

Probab=96.68  E-value=0.0052  Score=53.29  Aligned_cols=65  Identities=15%  Similarity=0.184  Sum_probs=52.6

Q ss_pred             HHHHHHHHhcCCCeEEEEEEecCCCCccc-cEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           53 DSQLYDLFNQMGQVVSVRVCRDLSTRRSL-GYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        53 e~~l~~~f~~~G~v~~v~i~~~~~~~~~~-g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      |+++.+-+.+||.|..|.|..+..---.. --.||+|...++|.+|+-.||+..|.|+.++..+..
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            35678889999999999999764322111 136999999999999999999999999999887654

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.55  E-value=0.0092  Score=46.05  Aligned_cols=75  Identities=19%  Similarity=0.210  Sum_probs=56.7

Q ss_pred             cCCCCceEEEecCCCCC----CHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccce
Q 012257          317 DKFEGLNLYVKNLDDSI----SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPL  392 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~----~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l  392 (467)
                      ..++..+|.|+=|..++    +-..+...++.||.|.+|.....      ..|.|.|.|..+|.+|+.+++. ...|..+
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGr------qsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGR------QSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCC------ceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            34566688887665544    33455566789999999987553      4899999999999999999886 5567778


Q ss_pred             EEehhh
Q 012257          393 YVALAQ  398 (467)
Q Consensus       393 ~v~~~~  398 (467)
                      .++|-.
T Consensus       155 qCsWqq  160 (166)
T PF15023_consen  155 QCSWQQ  160 (166)
T ss_pred             Eeeccc
Confidence            877743

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

Probab=96.49  E-value=0.0014  Score=55.95  Aligned_cols=62  Identities=21%  Similarity=0.349  Sum_probs=50.6

Q ss_pred             HHHHHHHh-hcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEeccc
Q 012257          142 KALHDTFS-TFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPF  203 (467)
Q Consensus       142 ~~l~~~f~-~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~  203 (467)
                      +++...|+ +||+|+++.+.....-.-.|-+||.|...++|++|+..|++..+.|+.|.....
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            44555555 999999987766544456788999999999999999999999999999987543

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.48  E-value=0.018  Score=38.11  Aligned_cols=54  Identities=19%  Similarity=0.292  Sum_probs=43.9

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcC----CCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHh
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQM----GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL  101 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~----G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l  101 (467)
                      ..+|+|+|+.. .+.++|+.+|..|    ++ ..|.-+-|.       .|-|.|.+.+.|.+|+..|
T Consensus         5 peavhirGvd~-lsT~dI~~y~~~y~~~~~~-~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVDE-LSTDDIKAYFSEYFDEEGP-FRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCCC-CCHHHHHHHHHHhcccCCC-ceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            35799999855 8999999999999    54 466666664       4899999999999999754

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

Probab=96.34  E-value=0.0032  Score=60.00  Aligned_cols=71  Identities=23%  Similarity=0.204  Sum_probs=60.2

Q ss_pred             CCCCCCCCccCeEEEcCCCCCCCHHHHHHHHh-cCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc
Q 012257           30 GVGDARQFVSTSLYVGDLDLSVNDSQLYDLFN-QMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL  106 (467)
Q Consensus        30 ~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~-~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  106 (467)
                      -+.+.+.+.+..|+|.||---.|.-.|+.++. .+|.|++.||-+-+.      .|||.|.+.++|...+..|++..+
T Consensus       435 vpSPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkIKS------hCyV~yss~eEA~atr~AlhnV~W  506 (718)
T KOG2416|consen  435 VPSPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKIKS------HCYVSYSSVEEAAATREALHNVQW  506 (718)
T ss_pred             CCCCCCCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHhhc------ceeEecccHHHHHHHHHHHhcccc
Confidence            34566888899999999999999999999998 566888887766554      699999999999999999987644

>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=96.30  E-value=0.055  Score=40.87  Aligned_cols=74  Identities=15%  Similarity=0.102  Sum_probs=56.6

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCC-CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMG-QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG  108 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G-~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g  108 (467)
                      ....+.+..+.+...|+.++-++|..+.+.+- .|..++|++|...  ++..+++.|.+.++|.......||+.|..
T Consensus         7 ~~~~~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p--nrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen    7 LPDERRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP--NRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CCCCCCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC--ceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            33445566677776667777778877777663 7889999988653  55689999999999999999999988744

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

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

Probab=96.18  E-value=0.0041  Score=57.70  Aligned_cols=87  Identities=20%  Similarity=0.260  Sum_probs=72.3

Q ss_pred             CCCCCCCCCCCccCeEEEcCCCCCCCH-HHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcc
Q 012257           27 NNGGVGDARQFVSTSLYVGDLDLSVND-SQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTP  105 (467)
Q Consensus        27 ~~~~~~~~~~~~~~~l~v~nLp~~~~e-~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~  105 (467)
                      .+.+.......+.+.|-+.-.|..... ++|..+|..||.|..|.+-...      -.|.|+|.+..+|-+|-. ..+..
T Consensus       360 rG~gv~g~~~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~~-s~~av  432 (526)
T KOG2135|consen  360 RGRGVPGHAVVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS------LHAVVTFKTRAEAGEAYA-SHGAV  432 (526)
T ss_pred             cCCCCCcchhcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCch------hhheeeeeccccccchhc-cccce
Confidence            444666677778889999999998776 7899999999999999886542      269999999999977776 57899


Q ss_pred             cCCceeeeeecccCc
Q 012257          106 LNGKPIRIMYSYRDP  120 (467)
Q Consensus       106 ~~g~~~~v~~~~~~~  120 (467)
                      |+++.|+|.|.+..+
T Consensus       433 lnnr~iKl~whnps~  447 (526)
T KOG2135|consen  433 LNNRFIKLFWHNPSP  447 (526)
T ss_pred             ecCceeEEEEecCCc
Confidence            999999999987654

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.86  E-value=0.004  Score=55.53  Aligned_cols=77  Identities=21%  Similarity=0.407  Sum_probs=60.4

Q ss_pred             ceEEEecCCCCCCHHHHH---HhhccCCceeEEEEeeCCC----CCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          322 LNLYVKNLDDSISDDKLK---ELFSEFGTITSCKVMRDPN----GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~---~~F~~~G~v~~v~i~~~~~----~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      .-+||-+|+..+-++.+.   ++|.+||.|..|.+..+..    ......++|+|...++|.+||...+|..+.|+.|+.
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            347888888776555544   4799999999998888652    122345899999999999999999999999988777


Q ss_pred             ehhh
Q 012257          395 ALAQ  398 (467)
Q Consensus       395 ~~~~  398 (467)
                      .+..
T Consensus       158 ~~gt  161 (327)
T KOG2068|consen  158 SLGT  161 (327)
T ss_pred             hhCC
Confidence            7653

>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=95.85  E-value=0.089  Score=39.76  Aligned_cols=66  Identities=23%  Similarity=0.231  Sum_probs=50.2

Q ss_pred             ceEEEecCC-CCCCHHHHHHhhccC-CceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEec
Q 012257          322 LNLYVKNLD-DSISDDKLKELFSEF-GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVV  388 (467)
Q Consensus       322 ~~l~V~nlp-~~~~~~~l~~~F~~~-G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~  388 (467)
                      ..+.|-..| ..++.++|..+.+.+ ..|..++|+++... ++.-+++.|.+.++|..-...+||+.+.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~p-nrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTP-NRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCC-ceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            345444444 555666776666666 46778899987643 5678999999999999999999999885

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>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=95.78  E-value=0.014  Score=48.61  Aligned_cols=69  Identities=9%  Similarity=0.167  Sum_probs=45.0

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhc-CCCe---EEEEEEe-cCCCCc-cccEEEEEecChHHHHHHHHHhCCccc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQ-MGQV---VSVRVCR-DLSTRR-SLGYGYVNYNAAHEATRALDELNFTPL  106 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~-~G~v---~~v~i~~-~~~~~~-~~g~afV~f~~~~~A~~A~~~l~~~~~  106 (467)
                      ...+|.||+||++++|+++.+.++. ++.-   ..+.-.. +...+. ...-|||.|.+.+++......+++..|
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F   80 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVF   80 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEE
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEE
Confidence            4579999999999999999998777 5544   2332111 111121 224699999999999999998888766

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.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.75  E-value=0.075  Score=37.18  Aligned_cols=55  Identities=20%  Similarity=0.337  Sum_probs=40.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCC
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNF  103 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~  103 (467)
                      ...+|+ .|..=...||.++|+.||.|. |.-+.|.       .|||...+.+.|..|+..+..
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            345555 999999999999999999974 4444442       699999999999999988753

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.49  E-value=0.024  Score=47.33  Aligned_cols=62  Identities=24%  Similarity=0.274  Sum_probs=47.1

Q ss_pred             CHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhC--CcEecccceEEehhhhh
Q 012257          334 SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN--GKMVVSKPLYVALAQRK  400 (467)
Q Consensus       334 ~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~--g~~~~g~~l~v~~~~~~  400 (467)
                      ..+.|+++|..|+.+..+..++.     =+-..|.|.+.++|.+|+..|+  +..+.|..++|-|+...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s-----FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS-----FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT-----TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC-----CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            45789999999999988887775     2378999999999999999999  99999999999998533

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.

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

Probab=95.06  E-value=0.083  Score=46.38  Aligned_cols=69  Identities=23%  Similarity=0.214  Sum_probs=51.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCce-eeeeec
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKP-IRIMYS  116 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~-~~v~~~  116 (467)
                      .=|-|-+.|+ -.-..|.++|++||.|+......      .-.+-.|.|.+.-+|++||. .+++.|.|.. |-|..+
T Consensus       198 ~WVTVfGFpp-g~~s~vL~~F~~cG~Vvkhv~~~------ngNwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpC  267 (350)
T KOG4285|consen  198 TWVTVFGFPP-GQVSIVLNLFSRCGEVVKHVTPS------NGNWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPC  267 (350)
T ss_pred             ceEEEeccCc-cchhHHHHHHHhhCeeeeeecCC------CCceEEEEecchhHHHHhhh-hcCeeeccceEEeeeec
Confidence            4566777777 44567899999999998775542      22488999999999999998 5888887755 445443

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.02  E-value=0.013  Score=52.34  Aligned_cols=78  Identities=21%  Similarity=0.389  Sum_probs=62.2

Q ss_pred             ccCeEEEcCCCCCCCHHHHH---HHHhcCCCeEEEEEEecCC----CCccccEEEEEecChHHHHHHHHHhCCcccCCce
Q 012257           38 VSTSLYVGDLDLSVNDSQLY---DLFNQMGQVVSVRVCRDLS----TRRSLGYGYVNYNAAHEATRALDELNFTPLNGKP  110 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~---~~f~~~G~v~~v~i~~~~~----~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  110 (467)
                      ...-+||-+|+.....+.+.   ++|.+||.|..|.+.++..    .+.. ..++|+|...+||..|+...++...+|+.
T Consensus        76 qknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~-~s~yITy~~~eda~rci~~v~g~~~dg~~  154 (327)
T KOG2068|consen   76 QKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGT-CSVYITYEEEEDADRCIDDVDGFVDDGRA  154 (327)
T ss_pred             hhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCC-CcccccccchHhhhhHHHHhhhHHhhhhh
Confidence            34668899999877666553   5899999999999988762    2222 35899999999999999999999999999


Q ss_pred             eeeeec
Q 012257          111 IRIMYS  116 (467)
Q Consensus       111 ~~v~~~  116 (467)
                      ++..+.
T Consensus       155 lka~~g  160 (327)
T KOG2068|consen  155 LKASLG  160 (327)
T ss_pred             hHHhhC
Confidence            777554

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=94.88  E-value=0.8  Score=40.46  Aligned_cols=182  Identities=14%  Similarity=0.189  Sum_probs=109.1

Q ss_pred             cccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECC--------CCCceeEEEEEeCCHHHHHHHH----HHhCC--C
Q 012257          217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA--------DGKSKCFGFVNFDDPDDAARSV----EALNG--K  282 (467)
Q Consensus       217 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~--------~~~~~g~afv~f~~~~~a~~a~----~~l~~--~  282 (467)
                      ..+.|.+.|+..+++...+...|-+||.|+++.++.+.        ..+......+.|-+.+.+..-.    ..+..  .
T Consensus        14 rTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~   93 (309)
T PF10567_consen   14 RTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKT   93 (309)
T ss_pred             eeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHH
Confidence            44789999999999999999999999999999999875        2233456788888877664332    22222  2


Q ss_pred             ccCCceEEEcccccchHHHH------Hhh-hhhhhhhh-ccccCCCCceEEEecCCCCCCHHHHHHhh---ccCC----c
Q 012257          283 KFDDKEWYVGKAQKKYEREM------ELK-GKFEQSLK-ETADKFEGLNLYVKNLDDSISDDKLKELF---SEFG----T  347 (467)
Q Consensus       283 ~~~~~~l~~~~~~~~~~~~~------~~~-~~~~~~~~-~~~~~~~~~~l~V~nlp~~~~~~~l~~~F---~~~G----~  347 (467)
                      .+....|.+.+..-......      .+. ........ .......+++|.|.--.....++-+.+.+   ..-+    .
T Consensus        94 ~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF~~~~~~~dl~~~kL~fL~~~~n~RYV  173 (309)
T PF10567_consen   94 KLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEFKDPVDKDDLIEKKLPFLKNSNNKRYV  173 (309)
T ss_pred             hcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEecCccchhHHHHHhhhhhccCCCceEE
Confidence            34555666655542111100      000 00011111 22333456677776544333443333322   2223    4


Q ss_pred             eeEEEEeeCC---CCCccceEEEEcCCHHHHHHHHHHhCCc--Eec-ccceEEehhh
Q 012257          348 ITSCKVMRDP---NGISRGSGFVAFSTAEEASKALTEMNGK--MVV-SKPLYVALAQ  398 (467)
Q Consensus       348 v~~v~i~~~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~--~~~-g~~l~v~~~~  398 (467)
                      +++|.++...   ...+..||.++|-+...|...+..|...  ..+ .+...|+...
T Consensus       174 lEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk~~~~~~~Iskc~fVs~~~  230 (309)
T PF10567_consen  174 LESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLKSNSKKLGISKCFFVSVQP  230 (309)
T ss_pred             EEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHHhcccccCcceEEEEeccC
Confidence            6778877654   3456789999999999999999877633  332 3455555544

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.77  E-value=0.079  Score=50.55  Aligned_cols=69  Identities=17%  Similarity=0.275  Sum_probs=54.9

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhc--CCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCC--cccCCceeeee
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQ--MGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNF--TPLNGKPIRIM  114 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~--~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~--~~~~g~~~~v~  114 (467)
                      .|.|+++-||..+.+|+|+.+|+.  |=.+.++..-....       =||+|++..||+.|.+.|..  ..|.|+.|..+
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-------WyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-------WYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-------eEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            466889999999999999999975  44677887765432       48999999999999998753  46888887543

>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=94.68  E-value=0.079  Score=44.17  Aligned_cols=81  Identities=15%  Similarity=0.251  Sum_probs=52.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcc-CCce---eEEEEeeCC--CC-CccceEEEEcCCHHHHHHHHHHhCCcEeccc--
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSE-FGTI---TSCKVMRDP--NG-ISRGSGFVAFSTAEEASKALTEMNGKMVVSK--  390 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~-~G~v---~~v~i~~~~--~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~--  390 (467)
                      ....|.|++||+.+|++++.+.++. ++.-   ..+.-....  .. ....-|+|.|.+.+++..-...++|+.|.+.  
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            3447999999999999999998887 6655   233211221  11 1245799999999999999999999988532  


Q ss_pred             ---ceEEehhhhh
Q 012257          391 ---PLYVALAQRK  400 (467)
Q Consensus       391 ---~l~v~~~~~~  400 (467)
                         ...|.||.-+
T Consensus        86 ~~~~~~VE~Apyq   98 (176)
T PF03467_consen   86 NEYPAVVEFAPYQ   98 (176)
T ss_dssp             -EEEEEEEE-SS-
T ss_pred             CCcceeEEEcchh
Confidence               4567776543

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.

>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=94.67  E-value=0.14  Score=34.51  Aligned_cols=55  Identities=18%  Similarity=0.258  Sum_probs=41.9

Q ss_pred             CCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           50 SVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        50 ~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      .++-++++..++.|+- ..|  ..|+ +    || ||.|.+.++|+++....++..+.+-.+.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~I--~~d~-t----Gf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DRI--RDDR-T----GF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ceE--EecC-C----EE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            5778999999999964 333  3454 3    34 89999999999999998888776655543

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

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

Probab=94.62  E-value=0.018  Score=57.60  Aligned_cols=74  Identities=30%  Similarity=0.424  Sum_probs=63.6

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEe--cccceEEehhhhhH
Q 012257          324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV--VSKPLYVALAQRKE  401 (467)
Q Consensus       324 l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~~~~~~  401 (467)
                      ..+.|.+...+-..|..+|+.||.|.+++.+++-+     .|.|+|.+.+.|..|+++|+|+.+  -|-+.+|.|++...
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N-----~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN-----MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheeccccc-----chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            44555566778889999999999999999988754     899999999999999999999987  48889999998665


Q ss_pred             H
Q 012257          402 E  402 (467)
Q Consensus       402 ~  402 (467)
                      .
T Consensus       376 ~  376 (1007)
T KOG4574|consen  376 M  376 (1007)
T ss_pred             c
Confidence            4

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=94.56  E-value=0.05  Score=53.13  Aligned_cols=79  Identities=13%  Similarity=0.097  Sum_probs=64.4

Q ss_pred             CCCCCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccC
Q 012257           28 NGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLN  107 (467)
Q Consensus        28 ~~~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~  107 (467)
                      +.++-...-.+.-++||+|+-..+..+-+..+...||-|.+.+...         |+|..|....-+.+|+..+....++
T Consensus        29 p~qp~~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~   99 (668)
T KOG2253|consen   29 PIQPVFQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNID   99 (668)
T ss_pred             CCcccccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCC
Confidence            3344444445678999999999999999999999999988876643         8999999999999999988888888


Q ss_pred             Cceeeeee
Q 012257          108 GKPIRIMY  115 (467)
Q Consensus       108 g~~~~v~~  115 (467)
                      |..+.+..
T Consensus       100 ~~kl~~~~  107 (668)
T KOG2253|consen  100 DQKLIENV  107 (668)
T ss_pred             cchhhccc
Confidence            87776644

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=94.55  E-value=1.1  Score=39.66  Aligned_cols=156  Identities=13%  Similarity=0.201  Sum_probs=102.1

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCC-------CCccccEEEEEecChHHHHHHH----HHhC
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLS-------TRRSLGYGYVNYNAAHEATRAL----DELN  102 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~-------~~~~~g~afV~f~~~~~A~~A~----~~l~  102 (467)
                      ...--+|.|...||..+++--.+...|-+||+|++|.++.+..       .........+.|-+.+.+...-    +.|.
T Consensus        10 dD~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLs   89 (309)
T PF10567_consen   10 DDEYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLS   89 (309)
T ss_pred             CccceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHH
Confidence            3445589999999999999999999999999999999998761       1122346889999999885533    3332


Q ss_pred             --CcccCCceeeeeeccc---Cc---------------------ccccCCCccEEEcCCCCcCCHHHHH-H---HHhhcC
Q 012257          103 --FTPLNGKPIRIMYSYR---DP---------------------TIRKSGAGNIFIKNLDKSIDNKALH-D---TFSTFG  152 (467)
Q Consensus       103 --~~~~~g~~~~v~~~~~---~~---------------------~~~~~~~~~l~v~nlp~~~t~~~l~-~---~f~~~g  152 (467)
                        ...+....+.+.+..-   ..                     ......-++|.|.= ...+.++++. +   ++..-+
T Consensus        90 EfK~~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF-~~~~~~~dl~~~kL~fL~~~~  168 (309)
T PF10567_consen   90 EFKTKLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEF-KDPVDKDDLIEKKLPFLKNSN  168 (309)
T ss_pred             HHHHhcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEe-cCccchhHHHHHhhhhhccCC
Confidence              2346777777766431   10                     01122234555543 2444344433 2   232223


Q ss_pred             ----CeEEEEEeeC---CCCCceeEEEEEeCCHHHHHHHHHHhcC
Q 012257          153 ----NILSCKVATD---SLGQSRGYGFVQFDNEESAKSAIDKLNG  190 (467)
Q Consensus       153 ----~v~~~~~~~~---~~g~~~~~afV~f~~~~~A~~a~~~l~~  190 (467)
                          -+++|.++..   ....+..||.+.|-+...|...+..+..
T Consensus       169 n~RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk~  213 (309)
T PF10567_consen  169 NKRYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLKS  213 (309)
T ss_pred             CceEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHHh
Confidence                3567777765   2234678999999999999999998863

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.35  E-value=0.036  Score=52.73  Aligned_cols=67  Identities=13%  Similarity=0.351  Sum_probs=52.4

Q ss_pred             ccEEEcCCCCcCCHHHHHHHHhh--cCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcC--CccCCeeeEe
Q 012257          128 GNIFIKNLDKSIDNKALHDTFST--FGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNG--MLLNDKQVFV  200 (467)
Q Consensus       128 ~~l~v~nlp~~~t~~~l~~~f~~--~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~--~~~~g~~~~v  200 (467)
                      +-|.++-||..+-.++++.+|..  +..+.+|.+-..      .-.||+|++..||+.|.+.|..  +.|.|+.|..
T Consensus       176 cIvilREIpettp~e~Vk~lf~~encPk~iscefa~N------~nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN------DNWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec------CceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            34668999999999999999984  557788887543      2369999999999999998854  3466766544

>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=94.13  E-value=0.16  Score=42.51  Aligned_cols=60  Identities=25%  Similarity=0.334  Sum_probs=45.7

Q ss_pred             CHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhC--CcccCCceeeeeecc
Q 012257           52 NDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN--FTPLNGKPIRIMYSY  117 (467)
Q Consensus        52 ~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~--~~~~~g~~~~v~~~~  117 (467)
                      ..+.|+++|..++.+..+..++.=+      =..|.|.+.++|.+|...|+  +..+.|..+++.+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFr------Ri~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~   69 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFR------RIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQ   69 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTT------EEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE---
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCC------EEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcc
Confidence            3478999999999988888876532      48999999999999999998  889999999998873

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.

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=93.70  E-value=0.1  Score=52.06  Aligned_cols=19  Identities=5%  Similarity=0.029  Sum_probs=11.2

Q ss_pred             EeCCHHHHHHHHHHhcCCc
Q 012257          174 QFDNEESAKSAIDKLNGML  192 (467)
Q Consensus       174 ~f~~~~~A~~a~~~l~~~~  192 (467)
                      .-++..++.++++.+-+..
T Consensus       205 ~~k~~~eiIrClka~mNn~  223 (1102)
T KOG1924|consen  205 DIKNLQEIIRCLKAFMNNK  223 (1102)
T ss_pred             HHHHHHHHHHHHHHHhccc
Confidence            3445667777777664443

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

Probab=93.68  E-value=0.22  Score=43.92  Aligned_cols=68  Identities=22%  Similarity=0.239  Sum_probs=51.9

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccc-eEEehh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP-LYVALA  397 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-l~v~~~  397 (467)
                      =|.|.+.|+.- ..-|..+|++||+|.+....  .+|.   +-.|.|.++-+|.+||.. ||+.|+|.. |-|+-.
T Consensus       199 WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~--~ngN---wMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpC  267 (350)
T KOG4285|consen  199 WVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP--SNGN---WMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPC  267 (350)
T ss_pred             eEEEeccCccc-hhHHHHHHHhhCeeeeeecC--CCCc---eEEEEecchhHHHHhhhh-cCeeeccceEEeeeec
Confidence            47788888663 35677899999999886554  3343   999999999999999984 999998764 445543

>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=93.62  E-value=0.35  Score=34.69  Aligned_cols=65  Identities=15%  Similarity=0.304  Sum_probs=45.0

Q ss_pred             EEEEecChHHHHHHHHHhCC-cccCCceeeeeeccc--C-----cccccCCCccEEEcCCCCcCCHHHHHHHH
Q 012257           84 GYVNYNAAHEATRALDELNF-TPLNGKPIRIMYSYR--D-----PTIRKSGAGNIFIKNLDKSIDNKALHDTF  148 (467)
Q Consensus        84 afV~f~~~~~A~~A~~~l~~-~~~~g~~~~v~~~~~--~-----~~~~~~~~~~l~v~nlp~~~t~~~l~~~f  148 (467)
                      |+|+|.+.+-|++.++.-.+ ..+.+..++|..+.-  .     ........++|.|.|||...++++|++.+
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeE
Confidence            68999999999999985332 345666666544321  1     11123446789999999999999988654

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=93.56  E-value=0.2  Score=46.73  Aligned_cols=67  Identities=19%  Similarity=0.298  Sum_probs=59.1

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccC-CceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEec
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEF-GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVV  388 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~-G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~  388 (467)
                      +..|.|-.+|..++..||..|+..| -.|.+++++++..+ .+...+|.|.+.++|..-.+.+||+.|.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p-nrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP-NRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC-ceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            5689999999999999999999877 46889999997544 3568999999999999999999999885

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=93.54  E-value=0.083  Score=52.62  Aligned_cols=10  Identities=20%  Similarity=0.597  Sum_probs=3.8

Q ss_pred             HHHHHHHHhc
Q 012257           53 DSQLYDLFNQ   62 (467)
Q Consensus        53 e~~l~~~f~~   62 (467)
                      ++++...|..
T Consensus        85 ~~e~~~~F~~   94 (1102)
T KOG1924|consen   85 SNEVLELFEL   94 (1102)
T ss_pred             HHHHHHHHHH
Confidence            3333333333

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=93.37  E-value=0.33  Score=45.34  Aligned_cols=68  Identities=18%  Similarity=0.213  Sum_probs=59.6

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCC-CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMG-QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG  108 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G-~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g  108 (467)
                      ++.|+|-.+|..++-.||..|+..+- .|.++++++|...  ++..++|.|.+.+||....+.+||..|..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p--nrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP--NRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC--ceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            88999999999999999999987764 7999999997654  44589999999999999999999987744

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

Probab=93.30  E-value=0.27  Score=34.30  Aligned_cols=60  Identities=23%  Similarity=0.328  Sum_probs=37.9

Q ss_pred             CCCCCHHHHHHhhccCC-----ceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          330 DDSISDDKLKELFSEFG-----TITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       330 p~~~~~~~l~~~F~~~G-----~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      -..++..+|..++...+     .|-++++..+       |+||+-.. +.|..+++.|++..+.|++++|+.|
T Consensus        10 ~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~-------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   10 KDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN-------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS--------EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             ccCCCHHHHHHHHHhccCCCHHhEEEEEEeee-------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            35678888988887664     4566787776       99999876 5899999999999999999999754

; PDB: 2G0C_A 3MOJ_B.

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

Probab=92.55  E-value=0.052  Score=50.73  Aligned_cols=73  Identities=19%  Similarity=0.236  Sum_probs=58.4

Q ss_pred             ceEEEecCCCCC-CHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          322 LNLYVKNLDDSI-SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       322 ~~l~V~nlp~~~-~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      +.|-+.-.|+.. +-.+|...|.+||+|..|.+-..     .-.|.|+|.+..+|-+|.. .++..|+++.|+|-|-.+.
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-----~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-----SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCc-----hhhheeeeeccccccchhc-cccceecCceeEEEEecCC
Confidence            345555556554 45789999999999999887554     2379999999999988875 6999999999999997753

>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=92.11  E-value=0.94  Score=30.59  Aligned_cols=55  Identities=13%  Similarity=0.363  Sum_probs=43.8

Q ss_pred             CCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          332 SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       332 ~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      .++-++++.-+..|+-.   +|..+.+|     -||.|.+.++|.++....+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~---~I~~d~tG-----fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD---RIRDDRTG-----FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcc---eEEecCCE-----EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            56788999999999543   34455443     479999999999999999999998877654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

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

Probab=91.91  E-value=0.11  Score=52.36  Aligned_cols=70  Identities=27%  Similarity=0.414  Sum_probs=57.1

Q ss_pred             cCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc--CCceeeeeecccCc
Q 012257           45 GDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL--NGKPIRIMYSYRDP  120 (467)
Q Consensus        45 ~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~--~g~~~~v~~~~~~~  120 (467)
                      .|.+...+-.-|..+|+.||.|.+.+.+++-.      .|.|+|.+.+.|..|+..++|++.  -|-+.+|.+++..+
T Consensus       304 ~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  304 ENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             hcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            33444556667889999999999999988764      799999999999999999998864  67778888876543

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.42  E-value=1.3  Score=42.91  Aligned_cols=83  Identities=18%  Similarity=0.290  Sum_probs=63.0

Q ss_pred             CCCCCccCeEEEcCCCCC-CCHHHHHHHHhcC----CCeEEEEEEecC----------CCCc------------------
Q 012257           33 DARQFVSTSLYVGDLDLS-VNDSQLYDLFNQM----GQVVSVRVCRDL----------STRR------------------   79 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~-~~e~~l~~~f~~~----G~v~~v~i~~~~----------~~~~------------------   79 (467)
                      +.....+++|-|.|+.|+ +.-++|.-+|+.|    |.|++|.|+...          .+|.                  
T Consensus       168 ~~~~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~  247 (650)
T KOG2318|consen  168 PVLGEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDD  247 (650)
T ss_pred             cccccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccch
Confidence            444667899999999995 5568999988877    589999987421          1111                  


Q ss_pred             -------------------cccEEEEEecChHHHHHHHHHhCCcccCC--ceeeeee
Q 012257           80 -------------------SLGYGYVNYNAAHEATRALDELNFTPLNG--KPIRIMY  115 (467)
Q Consensus        80 -------------------~~g~afV~f~~~~~A~~A~~~l~~~~~~g--~~~~v~~  115 (467)
                                         ...||.|+|.+.++|....+.|+|+.|..  ..+.+++
T Consensus       248 ee~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  248 EEEEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRF  304 (650)
T ss_pred             hhhhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeee
Confidence                               22699999999999999999999998844  4444444

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

Probab=90.18  E-value=1.6  Score=30.35  Aligned_cols=57  Identities=14%  Similarity=0.320  Sum_probs=34.8

Q ss_pred             CCCHHHHHHHHhcCC-----CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           50 SVNDSQLYDLFNQMG-----QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        50 ~~~e~~l~~~f~~~G-----~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      .++..+|..++...+     .|-.|.|..+        |+||+-.. +.|.++++.|++..+.|+.++|+.
T Consensus        12 g~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~   73 (74)
T PF03880_consen   12 GLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVER   73 (74)
T ss_dssp             T--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-T-T-HHHHHHHHTT--SSS----EEE
T ss_pred             CCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEE
Confidence            467778888887663     5777877543        78887654 488999999999999999999874

; PDB: 2G0C_A 3MOJ_B.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=87.66  E-value=0.34  Score=47.63  Aligned_cols=71  Identities=17%  Similarity=0.164  Sum_probs=62.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .++..++||+|+-..+..+-++.+...+|.|.++....        |+|.+|..+..+.+|+..++-..++|..+.+.-
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            44566899999999999999999999999998887655        999999999999999999998889888877765

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=85.88  E-value=1.1  Score=36.44  Aligned_cols=115  Identities=14%  Similarity=0.027  Sum_probs=73.4

Q ss_pred             eEEEcCCC--CCCCHHHHHHHHhc-CCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           41 SLYVGDLD--LSVNDSQLYDLFNQ-MGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        41 ~l~v~nLp--~~~~e~~l~~~f~~-~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ...|+.+.  .+.+-..|.+.+.+ ++....+.+..-.     .++..+.|.+.+|+.++++ .....+.|..+.+..-.
T Consensus        17 ~~lVg~~l~~~~~~~~~l~~~l~~~W~~~~~~~i~~l~-----~~~fl~~F~~~~d~~~vl~-~~p~~~~~~~~~l~~W~   90 (153)
T PF14111_consen   17 LCLVGRVLSPKPISLSALEQELAKIWKLKGGVKIRDLG-----DNLFLFQFESEEDRQRVLK-GGPWNFNGHFLILQRWS   90 (153)
T ss_pred             eEEEEEECCCCCCCHHHHHHHHHHHhCCCCcEEEEEeC-----CCeEEEEEEeccceeEEEe-cccccccccchhhhhhc
Confidence            34444443  24556677666654 2333333333221     1578999999999999997 45556778777776654


Q ss_pred             cCcccccCC----CccEEEcCCCCcC-CHHHHHHHHhhcCCeEEEEEee
Q 012257          118 RDPTIRKSG----AGNIFIKNLDKSI-DNKALHDTFSTFGNILSCKVAT  161 (467)
Q Consensus       118 ~~~~~~~~~----~~~l~v~nlp~~~-t~~~l~~~f~~~g~v~~~~~~~  161 (467)
                      +........    .-=|.|.|||... +++-++.+.+.+|.+..+....
T Consensus        91 ~~~~~~~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t  139 (153)
T PF14111_consen   91 PDFNPSEVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENT  139 (153)
T ss_pred             ccccccccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCC
Confidence            332221111    1226689999875 8888999999999998877544

>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=85.31  E-value=1.4  Score=31.68  Aligned_cols=70  Identities=19%  Similarity=0.235  Sum_probs=45.4

Q ss_pred             EEEEeCCHHHHHHHHHHhcCC-ccCCeeeEec--ccccccc-cccccccccccceeecCCCccCCHHHHHHhhc
Q 012257          171 GFVQFDNEESAKSAIDKLNGM-LLNDKQVFVG--PFLRKQE-RESTADKTRFNNVYVKNLSETTTEDDLKKIFG  240 (467)
Q Consensus       171 afV~f~~~~~A~~a~~~l~~~-~~~g~~~~v~--~~~~~~~-~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~  240 (467)
                      |.|+|..+.-|++.++.-... .+.+..+.+.  +...... .-........+++.++++|...+++++++.++
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            689999999999999743222 3556555443  2222221 11222334457899999999999999988643

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.82  E-value=3.2  Score=40.40  Aligned_cols=80  Identities=26%  Similarity=0.252  Sum_probs=62.6

Q ss_pred             CCCCceEEEecCCC-CCCHHHHHHhhccC----CceeEEEEeeCCC-----------CC---------------------
Q 012257          318 KFEGLNLYVKNLDD-SISDDKLKELFSEF----GTITSCKVMRDPN-----------GI---------------------  360 (467)
Q Consensus       318 ~~~~~~l~V~nlp~-~~~~~~l~~~F~~~----G~v~~v~i~~~~~-----------~~---------------------  360 (467)
                      ...+..|-|.|+.+ .+..++|.-+|+-|    |.|.+|.|.....           |.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            34566899999996 57889999888766    6999999876532           11                     


Q ss_pred             ----------------ccceEEEEcCCHHHHHHHHHHhCCcEecc--cceEEehh
Q 012257          361 ----------------SRGSGFVAFSTAEEASKALTEMNGKMVVS--KPLYVALA  397 (467)
Q Consensus       361 ----------------~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v~~~  397 (467)
                                      ...||.|+|++.+.|.+.....+|..+..  ..|.+.|-
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFI  305 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFI  305 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeec
Confidence                            13689999999999999999999999974  45555553

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	467
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-61
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		4e-20
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-61
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		3e-20
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		9e-33
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		2e-13
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		3e-32
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		2e-14
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		2e-26
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-20
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-16
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-07
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-20
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-16
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		9e-08
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		4e-20
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-19
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		9e-19
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-18
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		5e-06
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		7e-17
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		8e-17
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		2e-16
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		6e-16
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		1e-15
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		9e-15
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		1e-13
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		1e-14
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		3e-13
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-12
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		4e-07
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-12
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-07
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		4e-12
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		2e-07
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		4e-12
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		2e-07
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		4e-12
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		6e-08
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		6e-04
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		5e-12
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-06
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		5e-12
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		6e-12
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		8e-12
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-07
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-11
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-09
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-07
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-11
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		4e-09
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		1e-07
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		8e-11
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		2e-10
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		3e-08
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		3e-09
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		7e-09
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		8e-09
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-08
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		1e-07
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		9e-09
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		6e-08
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		1e-08
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		1e-08
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		3e-07
1sxl_A	97	Resonance Assignments And Solution Structure Of The		1e-08
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		4e-08
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		5e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		4e-08
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-07
1x5o_A	114	Solution Structure Of Rrm Domain In Rna Binding Mot		5e-08
2ghp_A	292	Crystal Structure Of The N-Terminal 3 Rna Binding D		5e-08
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		7e-08
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		7e-08
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		8e-08
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		1e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		1e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		4e-04
2khc_A	118	Bruno Rrm3+ Length = 118		1e-07
2khc_A	118	Bruno Rrm3+ Length = 118		1e-05
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		1e-07
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		3e-04
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		8e-04
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		1e-07
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		2e-07
2dno_A	102	Solution Structure Of Rna Binding Domain In Trinucl		2e-07
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		3e-07
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		4e-07
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		4e-05
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		4e-07
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		3e-04
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		8e-04
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		4e-07
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		4e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		6e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		4e-06
2dnh_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		8e-07
2f3j_A	177	The Solution Structure Of The Ref2-I Mrna Export Fa		1e-06
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		1e-06
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		2e-06
3ulh_A	107	Crystal Structure Of A Rna Binding Domain Of Tho Co		2e-06
2yka_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		3e-06
2kt5_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		3e-06
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		3e-06
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		3e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		3e-06
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		8e-06
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		2e-05
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		4e-06
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-05
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		4e-06
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		5e-06
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		6e-06
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		6e-06
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		6e-06
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		3e-05
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		8e-06
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		3e-05
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		8e-06
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		3e-04
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		8e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		9e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		1e-05
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		1e-05
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		9e-06
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		1e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-05
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		1e-05
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		1e-05
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		2e-05
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		4e-04
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		2e-05
1fht_A	116	Rna-Binding Domain Of The U1a Spliceosomal Protein		9e-05
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-05
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		2e-05
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		2e-05
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		1e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		2e-05
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		1e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-05
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		1e-04
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		3e-05
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		5e-04
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		4e-05
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		6e-04
1oia_A	95	U1a Rnp Domain 1-95 Length = 95		4e-05
1oia_A	95	U1a Rnp Domain 1-95 Length = 95		1e-04
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		4e-05
3pgw_A	282	Crystal Structure Of Human U1 Snrnp Length = 282		1e-04
2dhg_A	104	Solution Structure Of The C-Terminal Rna Recognitio		5e-05
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		5e-05
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		8e-05
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		5e-05
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		6e-05
1aud_A	101	U1a-Utrrna, Nmr, 31 Structures Length = 101		6e-05
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		9e-05
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		9e-05
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		6e-04
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		1e-04
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		1e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		1e-04
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		2e-04
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		2e-04
3l3c_A	90	Crystal Structure Of The Bacillus Anthracis Glms Ri		2e-04
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		2e-04
3iwn_C	91	Co-Crystal Structure Of A Bacterial C-Di-Gmp Ribosw		2e-04
1a9n_B	96	Crystal Structure Of The Spliceosomal U2b''-U2a' Pr		2e-04
2cqh_A	93	Solution Structure Of The Rna Binding Domain Of Igf		2e-04
2nz4_A	94	Structural Investigation Of The Glms Ribozyme Bound		2e-04
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		2e-04
3bo2_A	95	A Relaxed Active Site Following Exon Ligation By A		2e-04
2osq_A	74	Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length		2e-04
1urn_A	97	U1a MutantRNA COMPLEX + GLYCEROL Length = 97		2e-04
3k0j_A	96	Crystal Structure Of The E. Coli Thim Riboswitch In		3e-04
1u6b_A	98	Crystal Structure Of A Self-Splicing Group I Intron		3e-04
2dk2_A	97	Solution Structure Of Rrm Domain In Heterogeneous N		3e-04
1m5k_C	100	Crystal Structure Of A Hairpin Ribozyme In The Cata		3e-04
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		3e-04
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		7e-04
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		3e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		3e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		9e-04
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		3e-04
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		5e-04
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		6e-04
2dnp_A	90	Solution Structure Of Rna Binding Domain 2 In Rna-B		6e-04
1wf1_A	110	Solution Structure Of Rrm Domain In Rna-Binding Pro		6e-04
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		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 =  233 bits (595), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 109/178 (61%), Positives = 139/178 (78%), Gaps = 1/178 (0%)
Query: 34  ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
           A  +   SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +
Sbjct: 5   APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 64
Query: 94  ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
           A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct: 65  AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 124
Query: 154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
           ILSCKV  D  G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+
Sbjct: 125 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 181

>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 = 95.9 bits (237), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 65/192 (33%), Positives = 102/192 (53%), Gaps = 18/192 (9%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEA 278
           ++YV +L    TE  L + F   G I S  V RD    +S  + +VNF  P DA R+++ 
Sbjct: 12  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
           +N      K   +  +Q+            + SL+++       N+++KNLD SI +  L
Sbjct: 72  MNFDVIKGKPVRIMWSQR------------DPSLRKSGVG----NIFIKNLDKSIDNKAL 115
Query: 339 KELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ 398
            + FS FG I SCKV+ D NG S+G GFV F T E A +A+ +MNG ++  + ++V   +
Sbjct: 116 YDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK 174
Query: 399 RKEERRARLQAQ 410
            ++ER A L A+
Sbjct: 175 SRKEREAELGAR 186

>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 =  233 bits (593), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 109/178 (61%), Positives = 139/178 (78%), Gaps = 1/178 (0%)
Query: 34  ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
           A  +   SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +
Sbjct: 10  APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 69
Query: 94  ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
           A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGN
Sbjct: 70  AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGN 129
Query: 154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
           ILSCKV  D  G S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+
Sbjct: 130 ILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 186

>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 = 96.3 bits (238), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 66/201 (32%), Positives = 104/201 (51%), Gaps = 18/201 (8%)
Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDP 269
            +A      ++YV +L    TE  L + F   G I S  V RD    +S  + +VNF  P
Sbjct: 8   PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP 67
Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNL 329
            DA R+++ +N      K   +  +Q+            + SL+++       N+++KNL
Sbjct: 68  ADAERALDTMNFDVIKGKPVRIMWSQR------------DPSLRKSGVG----NIFIKNL 111
Query: 330 DDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVS 389
           D SI +  L + FS FG I SCKV+ D NG S+G GFV F T E A +A+ +MNG ++  
Sbjct: 112 DKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLND 170
Query: 390 KPLYVALAQRKEERRARLQAQ 410
           + ++V   + ++ER A L A+
Sbjct: 171 RKVFVGRFKSRKEREAELGAR 191

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score =  137 bits (346), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 65/93 (69%), Positives = 80/93 (86%), Gaps = 1/93 (1%)
Query: 119 DPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNE 178
           DP++RKSG GNIFIKNLDKSIDNKAL+DTFS FGNILSCKV  D  G S+GYGFV F+ +
Sbjct: 3   DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQ 61
Query: 179 ESAKSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
           E+A+ AI+K+NGMLLND++VFVG F  ++ERE+
Sbjct: 62  EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 94

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 73.9 bits (180), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/83 (44%), Positives = 55/83 (66%), Gaps = 1/83 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           N+++KNLD SI +  L + FS FG I SCKV+ D NG S+G GFV F T E A +A+ +M
Sbjct: 13  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 383 NGKMVVSKPLYVALAQRKEERRA 405
           NG ++  + ++V   + ++ER A
Sbjct: 72  NGMLLNDRKVFVGRFKSRKEREA 94

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score =  136 bits (342), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 68/108 (62%), Positives = 84/108 (77%), Gaps = 3/108 (2%)
Query: 126 GAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
           G+GNIFIKNLDKSIDNKAL+DTFS FGNILSCKV  D  G S+GYGFV F+ +E+A+ AI
Sbjct: 4   GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAI 62
Query: 186 DKLNGMLLNDKQVFVGPFLRKQEREST--ADKTRFNNVYVKNLSETTT 231
           +K+NGMLLND++VFVG F  ++ERE+   A    F NVY+KN    +T
Sbjct: 63  EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGST 110

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 77.0 bits (188), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 39/88 (44%), Positives = 58/88 (65%), Gaps = 1/88 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           N+++KNLD SI +  L + FS FG I SCKV+ D NG S+G GFV F T E A +A+ +M
Sbjct: 7   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 383 NGKMVVSKPLYVALAQRKEERRARLQAQ 410
           NG ++  + ++V   + ++ER A L A+
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREAELGAR 93

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 56/88 (63%), Positives = 74/88 (84%), Gaps = 1/88 (1%)
Query: 318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASK 377
           +++ +NLYVKNLDD I D++L++ FS FGTITS KVM +  G S+G GFV FS+ EEA+K
Sbjct: 12  RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATK 70
Query: 378 ALTEMNGKMVVSKPLYVALAQRKEERRA 405
           A+TEMNG++V +KPLYVALAQRKEER++
Sbjct: 71  AVTEMNGRIVATKPLYVALAQRKEERQS 98

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 97.4 bits (241), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 56/152 (36%), Positives = 85/152 (55%), Gaps = 3/152 (1%)
Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+L V  L  ++   +L  LF+ +G+V S ++ RD     SLGYG+VNY  A +A RA++
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKV 159
            LN   L  K I++  SY  P+       N++I  L +++  K + D FS FG I++ +V
Sbjct: 63  TLNGLRLQSKTIKV--SYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
Query: 160 ATD-SLGQSRGYGFVQFDNEESAKSAIDKLNG 190
             D + G SRG  F++FD    A+ AI   NG
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 83.6 bits (205), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 54/186 (29%), Positives = 90/186 (48%), Gaps = 22/186 (11%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+D+L+ +F   G + S  ++RD   G S  +GFVN+    DA R++  
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
           LNG +   K   V  A                  + +++  +  NLY+  L  +++   +
Sbjct: 64  LNGLRLQSKTIKVSYA------------------RPSSEVIKDANLYISGLPRTMTQKDV 105
Query: 339 KELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKMVV--SKPLYVA 395
           +++FS FG I + +V+ D   G+SRG  F+ F    EA +A+T  NG      S+P+ V 
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVK 165
Query: 396 LAQRKE 401
            A   E
Sbjct: 166 FAANLE 171

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NL V  L  +++ D+L+ LFS  G + S K++RD   G S G GFV + TA++A +A+  
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 382 MNGKMVVSKPLYVALAQRKEE 402
           +NG  + SK + V+ A+   E
Sbjct: 64  LNGLRLQSKTIKVSYARPSSE 84

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 97.4 bits (241), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 56/152 (36%), Positives = 85/152 (55%), Gaps = 3/152 (1%)
Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+L V  L  ++   +L  LF+ +G+V S ++ RD     SLGYG+VNY  A +A RA++
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKV 159
            LN   L  K I++  SY  P+       N++I  L +++  K + D FS FG I++ +V
Sbjct: 63  TLNGLRLQSKTIKV--SYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRV 120
Query: 160 ATD-SLGQSRGYGFVQFDNEESAKSAIDKLNG 190
             D + G SRG  F++FD    A+ AI   NG
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 84.0 bits (206), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 54/186 (29%), Positives = 90/186 (48%), Gaps = 22/186 (11%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+D+L+ +F   G + S  ++RD   G S  +GFVN+    DA R++  
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
           LNG +   K   V  A                  + +++  +  NLY+  L  +++   +
Sbjct: 64  LNGLRLQSKTIKVSYA------------------RPSSEVIKDANLYISGLPRTMTQKDV 105
Query: 339 KELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKMVV--SKPLYVA 395
           +++FS FG I + +V+ D   G+SRG  F+ F    EA +A+T  NG      S+P+ V 
Sbjct: 106 EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVX 165
Query: 396 LAQRKE 401
            A   E
Sbjct: 166 FAANLE 171

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 55.1 bits (131), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NL V  L  +++ D+L+ LFS  G + S K++RD   G S G GFV + TA++A +A+  
Sbjct: 4   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 382 MNGKMVVSKPLYVALAQRKEE 402
           +NG  + SK + V+ A+   E
Sbjct: 64  LNGLRLQSKTIKVSYARPSSE 84

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 95.9 bits (237), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 57/182 (31%), Positives = 96/182 (52%), Gaps = 22/182 (12%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+D+ K +FG  G I S  ++RD   G+S  +GFVN+ DP+DA +++  
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
           LNG K   K   V  A                  + ++      NLYV  L  ++S  ++
Sbjct: 66  LNGLKLQTKTIKVSYA------------------RPSSASIRDANLYVSGLPKTMSQKEM 107
Query: 339 KELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGK--MVVSKPLYVA 395
           ++LFS++G I + +++ D   G+SRG GF+ F    EA +A+  +NG+  +  ++P+ V 
Sbjct: 108 EQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVK 167
Query: 396 LA 397
            A
Sbjct: 168 FA 169

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 94.4 bits (233), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/152 (34%), Positives = 85/152 (55%), Gaps = 3/152 (1%)
Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+L V  L  ++   +   LF  +G++ S ++ RD  T +SLGYG+VNY    +A +A++
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKV 159
            LN   L  K I++  SY  P+       N+++  L K++  K L   FS +G I++ ++
Sbjct: 63  TLNGLRLQTKTIKV--SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 160 ATDSL-GQSRGYGFVQFDNEESAKSAIDKLNG 190
             D + G SRG GF++FD    A+ AI  LNG
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 91.7 bits (226), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 54/157 (34%), Positives = 89/157 (56%), Gaps = 8/157 (5%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+ +  L +++  +     F + G I SCK+  D + GQS GYGFV + + + A+ AI+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 188 LNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFG-IIT 246
           LNG+ L  K + V        R S+A   R  N+YV  L +T T+ +L+++F ++G IIT
Sbjct: 64  LNGLRLQTKTIKV-----SYARPSSAS-IRDANLYVSGLPKTMTQKELEQLFSQYGRIIT 117
Query: 247 STAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKK 283
           S  ++    G S+  GF+ FD   +A  +++ LNG+K
Sbjct: 118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK 154

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 90.5 bits (223), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 94/183 (51%), Gaps = 22/183 (12%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVE 277
            N+ V  L +  T+++ + +FG  G I S  ++RD   G+S  +GFVN+ DP DA +++ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 278 ALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDK 337
            LNG +   K   V  A                  + ++      NLYV  L  +++  +
Sbjct: 63  TLNGLRLQTKTIKVSYA------------------RPSSASIRDANLYVSGLPKTMTQKE 104
Query: 338 LKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMV--VSKPLYV 394
           L++LFS++G I + +++ D   G+SRG GF+ F    EA +A+  +NG+     ++P+ V
Sbjct: 105 LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 164
Query: 395 ALA 397
             A
Sbjct: 165 KFA 167

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NL V  L  +++ ++ + LF   G I SCK++RD   G S G GFV +   ++A KA+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 382 MNGKMVVSKPLYVALAQ 398
           +NG  + +K + V+ A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 85.5 bits (210), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 46/154 (29%), Positives = 86/154 (55%), Gaps = 2/154 (1%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYVG+LD ++ +  L   F   G + ++++  D    +++ Y +V Y+ +H+A  AL  L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 102 NFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVAT 161
           N   +    ++I ++++          N+F+ +L+ ++D++ L + F  F + LS  V  
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 162 D-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLN 194
           D   G SRGYGFV F +++ A++A+D + G  LN
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN 155

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 85.1 bits (209), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 93/180 (51%), Gaps = 17/180 (9%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV NL +  TED LK+ F   G I +  +M D + K+  + FV +    DA  +++ LN
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 281 GKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKE 340
           GK+ ++               +++   F+     + D F   NL+V +L+ ++ D+ L+ 
Sbjct: 63  GKQIENN-------------IVKINWAFQSQQSSSDDTF---NLFVGDLNVNVDDETLRN 106
Query: 341 LFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR 399
            F +F +  S  VM D   G SRG GFV+F++ ++A  A+  M G+ +  +PL +  A +
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 83.6 bits (205), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 59/182 (32%), Positives = 93/182 (51%), Gaps = 22/182 (12%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+ +L  +F   G I +  +MRD   G S  + FV+F    D+ R+++ 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
           LNG    +K   V  A+   E           S+K+T       NLYV NL  +I+DD+L
Sbjct: 65  LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 106
Query: 339 KELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVV--SKPLYVA 395
             +F ++G+I    ++RD   G  RG  FV ++  EEA +A++ +N  +    S+PL V 
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 166
Query: 396 LA 397
           LA
Sbjct: 167 LA 168

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 82.0 bits (201), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 48/155 (30%), Positives = 81/155 (52%), Gaps = 3/155 (1%)
Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           +T+L V  L     D +LY LF  +G + + R+ RD  T  S GY +V++ +  ++ RA+
Sbjct: 14  NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAI 73
Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCK 158
             LN   +  K  R+  SY  P        N+++ NL ++I +  L   F  +G+I+   
Sbjct: 74  KVLNGITVRNK--RLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 131
Query: 159 VATDSL-GQSRGYGFVQFDNEESAKSAIDKLNGML 192
           +  D L G+ RG  FV+++  E A+ AI  LN ++
Sbjct: 132 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 80.9 bits (198), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 58/183 (31%), Positives = 93/183 (50%), Gaps = 22/183 (12%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+ +L  +F   G I +  + RD   G S  + FV+F    D+ R+++ 
Sbjct: 16  NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
           LNG    +K   V  A+   E           S+K+T       NLYV NL  +I+DD+L
Sbjct: 76  LNGITVRNKRLKVSYARPGGE-----------SIKDT-------NLYVTNLPRTITDDQL 117
Query: 339 KELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVV--SKPLYVA 395
             +F ++G+I    ++RD   G  RG  FV ++  EEA +A++ +N  +    S+PL V 
Sbjct: 118 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 177
Query: 396 LAQ 398
           LA+
Sbjct: 178 LAE 180

>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 = 78.2 bits (191), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 45/176 (25%), Positives = 93/176 (52%), Gaps = 15/176 (8%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLG-QSRGYGFVQFDNEESAKSAIDKL 188
           +++ ++   +    +   F+ FG I S  ++ DS+  + +G+ FV+++  E+A+ A++++
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 189 NGMLLNDKQVFVG---------PFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIF 239
           N ++L  + + VG         P + +   E+ A    FN +YV ++ +  ++DD+K +F
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA----FNRIYVASVHQDLSDDDIKSVF 146
Query: 240 GEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA 294
             FG I S  + RD   GK K +GF+ ++    +  +V ++N      +   VGKA
Sbjct: 147 EAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202

>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 = 74.3 bits (181), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 83/169 (49%), Gaps = 11/169 (6%)
Query: 218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSV 276
            + VYV ++     ED +++ F  FG I S  +  D+   K K F FV ++ P+ A  ++
Sbjct: 28  MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 277 EALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLN-LYVKNLDDSISD 335
           E +N      +   VG+            G+ +  + + A++    N +YV ++   +SD
Sbjct: 88  EQMNSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRIYVASVHQDLSD 139
Query: 336 DKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMN 383
           D +K +F  FG I S  + RDP  G  +G GF+ +  A+ +  A++ MN
Sbjct: 140 DDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 77.8 bits (190), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 48/166 (28%), Positives = 83/166 (50%), Gaps = 11/166 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEAL 279
           VYV ++     ED +++ F  FG I S  +  D+   K K F FV ++ P+ A  ++E +
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 280 NGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLN-LYVKNLDDSISDDKL 338
           N      +   VG+            G+ +  + + A++    N +YV ++   +SDD +
Sbjct: 76  NSVMLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDI 127
Query: 339 KELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMN 383
           K +F  FG I SC + RDP  G  +G GF+ +  A+ +  A++ MN
Sbjct: 128 KSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173

>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 = 73.2 bits (178), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 47/166 (28%), Positives = 80/166 (48%), Gaps = 11/166 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEAL 279
           VYV ++     ED +++ F  FG I S     D+   K K F FV ++ P+ A  ++E  
Sbjct: 15  VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 280 NGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLN-LYVKNLDDSISDDKL 338
           N      +   VG+            G+ +  + + A++    N +YV ++   +SDD +
Sbjct: 75  NSVXLGGRNIKVGRPSNI--------GQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDI 126
Query: 339 KELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMN 383
           K +F  FG I SC + RDP  G  +G GF+ +  A+ +  A++  N
Sbjct: 127 KSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/150 (25%), Positives = 75/150 (50%), Gaps = 14/150 (9%)
Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           + L+VG+L   + + ++  LF + G+   V + +D       G+G++       A  A  
Sbjct: 23  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKV 76
Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKV 159
           EL+  PL GK +R+ ++          + ++ ++NL + + N+ L + FS FG +    V
Sbjct: 77  ELDNMPLRGKQLRVRFA--------CHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVV 128
Query: 160 ATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
             D  G+  G G V+F  + +A+ A+D+ +
Sbjct: 129 IVDDRGRPSGKGIVEFSGKPAARKALDRCS 158

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 52.8 bits (125), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 75/166 (45%), Gaps = 33/166 (19%)
Query: 216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARS 275
           T+ + ++V NL    TE++++K+F ++G      + +D     K FGF+  +      R+
Sbjct: 20  TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLE-----TRT 69
Query: 276 VEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKF--EGLNLYVKNLDDSI 333
           +  +   + D+               M L+GK      +   +F     +L V+NL   +
Sbjct: 70  LAEIAKVELDN---------------MPLRGK------QLRVRFACHSASLTVRNLPQYV 108
Query: 334 SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           S++ L+E FS FG +    V+ D  G   G G V FS    A KAL
Sbjct: 109 SNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKAL 154

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 69.3 bits (168), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 53/184 (28%), Positives = 82/184 (44%), Gaps = 13/184 (7%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L++G L     D  L   F Q G +    V RD +T+RS G+G+V Y    E   A   +
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 72
Query: 102 NFTP--LNGKPIRIMYSYRDPTIRKSGAG----NIFIKNLDKSIDNKALHDTFSTFGNIL 155
           N  P  ++G+ +    +      ++ GA      IF+  + +  +   L D F  +G I 
Sbjct: 73  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 132
Query: 156 SCKVATD-SLGQSRGYGFVQFDNEESA-KSAIDKLNGMLLNDKQVFVGPFLRKQERESTA 213
             ++ TD   G+ RG+ FV FD+ +S  K  I K +   +N     V   L KQE  S +
Sbjct: 133 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQEMASAS 190
Query: 214 DKTR 217
              R
Sbjct: 191 SSQR 194

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
           L++  L    +D+ L+  F ++GT+T C VMRDPN   SRG GFV ++T EE   A+   
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 381 --EMNGKMVVSK 390
             +++G++V  K
Sbjct: 76  PHKVDGRVVEPK 87

>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 = 69.3 bits (168), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 53/184 (28%), Positives = 82/184 (44%), Gaps = 13/184 (7%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L++G L     D  L   F Q G +    V RD +T+RS G+G+V Y    E   A   +
Sbjct: 17  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 73
Query: 102 NFTP--LNGKPIRIMYSYRDPTIRKSGAG----NIFIKNLDKSIDNKALHDTFSTFGNIL 155
           N  P  ++G+ +    +      ++ GA      IF+  + +  +   L D F  +G I 
Sbjct: 74  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 133
Query: 156 SCKVATD-SLGQSRGYGFVQFDNEESA-KSAIDKLNGMLLNDKQVFVGPFLRKQERESTA 213
             ++ TD   G+ RG+ FV FD+ +S  K  I K +   +N     V   L KQE  S +
Sbjct: 134 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQEMASAS 191
Query: 214 DKTR 217
              R
Sbjct: 192 SSQR 195

>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 = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
           L++  L    +D+ L+  F ++GT+T C VMRDPN   SRG GFV ++T EE   A+   
Sbjct: 17  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 76
Query: 381 --EMNGKMVVSK 390
             +++G++V  K
Sbjct: 77  PHKVDGRVVEPK 88

>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 = 69.3 bits (168), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 53/184 (28%), Positives = 82/184 (44%), Gaps = 13/184 (7%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L++G L     D  L   F Q G +    V RD +T+RS G+G+V Y    E   A   +
Sbjct: 15  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 71
Query: 102 NFTP--LNGKPIRIMYSYRDPTIRKSGAG----NIFIKNLDKSIDNKALHDTFSTFGNIL 155
           N  P  ++G+ +    +      ++ GA      IF+  + +  +   L D F  +G I 
Sbjct: 72  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 131
Query: 156 SCKVATD-SLGQSRGYGFVQFDNEESA-KSAIDKLNGMLLNDKQVFVGPFLRKQERESTA 213
             ++ TD   G+ RG+ FV FD+ +S  K  I K +   +N     V   L KQE  S +
Sbjct: 132 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQEMASAS 189
Query: 214 DKTR 217
              R
Sbjct: 190 SSQR 193

>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 = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
           L++  L    +D+ L+  F ++GT+T C VMRDPN   SRG GFV ++T EE   A+   
Sbjct: 15  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 74
Query: 381 --EMNGKMVVSK 390
             +++G++V  K
Sbjct: 75  PHKVDGRVVEPK 86

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 69.3 bits (168), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 77/165 (46%), Gaps = 18/165 (10%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG+L   + +     LF + G+   V + RD       G+G++   +   A  A  EL
Sbjct: 25  LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 102 NFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVAT 161
           + T L  +P+RI ++        +    + +KNL   + N+ L   FS FG +    V  
Sbjct: 79  DGTILKSRPLRIRFA--------THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV 130
Query: 162 DSLGQSRGYGFVQFDNEESAKSAIDKL-NGMLL---NDKQVFVGP 202
           D  G++ G GFV+F  +  A+ A+++  +G  L     + V V P
Sbjct: 131 DDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEP 175

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 55.8 bits (133), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 43/164 (26%), Positives = 69/164 (42%), Gaps = 29/164 (17%)
Query: 216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARS 275
           T+   ++V NL    TE+D K++F  +G  +   + RD     + FGF+  +    A  +
Sbjct: 20  TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIA 74
Query: 276 VEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISD 335
              L+G     +   +  A                          G  L VKNL   +S+
Sbjct: 75  KAELDGTILKSRPLRIRFAT------------------------HGAALTVKNLSPVVSN 110
Query: 336 DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           + L++ FS+FG +    V+ D  G + G GFV F+    A KAL
Sbjct: 111 ELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKAL 154

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            L+V NL   I+++  K LF  +G  +   + RD     RG GF+   +   A  A  E+
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAEL 78
Query: 383 NGKMVVSKPLYVALA 397
           +G ++ S+PL +  A
Sbjct: 79  DGTILKSRPLRIRFA 93

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 69.3 bits (168), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 46/164 (28%), Positives = 86/164 (52%), Gaps = 28/164 (17%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDP---DDAARSV 276
           +++  L+  TTED+L++ FG++G +T   +M+D A G+S+ FGF++F+ P   D+  ++ 
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 277 EALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDD 336
             L+GK  D K     +A  + E++   K                  ++V  +   +   
Sbjct: 66  HILDGKVIDPK-----RAIPRDEQDKTGK------------------IFVGGIGPDVRPK 102
Query: 337 KLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKAL 379
           + +E FS++GTI   ++M D + G SRG GFV + +A+   +  
Sbjct: 103 EFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC 146

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 46/75 (61%), Gaps = 4/75 (5%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAF---STAEEA 375
           E   +++  L+   ++D L+E F ++GT+T  K+M+DP  G SRG GF++F   S+ +E 
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 376 SKALTEMNGKMVVSK 390
            K    ++GK++  K
Sbjct: 62  VKTQHILDGKVIDPK 76

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 68.9 bits (167), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 47/183 (25%), Positives = 84/183 (45%), Gaps = 20/183 (10%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD---GKSKCFGFVNFDDPDDAARSVE 277
           ++V  +  T +E DL+++F ++G +    V+RD      +SK   FV F     A  +  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 278 ALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDK 337
           AL+  K                  M    + + +  E  +  E   L++  +    +++ 
Sbjct: 66  ALHNMKVLPG--------------MHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTEND 111
Query: 338 LKELFSEFGTITSCKVMRDPNGISRGSGFVAFST---AEEASKALTEMNGKMVVSKPLYV 394
           ++ +FS FG I  C+++R P+G+SRG  FV F+T   A+ A KA+ +       S P+ V
Sbjct: 112 IRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 171
Query: 395 ALA 397
             A
Sbjct: 172 KFA 174

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 68.9 bits (167), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 47/183 (25%), Positives = 84/183 (45%), Gaps = 20/183 (10%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD---GKSKCFGFVNFDDPDDAARSVE 277
           ++V  +  T +E DL+++F ++G +    V+RD      +SK   FV F     A  +  
Sbjct: 18  MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 278 ALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDK 337
           AL+  K                  M    + + +  E  +  E   L++  +    +++ 
Sbjct: 78  ALHNMKVLPG--------------MHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTEND 123
Query: 338 LKELFSEFGTITSCKVMRDPNGISRGSGFVAFST---AEEASKALTEMNGKMVVSKPLYV 394
           ++ +FS FG I  C+++R P+G+SRG  FV F+T   A+ A KA+ +       S P+ V
Sbjct: 124 IRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 183
Query: 395 ALA 397
             A
Sbjct: 184 KFA 186

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 68.6 bits (166), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 81/180 (45%), Gaps = 13/180 (7%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L++G L     D  L   F Q G +    V RD +T+RS G+G+V Y    E   A   +
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 65
Query: 102 NFTP--LNGKPIRIMYSYRDPTIRKSGAG----NIFIKNLDKSIDNKALHDTFSTFGNIL 155
           N  P  ++G+ +    +      ++ GA      IF+  + +  +   L D F  +G I 
Sbjct: 66  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 125
Query: 156 SCKVATD-SLGQSRGYGFVQFDNEESA-KSAIDKLNGMLLNDKQVFVGPFLRKQERESTA 213
             ++ TD   G+ RG+ FV FD+ +S  K  I K +   +N     V   L KQE  S +
Sbjct: 126 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQEMASAS 183

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
           L++  L    +D+ L+  F ++GT+T C VMRDPN   SRG GFV ++T EE   A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 381 --EMNGKMVVSK 390
             +++G++V  K
Sbjct: 69  PHKVDGRVVEPK 80

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/154 (28%), Positives = 72/154 (46%), Gaps = 14/154 (9%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L++G L     D  L   F Q G +    V RD +T+RS G+G+V Y    E   A   +
Sbjct: 14  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 70
Query: 102 NFTP--LNGKPIRIMYSYRDPTIRKSGAG----NIFIKNLDKSIDNKALHDTFSTFGNIL 155
           N  P  ++G+ +    +      ++ GA      IF+  + +  +   L D F  +G I 
Sbjct: 71  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 130
Query: 156 SCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
             ++ TD   G+ RG+ FV FD+ +S    +DK+
Sbjct: 131 VIEIMTDRGSGKKRGFAFVTFDDHDS----VDKI 160

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 59.3 bits (142), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 40/153 (26%), Positives = 72/153 (47%), Gaps = 11/153 (7%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAID-- 186
           +FI  L     +++L   F  +G +  C V  D +  +SRG+GFV +   E   +A++  
Sbjct: 14  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 187 --KLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGI 244
             K++G ++  K+      + +++ +          ++V  + E T E  L+  F ++G 
Sbjct: 74  PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 128
Query: 245 ITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSV 276
           I    +M D   GK + F FV FDD D   + V
Sbjct: 129 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
           L++  L    +D+ L+  F ++GT+T C VMRDPN   SRG GFV ++T EE   A+   
Sbjct: 14  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 73
Query: 381 --EMNGKMVVSK 390
             +++G++V  K
Sbjct: 74  PHKVDGRVVEPK 85

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 44/154 (28%), Positives = 72/154 (46%), Gaps = 14/154 (9%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L++G L     D  L   F Q G +    V RD +T+RS G+G+V Y    E   A   +
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 72
Query: 102 NFTP--LNGKPIRIMYSYRDPTIRKSGAG----NIFIKNLDKSIDNKALHDTFSTFGNIL 155
           N  P  ++G+ +    +      ++ GA      IF+  + +  +   L D F  +G I 
Sbjct: 73  NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 132
Query: 156 SCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
             ++ TD   G+ RG+ FV FD+ +S    +DK+
Sbjct: 133 VIEIMTDRGSGKKRGFAFVTFDDHDS----VDKI 162

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 40/153 (26%), Positives = 72/153 (47%), Gaps = 11/153 (7%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAID-- 186
           +FI  L     +++L   F  +G +  C V  D +  +SRG+GFV +   E   +A++  
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 187 --KLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGI 244
             K++G ++  K+      + +++ +          ++V  + E T E  L+  F ++G 
Sbjct: 76  PHKVDGRVVEPKRA-----VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130
Query: 245 ITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSV 276
           I    +M D   GK + F FV FDD D   + V
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALT-- 380
           L++  L    +D+ L+  F ++GT+T C VMRDPN   SRG GFV ++T EE   A+   
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 381 --EMNGKMVVSK 390
             +++G++V  K
Sbjct: 76  PHKVDGRVVEPK 87

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 65.1 bits (157), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 49/182 (26%), Positives = 81/182 (44%), Gaps = 20/182 (10%)
Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD---GKSKCFGFVNFDDPDDAARSVEA 278
           +V  +  T +E DL+++F ++G +    V+RD      +SK   FV F     A  +  A
Sbjct: 7   FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
           L+  K      +             ++ K   S K  A   E   L++  +    +++ +
Sbjct: 67  LHNXKVLPGXHH------------PIQXKPADSEKNNA--VEDRKLFIGXISKKCTENDI 112
Query: 339 KELFSEFGTITSCKVMRDPNGISRGSGFVAFST---AEEASKALTEMNGKMVVSKPLYVA 395
           +  FS FG I  C+++R P+G+SRG  FV F+T   A+ A KA  +       S P  V 
Sbjct: 113 RVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQAQTXEGCSSPXVVK 172
Query: 396 LA 397
            A
Sbjct: 173 FA 174

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 36/89 (40%), Positives = 54/89 (60%), Gaps = 2/89 (2%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNIL-SCKVATDS-LGQSRGYGFVQFDNEESAK 182
           SG+  IFI NLD  ID K L+DTFS FG IL + K+  D   G S+GY F+ F + +++ 
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 183 SAIDKLNGMLLNDKQVFVGPFLRKQERES 211
           +AI+ +NG  L ++ + V    +K  + S
Sbjct: 63  AAIEAMNGQYLCNRPITVSYAFKKDSKGS 91

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 52/82 (63%), Gaps = 2/82 (2%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTI-TSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           +++ NLD  I +  L + FS FG I  + K+MRDP+ G S+G  F+ F++ + +  A+  
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 382 MNGKMVVSKPLYVALAQRKEER 403
           MNG+ + ++P+ V+ A +K+ +
Sbjct: 68  MNGQYLCNRPITVSYAFKKDSK 89

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 48/79 (60%)
Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
           G  ++V NLD  +   KLKE+FS  G +    ++ D +G SRG G V F  + EA +A++
Sbjct: 15  GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAIS 74
Query: 381 EMNGKMVVSKPLYVALAQR 399
             NG+++  +P++V + +R
Sbjct: 75  MFNGQLLFDRPMHVKMDER 93

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 58.5 bits (140), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 32/81 (39%), Positives = 50/81 (61%), Gaps = 1/81 (1%)
Query: 319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASK 377
           F+G NL V  L  + + D+L+ LFS  G + S K++RD   G S G GFV + TA++A +
Sbjct: 17  FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 378 ALTEMNGKMVVSKPLYVALAQ 398
           A+  +NG  + SK + V+ A+
Sbjct: 77  AINTLNGLRLQSKTIKVSYAR 97

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 58.5 bits (140), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 48/77 (62%)
Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S+ LYVG L  ++ +  L  +F   G++ ++ + +D  T RS GYG++ ++ +  A RAL
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 99  DELNFTPLNGKPIRIMY 115
           ++LN   L G+P+R+ +
Sbjct: 65  EQLNGFELAGRPMRVGH 81

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
           + +YV +L    TED L+ IF  FG I +  +M+D+D G+SK +GF+ F D + A R++E
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 278 ALNGKKFDDKEWYVGKAQKKYE 299
            LNG +   +   VG   ++ +
Sbjct: 66  QLNGFELAGRPMRVGHVTERLD 87

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 47/74 (63%), Gaps = 1/74 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            LYV +L  +I++D L+ +F  FG I +  +M+D + G S+G GF+ FS +E A +AL +
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 382 MNGKMVVSKPLYVA 395
           +NG  +  +P+ V 
Sbjct: 67  LNGFELAGRPMRVG 80

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 58.2 bits (139), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 48/78 (61%)
Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L+VGDL+++V+D  L + F      +S  V  D+ T  S GYG+V++ +  +A  A+D 
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 101 LNFTPLNGKPIRIMYSYR 118
           +    LNG+P+RI ++ +
Sbjct: 63  MQGQDLNGRPLRINWAAK 80

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 55.8 bits (133), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 48/82 (58%), Gaps = 1/82 (1%)
Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALT 380
            NL+V +L+ ++ D+ L+  F +F +  S  VM D   G SRG GFV+F++ ++A  A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 381 EMNGKMVVSKPLYVALAQRKEE 402
            M G+ +  +PL +  A + E 
Sbjct: 62  SMQGQDLNGRPLRINWAAKLEH 83

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 47/75 (62%), Gaps = 1/75 (1%)
Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALT 380
           + LYV +L  +I++D L+ +F  FG I S ++M D   G S+G GF+ FS +E A KAL 
Sbjct: 27  MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 381 EMNGKMVVSKPLYVA 395
           ++NG  +  +P+ V 
Sbjct: 87  QLNGFELAGRPMKVG 101

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+D+ K +FG  G I S  ++RD   G+S  +GFVN+ DP+DA +++  
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 279 LNGKKFDDKEWYVGKAQ 295
           LNG K   K   V  A+
Sbjct: 66  LNGLKLQTKTIKVSYAR 82

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 53.1 bits (126), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NL V  L  +++ D+ K LF   G I SCK++RD   G S G GFV +S   +A KA+  
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 382 MNGKMVVSKPLYVALAQ 398
           +NG  + +K + V+ A+
Sbjct: 66  LNGLKLQTKTIKVSYAR 82

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 34/92 (36%), Positives = 55/92 (59%), Gaps = 10/92 (10%)
Query: 310 QSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVA 368
           +S+K+T       NLYV NL  +I+DD+L  +F ++G+I    ++RD   G  RG  FV 
Sbjct: 9   ESIKDT-------NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 61
Query: 369 FSTAEEASKALTEMNGKMVV--SKPLYVALAQ 398
           ++  EEA +A++ +N  +    S+PL V LA+
Sbjct: 62  YNKREEAQEAISALNNVIPEGGSQPLSVRLAE 93

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 55.8 bits (133), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 45/74 (60%)
Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
            ++YVG LD  V++  L++LF Q G VV+  + +D  T +  GYG+V + +  +A  A+ 
Sbjct: 16  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 100 ELNFTPLNGKPIRI 113
            ++   L GKPIR+
Sbjct: 76  IMDMIKLYGKPIRV 89

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNE 178
           P   ++    +++  LD+ +    L + F   G +++  +  D + GQ +GYGFV+F +E
Sbjct: 8   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67
Query: 179 ESAKSAIDKLNGMLLNDKQVFV 200
           E A  AI  ++ + L  K + V
Sbjct: 68  EDADYAIKIMDMIKLYGKPIRV 89

>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 = 55.8 bits (133), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 46/77 (59%)
Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+L V  L  ++   +L  LF+ +G+V S ++ RD     SLGYG+VNY  A +A RA++
Sbjct: 5   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 100 ELNFTPLNGKPIRIMYS 116
            LN   L  K I++ Y+
Sbjct: 65  TLNGLRLQSKTIKVSYA 81

>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 = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 48/77 (62%), Gaps = 1/77 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NL V  L  +++ D+L+ LFS  G + S K++RD   G S G GFV + TA++A +A+  
Sbjct: 6   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 382 MNGKMVVSKPLYVALAQ 398
           +NG  + SK + V+ A+
Sbjct: 66  LNGLRLQSKTIKVSYAR 82

>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 1 Length = 114

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 23/69 (33%), Positives = 39/69 (56%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           NLY+ NL  S+ + +L+ +   FG + S +++RD +G SRG GF    + E+    +   
Sbjct: 27  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 383 NGKMVVSKP 391
           NGK + + P
Sbjct: 87  NGKFIKTPP 95

>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains Of The Yeast Splicing Factor Prp24 Length = 292

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 57/275 (20%), Positives = 120/275 (43%), Gaps = 31/275 (11%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + +KNL KS +   ++  F   G I+   VA DSL ++  +  ++F   + A +AI K +
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA-DSLKKNFRFARIEFARYDGALAAITKTH 102
Query: 190 GMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTA 249
            ++    ++ V         E T        ++  N   + T+ +++ +  +  ++  + 
Sbjct: 103 KVV-GQNEIIVSHLT-----ECT--------LWXTNFPPSYTQRNIRDLLQDINVVALSI 148
Query: 250 VMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKF 308
            +       S+ F +++    +DA   VE LNG K +            Y    ++    
Sbjct: 149 RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG-----------YTLVTKVSNPL 197
Query: 309 EQSLKETADKFEGLNLYVKNLDDSISDDK-LKELFSEFGTITSCKVM--RDPNGISRGSG 365
           E+S +  +   EG  + ++NL   + D+  L+E F  FG+I    +   +  +  +    
Sbjct: 198 EKSKRTDSATLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCA 257
Query: 366 FVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK 400
           F  F   + A +AL + N  ++ ++ + V+LA +K
Sbjct: 258 FXVFENKDSAERAL-QXNRSLLGNREISVSLADKK 291

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 55.1 bits (131), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 60/257 (23%), Positives = 105/257 (40%), Gaps = 35/257 (13%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           I I+ L   + N+ +HD  S +  +  C V      + +G  FV   N E A++AI+  +
Sbjct: 25  ILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAAINAFH 78
Query: 190 GMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITST- 248
              L ++++ V      Q + + A       + V NL  + T+   +++   FG +    
Sbjct: 79  QSRLRERELSV------QLQPTDA------LLCVANLPPSLTQQQFEELVRPFGSLERCF 126
Query: 249 AVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKF 308
            V  +  G+SK +GF  +   D AAR+   L GK    +  YV                +
Sbjct: 127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV---------------HW 171
Query: 309 EQSLKETADKFEGLNLYVKNLDDSISD-DKLKELFSEFGTITSCKVMRDPNGISRGSGFV 367
             + + T        L V  L    +D D L    S   + T C++    +G  +G   +
Sbjct: 172 TDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVL 231
Query: 368 AFSTAEEASKALTEMNG 384
            + TAE A +A  + +G
Sbjct: 232 EYETAEMAEEAQQQADG 248

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 55.1 bits (131), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 60/257 (23%), Positives = 105/257 (40%), Gaps = 35/257 (13%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           I I+ L   + N+ +HD  S +  +  C V      + +G  FV   N E A++AI+  +
Sbjct: 23  ILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAAINAFH 76
Query: 190 GMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITST- 248
              L ++++ V      Q + + A       + V NL  + T+   +++   FG +    
Sbjct: 77  QSRLRERELSV------QLQPTDA------LLCVANLPPSLTQQQFEELVRPFGSLERCF 124
Query: 249 AVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKF 308
            V  +  G+SK +GF  +   D AAR+   L GK    +  YV                +
Sbjct: 125 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV---------------HW 169
Query: 309 EQSLKETADKFEGLNLYVKNLDDSISD-DKLKELFSEFGTITSCKVMRDPNGISRGSGFV 367
             + + T        L V  L    +D D L    S   + T C++    +G  +G   +
Sbjct: 170 TDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVL 229
Query: 368 AFSTAEEASKALTEMNG 384
            + TAE A +A  + +G
Sbjct: 230 EYETAEMAEEAQQQADG 246

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 55.1 bits (131), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 60/257 (23%), Positives = 105/257 (40%), Gaps = 35/257 (13%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           I I+ L   + N+ +HD  S +  +  C V      + +G  FV   N E A++AI+  +
Sbjct: 25  ILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAAINAFH 78
Query: 190 GMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITST- 248
              L ++++ V      Q + + A       + V NL  + T+   +++   FG +    
Sbjct: 79  QSRLRERELSV------QLQPTDA------LLCVANLPPSLTQQQFEELVRPFGSLERCF 126
Query: 249 AVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKF 308
            V  +  G+SK +GF  +   D AAR+   L GK    +  YV                +
Sbjct: 127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV---------------HW 171
Query: 309 EQSLKETADKFEGLNLYVKNLDDSISD-DKLKELFSEFGTITSCKVMRDPNGISRGSGFV 367
             + + T        L V  L    +D D L    S   + T C++    +G  +G   +
Sbjct: 172 TDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVL 231
Query: 368 AFSTAEEASKALTEMNG 384
            + TAE A +A  + +G
Sbjct: 232 EYETAEMAEEAQQQADG 248

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 49/78 (62%), Gaps = 3/78 (3%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
           NLYV  L  ++S  ++++LFS++G I + +++ D   G+SRG GF+ F    EA +A+  
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 382 MNGK--MVVSKPLYVALA 397
           +NG+  +  ++P+ V  A
Sbjct: 63  LNGQKPLGAAEPITVKFA 80

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 44/76 (57%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +++  L+  T E  LK +FG+ G I+   +++D   KS+ F F+ F++P DA  + + +N
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 281 GKKFDDKEWYVGKAQK 296
           GK    K   V +A+K
Sbjct: 70  GKSLHGKAIKVEQAKK 85

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 40/76 (52%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L++  L+   ++  LK +F + G I+   +++D    SRG  F+ F    +A  A  +MN
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 384 GKMVVSKPLYVALAQR 399
           GK +  K + V  A++
Sbjct: 70  GKSLHGKAIKVEQAKK 85

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEA 278
           N+++ +L +  T+ DL   F  FG + S  V  D     SKCFGFV+FD+PD A  +++A
Sbjct: 42  NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 279 LNGKKFDDKEWYV 291
           +NG +   K   V
Sbjct: 102 MNGFQVGTKRLKV 114

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKA 378
           EG NL++ +L    +D  L   F  FG + S KV  D    +S+  GFV+F   + A  A
Sbjct: 39  EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 379 LTEMNGKMVVSKPLYVAL 396
           +  MNG  V +K L V L
Sbjct: 99  IKAMNGFQVGTKRLKVQL 116

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/186 (26%), Positives = 90/186 (48%), Gaps = 30/186 (16%)
Query: 29  GGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFN-QM----------GQVVSVRVCRDLST 77
           G +G AR+     LYVG++   + +  + D FN QM            V++V++ +D + 
Sbjct: 1   GPLGSARR-----LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN- 54
Query: 78  RRSLGYGYVNYNAAHEATRAL--DELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNL 135
                + ++ + +  E T+A+  D + F   + K IR  + Y+       GA  +FI  L
Sbjct: 55  -----FAFLEFRSVDETTQAMAFDGIIFQGQSLK-IRRPHDYQP----LPGAHKLFIGGL 104
Query: 136 DKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKLNGMLLN 194
              +++  + +  ++FG + +  +  DS  G S+GY F ++ +      AI  LNGM L 
Sbjct: 105 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG 164
Query: 195 DKQVFV 200
           DK++ V
Sbjct: 165 DKKLLV 170

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 35/175 (20%), Positives = 77/175 (44%), Gaps = 14/175 (8%)
Query: 127 AGNIFIKNLDKSIDNKALHDTFST---FGNILSCK---VATDSLGQSRGYGFVQFDNEES 180
           A  +++ N+   I  +A+ D F+     G +       V    + Q + + F++F     
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF----- 60
Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240
              ++D+    +  D  +F G  L+ +           + +++  L     +D +K++  
Sbjct: 61  --RSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLT 118
Query: 241 EFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA 294
            FG + +  +++D A G SK + F  + D +   +++  LNG +  DK+  V +A
Sbjct: 119 SFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 173

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 40/184 (21%), Positives = 79/184 (42%), Gaps = 26/184 (14%)
Query: 221 VYVKNLSETTTEDDLKKIF------GEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
           +YV N+    TE+ +   F      G         V+     + K F F+ F   D+  +
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 275 SVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSIS 334
           ++ A +G  F  +     K ++ ++ +  L G  +              L++  L + ++
Sbjct: 69  AM-AFDGIIFQGQSL---KIRRPHDYQ-PLPGAHK--------------LFIGGLPNYLN 109
Query: 335 DDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY 393
           DD++KEL + FG + +  +++D   G+S+G  F  +       +A+  +NG  +  K L 
Sbjct: 110 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 169
Query: 394 VALA 397
           V  A
Sbjct: 170 VQRA 173

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 47/80 (58%), Gaps = 4/80 (5%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG----ISRGSGFVAFSTAEEASKAL 379
           L++KNL+ S +++ LK +FS+ G I SC + +  N     +S G GFV +   E+A KAL
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 380 TEMNGKMVVSKPLYVALAQR 399
            ++ G  V    L V +++R
Sbjct: 68  KQLQGHTVDGHKLEVRISER 87

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 28/82 (34%), Positives = 44/82 (53%), Gaps = 3/82 (3%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V  L+   S+D ++ LF  FG I  C ++R P+G S+G  FV +S+  EA  A+  ++
Sbjct: 18  LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 384 GKMVV---SKPLYVALAQRKEE 402
           G   +   S  L V  A   +E
Sbjct: 78  GSQTMPGASSSLVVKFADTDKE 99

>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide Repeat Containing 4 Variant Length = 102

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/86 (33%), Positives = 45/86 (52%), Gaps = 3/86 (3%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           E   L+V  L    +D+ ++++F  FGTI  C V+R P+G S+G  FV F T  EA  A+
Sbjct: 11  EDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAI 70
Query: 380 TEMNGKMVV---SKPLYVALAQRKEE 402
             ++    +   S  L V  A  ++E
Sbjct: 71  NTLHSSRTLPGASSSLVVKFADTEKE 96

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 53.1 bits (126), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 42/72 (58%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG L    N+  L  +F++ GQ+  V V +D  T+RS G+G+V +    +A  A+  +
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 102 NFTPLNGKPIRI 113
           N   ++G+ IR+
Sbjct: 75  NGKSVDGRQIRV 86

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 52.8 bits (125), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 49/77 (63%), Gaps = 1/77 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVEAL 279
           ++V  LS  T E  L+++F ++G I+   V++D +  +S+ FGFV F++ DDA  ++ A+
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 280 NGKKFDDKEWYVGKAQK 296
           NGK  D ++  V +A K
Sbjct: 75  NGKSVDGRQIRVDQAGK 91

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 46/83 (55%), Gaps = 1/83 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEM 382
           L+V  L    ++  L+++FS++G I+   V++D     SRG GFV F   ++A  A+  M
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 383 NGKMVVSKPLYVALAQRKEERRA 405
           NGK V  + + V  A +  + R+
Sbjct: 75  NGKSVDGRQIRVDQAGKSSDNRS 97

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 48/184 (26%), Positives = 89/184 (48%), Gaps = 30/184 (16%)
Query: 31  VGDARQFVSTSLYVGDLDLSVNDSQLYDLFN-QM----------GQVVSVRVCRDLSTRR 79
           +G AR+     LYVG++   + +  + D FN QM            V++V++ +D +   
Sbjct: 1   LGSARR-----LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN--- 52
Query: 80  SLGYGYVNYNAAHEATRAL--DELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDK 137
              + ++ + +  E T+A+  D + F   + K IR  + Y+       GA  +FI  L  
Sbjct: 53  ---FAFLEFRSVDETTQAMAFDGIIFQGQSLK-IRRPHDYQP----LPGAHKLFIGGLPN 104
Query: 138 SIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDK 196
            +++  + +  ++FG + +  +  DS  G S+GY F ++ +      AI  LNGM L DK
Sbjct: 105 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 164
Query: 197 QVFV 200
           ++ V
Sbjct: 165 KLLV 168

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 35/175 (20%), Positives = 77/175 (44%), Gaps = 14/175 (8%)
Query: 127 AGNIFIKNLDKSIDNKALHDTFST---FGNILSCK---VATDSLGQSRGYGFVQFDNEES 180
           A  +++ N+   I  +A+ D F+     G +       V    + Q + + F++F     
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF----- 58
Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFG 240
              ++D+    +  D  +F G  L+ +           + +++  L     +D +K++  
Sbjct: 59  --RSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLT 116
Query: 241 EFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA 294
            FG + +  +++D A G SK + F  + D +   +++  LNG +  DK+  V +A
Sbjct: 117 SFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 40/184 (21%), Positives = 79/184 (42%), Gaps = 26/184 (14%)
Query: 221 VYVKNLSETTTEDDLKKIF------GEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
           +YV N+    TE+ +   F      G         V+     + K F F+ F   D+  +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 275 SVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSIS 334
           ++ A +G  F  +     K ++ ++ +  L G  +              L++  L + ++
Sbjct: 67  AM-AFDGIIFQGQSL---KIRRPHDYQ-PLPGAHK--------------LFIGGLPNYLN 107
Query: 335 DDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY 393
           DD++KEL + FG + +  +++D   G+S+G  F  +       +A+  +NG  +  K L 
Sbjct: 108 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Query: 394 VALA 397
           V  A
Sbjct: 168 VQRA 171

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score = 52.8 bits (125), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 42/73 (57%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L V NLD  +SD  ++ELF+EFGT+    V  D +G S G+  V F    +A KA+ + N
Sbjct: 31  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 384 GKMVVSKPLYVAL 396
           G  +  +P+ + L
Sbjct: 91  GVPLDGRPMNIQL 103

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 52.8 bits (125), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 29/82 (35%), Positives = 47/82 (57%), Gaps = 1/82 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
           NL V  +  ++ + +L++LF  +G I S K++ D     SRG GFV F +   A +A+  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 382 MNGKMVVSKPLYVALAQRKEER 403
           +NG  +++K L VALA    +R
Sbjct: 104 LNGFNILNKRLKVALAASGHQR 125

>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 = 52.4 bits (124), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 41/73 (56%)
Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           S++VG++     + QL D+F+++G VVS R+  D  T +  GYG+  Y     A  A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 101 LNFTPLNGKPIRI 113
           LN    +G+ +R+
Sbjct: 70  LNGREFSGRALRV 82

>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 = 49.3 bits (116), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 30/89 (33%), Positives = 48/89 (53%), Gaps = 2/89 (2%)
Query: 218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSV 276
             +V+V N+    TE+ LK IF E G + S  ++ D + GK K +GF  + D + A  ++
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 277 EALNGKKFDDKEWYVGKAQKKYEREMELK 305
             LNG++F  +   V  A  +  +E ELK
Sbjct: 68  RNLNGREFSGRALRVDNAASEKNKE-ELK 95

>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5 Rna Binding Protein Length = 105

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 3/82 (3%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V  L+   S++ +  LF  FG I  C V+R P+G S+G  FV FS+  EA  A+  ++
Sbjct: 18  LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 384 GKMVV---SKPLYVALAQRKEE 402
           G   +   S  L V  A   +E
Sbjct: 78  GSQTMPGASSSLVVKFADTDKE 99

>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor (Residues 1-155) Length = 177

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 53/104 (50%), Gaps = 5/104 (4%)
Query: 298 YEREMELKGKFEQSLKETA----DKFE-GLNLYVKNLDDSISDDKLKELFSEFGTITSCK 352
           Y R   L  K++  L ++     +  E G  L V NLD  +SD  ++ELF+EFGT+    
Sbjct: 60  YSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA 119
Query: 353 VMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL 396
           V  D +G S G+  V F    +A KA+ +  G  +  +P+ + L
Sbjct: 120 VDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL 163

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 5/74 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
           + V NLSE T E DL+++F  FG I+   + +D   G+SK F F++F   +DAAR++  +
Sbjct: 18  IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 280 NGKKFD----DKEW 289
           +G  +D    + EW
Sbjct: 78  SGFGYDHLILNVEW 91

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
           NL V  L   ++D +L  LF   G I +C++MRD   G S G  FV F++  ++ +A+  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 382 MNGKMVVSKPLYVALAQ 398
           +NG  V +K L V+ A+
Sbjct: 65  LNGITVRNKRLKVSYAR 81

>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A Resolution Length = 107

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 40/73 (54%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L V NLD  +SD  ++ELF+EFGT+    V  D +G S G+  V F    +A KA  + N
Sbjct: 32  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 384 GKMVVSKPLYVAL 396
           G  +  +P  + L
Sbjct: 92  GVPLDGRPXNIQL 104

>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs Orf57 Peptide Length = 124

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 42/76 (55%)
Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
           G  L V NLD  +SD  ++ELF+EFGT+    V  D +G S G+  V F    +A KA+ 
Sbjct: 35  GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 381 EMNGKMVVSKPLYVAL 396
           +  G  +  +P+ + L
Sbjct: 95  QYKGVPLDGRPMDIQL 110

>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1 Icp27 Peptide Length = 124

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 42/76 (55%)
Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
           G  L V NLD  +SD  ++ELF+EFGT+    V  D +G S G+  V F    +A KA+ 
Sbjct: 35  GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 381 EMNGKMVVSKPLYVAL 396
           +  G  +  +P+ + L
Sbjct: 95  QYKGVPLDGRPMDIQL 110

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID-- 186
           +FI  L      K L D FS FG ++ C +  D + G+SRG+GFV F   ES    +D  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 187 --KLNGMLLNDKQ 197
             KLNG +++ K+
Sbjct: 62  EHKLNGKVIDPKR 74

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE- 381
           +++  L    +   LK+ FS+FG +  C +  DP  G SRG GFV F  +E   K + + 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 382 ---MNGKMVVSK 390
              +NGK++  K
Sbjct: 62  EHKLNGKVIDPK 73

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/101 (29%), Positives = 51/101 (50%), Gaps = 4/101 (3%)
Query: 29  GGVGDARQFVSTS----LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYG 84
           G  G + Q   TS    ++VGDL   +    +   F   G++   RV +D++T +S GYG
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 85  YVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKS 125
           +V++    +A  A+ ++    L G+ IR  ++ R P   KS
Sbjct: 61  FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKS 101

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 28/85 (32%), Positives = 48/85 (56%), Gaps = 1/85 (1%)
Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDA 272
           D +   +V+V +LS   T +D+K  F  FG I+   V++D A GKSK +GFV+F +  DA
Sbjct: 11  DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70
Query: 273 ARSVEALNGKKFDDKEWYVGKAQKK 297
             +++ + G+    ++     A +K
Sbjct: 71  ENAIQQMGGQWLGGRQIRTNWATRK 95

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/89 (30%), Positives = 51/89 (57%), Gaps = 4/89 (4%)
Query: 313 KETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFST 371
           K+T++ F   +++V +L   I+ + +K  F+ FG I+  +V++D   G S+G GFV+F  
Sbjct: 10  KDTSNHF---HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66
Query: 372 AEEASKALTEMNGKMVVSKPLYVALAQRK 400
             +A  A+ +M G+ +  + +    A RK
Sbjct: 67  KWDAENAIQQMGGQWLGGRQIRTNWATRK 95

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYVG L   V+D  L+  F   G +  +++  D  T +  G+ +V +  A +A  A+D +
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 102 NFTPLNGKPIRI 113
           N + L G+ IR+
Sbjct: 75  NESELFGRTIRV 86

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +++  L + +D+K LH  F  FG+I   ++  D    + RG+ FV+F+  E A +AID +
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 189 N 189
           N
Sbjct: 75  N 75

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 49.3 bits (116), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/90 (31%), Positives = 54/90 (60%), Gaps = 11/90 (12%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V+NL ++++++ L++ FS+FG +   K ++D         F+ F   + A KA+ EMN
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 66
Query: 384 GKMVVSKPLYVALA----QRKEERRARLQA 409
           GK +  + + +  A    Q+++ER+A+ QA
Sbjct: 67  GKDLEGENIEIVFAKPPDQKRKERKAQRQA 96

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID-K 187
            +F+  +D  +D   +   F+ +G++   K+ TD  G S+GYGFV F N+   +  ++ +
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 188 LNGMLLNDKQVFVGPFLRKQ 207
           +N    + K++ +GP +RKQ
Sbjct: 71  IN---FHGKKLKLGPAIRKQ 87

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 46/79 (58%), Gaps = 4/79 (5%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID-KL 188
           +F+  +D  +D   +   F+ +G++   K+ TD  G S+GYGFV F N+   +  ++ ++
Sbjct: 13  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI 72
Query: 189 NGMLLNDKQVFVGPFLRKQ 207
           N    + K++ +GP +RKQ
Sbjct: 73  N---FHGKKLKLGPAIRKQ 88

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 46/79 (58%), Gaps = 4/79 (5%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID-KL 188
           +F+  +D  +D   +   F+ +G++   K+ TD  G S+GYGFV F N+   +  ++ ++
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI 71
Query: 189 NGMLLNDKQVFVGPFLRKQ 207
           N    + K++ +GP +RKQ
Sbjct: 72  N---FHGKKLKLGPAIRKQ 87

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 4/72 (5%)
Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDP 269
           +  AD+T    V+V NL     E+ L ++F + G +T   + +D +GK K FGFV F  P
Sbjct: 12  QEEADRT----VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHP 67
Query: 270 DDAARSVEALNG 281
           +  + ++  LNG
Sbjct: 68  ESVSYAIALLNG 79

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/83 (30%), Positives = 44/83 (53%), Gaps = 4/83 (4%)
Query: 313 KETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTA 372
           +E AD+     ++V NL+  + ++ L ELF + G +T   + +D  G  +  GFV F   
Sbjct: 12  QEEADR----TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHP 67
Query: 373 EEASKALTEMNGKMVVSKPLYVA 395
           E  S A+  +NG  +  +P+ V+
Sbjct: 68  ESVSYAIALLNGIRLYGRPINVS 90

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYVG L   V+D  L+  F   G +  +++  D  T +  G+ +V +  A +A  A+D +
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 102 NFTPLNGKPIRI 113
           N + L G+ IR+
Sbjct: 126 NESELFGRTIRV 137

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +++  L + +D+K LH  F  FG+I   ++  D    + RG+ FV+F+  E A +AID +
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 189 N 189
           N
Sbjct: 126 N 126

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 45/190 (23%), Positives = 87/190 (45%), Gaps = 39/190 (20%)
Query: 42  LYVGDLDLSVNDSQLYDLFN-QM----------GQVVSVRVCRDLSTRRSLGYGYVNYNA 90
           LYVG++   + +  + D FN QM            V++V++ +D +      + ++ + +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRS 60
Query: 91  AHEATRAL--DELNFT--------PLNGKPIRIMYSYRDPTIRKSG---------AGNIF 131
             E T+A+  D + F         P + +P+  M    +P++   G         A  +F
Sbjct: 61  VDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMS--ENPSVYVPGVVSTVVPDSAHKLF 118
Query: 132 IKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKLNG 190
           I  L   +++  + +  ++FG + +  +  DS  G S+GY F ++ +      AI  LNG
Sbjct: 119 IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 178
Query: 191 MLLNDKQVFV 200
           M L DK++ V
Sbjct: 179 MQLGDKKLLV 188

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 40/193 (20%), Positives = 83/193 (43%), Gaps = 24/193 (12%)
Query: 221 VYVKNLSETTTEDDLKKIF------GEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
           +YV N+    TE+ +   F      G         V+     + K F F+ F   D+  +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 275 SV---------EALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLY 325
           ++         ++L  ++  D +   G ++      + + G     + ++A K     L+
Sbjct: 67  AMAFDGIIFQGQSLKIRRPHDYQPLPGMSENP---SVYVPGVVSTVVPDSAHK-----LF 118
Query: 326 VKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNG 384
           +  L + ++DD++KEL + FG + +  +++D   G+S+G  F  +       +A+  +NG
Sbjct: 119 IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 178
Query: 385 KMVVSKPLYVALA 397
             +  K L V  A
Sbjct: 179 MQLGDKKLLVQRA 191

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 27/76 (35%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           SGA  IF++NL      K L D F+  G++L   +  ++ G+S+G G V+F++ E A+ A
Sbjct: 6   SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAERA 64
Query: 185 IDKLNGMLLNDKQVFV 200
              +NGM L+ +++ V
Sbjct: 65  CRMMNGMKLSGREIDV 80

>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 = 48.5 bits (114), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           N+FI +L +   ++ L   F  FGN++S KV  D     S+ +GFV +DN  SA++AI  
Sbjct: 27  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 188 LNGMLLNDKQVFV 200
           +NG  +  K++ V
Sbjct: 87  MNGFQIGMKRLKV 99

>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 = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEA 278
           N+++ +L +   + DL ++F  FG + S  V  D     SKCFGFV++D+P  A  ++++
Sbjct: 27  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 279 LNGKKFDDKEWYV 291
           +NG +   K   V
Sbjct: 87  MNGFQIGMKRLKV 99

>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 = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/87 (32%), Positives = 44/87 (50%), Gaps = 1/87 (1%)
Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKA 378
           EG NL++ +L     D  L ++F  FG + S KV  D    +S+  GFV++     A  A
Sbjct: 24  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 379 LTEMNGKMVVSKPLYVALAQRKEERRA 405
           +  MNG  +  K L V L + K + ++
Sbjct: 84  IQSMNGFQIGMKRLKVQLKRSKNDSKS 110

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 48.1 bits (113), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITST-AVMRDADGKSKCFGFVNFDDPDDAARSVE 277
           + +Y++ L   TT+ DL K+   +G I ST A++     K K +GFV+FD P  A ++V 
Sbjct: 6   SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 278 AL 279
           AL
Sbjct: 66  AL 67

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVEAL 279
           VYV NL  + T +DL +IF ++G +    +M+D D  KSK   F+ F D D A     A+
Sbjct: 19  VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 280 NGKKF 284
           N K+ 
Sbjct: 79  NNKQL 83

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/96 (29%), Positives = 48/96 (50%), Gaps = 4/96 (4%)
Query: 29  GGVGDARQFVSTS----LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYG 84
           G  G + Q   TS    ++VGDL   +    +   F   G++   RV +D++T +S GYG
Sbjct: 1   GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
Query: 85  YVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP 120
           +V++    +A  A+  +    L G+ IR  ++ R P
Sbjct: 61  FVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKP 96

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           ++F+ +L   I  + +   F+ FG I   +V  D + G+S+GYGFV F N+  A++AI  
Sbjct: 17  HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 188 LNGMLLNDKQV 198
           + G  L  +Q+
Sbjct: 77  MGGQWLGGRQI 87

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/89 (30%), Positives = 50/89 (56%), Gaps = 4/89 (4%)
Query: 313 KETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFST 371
           K+T++ F   +++V +L   I+ + +K  F+ FG I+  +V++D   G S+G GFV+F  
Sbjct: 10  KDTSNHF---HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYN 66
Query: 372 AEEASKALTEMNGKMVVSKPLYVALAQRK 400
             +A  A+  M G+ +  + +    A RK
Sbjct: 67  KLDAENAIVHMGGQWLGGRQIRTNWATRK 95

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/76 (34%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           SG+  IF++NL      K L D F+  G++L   +  ++ G+S+G G V+F++ E A+ A
Sbjct: 3   SGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAERA 61
Query: 185 IDKLNGMLLNDKQVFV 200
              +NGM L+ +++ V
Sbjct: 62  CRMMNGMKLSGREIDV 77

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           VYV NL     + +L++ FG +G + S  V R+  G    F FV F+DP DAA +V  L+
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELD 131
Query: 281 GK 282
           G+
Sbjct: 132 GR 133

>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 = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/87 (31%), Positives = 50/87 (57%), Gaps = 1/87 (1%)
Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPD 270
           +T +K++   ++V N+     + DL+++FG+FG I    ++ +  G SK FGFV F++  
Sbjct: 22  NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSA 80
Query: 271 DAARSVEALNGKKFDDKEWYVGKAQKK 297
           DA R+ E L+G   + ++  V  A  +
Sbjct: 81  DADRAREKLHGTVVEGRKIEVNNATAR 107

>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 = 42.7 bits (99), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/80 (28%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 315 TADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEE 374
           T +K +   L+V N+     D  L+++F +FG I   +++ +  G S+G GFV F  + +
Sbjct: 23  TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSAD 81
Query: 375 ASKALTEMNGKMVVSKPLYV 394
           A +A  +++G +V  + + V
Sbjct: 82  ADRAREKLHGTVVEGRKIEV 101

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41  SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
           ++Y+ +L+  +   +L    Y +F+Q GQ++ + V R L  R   G  +V +     AT 
Sbjct: 10  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 66
Query: 97  ALDELNFTPLNGKPIRIMYSYRDPTI 122
           AL  +   P   KP+RI Y+  D  I
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKTDSDI 92

>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117, Nmr, 43 Structures Length = 116

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 45/92 (48%), Gaps = 6/92 (6%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK+    +FS+FG I    V R      RG  FV F     A+ AL
Sbjct: 11  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 68
Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQAQF 411
             M G     KP+ +  A+   +  A+++  F
Sbjct: 69  RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           ++YVG+L  S    Q+ +LF+Q G+V +V++  D  T++  G+G+V        + A+ +
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 101 LNFTPLNGKPIRI 113
           L+ T   G+ IR+
Sbjct: 62  LDNTDFMGRTIRV 74

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           VYV NL     + +L++ FG +G + S  V R+  G    F FV F+DP DAA +V  L+
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRDLD 131
Query: 281 GK 282
           G+
Sbjct: 132 GR 133

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYVG L   V+D  L+  F   G +  +++  D  T +  G+ +V +  A +A  A+D +
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 102 NFTPLNGKPIRI 113
           N + L G+ IR+
Sbjct: 65  NESELFGRTIRV 76

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +++  L + +D+K LH  F  FG+I   ++  D    + RG+ FV+F+  E A +AID +
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 189 N 189
           N
Sbjct: 65  N 65

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYVG L   V+D  L+  F   G +  +++  D  T +  G+ +V +  A +A  A+D +
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 102 NFTPLNGKPIRI 113
           N + L G+ IR+
Sbjct: 70  NESELFGRTIRV 81

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +++  L + +D+K LH  F  FG+I   ++  D    + RG+ FV+F+  E A +AID +
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 189 N 189
           N
Sbjct: 70  N 70

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYVG L   V+D  L+  F   G +  +++  D  T +  G+ +V +  A +A  A+D +
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 102 NFTPLNGKPIRI 113
           N + L G+ IR+
Sbjct: 68  NESELFGRTIRV 79

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
           +++  L + +D+K LH  F  FG+I   ++  D    + RG+ FV+F+  E A +AID +
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 189 N 189
           N
Sbjct: 68  N 68

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAI 185
           AG  F+  L      K L D F+ FG ++ C +  D + G+SRG+GF+ F +  S +  +
Sbjct: 11  AGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL 70
Query: 186 D----KLNGMLLNDKQV 198
           D    +L+G +++ K+ 
Sbjct: 71  DQKEHRLDGRVIDPKKA 87

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 325 YVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE-- 381
           +V  L    S   LK+ F++FG +  C +  DPN G SRG GF+ F  A    K L +  
Sbjct: 15  FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 382 --MNGKMVVSK 390
             ++G+++  K
Sbjct: 75  HRLDGRVIDPK 85

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 45/169 (26%), Positives = 77/169 (45%), Gaps = 14/169 (8%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           N+FI NL+ +     L    S         V     G +R +G+V F++ E  + A++ L
Sbjct: 15  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 73
Query: 189 NGMLLNDKQVFVGPFLRKQERESTADKTRF-NNVYVKNLSETTTEDDLKKIFGEFGIITS 247
            G+     +VF      ++ +   + K R    +  KNLS   TED+LK++F +   I  
Sbjct: 74  TGL-----KVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR- 127
Query: 248 TAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKE---WYVGK 293
              +   DGKSK   ++ F    DA +++E   G + D +    +Y G+
Sbjct: 128 ---LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 45/178 (25%), Positives = 81/178 (45%), Gaps = 22/178 (12%)
Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDP 269
           E +   T FN +++ NL+   +  +LK    E       AV+    G ++ FG+V+F+  
Sbjct: 6   EGSESTTPFN-LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 64
Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNL 329
           +D  +++E L G K    E  + K           KG+  + ++          L  KNL
Sbjct: 65  EDLEKALE-LTGLKVFGNEIKLEKP----------KGRDSKKVRAAR------TLLAKNL 107
Query: 330 DDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV 387
             +I++D+LKE+F +   I     +   +G S+G  ++ F +  +A K L E  G  +
Sbjct: 108 SFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161

>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95 Length = 95

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41  SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
           ++Y+ +L+  +   +L    Y +F+Q GQ++ + V R L  R   G  +V +     AT 
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 97  ALDELNFTPLNGKPIRIMYSYRDPTI 122
           AL  +   P   KP+RI Y+  D  I
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDI 93

>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95 Length = 95

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK+    +FS+FG I    V R      RG  FV F     A+ AL
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 69
Query: 380 TEMNGKMVVSKPLYVALAQ 398
             M G     KP+ +  A+
Sbjct: 70  RSMQGFPFYDKPMRIQYAK 88

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 7/83 (8%)
Query: 41  SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
           ++Y+ +L+  +   +L    Y +F+Q GQ++ + V R L  R   G  +V +     AT 
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 97  ALDELNFTPLNGKPIRIMYSYRD 119
           AL  +   P   KP+RI Y+  D
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTD 90

>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp Length = 282

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 46/92 (50%), Gaps = 6/92 (6%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK+    +FS+FG I    V R  +   RG  FV F     A+ AL
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 69
Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQAQF 411
             M G     KP+ +  A+   +  A+++  F
Sbjct: 70  RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 101

>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif In Trna Selenocysteine Associated Protein Length = 104

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 31/85 (36%), Positives = 47/85 (55%), Gaps = 6/85 (7%)
Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSC---KVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +L+V +L   + D  L E F +     SC   KV+ D  G+S+G GFV F+   E  +AL
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVK--VYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRAL 68
Query: 380 TEMNGKM-VVSKPLYVALAQRKEER 403
           TE  G + + SKP+ +++A  K  R
Sbjct: 69  TECQGAVGLGSKPVRLSVAIPKASR 93

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 29/82 (35%), Positives = 44/82 (53%), Gaps = 5/82 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDA----ARS 275
           +++  LS  TT++ L++ FG+FG +    VMRD    +S+ FGFV F D        A+S
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Query: 276 VEALNGKKFDDKEWYVGKAQKK 297
              L+ K  D K  +  +AQ K
Sbjct: 88  RHELDSKTIDPKVAFPRRAQPK 109

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/85 (32%), Positives = 40/85 (47%), Gaps = 5/85 (5%)
Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKAL 379
           G  +++  L    + + L+E F +FG +  C VMRDP    SRG GFV F       K L
Sbjct: 25  GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Query: 380 T----EMNGKMVVSKPLYVALAQRK 400
                E++ K +  K  +   AQ K
Sbjct: 85  AQSRHELDSKTIDPKVAFPRRAQPK 109

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V+     + + +L E+F  FG +   K++        G  FV F  AE A+KA+ E++
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 86
Query: 384 GKMVVSKPLYVALAQRKEER 403
           GK   ++PL V  ++   +R
Sbjct: 87  GKSFANQPLEVVYSKLPAKR 106

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 24/66 (36%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEALNG 281
           V  LS  TTE DL+++F ++G I   +++ D   + S+ F FV F++ DDA  + E  NG
Sbjct: 51  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 282 KKFDDK 287
            + D +
Sbjct: 111 MELDGR 116

>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures Length = 101

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 44/92 (47%), Gaps = 6/92 (6%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK+    +FS FG I    V R      RG  FV F     A+ AL
Sbjct: 11  IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 68
Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQAQF 411
             M G     KP+ +  A+   +  A+++  F
Sbjct: 69  RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEALNG 281
           V NL+  T+ D L+++F ++G +    + RD   K S+ F FV F D  DA  +++A++G
Sbjct: 52  VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 282 KKFDDKEWYVGKAQ 295
              D +E  V  A+
Sbjct: 112 AVLDGRELRVQMAR 125

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           ++V N+     + DL+++FG+FG I    ++ +  G SK FGFV F++  DA R+ E L+
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 281 GKKFDDKEWYVGKAQKK 297
           G   + ++  V  A  +
Sbjct: 77  GTVVEGRKIEVNNATAR 93

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V N+     D  L+++F +FG I   +++ +  G S+G GFV F  + +A +A  +++
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 384 GKMVVSKPLYV 394
           G +V  + + V
Sbjct: 77  GTVVEGRKIEV 87

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 42/74 (56%)
Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S +LYVG+L     + Q+Y+LF++ G +  + +  D   + + G+ +V Y +  +A  A+
Sbjct: 39  SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 99  DELNFTPLNGKPIR 112
             +N T L+ + IR
Sbjct: 99  RYINGTRLDDRIIR 112

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 43/173 (24%), Positives = 78/173 (45%), Gaps = 14/173 (8%)
Query: 127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID 186
           A N+F+ NL+ +     L    S         V    +G +R +G+V F++ E  + A++
Sbjct: 7   AFNLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALE 66
Query: 187 KLNGMLLNDKQVFVGPFLRKQERESTADKTR-FNNVYVKNLSETTTEDDLKKIFGEFGII 245
            L G+     +VF      ++ +   + K R    +  KNL    T+D+LK++F +   I
Sbjct: 67  -LTGL-----KVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEI 120
Query: 246 TSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKE---WYVGKAQ 295
                +   DGKSK   ++ F    DA ++ E   G + D +    +Y G+ +
Sbjct: 121 R----LVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYTGEPK 169

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEALNG 281
           V  LS  TTE DL+++F ++G I   +++ D   + S+ F FV F++ DDA  + E  NG
Sbjct: 17  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 282 KKFDDKEWYV 291
            + D +   V
Sbjct: 77  MELDGRRIRV 86

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/80 (31%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEAL 279
           ++V+NLS T++E+DL+K+F  +G ++      D+   K K F FV F  P+ A ++   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 280 NGKKFDDKEWYVGKAQKKYE 299
           +G+ F  +  +V  +  K E
Sbjct: 71  DGQVFQGRMLHVLPSTIKKE 90

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEALNG 281
           V  LS  TTE DL+++F ++G I   +++ D   + S+ F FV F++ DDA  + E  NG
Sbjct: 20  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 282 KKFDDKEWYV 291
            + D +   V
Sbjct: 80  MELDGRRIRV 89

>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme Bound To Glc6p Length = 90

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK+    +FS FG I    V R      RG  FV F     A+ AL
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 63
Query: 380 TEMNGKMVVSKPLYVALAQ 398
             M G     KP+ +  A+
Sbjct: 64  RSMQGFPFYDKPMRIQYAK 82

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEALNG 281
           V  LS  TTE DL+++F ++G I   +++ D   + S+ F FV F++ DDA  + E  NG
Sbjct: 20  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 282 KKFDDKEWYV 291
            + D +   V
Sbjct: 80  MELDGRRIRV 89

>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch Length = 91

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK+    +FS FG I    V R      RG  FV F     A+ AL
Sbjct: 7   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 64
Query: 380 TEMNGKMVVSKPLYVALAQ 398
             M G     KP+ +  A+
Sbjct: 65  RSMQGFPFYDKPMRIQYAK 83

>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein Complex Bound To A Fragment Of U2 Small Nuclear Rna Length = 96

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 41  SLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
           ++Y+ +++  +   +L    Y LF+Q G VV +   + +  R   G  +V +     +T 
Sbjct: 8   TIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMR---GQAFVIFKELGSSTN 64
Query: 97  ALDELNFTPLNGKPIRIMYSYRDPTI 122
           AL +L   P  GKP+RI Y+  D  I
Sbjct: 65  ALRQLQGFPFYGKPMRIQYAKTDSDI 90

>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii Mrna- Binding Protein 2 Length = 93

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 5/71 (7%)
Query: 212 TADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
           ++  +  N +Y+ NLS   T DDL+++FG+  +  +  V+  +      + FV++ D + 
Sbjct: 2   SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS-----GYAFVDYPDQNW 56
Query: 272 AARSVEALNGK 282
           A R++E L+GK
Sbjct: 57  AIRAIETLSGK 67

>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its Catalytic Cofactor Length = 94

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK+    +FS FG I    V R      RG  FV F     A+ AL
Sbjct: 8   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 65
Query: 380 TEMNGKMVVSKPLYVALAQ 398
             M G     KP+ +  A+
Sbjct: 66  RSMQGFPFYDKPMRIQYAK 84

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/83 (30%), Positives = 46/83 (55%), Gaps = 5/83 (6%)
Query: 313 KETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFST 371
           ++  +K +   L++  L    +++ L+  + ++G +T C VMRDP +  SRG GFV FS+
Sbjct: 19  RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 78
Query: 372 AEEASKALT----EMNGKMVVSK 390
             E   A+      ++G++V  K
Sbjct: 79  MAEVDAAMAARPHSIDGRVVEPK 101

>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I Intron Length = 95

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK+    +FS FG I    V R      RG  FV F     A+ AL
Sbjct: 9   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 66
Query: 380 TEMNGKMVVSKPLYVALAQ 398
             M G     KP+ +  A+
Sbjct: 67  RSMQGFPFYDKPMRIQYAK 85

>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length = 74

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V+     + + +L E+F  FG +   K++        G  FV F  AE A+KA+ E++
Sbjct: 7   LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 59
Query: 384 GKMVVSKPLYVALAQ 398
           GK   ++PL V  ++
Sbjct: 60  GKSFANQPLEVVYSK 74

>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL Length = 97

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK+    +FS FG I    V R      RG  FV F     A+ AL
Sbjct: 11  IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 68
Query: 380 TEMNGKMVVSKPLYVALAQ 398
             M G     KP+ +  A+
Sbjct: 69  RSMQGFPFYDKPMRIQYAK 87

>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In Complex With Thiamine Pyrophosphate And The U1a Crystallization Module Length = 96

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK+    +FS FG I    V R      RG  FV F     A+ AL
Sbjct: 11  IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 68
Query: 380 TEMNGKMVVSKPLYVALAQ 398
             M G     KP+ +  A+
Sbjct: 69  RSMQGFPFYDKPMRIQYAK 87

>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With Both Exons Length = 98

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK+    +FS FG I    V R      RG  FV F     A+ AL
Sbjct: 12  IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 69
Query: 380 TEMNGKMVVSKPLYVALAQ 398
             M G     KP+ +  A+
Sbjct: 70  RSMQGFPFYDKPMRIQYAK 88

>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleoprotein R (Hnrnp R) Length = 97

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 48/82 (58%), Gaps = 7/82 (8%)
Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L+V+NL  +++++ L++ FSEFG +   K ++D         FV F     A KA+ EMN
Sbjct: 18  LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAVKAMDEMN 70
Query: 384 GKMVVSKPLYVALAQRKEERRA 405
           GK +  + + + LA+  +++R+
Sbjct: 71  GKEIEGEEIEIVLAKPPDKKRS 92

>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The Catalytically-Active Conformation Length = 100

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 324 LYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK+    +FS FG I    V R      RG  FV F     A+ AL
Sbjct: 12  IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 69
Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQ 408
             M G     KP+ +  A+   +  A+++
Sbjct: 70  RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/79 (29%), Positives = 44/79 (55%)
Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VGDL   +  + +   F   G++   RV +D++T +S GYG+V++    +A  A+ ++
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 102 NFTPLNGKPIRIMYSYRDP 120
               L G+ IR  ++ R P
Sbjct: 69  GGQWLGGRQIRTNWATRKP 87

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           ++F+ +L   I   A+   F+ FG I   +V  D + G+S+GYGFV F N+  A++AI +
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 188 LNGMLLNDKQV 198
           + G  L  +Q+
Sbjct: 68  MGGQWLGGRQI 78

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           VYV NL     + +L++ F  +G + +  + R+  G    F FV F+DP DA  +V  L+
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG----FAFVEFEDPRDAEDAVRGLD 58
Query: 281 GK 282
           GK
Sbjct: 59  GK 60

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDN 177
           G +F+  LD S   + L   FS +G ++ C +  D +  QSRG+GFV+F +
Sbjct: 17  GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 41.6 bits (96), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDA----ARS 275
           ++V  L  +TT++ L+  F ++G +    +M+D    +S+ FGFV F DP+      A  
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 276 VEALNGKKFDDK 287
              L+G+  D K
Sbjct: 79  PHTLDGRNIDPK 90

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 223 VKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEALNG 281
           V NL+  T+ D L+++F ++G +    + RD   K S+ F FV F D  DA  +++A++G
Sbjct: 75  VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 282 KKFDDKEWYVGKAQ 295
              D +E  V  A+
Sbjct: 135 AVLDGRELRVQMAR 148

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S +LYVG+L     + Q+Y+LF++ G +  + +  D   + + G+ +V Y +  +A  A+
Sbjct: 18  SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD-KMKTACGFCFVEYYSRADAENAM 76
Query: 99  DELNFTPLNGKPIR 112
             +N T L+ + IR
Sbjct: 77  RYINGTRLDDRIIR 90

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 30/85 (35%), Positives = 44/85 (51%), Gaps = 11/85 (12%)
Query: 201 GPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKC 260
           GP  R Q  ++         ++VK LSE TTE+ LK+ F   G + +  V     G SK 
Sbjct: 7   GPNARSQPSKT---------LFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKG 55
Query: 261 FGFVNFDDPDDAARSVEALNGKKFD 285
           FGFV+F+  +DA  + EA+   + D
Sbjct: 56  FGFVDFNSEEDAKAAKEAMEDGEID 80

>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding Protein 14 Length = 90

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           IF+ N+  +  ++ L   F   G ++ C V  D       Y FV  + E  AK+AI +LN
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64
Query: 190 GMLLNDKQVFV 200
           G  +  K++ V
Sbjct: 65  GKEVKGKRINV 75

>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein Np_057951 Length = 110

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 130 IFIKNLDKSIDNKA-LHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +FI NL+ ++  K+ +   FS +G +  C V        +GY FVQ+ NE  A++A+   
Sbjct: 30  VFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGE 82
Query: 189 NGMLL 193
           NG +L
Sbjct: 83  NGRVL 87

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDA----ARS 275
           +++  LS  TT++ L++ FG+FG +    VMRD    +S+ FGFV F D        A+S
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 276 VEALNGKKFDDK 287
              L+ K  D K
Sbjct: 63  RHELDSKTIDPK 74

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	467
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-124
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-87
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-124
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-75
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-52
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-43
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-96
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-60
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-58
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-82
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-60
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-50
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-25
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-21
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-80
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-73
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-60
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-76
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-61
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-48
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-25
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-18
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-74
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-74
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-56
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	7e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-71
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-59
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-47
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-24
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-70
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-68
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-55
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-28
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-18
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-69
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-66
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-51
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-28
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	8e-60
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-46
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-44
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-18
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-58
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-45
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-45
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-15
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-52
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-34
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-34
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	9e-22
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-49
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-30
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-29
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-18
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-48
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-32
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-32
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-21
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-47
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-32
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	9e-30
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-21
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-46
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-30
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-26
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-18
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-45
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-27
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-23
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-20
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-45
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-28
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-17
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-14
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-44
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-24
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	6e-22
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-17
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	7e-43
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-28
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	8e-27
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-20
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-41
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-26
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	9e-23
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-20
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	8e-41
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-28
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	6e-26
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-20
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-40
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-36
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-28
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-19
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-40
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	6e-29
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	8e-19
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-14
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-40
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-36
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-32
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-17
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	8e-40
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	8e-30
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	7e-24
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-20
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-39
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	8e-24
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-22
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-16
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-38
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-36
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-28
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-17
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-10
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-37
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-35
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	5e-29
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-36
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-27
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-25
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-18
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-36
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-25
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	6e-22
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-12
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-36
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-30
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-25
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-17
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-36
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	6e-33
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-28
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	7e-17
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-11
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	8e-36
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	9e-34
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-23
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-16
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	5e-35
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-31
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-19
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-15
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	6e-35
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-22
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-20
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-16
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-33
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-31
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-21
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-16
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-32
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-29
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-22
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-22
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-32
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-21
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-19
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-17
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	6e-31
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	9e-22
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-18
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-16
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-31
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-29
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	9e-29
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-12
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-29
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-24
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	7e-21
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-18
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-28
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-23
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-19
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	5e-18
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-28
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-26
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-20
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-19
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-28
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-24
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-22
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-20
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-27
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-24
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-17
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-15
2div_A	99	TRNA selenocysteine associated protein; structural	3e-27
2div_A	99	TRNA selenocysteine associated protein; structural	1e-17
2div_A	99	TRNA selenocysteine associated protein; structural	2e-17
2div_A	99	TRNA selenocysteine associated protein; structural	2e-16
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-26
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-24
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-17
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-26
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-21
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-21
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	9e-21
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-26
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-18
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-18
1x5p_A	97	Negative elongation factor E; structure genomics,	3e-13
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-26
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	5e-25
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-21
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-19
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	8e-26
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-25
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	7e-22
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-16
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-25
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-20
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-16
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-15
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-25
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-18
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-17
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-15
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	7e-25
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-22
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-19
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-15
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-24
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-24
1x4e_A	85	RNA binding motif, single-stranded interacting pro	8e-22
1x4e_A	85	RNA binding motif, single-stranded interacting pro	9e-18
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-24
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	9e-22
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-17
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-16
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	7e-24
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-23
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	8e-14
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-23
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-17
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-16
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-15
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-23
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-21
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-17
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-16
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-23
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-22
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-22
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-20
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-23
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-22
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-18
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-18
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-23
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	9e-21
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-16
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-16
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	9e-23
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-22
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	6e-18
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-17
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-22
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-20
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-16
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-15
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	6e-22
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-21
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-17
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-17
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-21
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-21
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-19
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-16
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-21
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-21
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-18
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-17
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-21
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-21
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-18
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	6e-18
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-21
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-20
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-16
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	6e-16
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-21
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	8e-19
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-16
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	9e-15
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-21
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-20
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-18
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-17
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-21
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	5e-18
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-16
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-21
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	9e-20
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-18
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	8e-18
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	8e-21
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	8e-18
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-16
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-13
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	8e-21
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	6e-20
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	9e-17
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-14
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-20
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-19
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-18
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	5e-18
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-20
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-20
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	7e-17
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	8e-17
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-20
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	6e-20
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	7e-17
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-16
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-20
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-18
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-18
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-17
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-20
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-19
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-17
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-16
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-20
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-20
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-19
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-19
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-20
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-19
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-18
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-17
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-20
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	8e-19
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-18
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-17
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	9e-20
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	6e-19
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	6e-16
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	6e-16
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	9e-20
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-18
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-16
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-14
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-19
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-17
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-15
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-19
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-18
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	9e-17
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-16
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-19
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-15
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-11
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-19
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	8e-19
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-13
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-10
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-19
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	9e-19
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-15
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-13
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-19
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-19
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-16
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-15
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-19
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-18
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-16
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-15
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	8e-19
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-18
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	8e-15
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-14
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-18
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-16
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-14
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-12
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-18
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	7e-17
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-15
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-15
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-18
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-17
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-13
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-11
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-18
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-16
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-15
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-15
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-18
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	7e-16
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-09
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-18
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	8e-17
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	7e-16
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-15
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-18
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-17
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-13
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-11
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-18
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	8e-18
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	8e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-13
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	5e-18
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-15
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	6e-13
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	7e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	6e-18
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-17
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-14
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-11
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	8e-18
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-15
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-14
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-14
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-17
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-17
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-14
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-17
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-17
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-13
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	9e-11
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-17
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	4e-15
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	8e-12
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	7e-11
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-17
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-17
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-17
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-16
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-17
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-16
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-13
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-17
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-16
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-12
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-10
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-17
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-16
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-15
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-14
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	9e-17
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-15
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	4e-13
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-08
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-16
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	6e-14
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-13
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-12
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-16
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	6e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	4e-16
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	4e-10
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	5e-09
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	4e-16
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-14
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	4e-11
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	9e-07
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-16
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	9e-15
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	8e-12
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-16
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-15
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-15
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-13
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	6e-16
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	4e-14
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	6e-12
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	4e-08
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	8e-16
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	6e-15
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-13
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	7e-10
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-15
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	9e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-08
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-15
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-12
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-11
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-10
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-15
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-15
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	4e-14
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-13
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-15
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-14
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-11
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-06
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-15
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-14
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-11
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	4e-08
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-15
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	9e-15
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-12
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	4e-08
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-15
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	9e-12
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-11
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-06
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-15
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	7e-14
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	8e-13
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	5e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-15
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-14
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-12
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-15
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-14
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-10
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-09
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	7e-15
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-13
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-10
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	9e-05
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-14
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	4e-14
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	7e-12
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	4e-11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-14
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	9e-14
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	5e-11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-14
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-11
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	8e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-14
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-11
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-14
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	4e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-14
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	5e-14
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-11
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-10
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-14
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	3e-12
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-11
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	8e-14
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-13
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-11
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	8e-11
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-13
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	8e-11
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-07
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-13
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-12
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	8e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-10
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-13
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	6e-13
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-10
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-04
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-13
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-13
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-12
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	6e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-13
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	6e-11
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	8e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-08
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-13
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-10
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-13
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	8e-12
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-11
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	5e-13
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	6e-13
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	9e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	6e-13
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-10
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	6e-13
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-12
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-09
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-13
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-11
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-12
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-10
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-10
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	9e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-12
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-10
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	6e-12
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-11
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	8e-10
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	9e-12
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-10
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-09
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-11
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-11
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	8e-11
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-09
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-11
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-09
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-09
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	8e-09
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-11
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-10
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-10
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-07
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	1e-09
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-07
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	5e-04
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	8e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-09
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-08
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	9e-07
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	9e-09
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	3e-07
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	9e-09
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	3e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	5e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	1e-04
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	7e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	5e-07
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-05
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-08
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-08
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-06
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	2e-08
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	3e-07
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	4e-06
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	4e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-05
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	2e-06
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	4e-06
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	3e-05
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	8e-05
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	2e-05
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	2e-05
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	2e-04
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	4e-05
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	6e-05
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	6e-05
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	1e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	2e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	5e-04
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	2e-04
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	2e-04
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	7e-04

>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 =  361 bits (928), Expect = e-124
 Identities = 65/312 (20%), Positives = 117/312 (37%), Gaps = 37/312 (11%)

Query: 106 LNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLG 165
           L+ + IR    + +   +      I I+ L   + N+ +HD  S +  +  C V      
Sbjct: 3   LDPEEIRKRLEHTER--QFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----D 54

Query: 166 QSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKN 225
           + +G  FV   N E A++AI+  +   L ++++ V              +     + V N
Sbjct: 55  KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL------------QPTDALLCVAN 102

Query: 226 LSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKF 284
           L  + T+   +++   FG +    ++     G+SK +GF  +   D AAR+   L GK  
Sbjct: 103 LPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL 162

Query: 285 DDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISD-DKLKELFS 343
             +  YV            L  +                L V  L    +D D L    S
Sbjct: 163 GPRTLYVHWTDAGQLTPALLHSR---------------CLCVDRLPPGFNDVDALCRALS 207

Query: 344 EFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEER 403
              + T C++    +G  +G   + + TAE A +A  + +G  +    L V+        
Sbjct: 208 AVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG 267

Query: 404 RARLQAQFSQMR 415
           R+ L A  +   
Sbjct: 268 RSMLAALIAAQA 279

>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 =  268 bits (688), Expect = 1e-87
 Identities = 45/274 (16%), Positives = 92/274 (33%), Gaps = 20/274 (7%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              + +  L   V + +++DL +    +    V       +  G  +V      +A  A+
Sbjct: 22  RRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAI 74

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCK 158
           +  + + L  + + +     D          + + NL  S+  +   +    FG++  C 
Sbjct: 75  NAFHQSRLRERELSVQLQPTDA--------LLCVANLPPSLTQQQFEELVRPFGSLERCF 126

Query: 159 VATDSL-GQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTR 217
           +      GQS+GYGF ++  ++SA  A   L G  L  + ++V      Q   +      
Sbjct: 127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALL---H 183

Query: 218 FNNVYVKNLSETTTEDD-LKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSV 276
              + V  L     + D L +        T   +    DG+ K F  + ++  + A  + 
Sbjct: 184 SRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQ 243

Query: 277 EALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQ 310
           +  +G         V            L      
Sbjct: 244 QQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAA 277

>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 =  361 bits (929), Expect = e-124
 Identities = 63/328 (19%), Positives = 134/328 (40%), Gaps = 44/328 (13%)

Query: 80  SLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDP---TIRKSGAGNIFIKNLD 136
           S+ YG+   +A  ++ R LDE       G P     + +       R      + +KNL 
Sbjct: 1   SMEYGH---HARPDSKRPLDE-------GSPAAAGLTSKKANEALTRNRELTTVLVKNLP 50

Query: 137 KSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDK 196
           KS +   ++  F   G I+   VA     ++  +  ++F   + A +AI K + + +   
Sbjct: 51  KSYNQNKVYKYFKHCGPIIHVDVADSL-KKNFRFARIEFARYDGALAAITKTHKV-VGQN 108

Query: 197 QVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVM-RDAD 255
           ++ V                    +++ N   + T+ +++ +  +  ++  +  +     
Sbjct: 109 EIIVSHL-------------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF 155

Query: 256 GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKET 315
             S+ F +++    +DA   VE LNG K +                 ++    E+S +  
Sbjct: 156 NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVT-----------KVSNPLEKSKRTD 204

Query: 316 ADKFEGLNLYVKNLDDSISDDK-LKELFSEFGTITSCKVMRD--PNGISRGSGFVAFSTA 372
           +   EG  + ++NL   + D+  L+E F  FG+I    +      +  +    F+ F   
Sbjct: 205 SATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENK 264

Query: 373 EEASKALTEMNGKMVVSKPLYVALAQRK 400
           + A +AL +MN  ++ ++ + V+LA +K
Sbjct: 265 DSAERAL-QMNRSLLGNREISVSLADKK 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 =  237 bits (608), Expect = 1e-75
 Identities = 52/264 (19%), Positives = 111/264 (42%), Gaps = 20/264 (7%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T++ V +L  S N +++Y  F   G ++ V V      +++  +  + +     A  A+ 
Sbjct: 42  TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAIT 99

Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNI-LSCK 158
           + +   +    I + +              +++ N   S   + + D       + LS +
Sbjct: 100 KTHKV-VGQNEIIVSHLTEC---------TLWMTNFPPSYTQRNIRDLLQDINVVALSIR 149

Query: 159 VATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVG--PFLRKQERESTADKT 216
           + +     SR + ++   ++E A+  ++KLNG+ +    +       L K +R  +A   
Sbjct: 150 LPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSA-TL 208

Query: 217 RFNNVYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDAD--GKSKCFGFVNFDDPDDAA 273
               + ++NLS E   E+ L++ F  FG I    +         + C  F+ F++ D A 
Sbjct: 209 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 268

Query: 274 RSVEALNGKKFDDKEWYVGKAQKK 297
           R+++ +N     ++E  V  A KK
Sbjct: 269 RALQ-MNRSLLGNREISVSLADKK 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 =  178 bits (453), Expect = 1e-52
 Identities = 38/248 (15%), Positives = 79/248 (31%), Gaps = 40/248 (16%)

Query: 167 SRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNL 226
           S  YG         +K  +D+ +                K+  E+         V VKNL
Sbjct: 1   SMEYGHH---ARPDSKRPLDEGSPAAAGLTS--------KKANEALTRNRELTTVLVKNL 49

Query: 227 SETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDD 286
            ++  ++ + K F   G I    V      K+  F  + F   D A  ++   +      
Sbjct: 50  PKSYNQNKVYKYFKHCGPIIHVDVADS-LKKNFRFARIEFARYDGALAAITKTHKV-VGQ 107

Query: 287 KEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFG 346
            E  V    +                           L++ N   S +   +++L  +  
Sbjct: 108 NEIIVSHLTEC-------------------------TLWMTNFPPSYTQRNIRDLLQDIN 142

Query: 347 TIT-SCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRA 405
            +  S ++       SR   ++  ++ E+A   + ++NG  +    L   ++    E+  
Sbjct: 143 VVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS-NPLEKSK 201

Query: 406 RLQAQFSQ 413
           R  +   +
Sbjct: 202 RTDSATLE 209

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

 Score =  152 bits (385), Expect = 7e-43
 Identities = 34/187 (18%), Positives = 74/187 (39%), Gaps = 9/187 (4%)

Query: 28  NGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVN 87
                        +L++ +   S     + DL   +  V        L    S  + Y++
Sbjct: 106 GQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYID 165

Query: 88  YNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAG-----NIFIKNLDKSI-DN 141
             +  +A   +++LN   + G  +    S      +++ +       I I+NL   + D 
Sbjct: 166 VTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDE 225

Query: 142 KALHDTFSTFGNILSCKVATD--SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVF 199
             L ++F  FG+I    +         +    F+ F+N++SA+ A+ ++N  LL ++++ 
Sbjct: 226 NLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREIS 284

Query: 200 VGPFLRK 206
           V    +K
Sbjct: 285 VSLADKK 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 = 73.5 bits (181), Expect = 1e-14
 Identities = 14/90 (15%), Positives = 34/90 (37%), Gaps = 3/90 (3%)

Query: 33  DARQFVSTSLYVGDLDLSVNDSQ-LYDLFNQMGQVVSVRVCRDL-STRRSLGYGYVNYNA 90
           D+       + + +L   + D   L + F   G +  + +         +    ++ +  
Sbjct: 204 DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFEN 263

Query: 91  AHEATRALDELNFTPLNGKPIRIMYSYRDP 120
              A RAL ++N + L  + I +  + + P
Sbjct: 264 KDSAERAL-QMNRSLLGNREISVSLADKKP 292

>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 =  287 bits (736), Expect = 5e-96
 Identities = 113/215 (52%), Positives = 146/215 (67%), Gaps = 11/215 (5%)

Query: 33  DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAH 92
            A  +   SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    
Sbjct: 9   SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 68

Query: 93  EATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFG 152
           +A RALD +NF  + GKP+RIM+S RDP++RKSG GNIFIKNLDKSIDNKAL+DTFS FG
Sbjct: 69  DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 128

Query: 153 NILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST 212
           NILSCKV  D    S+GYGFV F+ +E+A+ AI+K+NGMLLND++VFVG F  ++ERE+ 
Sbjct: 129 NILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 187

Query: 213 ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITS 247
               R    Y  +         +    G  G I +
Sbjct: 188 LGA-RAKEFYPYD---------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 =  196 bits (500), Expect = 1e-60
 Identities = 67/216 (31%), Positives = 103/216 (47%), Gaps = 18/216 (8%)

Query: 208 ERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNF 266
               +A      ++YV +L    TE  L + F   G I S  V RD    +S  + +VNF
Sbjct: 5   SMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNF 64

Query: 267 DDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYV 326
             P DA R+++ +N      K   +  +Q+                  +  K    N+++
Sbjct: 65  QQPADAERALDTMNFDVIKGKPVRIMWSQRD----------------PSLRKSGVGNIFI 108

Query: 327 KNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKM 386
           KNLD SI +  L + FS FG I SCKV+ D NG S+G GFV F T E A +A+ +MNG +
Sbjct: 109 KNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGML 167

Query: 387 VVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPRM 422
           +  + ++V   + ++ER A L A+  +  P   P  
Sbjct: 168 LNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDY 203

>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 =  190 bits (485), Expect = 2e-58
 Identities = 56/209 (26%), Positives = 106/209 (50%), Gaps = 6/209 (2%)

Query: 116 SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQ 174
              +P+       ++++ +L   +    L++ FS  G ILS +V  D +  +S GY +V 
Sbjct: 4   GSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 63

Query: 175 FDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDD 234
           F     A+ A+D +N  ++  K V +       +R+ +  K+   N+++KNL ++     
Sbjct: 64  FQQPADAERALDTMNFDVIKGKPVRIM----WSQRDPSLRKSGVGNIFIKNLDKSIDNKA 119

Query: 235 LKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA 294
           L   F  FG I S  V+ D +  SK +GFV+F+  + A R++E +NG   +D++ +VG+ 
Sbjct: 120 LYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 178

Query: 295 QKKYEREMELKGKFEQSLKETADKFEGLN 323
           + + ERE EL  + ++        + G +
Sbjct: 179 KSRKEREAELGARAKEFYPYDVPDYAGSS 207

>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 =  249 bits (639), Expect = 6e-82
 Identities = 46/162 (28%), Positives = 89/162 (54%), Gaps = 2/162 (1%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
            LYVG+LD ++ +  L   F   G + ++++  D    +++ Y +V Y+ +H+A  AL  
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQT 60

Query: 101 LNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVA 160
           LN   +    ++I ++++          N+F+ +L+ ++D++ L + F  F + LS  V 
Sbjct: 61  LNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVM 120

Query: 161 TDSL-GQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVG 201
            D   G SRGYGFV F +++ A++A+D + G  LN + + + 
Sbjct: 121 WDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 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 =  193 bits (493), Expect = 3e-60
 Identities = 51/180 (28%), Positives = 91/180 (50%), Gaps = 17/180 (9%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV NL +  TED LK+ F   G I +  +M D + K+  + FV +    DA  +++ LN
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 281 GKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKE 340
           GK+ ++    +  A +  +   +                +  NL+V +L+ ++ D+ L+ 
Sbjct: 63  GKQIENNIVKINWAFQSQQSSSD----------------DTFNLFVGDLNVNVDDETLRN 106

Query: 341 LFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR 399
            F +F +  S  VM D   G SRG GFV+F++ ++A  A+  M G+ +  +PL +  A +
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>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 =  167 bits (425), Expect = 4e-50
 Identities = 42/168 (25%), Positives = 78/168 (46%), Gaps = 5/168 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +++ NLDK+I    L   F   G I + K+  D   ++  Y FV++     A  A+  LN
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 190 GMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTA 249
           G  + +  V +        +   +      N++V +L+    ++ L+  F +F    S  
Sbjct: 63  GKQIENNIVKIN----WAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118

Query: 250 VMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQK 296
           VM D   G S+ +GFV+F   DDA  +++++ G+  + +   +  A K
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>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 =  100 bits (251), Expect = 4e-25
 Identities = 26/81 (32%), Positives = 45/81 (55%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LYV NLD +I++D LK+ F   G I + K+M D N  +    FV +  + +A+ AL  +N
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 384 GKMVVSKPLYVALAQRKEERR 404
           GK + +  + +  A + ++  
Sbjct: 63  GKQIENNIVKINWAFQSQQSS 83

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 90.7 bits (226), Expect = 1e-21
 Identities = 27/78 (34%), Positives = 48/78 (61%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L+VGDL+++V+D  L + F      +S  V  D+ T  S GYG+V++ +  +A  A+D 
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148

Query: 101 LNFTPLNGKPIRIMYSYR 118
           +    LNG+P+RI ++ +
Sbjct: 149 MQGQDLNGRPLRINWAAK 166

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

 Score =  246 bits (630), Expect = 5e-80
 Identities = 47/203 (23%), Positives = 99/203 (48%), Gaps = 16/203 (7%)

Query: 106 LNGKPIRIMYSYRDPTIRKSGA----GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVAT 161
             G+ +      R    ++ GA      +++ ++   +    +   F+ FG I S  ++ 
Sbjct: 8   TGGQQMG-----RGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSW 62

Query: 162 DSL-GQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTR--- 217
           DS+  + +G+ FV+++  E+A+ A++++N ++L  + + VG      + +   D+     
Sbjct: 63  DSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEA 122

Query: 218 --FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAAR 274
             FN +YV ++ +  ++DD+K +F  FG I S  + RD   GK K +GF+ ++    +  
Sbjct: 123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQD 182

Query: 275 SVEALNGKKFDDKEWYVGKAQKK 297
           +V ++N      +   VGKA   
Sbjct: 183 AVSSMNLFDLGGQYLRVGKAVTP 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 =  227 bits (582), Expect = 8e-73
 Identities = 56/244 (22%), Positives = 100/244 (40%), Gaps = 34/244 (13%)

Query: 190 GMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTA 249
             +   +Q+  G   ++Q   +       + VYV ++     ED +++ F  FG I S  
Sbjct: 5   ASMTGGQQMGRGSAAQRQGALAI-----MSRVYVGSIYYELGEDTIRQAFAPFGPIKSID 59

Query: 250 VMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKF 308
           +  D+   K K F FV ++ P+ A  ++E +N      +   VG+     + +  +    
Sbjct: 60  MSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLA 119

Query: 309 EQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFV 367
           E++            +YV ++   +SDD +K +F  FG I S  + RDP  G  +G GF+
Sbjct: 120 EEARAFN-------RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFI 172

Query: 368 AFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPRMPMYPP 427
            +  A+ +  A++ MN   +  + L V  A                        MP+  P
Sbjct: 173 EYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP--------------------PMPLLTP 212

Query: 428 VAPG 431
             PG
Sbjct: 213 ATPG 216

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

 Score =  194 bits (495), Expect = 8e-60
 Identities = 47/223 (21%), Positives = 91/223 (40%), Gaps = 24/223 (10%)

Query: 1   MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLF 60
           MA +    Q     AAQ   A   ++               +YVG +   + +  +   F
Sbjct: 4   MASMTGGQQMGRGSAAQRQGALAIMSR--------------VYVGSIYYELGEDTIRQAF 49

Query: 61  NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY--- 117
              G + S+ +  D  T +  G+ +V Y     A  AL+++N   L G+ I++       
Sbjct: 50  APFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIG 109

Query: 118 -RDPTIRKSGAG-----NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGY 170
              P I +          I++ ++ + + +  +   F  FG I S  +A D   G+ +GY
Sbjct: 110 QAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGY 169

Query: 171 GFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTA 213
           GF++++  +S++ A+  +N   L  + + VG  +       T 
Sbjct: 170 GFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTP 212

>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 =  234 bits (598), Expect = 7e-76
 Identities = 53/165 (32%), Positives = 89/165 (53%), Gaps = 5/165 (3%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
            T+L V  L  ++   +   LF  +G++ S ++ RD  T +SLGYG+VNY    +A +A+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCK 158
           + LN   L  K I++ Y+   P+       N+++  L K++  K L   FS +G I++ +
Sbjct: 62  NTLNGLRLQTKTIKVSYA--RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSR 119

Query: 159 VATDSL-GQSRGYGFVQFDNEESAKSAIDKLNGMLLN--DKQVFV 200
           +  D + G SRG GF++FD    A+ AI  LNG   +   + + V
Sbjct: 120 ILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 164

>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 =  196 bits (501), Expect = 2e-61
 Identities = 54/182 (29%), Positives = 92/182 (50%), Gaps = 22/182 (12%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+++ + +FG  G I S  ++RD   G+S  +GFVN+ DP DA +++  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
           LNG +   K   V  A+                           NLYV  L  +++  +L
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASI------------------RDANLYVSGLPKTMTQKEL 105

Query: 339 KELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMV--VSKPLYVA 395
           ++LFS++G I + +++ D   G+SRG GF+ F    EA +A+  +NG+     ++P+ V 
Sbjct: 106 EQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK 165

Query: 396 LA 397
            A
Sbjct: 166 FA 167

>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 =  162 bits (412), Expect = 3e-48
 Identities = 51/170 (30%), Positives = 88/170 (51%), Gaps = 10/170 (5%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+ +  L +++  +     F + G I SCK+  D + GQS GYGFV + + + A+ AI+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 188 LNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITS 247
           LNG+ L  K + V            A      N+YV  L +T T+ +L+++F ++G I +
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASIRDA------NLYVSGLPKTMTQKELEQLFSQYGRIIT 117

Query: 248 TAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFD--DKEWYVGKA 294
           + ++ D   G S+  GF+ FD   +A  +++ LNG+K     +   V  A
Sbjct: 118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>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 =  101 bits (253), Expect = 2e-25
 Identities = 27/82 (32%), Positives = 45/82 (54%), Gaps = 1/82 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NL V  L  +++ ++ + LF   G I SCK++RD   G S G GFV +   ++A KA+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 382 MNGKMVVSKPLYVALAQRKEER 403
           +NG  + +K + V+ A+     
Sbjct: 64  LNGLRLQTKTIKVSYARPSSAS 85

>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 = 80.3 bits (199), Expect = 5e-18
 Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 2/85 (2%)

Query: 33  DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAH 92
            +      +LYV  L  ++   +L  LF+Q G++++ R+  D  T  S G G++ ++   
Sbjct: 82  SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 141

Query: 93  EATRALDELNFTPLNG--KPIRIMY 115
           EA  A+  LN    +G  +PI + +
Sbjct: 142 EAEEAIKGLNGQKPSGATEPITVKF 166

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score =  233 bits (597), Expect = 2e-74
 Identities = 56/277 (20%), Positives = 107/277 (38%), Gaps = 46/277 (16%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
             L+VG+L   + +     LF + G+   V + RD       G+G++   +   A  A  
Sbjct: 23  CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKA 76

Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKV 159
           EL+ T L  +P+RI ++             + +KNL   + N+ L   FS FG +    V
Sbjct: 77  ELDGTILKSRPLRIRFATHGA--------ALTVKNLSPVVSNELLEQAFSQFGPVEKAVV 128

Query: 160 ATDSLGQSRGYGFVQFDNEESAKSAIDKLNG----MLLNDKQVFVGPFLRKQERESTADK 215
             D  G++ G GFV+F  +  A+ A+++       +    + V V P  +  + +   +K
Sbjct: 129 VVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEK 188

Query: 216 T-RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
             +    Y K   +          F + G        R                     +
Sbjct: 189 LMQKTQQYHKEREQPP-------RFAQPGTFEFEYASR--------------------WK 221

Query: 275 SVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQS 311
           +++ +  ++ +  +  + +A++K E EME      Q 
Sbjct: 222 ALDEMEKQQREQVDRNIREAKEKLEAEMEAARHEHQL 258

>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 =  233 bits (596), Expect = 3e-74
 Identities = 51/240 (21%), Positives = 91/240 (37%), Gaps = 37/240 (15%)

Query: 196 KQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD 255
             + +  FL+  E+      T+   ++V NL    TE+D K++F  +G  +   + RD  
Sbjct: 4   FTIDIKSFLKPGEKT----YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-- 57

Query: 256 GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKET 315
              + FGF+  +    A  +   L+G     +   +  A                     
Sbjct: 58  ---RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH------------------- 95

Query: 316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEA 375
                G  L VKNL   +S++ L++ FS+FG +    V+ D  G + G GFV F+    A
Sbjct: 96  -----GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPA 150

Query: 376 SKALTEMNGKMVV----SKPLYVALAQRKEERRARLQAQFSQMRPPVGPRMPMYPPVAPG 431
            KAL        +     +P+ V   ++ ++     +    + +     R        PG
Sbjct: 151 RKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPG 210

>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 =  186 bits (473), Expect = 5e-56
 Identities = 44/256 (17%), Positives = 95/256 (37%), Gaps = 40/256 (15%)

Query: 108 GKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQS 167
           G  I I    +      +    +F+ NL   I  +     F  +G      +  D     
Sbjct: 3   GFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD----- 57

Query: 168 RGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLS 227
           RG+GF++ ++   A+ A  +L+G +L  + + +    R     +         + VKNLS
Sbjct: 58  RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI----RFATHGA--------ALTVKNLS 105

Query: 228 ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKF--- 284
              + + L++ F +FG +    V+ D  G++   GFV F     A +++E      F   
Sbjct: 106 PVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLT 165

Query: 285 -DDKEWYVGKAQKKYEREMELKGKFEQSLK-------------------ETADKFEGLNL 324
              +   V   ++  + +   +   +++ +                   E A +++ L+ 
Sbjct: 166 TTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRWKALDE 225

Query: 325 YVKNLDDSISDDKLKE 340
             K   + +  +  + 
Sbjct: 226 MEKQQREQVDRNIREA 241

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 67.4 bits (165), Expect = 7e-13
 Identities = 25/126 (19%), Positives = 44/126 (34%), Gaps = 5/126 (3%)

Query: 31  VGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNA 90
           +  A      +L V +L   V++  L   F+Q G V    V  D    R+ G G+V + A
Sbjct: 90  IRFATH--GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAA 146

Query: 91  AHEATRALDELN-FTPLNGKPIRIMY-SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTF 148
              A +AL+       L     R +     +    + G     ++   +    +     F
Sbjct: 147 KPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRF 206

Query: 149 STFGNI 154
           +  G  
Sbjct: 207 AQPGTF 212

>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 =  221 bits (566), Expect = 5e-71
 Identities = 45/184 (24%), Positives = 82/184 (44%), Gaps = 20/184 (10%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG---KSKCFGFVNFDDPDDAARSV 276
            ++V  +  T +E DL+++F ++G +    V+RD      +SK   FV F     A  + 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 277 EALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDD 336
            AL+  K      +  + +                  E  +  E   L++  +    +++
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADS--------------EKNNAVEDRKLFIGMISKKCTEN 110

Query: 337 KLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVV---SKPLY 393
            ++ +FS FG I  C+++R P+G+SRG  FV F+T   A  A+  M+    +   S P+ 
Sbjct: 111 DIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 170

Query: 394 VALA 397
           V  A
Sbjct: 171 VKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  190 bits (485), Expect = 6e-59
 Identities = 37/163 (22%), Positives = 73/163 (44%), Gaps = 5/163 (3%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLG---QSRGYGFVQFDNEESA 181
           S A  +F+  + ++   K L + F  +G +    V  D      QS+G  FV F   ++A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 182 KSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGE 241
             A + L+ M +          ++  + E   +      +++  +S+  TE+D++ +F  
Sbjct: 61  LEAQNALHNMKVLPGMHHPI-QMKPADSEKN-NAVEDRKLFIGMISKKCTENDIRVMFSS 118

Query: 242 FGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKF 284
           FG I    ++R  DG S+   FV F     A  +++A++  + 
Sbjct: 119 FGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQT 161

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  160 bits (406), Expect = 3e-47
 Identities = 42/170 (24%), Positives = 71/170 (41%), Gaps = 9/170 (5%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLST--RRSLGYGYVNYNAAHEATR 96
           +  ++VG +  + ++  L +LF Q G V  + V RD S    +S G  +V +     A  
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62

Query: 97  ALDELN---FTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
           A + L+     P    PI++  +  +          +FI  + K      +   FS+FG 
Sbjct: 63  AQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDR-KLFIGMISKKCTENDIRVMFSSFGQ 121

Query: 154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNG---MLLNDKQVFV 200
           I  C++     G SRG  FV F     A++AI  ++    M      + V
Sbjct: 122 IEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 171

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 99.6 bits (249), Expect = 1e-24
 Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 3/87 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG---ISRGSGFVAFSTAEEASKAL 379
            ++V  +  + S+  L+ELF ++G +    V+RD +     S+G  FV F T + A +A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 380 TEMNGKMVVSKPLYVALAQRKEERRAR 406
             ++   V+    +    +  +  +  
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADSEKNN 91

>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 = 67.3 bits (165), Expect = 2e-13
 Identities = 13/82 (15%), Positives = 30/82 (36%), Gaps = 4/82 (4%)

Query: 35  RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEA 94
                  L++G +     ++ +  +F+  GQ+   R+ R      S G  +V +     A
Sbjct: 91  NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMA 149

Query: 95  TRALDELN---FTPLNGKPIRI 113
             A+  ++          P+ +
Sbjct: 150 QTAIKAMHQAQTMEGCSSPMVV 171

>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 =  218 bits (558), Expect = 6e-70
 Identities = 47/165 (28%), Positives = 86/165 (52%), Gaps = 5/165 (3%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           +T+L V  L   + D +LY LF  +G + + R+ RD  T  S GY +V++ +  ++ RA+
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCK 158
             LN   +  K +++ Y+   P        N+++ NL ++I +  L   F  +G+I+   
Sbjct: 63  KVLNGITVRNKRLKVSYA--RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 120

Query: 159 VATDSL-GQSRGYGFVQFDNEESAKSAIDKLNGMLLN--DKQVFV 200
           +  D L G+ RG  FV+++  E A+ AI  LN ++     + + V
Sbjct: 121 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165

>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 =  213 bits (546), Expect = 4e-68
 Identities = 56/182 (30%), Positives = 89/182 (48%), Gaps = 22/182 (12%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+ +L  +F   G I +  +MRD   G S  + FV+F    D+ R+++ 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKL 338
           LNG    +K   V  A+   E                    +  NLYV NL  +I+DD+L
Sbjct: 65  LNGITVRNKRLKVSYARPGGESI------------------KDTNLYVTNLPRTITDDQL 106

Query: 339 KELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMV--VSKPLYVA 395
             +F ++G+I    ++RD   G  RG  FV ++  EEA +A++ +N  +    S+PL V 
Sbjct: 107 DTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR 166

Query: 396 LA 397
           LA
Sbjct: 167 LA 168

>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 =  181 bits (462), Expect = 1e-55
 Identities = 49/174 (28%), Positives = 84/174 (48%), Gaps = 10/174 (5%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKS 183
           +   N+ +  L + + ++ L+  F   G I +C++  D   G S GY FV F +E  ++ 
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60

Query: 184 AIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFG 243
           AI  LNG+ + +K++ V       E           N+YV NL  T T+D L  IFG++G
Sbjct: 61  AIKVLNGITVRNKRLKVSYARPGGESIKDT------NLYVTNLPRTITDDQLDTIFGKYG 114

Query: 244 IITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFD--DKEWYVGKA 294
            I    ++RD   G+ +   FV ++  ++A  ++ ALN    +   +   V  A
Sbjct: 115 SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>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 =  109 bits (274), Expect = 2e-28
 Identities = 29/86 (33%), Positives = 45/86 (52%), Gaps = 1/86 (1%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKA 378
              NL V  L   ++D +L  LF   G I +C++MRD   G S G  FV F++  ++ +A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 379 LTEMNGKMVVSKPLYVALAQRKEERR 404
           +  +NG  V +K L V+ A+   E  
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESI 87

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 81.1 bits (201), Expect = 3e-18
 Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 33  DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAH 92
                  T+LYV +L  ++ D QL  +F + G +V   + RD  T R  G  +V YN   
Sbjct: 83  GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 142

Query: 93  EATRALDELNFTPLNG--KPIRI 113
           EA  A+  LN     G  +P+ +
Sbjct: 143 EAQEAISALNNVIPEGGSQPLSV 165

>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 =  217 bits (554), Expect = 3e-69
 Identities = 42/182 (23%), Positives = 78/182 (42%), Gaps = 9/182 (4%)

Query: 116 SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQF 175
           S+       +   N+FI NL+ +     L    S         V     G +R +G+V F
Sbjct: 2   SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 61

Query: 176 DNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDL 235
           ++ E  + A+ +L G+ +   ++ +     +  ++  A       +  KNLS   TED+L
Sbjct: 62  ESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRA----ARTLLAKNLSFNITEDEL 116

Query: 236 KKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQ 295
           K++F +   I     +   DGKSK   ++ F    DA +++E   G + D +   +    
Sbjct: 117 KEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 172

Query: 296 KK 297
           +K
Sbjct: 173 EK 174

>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 =  208 bits (533), Expect = 5e-66
 Identities = 42/194 (21%), Positives = 83/194 (42%), Gaps = 21/194 (10%)

Query: 207 QERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNF 266
                 ++ T   N+++ NL+   +  +LK    E       AV+    G ++ FG+V+F
Sbjct: 2   SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 61

Query: 267 DDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYV 326
           +  +D  +++E L G K    E  + K + +  +++                     L  
Sbjct: 62  ESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVR----------------AARTLLA 104

Query: 327 KNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKM 386
           KNL  +I++D+LKE+F +   I     +   +G S+G  ++ F +  +A K L E  G  
Sbjct: 105 KNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 160

Query: 387 VVSKPLYVALAQRK 400
           +  + + +     K
Sbjct: 161 IDGRSVSLYYTGEK 174

>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 =  170 bits (432), Expect = 5e-51
 Identities = 32/163 (19%), Positives = 77/163 (47%), Gaps = 6/163 (3%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             +L++G+L+ + + ++L    +++     + V     T  +  +GYV++ +A +  +AL
Sbjct: 13  PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKAL 71

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCK 158
            EL    + G  I++       + +   A  +  KNL  +I    L + F     I   +
Sbjct: 72  -ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI---R 127

Query: 159 VATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVG 201
           + +   G+S+G  +++F +E  A+  +++  G  ++ + V + 
Sbjct: 128 LVSQD-GKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY 169

>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 =  109 bits (274), Expect = 3e-28
 Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 1/93 (1%)

Query: 314 ETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAE 373
           E ++     NL++ NL+ + S  +LK   SE        V+    G +R  G+V F +AE
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 65

Query: 374 EASKALTEMNGKMVVSKPLYVALAQRKEERRAR 406
           +  KAL E+ G  V    + +   + ++ ++ R
Sbjct: 66  DLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVR 97

>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 = 73.4 bits (181), Expect = 2e-15
 Identities = 13/80 (16%), Positives = 37/80 (46%), Gaps = 5/80 (6%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           + +L   +L  ++ + +L ++F    ++  V         +S G  Y+ + +  +A + L
Sbjct: 99  ARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNL 153

Query: 99  DELNFTPLNGKPIRIMYSYR 118
           +E     ++G+ + + Y+  
Sbjct: 154 EEKQGAEIDGRSVSLYYTGE 173

>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 =  193 bits (493), Expect = 8e-60
 Identities = 38/191 (19%), Positives = 77/191 (40%), Gaps = 10/191 (5%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITS------TAVMRDADGKSKCFGFVNFDDPDDAAR 274
           +YV N+    TE+ +   F     +          V+     + K F F+ F   D+  +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 275 SVEALNGKKFDDKEWYVGKAQKKYEREM--ELKGKFEQSLKETADKFEGLNLYVKNLDDS 332
           ++ A +G  F  +   + +           E    +   +  T        L++  L + 
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125

Query: 333 ISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEMNGKMVVSKP 391
           ++DD++KEL + FG + +  +++D   G+S+G  F  +       +A+  +NG  +  K 
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185

Query: 392 LYVALAQRKEE 402
           L V  A    +
Sbjct: 186 LLVQRASVGAK 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 =  159 bits (403), Expect = 1e-46
 Identities = 31/192 (16%), Positives = 79/192 (41%), Gaps = 22/192 (11%)

Query: 127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS------LGQSRGYGFVQFDNEES 180
           A  +++ N+   I  +A+ D F+    +     A  +      + Q + + F++F + + 
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTR--------------FNNVYVKNL 226
              A+   +G++   + + +      Q     ++                  + +++  L
Sbjct: 64  TTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGL 122

Query: 227 SETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFD 285
                +D +K++   FG + +  +++D+  G SK + F  + D +   +++  LNG +  
Sbjct: 123 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG 182

Query: 286 DKEWYVGKAQKK 297
           DK+  V +A   
Sbjct: 183 DKKLLVQRASVG 194

>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 =  153 bits (388), Expect = 2e-44
 Identities = 36/187 (19%), Positives = 77/187 (41%), Gaps = 25/187 (13%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSV-----RVCRDLSTRRSLGYGYVNYNAAHE 93
           +  LYVG++   + +  + D FN   ++  +          +   +   + ++ + +  E
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 94  ATRALDELNFTPLNGKPIRIMYSY------------------RDPTIRKSGAGNIFIKNL 135
            T+A+   +     G+ ++I   +                     T+    A  +FI  L
Sbjct: 64  TTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGL 122

Query: 136 DKSIDNKALHDTFSTFGNILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKLNGMLLN 194
              +++  + +  ++FG + +  +  DS  G S+GY F ++ +      AI  LNGM L 
Sbjct: 123 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG 182

Query: 195 DKQVFVG 201
           DK++ V 
Sbjct: 183 DKKLLVQ 189

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 82.8 bits (205), Expect = 1e-18
 Identities = 21/97 (21%), Positives = 39/97 (40%)

Query: 17  QPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLS 76
                   +   G V       +  L++G L   +ND Q+ +L    G + +  + +D +
Sbjct: 92  PGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA 151

Query: 77  TRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI 113
           T  S GY +  Y   +   +A+  LN   L  K + +
Sbjct: 152 TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 188

>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 = 81.2 bits (201), Expect = 5e-18
 Identities = 15/109 (13%), Positives = 39/109 (35%), Gaps = 7/109 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCK------VMRDPNGISRGSGFVAFSTAEEASK 377
           LYV N+   I+++ + + F+    +          V+       +   F+ F + +E ++
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 378 ALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPRMPMYP 426
           A+   +G +   + L +      +      +     +   V   +P   
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSA 114

>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 =  187 bits (477), Expect = 9e-58
 Identities = 34/169 (20%), Positives = 76/169 (44%), Gaps = 9/169 (5%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSV-----RVCRDLSTRRSLGYGYVNYNAAHE 93
           +  LYVG++   + +  + D FN   ++  +          +   +   + ++ + +  E
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63

Query: 94  ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN 153
            T+A+   +     G+ ++I   +    +  +    +FI  L   +++  + +  ++FG 
Sbjct: 64  TTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAH--KLFIGGLPNYLNDDQVKELLTSFGP 120

Query: 154 ILSCKVATDS-LGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVG 201
           + +  +  DS  G S+GY F ++ +      AI  LNGM L DK++ V 
Sbjct: 121 LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 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 =  155 bits (394), Expect = 1e-45
 Identities = 36/184 (19%), Positives = 72/184 (39%), Gaps = 26/184 (14%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTA------VMRDADGKSKCFGFVNFDDPDDAAR 274
           +YV N+    TE+ +   F     +          V+     + K F F+ F   D+  +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 275 SVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSIS 334
           ++ A +G  F  +   + +                              L++  L + ++
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDY------------------QPLPGAHKLFIGGLPNYLN 107

Query: 335 DDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY 393
           DD++KEL + FG + +  +++D   G+S+G  F  +       +A+  +NG  +  K L 
Sbjct: 108 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167

Query: 394 VALA 397
           V  A
Sbjct: 168 VQRA 171

>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 =  154 bits (392), Expect = 3e-45
 Identities = 31/177 (17%), Positives = 77/177 (43%), Gaps = 14/177 (7%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS------LGQSRGYGFVQFDNE 178
             A  +++ N+   I  +A+ D F+    +     A  +      + Q + + F++F + 
Sbjct: 2   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 179 ESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKI 238
           +    A+   +G++   + + +      Q           + +++  L     +D +K++
Sbjct: 62  DETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGA------HKLFIGGLPNYLNDDQVKEL 114

Query: 239 FGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA 294
              FG + +  +++D+  G SK + F  + D +   +++  LNG +  DK+  V +A
Sbjct: 115 LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>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 = 72.6 bits (179), Expect = 3e-15
 Identities = 13/87 (14%), Positives = 34/87 (39%), Gaps = 7/87 (8%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCK------VMRDPNGISRGSGFVAFSTAEEASK 377
           LYV N+   I+++ + + F+    +          V+       +   F+ F + +E ++
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 378 ALTEMNGKMVVSKPLYVALAQRKEERR 404
           A+   +G +   + L +      +   
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDYQPLP 92

>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 =  170 bits (433), Expect = 4e-52
 Identities = 67/111 (60%), Positives = 83/111 (74%), Gaps = 3/111 (2%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
            G+GNIFIKNLDKSIDNKAL+DTFS FGNILSCKV  D    S+GYGFV F+ +E+A+ A
Sbjct: 3   LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERA 61

Query: 185 IDKLNGMLLNDKQVFVGPFLRKQEREST--ADKTRFNNVYVKNLSETTTED 233
           I+K+NGMLLND++VFVG F  ++ERE+   A    F NVY+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 =  124 bits (314), Expect = 1e-34
 Identities = 39/91 (42%), Positives = 59/91 (64%), Gaps = 1/91 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           N+++KNLD SI +  L + FS FG I SCKV+ D NG S+G GFV F T E A +A+ +M
Sbjct: 7   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65

Query: 383 NGKMVVSKPLYVALAQRKEERRARLQAQFSQ 413
           NG ++  + ++V   + ++ER A L A+  +
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREAELGARAKE 96

>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 =  124 bits (313), Expect = 2e-34
 Identities = 35/118 (29%), Positives = 62/118 (52%), Gaps = 11/118 (9%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
            N+++KNL ++     L   F  FG I S  V+ D +  SK +GFV+F+  + A R++E 
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEK 64

Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDD 336
           +NG   +D++ +VG+ + + ERE EL  + ++            N+Y+KN     +  
Sbjct: 65  MNGMLLNDRKVFVGRFKSRKEREAELGARAKEF----------TNVYIKNFGPGSTRA 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 = 89.2 bits (222), Expect = 9e-22
 Identities = 31/111 (27%), Positives = 57/111 (51%), Gaps = 8/111 (7%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S ++++ +LD S+++  LYD F+  G ++S +V  D     S GYG+V++     A RA+
Sbjct: 5   SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAI 62

Query: 99  DELNFTPLNGKPIRI-MYSYRDPTIRKSGAG-----NIFIKNLDKSIDNKA 143
           +++N   LN + + +  +  R     + GA      N++IKN        A
Sbjct: 63  EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAA 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 =  163 bits (414), Expect = 3e-49
 Identities = 27/108 (25%), Positives = 49/108 (45%)

Query: 299 EREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN 358
                LK    Q+      + +  NLY+ NL  S+ + +L+ +   FG + S +++RD +
Sbjct: 3   SGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS 62

Query: 359 GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRAR 406
           G SRG GF    + E+    +   NGK + + P   A  +    + + 
Sbjct: 63  GTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSG 110

>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 =  112 bits (283), Expect = 3e-30
 Identities = 20/94 (21%), Positives = 39/94 (41%)

Query: 207 QERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNF 266
           Q + +   +    N+Y+ NL  +  E +L+ +   FG + ST ++RD+ G S+  GF   
Sbjct: 14  QAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARM 73

Query: 267 DDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           +  +     +   NGK            +    +
Sbjct: 74  ESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCK 107

>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 =  109 bits (275), Expect = 4e-29
 Identities = 23/92 (25%), Positives = 42/92 (45%)

Query: 118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDN 177
           +    ++    N++I NL  S+D + L +    FG ++S ++  DS G SRG GF + ++
Sbjct: 16  QMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMES 75

Query: 178 EESAKSAIDKLNGMLLNDKQVFVGPFLRKQER 209
            E  ++ I   NG  +        P      +
Sbjct: 76  TEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCK 107

>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 = 78.8 bits (195), Expect = 4e-18
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
            T+LY+ +L LS+++ +L ++    GQV+S R+ RD S+  S G G+    +  +    +
Sbjct: 25  PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVI 83

Query: 99  DELNFTPLNGKPIRI 113
              N   +   P   
Sbjct: 84  GHFNGKFIKTPPGVS 98

>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 =  166 bits (420), Expect = 3e-48
 Identities = 48/278 (17%), Positives = 93/278 (33%), Gaps = 13/278 (4%)

Query: 129 NIFIKNLDKSID----NKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
            I+I NL++ I      K+L+  FS FG IL   V+     + RG  FV F    SA +A
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRS--LKMRGQAFVIFKEVSSATNA 68

Query: 185 IDKLNGMLLNDKQVFVGPFLRKQERESTADKT--RFNNVYVKNLSETTTEDDLKKIFGEF 242
           +  + G    DK + +       +  +    T    +    K   ++      KK     
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128

Query: 243 GIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREM 302
           G       ++                     +                 G+         
Sbjct: 129 GATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQ 188

Query: 303 ELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISR 362
           +L        +  ++      L++ NL +  ++  L  LF++F      +++   + I  
Sbjct: 189 QLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDI-- 246

Query: 363 GSGFVAFSTAEEASKALTEMNG-KMVVSKPLYVALAQR 399
              FV F    +A  A   + G K+  +  + ++ A++
Sbjct: 247 --AFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282

>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 =  123 bits (309), Expect = 3e-32
 Identities = 49/281 (17%), Positives = 92/281 (32%), Gaps = 30/281 (10%)

Query: 39  STSLYVGDLDLSVND----SQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEA 94
           + ++Y+ +L+  +        LY +F+Q GQ++ + V R L  R   G  +V +     A
Sbjct: 9   NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSA 65

Query: 95  TRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDT------F 148
           T AL  +   P   KP+RI Y+  D  I     G    ++  +        +T       
Sbjct: 66  TNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAV 125

Query: 149 STFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGP------ 202
              G           +                           ++    +  G       
Sbjct: 126 QGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAM 185

Query: 203 ------FLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG 256
                   +    +  ++    + +++ NL E T E  L  +F +F       ++     
Sbjct: 186 PPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD 245

Query: 257 KSKCFGFVNFDDPDDAARSVEALNGKKF-DDKEWYVGKAQK 296
                 FV FD+   A  + +AL G K   +    +  A+K
Sbjct: 246 ----IAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282

>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 =  122 bits (306), Expect = 7e-32
 Identities = 36/136 (26%), Positives = 54/136 (39%), Gaps = 12/136 (8%)

Query: 323 NLYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKA 378
            +Y+ NL++ I  D+LK+    +FS+FG I    V R      RG  FV F     A+ A
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK--MRGQAFVIFKEVSSATNA 68

Query: 379 LTEMNGKMVVSKPLYVALAQRKEERRARLQAQF------SQMRPPVGPRMPMYPPVAPGL 432
           L  M G     KP+ +  A+   +  A+++  F       + R P     P       G 
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128

Query: 433 GQQLFYGQGPPIIPPQ 448
           G     G     +P  
Sbjct: 129 GATPVVGAVQGPVPGM 144

>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 = 92.6 bits (229), Expect = 3e-21
 Identities = 39/229 (17%), Positives = 72/229 (31%), Gaps = 16/229 (6%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNF 266
           +  +    + +Y+ NL+E   +D+LKK    IF +FG I    V R    K +   FV F
Sbjct: 2   AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRS--LKMRGQAFVIF 59

Query: 267 DDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYV 326
            +   A  ++ ++ G  F DK   +  A+   +   ++KG F +  ++            
Sbjct: 60  KEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRK----------RE 109

Query: 327 KNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKM 386
           K    S      K+     G       ++ P                   +        M
Sbjct: 110 KRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGM 169

Query: 387 VVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPRMPMYPPVAPGLGQQ 435
           +    L             +L         P+    P +      L ++
Sbjct: 170 IPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEE 218

>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 =  157 bits (399), Expect = 3e-47
 Identities = 57/97 (58%), Positives = 76/97 (78%), Gaps = 1/97 (1%)

Query: 311 SLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFS 370
           S  +   +++ +NLYVKNLDD I D++L++ FS FGTITS KVM +  G S+G GFV FS
Sbjct: 5   SSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFS 63

Query: 371 TAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARL 407
           + EEA+KA+TEMNG++V +KPLYVALAQRKEER++  
Sbjct: 64  SPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGP 100

>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 =  116 bits (294), Expect = 5e-32
 Identities = 39/101 (38%), Positives = 57/101 (56%), Gaps = 4/101 (3%)

Query: 201 GPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKC 260
           G      +R     + +  N+YVKNL +   ++ L+K F  FG ITS  VM +  G+SK 
Sbjct: 1   GSSGSSGDR---ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKG 56

Query: 261 FGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
           FGFV F  P++A ++V  +NG+    K  YV  AQ+K ER+
Sbjct: 57  FGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQ 97

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score =  110 bits (278), Expect = 9e-30
 Identities = 36/90 (40%), Positives = 56/90 (62%), Gaps = 1/90 (1%)

Query: 122 IRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESA 181
           I +    N+++KNLD  ID++ L   FS FG I S KV  +  G+S+G+GFV F + E A
Sbjct: 10  ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEA 68

Query: 182 KSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
             A+ ++NG ++  K ++V    RK+ER+S
Sbjct: 69  TKAVTEMNGRIVATKPLYVALAQRKEERQS 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 = 87.3 bits (217), Expect = 4e-21
 Identities = 28/96 (29%), Positives = 53/96 (55%), Gaps = 3/96 (3%)

Query: 34  ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
             ++   +LYV +LD  ++D +L   F+  G + S +V  +    RS G+G+V +++  E
Sbjct: 10  ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEE 67

Query: 94  ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
           AT+A+ E+N   +  KP+ +  + R    R+SG  +
Sbjct: 68  ATKAVTEMNGRIVATKPLYVALAQRKEE-RQSGPSS 102

>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 =  155 bits (395), Expect = 2e-46
 Identities = 30/98 (30%), Positives = 52/98 (53%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
            G  ++V NLD  +   KLKE+FS  G +    ++ D +G SRG G V F  + EA +A+
Sbjct: 14  LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAI 73

Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPP 417
           +  NG+++  +P++V + +R   +      +  Q   P
Sbjct: 74  SMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGP 111

>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 =  113 bits (284), Expect = 2e-30
 Identities = 22/92 (23%), Positives = 43/92 (46%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           + V+V NL        LK++F   G++    ++ D DGKS+  G V F+   +A +++  
Sbjct: 16  STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75

Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQ 310
            NG+   D+  +V   ++   +      +  Q
Sbjct: 76  FNGQLLFDRPMHVKMDERALPKGDFFPPERPQ 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 =  101 bits (254), Expect = 3e-26
 Identities = 27/83 (32%), Positives = 39/83 (46%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            +F+ NLD  +  K L + FS  G ++   +  D  G+SRG G V F+    A  AI   
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76

Query: 189 NGMLLNDKQVFVGPFLRKQERES 211
           NG LL D+ + V    R   +  
Sbjct: 77  NGQLLFDRPMHVKMDERALPKGD 99

>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 = 78.9 bits (195), Expect = 4e-18
 Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 38  VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
           + ++++V +LD  V   +L ++F+  G VV   +  D    +S G G V +  + EA +A
Sbjct: 14  LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQA 72

Query: 98  LDELNFTPLNGKPIRI 113
           +   N   L  +P+ +
Sbjct: 73  ISMFNGQLLFDRPMHV 88

>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 =  154 bits (390), Expect = 1e-45
 Identities = 31/119 (26%), Positives = 50/119 (42%)

Query: 292 GKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSC 351
           G  Q   + +      F+           G  L V NLD  +SD  ++ELF+EFGT+   
Sbjct: 6   GGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA 65

Query: 352 KVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQ 410
            V  D +G S G+  V F    +A KA+ +  G  +  +P+ + L   + +        
Sbjct: 66  AVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHHH 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 =  104 bits (261), Expect = 4e-27
 Identities = 20/99 (20%), Positives = 39/99 (39%)

Query: 207 QERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNF 266
                         + V NL    ++ D++++F EFG +   AV  D  G+S     V+F
Sbjct: 24  SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHF 83

Query: 267 DDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELK 305
           +   DA ++++   G   D +   +     + + E    
Sbjct: 84  ERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 122

>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 = 93.6 bits (233), Expect = 3e-23
 Identities = 18/88 (20%), Positives = 37/88 (42%)

Query: 124 KSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKS 183
                 + + NLD  + +  + + F+ FG +    V  D  G+S G   V F+    A  
Sbjct: 32  VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALK 91

Query: 184 AIDKLNGMLLNDKQVFVGPFLRKQERES 211
           A+ +  G+ L+ + + +     + + E 
Sbjct: 92  AMKQYKGVPLDGRPMDIQLVASQIDLEH 119

>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 = 7e-20
 Identities = 26/100 (26%), Positives = 48/100 (48%), Gaps = 1/100 (1%)

Query: 14  VAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCR 73
           +   P    + + ++G  G         L V +LD  V+D+ + +LF + G +    V  
Sbjct: 10  MGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDY 69

Query: 74  DLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI 113
           D  + RSLG   V++    +A +A+ +    PL+G+P+ I
Sbjct: 70  D-RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI 108

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score =  153 bits (388), Expect = 3e-45
 Identities = 28/146 (19%), Positives = 58/146 (39%), Gaps = 13/146 (8%)

Query: 272 AARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDD 331
                + +  +    +E   G+  ++    + +   +E              +YVKNL  
Sbjct: 3   LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNC-------RIYVKNLAK 55

Query: 332 SISDDKLKELFSEFGTITS--CKVMRD----PNGISRGSGFVAFSTAEEASKALTEMNGK 385
            + +  LK +F  +   +S   ++M D      G  +G  F+     + A+KAL E NG 
Sbjct: 56  HVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGY 115

Query: 386 MVVSKPLYVALAQRKEERRARLQAQF 411
           ++  KP+ V  A+    ++   + + 
Sbjct: 116 VLFGKPMVVQFARSARPKQDPKEGKR 141

>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 =  108 bits (271), Expect = 3e-28
 Identities = 30/140 (21%), Positives = 59/140 (42%), Gaps = 11/140 (7%)

Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTR-----FNNVYVKNLSETTTEDDL 235
             S  D++    ++ +++  G   R++    +  ++         +YVKNL++   E DL
Sbjct: 3   LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDL 62

Query: 236 KKIFGEFGIITSTAVMRDAD------GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEW 289
           K IFG +   +S       D      G+ K   F+   +   AA++++  NG     K  
Sbjct: 63  KYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM 122

Query: 290 YVGKAQKKYEREMELKGKFE 309
            V  A+    ++   +GK +
Sbjct: 123 VVQFARSARPKQDPKEGKRK 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 = 78.3 bits (193), Expect = 1e-17
 Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 6/95 (6%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCK------VATDSLGQSRGYGFVQFDNEESAK 182
            I++KNL K +  K L   F  + +  S        +     G+ +G  F+   NE++A 
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 183 SAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTR 217
            A+ + NG +L  K + V      + ++   +  R
Sbjct: 107 KALKEANGYVLFGKPMVVQFARSARPKQDPKEGKR 141

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 69.5 bits (170), Expect = 2e-14
 Identities = 20/96 (20%), Positives = 36/96 (37%), Gaps = 5/96 (5%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVS-----VRVCRDLSTRRSLGYGYVNYNAAHE 93
           +  +YV +L   V +  L  +F +     S     +   R +   R  G  ++       
Sbjct: 45  NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 94  ATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
           A +AL E N   L GKP+ + ++      +    G 
Sbjct: 105 AAKALKEANGYVLFGKPMVVQFARSARPKQDPKEGK 140

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score =  152 bits (386), Expect = 2e-44
 Identities = 30/121 (24%), Positives = 50/121 (41%)

Query: 290 YVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTIT 349
               ++ K   +      F+           G  L V NLD  +SD  ++ELF+EFGT+ 
Sbjct: 57  PAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLK 116

Query: 350 SCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQA 409
              V  D +G S G+  V F    +A KA+ +  G  +  +P+ + L   + +       
Sbjct: 117 KAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHH 176

Query: 410 Q 410
            
Sbjct: 177 H 177

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 97.6 bits (243), Expect = 4e-24
 Identities = 20/100 (20%), Positives = 39/100 (39%)

Query: 206 KQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVN 265
                          + V NL    ++ D++++F EFG +   AV  D  G+S     V+
Sbjct: 76  DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVH 135

Query: 266 FDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELK 305
           F+   DA ++++   G   D +   +     + + E    
Sbjct: 136 FERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 175

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 91.8 bits (228), Expect = 6e-22
 Identities = 22/108 (20%), Positives = 43/108 (39%), Gaps = 1/108 (0%)

Query: 105 PLNGKPIRIMY-SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS 163
           PL  K    ++ S             + + NLD  + +  + + F+ FG +    V  D 
Sbjct: 65  PLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR 124

Query: 164 LGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
            G+S G   V F+    A  A+ +  G+ L+ + + +     + + E 
Sbjct: 125 SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEH 172

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 79.5 bits (196), Expect = 1e-17
 Identities = 27/106 (25%), Positives = 48/106 (45%), Gaps = 1/106 (0%)

Query: 8   PQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVV 67
           P         P    + + ++G  G         L V +LD  V+D+ + +LF + G + 
Sbjct: 57  PAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLK 116

Query: 68  SVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI 113
              V  D  + RSLG   V++    +A +A+ +    PL+G+P+ I
Sbjct: 117 KAAVDYD-RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI 161

>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 =  146 bits (370), Expect = 7e-43
 Identities = 29/107 (27%), Positives = 49/107 (45%), Gaps = 1/107 (0%)

Query: 304 LKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISR 362
           L  +   +     +  EG NL++ +L     D  L ++F  FG + S KV  D    +S+
Sbjct: 8   LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67

Query: 363 GSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQA 409
             GFV++     A  A+  MNG  +  K L V L + K + ++   +
Sbjct: 68  CFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPSS 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 =  107 bits (268), Expect = 4e-28
 Identities = 26/92 (28%), Positives = 48/92 (52%), Gaps = 1/92 (1%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDP 269
           S  +     N+++ +L +   + DL ++F  FG + S  V  D     SKCFGFV++D+P
Sbjct: 18  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 77

Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
             A  +++++NG +   K   V   + K + +
Sbjct: 78  VSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 109

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score =  103 bits (258), Expect = 8e-27
 Identities = 29/97 (29%), Positives = 47/97 (48%), Gaps = 1/97 (1%)

Query: 116 SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQ 174
                        N+FI +L +   ++ L   F  FGN++S KV  D     S+ +GFV 
Sbjct: 14  GAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVS 73

Query: 175 FDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
           +DN  SA++AI  +NG  +  K++ V     K + +S
Sbjct: 74  YDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKS 110

>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 = 85.4 bits (212), Expect = 2e-20
 Identities = 23/98 (23%), Positives = 41/98 (41%), Gaps = 11/98 (11%)

Query: 26  ANNGGVGDARQFVSTS-----------LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRD 74
            ++G  G  +Q +  +           L++  L     D  L  +F   G VVS +V  D
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60

Query: 75  LSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR 112
             T  S  +G+V+Y+    A  A+  +N   +  K ++
Sbjct: 61  KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK 98

>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 =  143 bits (362), Expect = 1e-41
 Identities = 34/105 (32%), Positives = 50/105 (47%), Gaps = 5/105 (4%)

Query: 299 EREMELKGK-----FEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKV 353
            R  +L  K     F+      A    G  L V NLD  +SD  ++ELF+EFGT+    V
Sbjct: 2   SRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 61

Query: 354 MRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ 398
             D +G S G+  V F    +A KA+ + NG  +  +P+ + L  
Sbjct: 62  HYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>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 =  101 bits (253), Expect = 4e-26
 Identities = 21/89 (23%), Positives = 38/89 (42%)

Query: 207 QERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNF 266
                 A       + V NL    ++ D++++F EFG +   AV  D  G+S     V+F
Sbjct: 18  SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHF 77

Query: 267 DDPDDAARSVEALNGKKFDDKEWYVGKAQ 295
           +   DA ++++  NG   D +   +    
Sbjct: 78  ERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>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 = 92.0 bits (229), Expect = 9e-23
 Identities = 19/78 (24%), Positives = 37/78 (47%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAK 182
                G + + NLD  + +  + + F+ FG +    V  D  G+S G   V F+ +  A 
Sbjct: 25  GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADAL 84

Query: 183 SAIDKLNGMLLNDKQVFV 200
            A+ + NG+ L+ + + +
Sbjct: 85  KAMKQYNGVPLDGRPMNI 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 = 85.0 bits (211), Expect = 3e-20
 Identities = 28/96 (29%), Positives = 49/96 (51%), Gaps = 1/96 (1%)

Query: 18  PSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLST 77
           P    + + ++G  G A       L V +LD  V+D+ + +LF + G +    V  D  +
Sbjct: 8   PDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RS 66

Query: 78  RRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI 113
            RSLG   V++    +A +A+ + N  PL+G+P+ I
Sbjct: 67  GRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 102

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  140 bits (356), Expect = 8e-41
 Identities = 30/97 (30%), Positives = 45/97 (46%), Gaps = 1/97 (1%)

Query: 303 ELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GIS 361
            L      +  +  +  EG NL++ +L    +D  L   F  FG + S KV  D    +S
Sbjct: 22  ALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLS 81

Query: 362 RGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ 398
           +  GFV+F   + A  A+  MNG  V +K L V L +
Sbjct: 82  KCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  107 bits (270), Expect = 2e-28
 Identities = 34/113 (30%), Positives = 53/113 (46%), Gaps = 2/113 (1%)

Query: 90  AAHEATRALDELNFTPLNGKPIRIMYSY-RDPTIRKSGAGNIFIKNLDKSIDNKALHDTF 148
           A      +   L+ +PL    +    +      I      N+FI +L +   +  L  TF
Sbjct: 2   AGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTF 61

Query: 149 STFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
             FGN++S KV  D     S+ +GFV FDN +SA+ AI  +NG  +  K++ V
Sbjct: 62  LPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV 114

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  100 bits (252), Expect = 6e-26
 Identities = 28/90 (31%), Positives = 44/90 (48%), Gaps = 1/90 (1%)

Query: 207 QERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVN 265
                  +     N+++ +L +  T+ DL   F  FG + S  V  D     SKCFGFV+
Sbjct: 29  AAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVS 88

Query: 266 FDDPDDAARSVEALNGKKFDDKEWYVGKAQ 295
           FD+PD A  +++A+NG +   K   V   +
Sbjct: 89  FDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 85.1 bits (211), Expect = 3e-20
 Identities = 24/112 (21%), Positives = 45/112 (40%), Gaps = 8/112 (7%)

Query: 1   MAQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLF 60
            + +   P A VA++A  + A                   +L++  L     D+ L   F
Sbjct: 10  ASALSTSPLASVALSAAAAAAAGKQIE--------GPEGCNLFIYHLPQEFTDTDLASTF 61

Query: 61  NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR 112
              G V+S +V  D  T  S  +G+V+++    A  A+  +N   +  K ++
Sbjct: 62  LPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK 113

>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 =  142 bits (359), Expect = 3e-40
 Identities = 40/200 (20%), Positives = 77/200 (38%), Gaps = 26/200 (13%)

Query: 220 NVYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
            + V NL+ E  T   L  +FG +G +    ++ +     K    V   D + A  ++  
Sbjct: 5   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSH 60

Query: 279 LNGKKFDDKEWYVGKA-------QKKYEREMELKGKFEQSLKETADKFEGLN-------- 323
           LNG K   K   +  +        ++ + +  L   +  S      K    N        
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120

Query: 324 --LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
             L++ N+  S+S++ LK LFS  G +         +   R    +   + EEA +AL +
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---RKMALIQMGSVEEAVQALID 177

Query: 382 MNGKMVV-SKPLYVALAQRK 400
           ++   +  +  L V+ ++  
Sbjct: 178 LHNHDLGENHHLRVSFSKST 197

>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 =  133 bits (335), Expect = 1e-36
 Identities = 30/191 (15%), Positives = 70/191 (36%), Gaps = 37/191 (19%)

Query: 126 GAGNIFIKNLD-KSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           G   + + NL+ + +  ++L   F  +G++   K+  +     +    VQ  +   A+ A
Sbjct: 2   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLA 57

Query: 185 IDKLNGMLLNDKQVFVG-------PFLRKQERESTADKT-------RF------------ 218
           +  LNG  L+ K + +           R+ + +    K        RF            
Sbjct: 58  MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117

Query: 219 ---NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARS 275
                +++ N+  + +E+DLK +F   G +           K +    +     ++A ++
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQA 174

Query: 276 VEALNGKKFDD 286
           +  L+     +
Sbjct: 175 LIDLHNHDLGE 185

>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 =  109 bits (274), Expect = 4e-28
 Identities = 36/191 (18%), Positives = 62/191 (32%), Gaps = 42/191 (21%)

Query: 39  STSLYVGDLD-LSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
           ++ L V +L+   V    L+ LF   G V  V++  +           V     ++A  A
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLA 57

Query: 98  LDELNFTPLNGKPIRIMYSYRDPTIRKSGAGN---------------------------- 129
           +  LN   L+GKPIRI  S                                         
Sbjct: 58  MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117

Query: 130 -----IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
                + + N+  S+  + L   FS+ G ++          + R    +Q  + E A  A
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQA 174

Query: 185 IDKLNGMLLND 195
           +  L+   L +
Sbjct: 175 LIDLHNHDLGE 185

>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 = 85.3 bits (211), Expect = 2e-19
 Identities = 20/117 (17%), Positives = 47/117 (40%), Gaps = 6/117 (5%)

Query: 323 NLYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
            L V NL+ + ++   L  LF  +G +   K++ +     + +  V  +   +A  A++ 
Sbjct: 5   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSH 60

Query: 382 MNGKMVVSKPLYVALAQRKE-ERRARLQAQFSQMRPPVGPRMPMYPPVAPGLGQQLF 437
           +NG  +  KP+ + L++ +  +     Q      +      +  +        Q +F
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117

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

 Score = 57.6 bits (139), Expect = 6e-10
 Identities = 21/113 (18%), Positives = 41/113 (36%), Gaps = 5/113 (4%)

Query: 5   QVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMG 64
           + Q    +      SP                  S +L++ ++  SV++  L  LF+  G
Sbjct: 86  EGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNG 145

Query: 65  QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL-NGKPIRIMYS 116
            VV          ++      +   +  EA +AL +L+   L     +R+ +S
Sbjct: 146 GVVKGFK----FFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 194

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score =  138 bits (350), Expect = 5e-40
 Identities = 26/114 (22%), Positives = 49/114 (42%), Gaps = 7/114 (6%)

Query: 291 VGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITS 350
           +G +   +     L  +          +     L+V+     + + +L E+F  FG +  
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE 60

Query: 351 CKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERR 404
            K++        G  FV F  AE A+KA+ E++GK   ++PL V  ++   +R 
Sbjct: 61  VKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score =  108 bits (273), Expect = 6e-29
 Identities = 20/94 (21%), Positives = 42/94 (44%), Gaps = 7/94 (7%)

Query: 207 QERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNF 266
                   +     ++V+       E +L +IFG FG +    ++         F FV F
Sbjct: 20  HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEF 72

Query: 267 DDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           ++ + AA+++E ++GK F ++   V  ++   +R
Sbjct: 73  EEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR 106

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 80.8 bits (200), Expect = 8e-19
 Identities = 18/87 (20%), Positives = 38/87 (43%), Gaps = 7/87 (8%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAK 182
            +     +F++     +    L++ F  FG +   K+         G+ FV+F+  ESA 
Sbjct: 27  GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAA 79

Query: 183 SAIDKLNGMLLNDKQVFVGPFLRKQER 209
            AI++++G    ++ + V       +R
Sbjct: 80  KAIEEVHGKSFANQPLEVVYSKLPAKR 106

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 67.7 bits (166), Expect = 3e-14
 Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 8/78 (10%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           +T L+V    L V +S+L ++F   G +  V++          G+ +V +  A  A +A+
Sbjct: 31  NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAI 82

Query: 99  DELNFTPLNGKPIRIMYS 116
           +E++      +P+ ++YS
Sbjct: 83  EEVHGKSFANQPLEVVYS 100

>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 =  140 bits (355), Expect = 7e-40
 Identities = 39/173 (22%), Positives = 78/173 (45%), Gaps = 11/173 (6%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID 186
             +FI  L+       L + F  +G +   K+  D   G+SRG+GF+ F+   S    + 
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63

Query: 187 KLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIIT 246
             +  +L+ K +     + + E++ T        ++V  +       + ++ F ++G I 
Sbjct: 64  TQH--ILDGKVIDPKRAIPRDEQDKT------GKIFVGGIGPDVRPKEFEEFFSQWGTII 115

Query: 247 STAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKY 298
              +M D D G+S+ FGFV +D  D   R  +      F D++  + +A+ ++
Sbjct: 116 DAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPRH 167

>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 =  129 bits (328), Expect = 5e-36
 Identities = 43/182 (23%), Positives = 87/182 (47%), Gaps = 23/182 (12%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           +++  L+  TTED+L++ FG++G +T   +M+D   G+S+ FGF++F+ P      V+  
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65

Query: 280 NGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLK 339
           +    D K     +A  + E++   K                  ++V  +   +   + +
Sbjct: 66  H--ILDGKVIDPKRAIPRDEQDKTGK------------------IFVGGIGPDVRPKEFE 105

Query: 340 ELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ 398
           E FS++GTI   ++M D + G SRG GFV + +A+   +   +        + + +  A+
Sbjct: 106 EFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRAE 164

Query: 399 RK 400
            +
Sbjct: 165 PR 166

>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 =  120 bits (303), Expect = 2e-32
 Identities = 36/167 (21%), Positives = 78/167 (46%), Gaps = 6/167 (3%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           +++G L+    +  L + F + G V  +++ +D +T RS G+G++++         +   
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65

Query: 102 NFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVAT 161
           +   L+GK I    +   P   +   G IF+  +   +  K   + FS +G I+  ++  
Sbjct: 66  HI--LDGKVIDPKRA--IPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLML 121

Query: 162 D-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQ 207
           D   GQSRG+GFV +D+ ++      +   +   D+++ +     + 
Sbjct: 122 DKDTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRAEPRH 167

>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 = 78.7 bits (195), Expect = 2e-17
 Identities = 24/92 (26%), Positives = 51/92 (55%), Gaps = 7/92 (7%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKA 378
           E   +++  L+   ++D L+E F ++GT+T  K+M+DP  G SRG GF++F       + 
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 379 LTEM---NGKMVVSKPLYVALAQRKEERRARL 407
           +      +GK++  K    A+ + ++++  ++
Sbjct: 62  VKTQHILDGKVIDPKR---AIPRDEQDKTGKI 90

>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 =  137 bits (348), Expect = 8e-40
 Identities = 36/89 (40%), Positives = 53/89 (59%), Gaps = 2/89 (2%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSC-KVATDSL-GQSRGYGFVQFDNEESAK 182
           SG+  IFI NLD  ID K L+DTFS FG IL   K+  D   G S+GY F+ F + +++ 
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62

Query: 183 SAIDKLNGMLLNDKQVFVGPFLRKQERES 211
           +AI+ +NG  L ++ + V    +K  + S
Sbjct: 63  AAIEAMNGQYLCNRPITVSYAFKKDSKGS 91

>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 =  110 bits (278), Expect = 8e-30
 Identities = 28/88 (31%), Positives = 51/88 (57%), Gaps = 2/88 (2%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSC-KVMRDP-NGISRGSGFVAFSTAEEASKALT 380
            +++ NLD  I +  L + FS FG I    K+MRDP  G S+G  F+ F++ + +  A+ 
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 381 EMNGKMVVSKPLYVALAQRKEERRARLQ 408
            MNG+ + ++P+ V+ A +K+ + +   
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSKGSGPS 94

>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 = 94.6 bits (236), Expect = 7e-24
 Identities = 28/84 (33%), Positives = 43/84 (51%), Gaps = 2/84 (2%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTA-VMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
            +++ NL     E  L   F  FG+I  T  +MRD D G SK + F+NF   D +  ++E
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 278 ALNGKKFDDKEWYVGKAQKKYERE 301
           A+NG+   ++   V  A KK  + 
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSKG 90

>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 = 84.9 bits (211), Expect = 2e-20
 Identities = 24/92 (26%), Positives = 53/92 (57%), Gaps = 2/92 (2%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSV-RVCRDLSTRRSLGYGYVNYNAAHEATRA 97
           S+ +++G+LD  +++  LYD F+  G ++   ++ RD  T  S GY ++N+ +   +  A
Sbjct: 5   SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64

Query: 98  LDELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
           ++ +N   L  +PI + Y+++  + + SG  +
Sbjct: 65  IEAMNGQYLCNRPITVSYAFKKDS-KGSGPSS 95

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score =  137 bits (346), Expect = 2e-39
 Identities = 30/93 (32%), Positives = 51/93 (54%), Gaps = 2/93 (2%)

Query: 323 NLYVKNLDDSISDDKLKELFSE-FGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
           +L+V +L   + D  L E F + + +    KV+ D  G+S+G GFV F+   E  +ALTE
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 382 MNGKMVV-SKPLYVALAQRKEERRARLQAQFSQ 413
             G + + SKP+ +++A  K  R   +++  S 
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRVKPVESGPSS 103

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 94.7 bits (236), Expect = 8e-24
 Identities = 21/97 (21%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGE-FGIITSTAVMRDADGKSKCFGFVNFDDP 269
           S+       +++V +L+    +  L + F + +       V+ D  G SK +GFV F D 
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDE 61

Query: 270 DDAARSVEALNGKKF-DDKEWYVGKAQKKYEREMELK 305
            +  R++    G      K   +  A  K  R   ++
Sbjct: 62  LEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVE 98

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 91.2 bits (227), Expect = 1e-22
 Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 2/85 (2%)

Query: 129 NIFIKNLDKSIDNKALHDTFS-TFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
           ++F+ +L   +D+  L++ F   + +    KV  D  G S+GYGFV+F +E   K A+ +
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 188 LNG-MLLNDKQVFVGPFLRKQERES 211
             G + L  K V +   + K  R  
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRVK 95

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 73.9 bits (182), Expect = 2e-16
 Identities = 29/88 (32%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQM-GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           SL+VGDL   V+D  LY+ F ++       +V  D  T  S GYG+V +    E  RAL 
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRALT 69

Query: 100 ELN-FTPLNGKPIRIMYSYRDPTIRKSG 126
           E      L  KP+R+  +    +  K  
Sbjct: 70  ECQGAVGLGSKPVRLSVAIPKASRVKPV 97

>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 =  138 bits (349), Expect = 2e-38
 Identities = 30/199 (15%), Positives = 72/199 (36%), Gaps = 37/199 (18%)

Query: 118 RDPTIRKSGAGNIFIKNLD-KSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFD 176
             P +  +G   + + NL+ + +  ++L   F  +G++   K+  +     +    VQ  
Sbjct: 25  AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMA 80

Query: 177 NEESAKSAIDKLNGMLLNDKQVFVGPFLRK-----QERESTADKTRF------------- 218
           +   A+ A+  LNG  L+ K + +     +     +E +     T+              
Sbjct: 81  DGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPG 140

Query: 219 -----------NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFD 267
                        +++ N+  + +E+DLK +F   G +         D K      +   
Sbjct: 141 SKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK---MALIQMG 197

Query: 268 DPDDAARSVEALNGKKFDD 286
             ++A +++  L+     +
Sbjct: 198 SVEEAVQALIDLHNHDLGE 216

>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 =  133 bits (336), Expect = 1e-36
 Identities = 37/213 (17%), Positives = 77/213 (36%), Gaps = 26/213 (12%)

Query: 207 QERESTADKTRFNNVYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVN 265
           +           + + V NL+ E  T   L  +FG +G +    ++       K    V 
Sbjct: 23  RIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF----NKKENALVQ 78

Query: 266 FDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFE----- 320
             D + A  ++  LNG K   K   +  ++ +  +      + +   K+  +        
Sbjct: 79  MADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 138

Query: 321 ------------GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVA 368
                          L++ N+  S+S++ LK LFS  G +         +   R    + 
Sbjct: 139 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---RKMALIQ 195

Query: 369 FSTAEEASKALTEMNGKMVV-SKPLYVALAQRK 400
             + EEA +AL +++   +  +  L V+ ++  
Sbjct: 196 MGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score =  110 bits (276), Expect = 4e-28
 Identities = 40/224 (17%), Positives = 68/224 (30%), Gaps = 45/224 (20%)

Query: 8   PQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDL-SVNDSQLYDLFNQMGQV 66
                +    P  +  G     G+  A    ++ L V +L+   V    L+ LF   G V
Sbjct: 6   HHHHHSSGLVPRGSHMGRIAIPGLAGAG---NSVLLVSNLNPERVTPQSLFILFGVYGDV 62

Query: 67  VSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSG 126
             V++              V     ++A  A+  LN   L+GKPIRI  S          
Sbjct: 63  QRVKI-----LFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPRE 117

Query: 127 AGN---------------------------------IFIKNLDKSIDNKALHDTFSTFGN 153
                                               + + N+  S+  + L   FS+ G 
Sbjct: 118 GQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG 177

Query: 154 ILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQ 197
           ++          + R    +Q  + E A  A+  L+   L +  
Sbjct: 178 VVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGENH 218

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 81.2 bits (200), Expect = 1e-17
 Identities = 21/117 (17%), Positives = 48/117 (41%), Gaps = 6/117 (5%)

Query: 323 NLYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
            L V NL+ + ++   L  LF  +G +   K++ +     + +  V  +   +A  A++ 
Sbjct: 36  VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSH 91

Query: 382 MNGKMVVSKPLYVALAQRKEERRAR-LQAQFSQMRPPVGPRMPMYPPVAPGLGQQLF 437
           +NG  +  KP+ + L++ +  +  R  Q      +      +  +        Q +F
Sbjct: 92  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 148

>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 = 58.1 bits (140), Expect = 7e-10
 Identities = 20/113 (17%), Positives = 40/113 (35%), Gaps = 5/113 (4%)

Query: 5   QVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMG 64
           + Q    +      SP                  S +L++ ++  SV++  L  LF+  G
Sbjct: 117 EGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNG 176

Query: 65  QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN-FTPLNGKPIRIMYS 116
            VV          ++      +   +  EA +AL +L+         +R+ +S
Sbjct: 177 GVVKGFK----FFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 225

>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 =  133 bits (336), Expect = 6e-37
 Identities = 45/208 (21%), Positives = 87/208 (41%), Gaps = 16/208 (7%)

Query: 208 ERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNF 266
           + ES  +  +   +++  LS  TT++ L+  F ++G +T   VMRD +  +S+ FGFV +
Sbjct: 3   KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62

Query: 267 DDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYV 326
              ++   ++ A    K D +     +A  +   + +  G      K          ++V
Sbjct: 63  ATVEEVDAAMNA-RPHKVDGRVVEPKRAVSR--EDSQRPGAHLTVKK----------IFV 109

Query: 327 KNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEMNGK 385
             + +   +  L++ F ++G I   ++M D   G  RG  FV F   +   K +      
Sbjct: 110 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYH 168

Query: 386 MVVSKPLYVALAQRKEERRARLQAQFSQ 413
            V      V  A  K+E  +   +Q  +
Sbjct: 169 TVNGHNCEVRKALSKQEMASASSSQRGR 196

>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 =  129 bits (327), Expect = 1e-35
 Identities = 43/175 (24%), Positives = 73/175 (41%), Gaps = 4/175 (2%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID 186
             +FI  L     +++L   F  +G +  C V  D    +SRG+GFV +   E   +A++
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73

Query: 187 KLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIIT 246
                 ++ + V     + +++ +          ++V  + E T E  L+  F ++G I 
Sbjct: 74  A-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 132

Query: 247 STAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
              +M D   GK + F FV FDD D   + V        +     V KA  K E 
Sbjct: 133 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM 186

>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 =  112 bits (281), Expect = 5e-29
 Identities = 48/181 (26%), Positives = 79/181 (43%), Gaps = 7/181 (3%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L++G L     D  L   F Q G +    V RD +T+RS G+G+V Y    E   A++  
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75

Query: 102 NFTPLNGKPIRIMYSYRDPTIRKSGAGN----IFIKNLDKSIDNKALHDTFSTFGNILSC 157
               ++G+ +    +      ++ GA      IF+  + +  +   L D F  +G I   
Sbjct: 76  PHK-VDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 134

Query: 158 KVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKT 216
           ++ TD   G+ RG+ FV FD+ +S    + +     +N     V   L KQE  S +   
Sbjct: 135 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMASASSSQ 193

Query: 217 R 217
           R
Sbjct: 194 R 194

>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 =  129 bits (326), Expect = 1e-36
 Identities = 29/88 (32%), Positives = 49/88 (55%), Gaps = 4/88 (4%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG----ISRGSGFVAFSTAEEASKA 378
            L++KNL+ S +++ LK +FS+ G I SC + +  N     +S G GFV +   E+A KA
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 379 LTEMNGKMVVSKPLYVALAQRKEERRAR 406
           L ++ G  V    L V +++R  +  + 
Sbjct: 67  LKQLQGHTVDGHKLEVRISERATKPASG 94

>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 =  103 bits (259), Expect = 4e-27
 Identities = 23/87 (26%), Positives = 46/87 (52%), Gaps = 4/87 (4%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK----SKCFGFVNFDDPDDAAR 274
           + +++KNL+ +TTE+ LK +F + G I S  + +  +      S  FGFV +  P+ A +
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 275 SVEALNGKKFDDKEWYVGKAQKKYERE 301
           +++ L G   D  +  V  +++  +  
Sbjct: 66  ALKQLQGHTVDGHKLEVRISERATKPA 92

>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 = 99.6 bits (249), Expect = 1e-25
 Identities = 28/91 (30%), Positives = 46/91 (50%), Gaps = 4/91 (4%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD----SLGQSRGYGFVQFDNEES 180
           SG+  +FIKNL+ S   + L   FS  G I SC ++       +  S G+GFV++   E 
Sbjct: 3   SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
           A+ A+ +L G  ++  ++ V    R  +  S
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 = 80.0 bits (198), Expect = 1e-18
 Identities = 22/94 (23%), Positives = 47/94 (50%), Gaps = 4/94 (4%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLST---RRSLGYGYVNYNAAHEAT 95
           S+ L++ +L+ S  +  L  +F+++G + S  + +  +      S+G+G+V Y    +A 
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64

Query: 96  RALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
           +AL +L    ++G  + +  S R      SG  +
Sbjct: 65  KALKQLQGHTVDGHKLEVRISERATK-PASGPSS 97

>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 =  129 bits (326), Expect = 1e-36
 Identities = 29/94 (30%), Positives = 44/94 (46%), Gaps = 3/94 (3%)

Query: 316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEA 375
           +       L+V  L+   S++ +  LF  FG I  C V+R P+G S+G  FV FS+  EA
Sbjct: 10  SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEA 69

Query: 376 SKALTEMNGKMVV---SKPLYVALAQRKEERRAR 406
             A+  ++G   +   S  L V  A   +E    
Sbjct: 70  QAAIHALHGSQTMPGASSSLVVKFADTDKESGPS 103

>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 =  100 bits (250), Expect = 1e-25
 Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 3/93 (3%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPD 270
           S +   R   ++V  L++  +E+D+ ++F  FG+I    V+R  DG SK   FV F    
Sbjct: 8   SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHT 67

Query: 271 DAARSVEALNGKKFDD---KEWYVGKAQKKYER 300
           +A  ++ AL+G +          V  A    E 
Sbjct: 68  EAQAAIHALHGSQTMPGASSSLVVKFADTDKES 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 = 89.3 bits (222), Expect = 6e-22
 Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 3/90 (3%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAK 182
           R      +F+  L+K    + +   F  FG I  C V     G S+G  FV+F +   A+
Sbjct: 11  RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQ 70

Query: 183 SAIDKLNG---MLLNDKQVFVGPFLRKQER 209
           +AI  L+G   M      + V      +E 
Sbjct: 71  AAIHALHGSQTMPGASSSLVVKFADTDKES 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 = 63.5 bits (155), Expect = 1e-12
 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 4/85 (4%)

Query: 32  GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
            ++R      L+VG L+   ++  +  LF   G +    V R      S G  +V +++ 
Sbjct: 8   SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSSH 66

Query: 92  HEATRALDELN---FTPLNGKPIRI 113
            EA  A+  L+     P     + +
Sbjct: 67  TEAQAAIHALHGSQTMPGASSSLVV 91

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

 Score =  128 bits (324), Expect = 2e-36
 Identities = 28/91 (30%), Positives = 48/91 (52%), Gaps = 1/91 (1%)

Query: 121 TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEES 180
           +   SGA  IF++NL      K L D F+  G++L   +  ++ G+S+G G V+F++ E 
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEV 60

Query: 181 AKSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
           A+ A   +NGM L+ +++ V          S
Sbjct: 61  AERACRMMNGMKLSGREIDVRIDRNASGPSS 91

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

 Score =  111 bits (281), Expect = 3e-30
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 1/85 (1%)

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
              ++V+NL    +   LK+ F+E G +    +  + NG S+G G V F + E A +A  
Sbjct: 8   ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACR 66

Query: 381 EMNGKMVVSKPLYVALAQRKEERRA 405
            MNG  +  + + V + +      +
Sbjct: 67  MMNGMKLSGREIDVRIDRNASGPSS 91

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

 Score = 98.4 bits (246), Expect = 2e-25
 Identities = 24/90 (26%), Positives = 40/90 (44%), Gaps = 1/90 (1%)

Query: 212 TADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
           ++  +    ++V+NL    T   LK  F E G +    +  + +GKSK  G V F+ P+ 
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEV 60

Query: 272 AARSVEALNGKKFDDKEWYVGKAQKKYERE 301
           A R+   +NG K   +E  V   +      
Sbjct: 61  AERACRMMNGMKLSGREIDVRIDRNASGPS 90

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

 Score = 76.5 bits (189), Expect = 1e-17
 Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 3/95 (3%)

Query: 32  GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
           G +    +  ++V +L        L D FN+ G V+   +  +    +S G G V + + 
Sbjct: 1   GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESP 58

Query: 92  HEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSG 126
             A RA   +N   L+G+ I +    R+ +   SG
Sbjct: 59  EVAERACRMMNGMKLSGREIDVRID-RNASGPSSG 92

>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 =  131 bits (331), Expect = 3e-36
 Identities = 27/204 (13%), Positives = 56/204 (27%), Gaps = 29/204 (14%)

Query: 219 NNVYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
             + V  L       D +  +F  +G +     M+           V   D     R++ 
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAIT 60

Query: 278 ALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKF------------------ 319
            LN      ++  V  +++      +  G  + S                          
Sbjct: 61  HLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ 120

Query: 320 -EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASK 377
                L+  N    ++++   E+  E G      V           SG + + +  +A +
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180

Query: 378 ALTEMNGKMV----VSKPLYVALA 397
            L  +N   +       P  + L 
Sbjct: 181 TLGFLNHYQMKNPNGPYPYTLKLC 204

>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 =  122 bits (308), Expect = 6e-33
 Identities = 30/198 (15%), Positives = 64/198 (32%), Gaps = 39/198 (19%)

Query: 126 GAGN--IFIKNLDKS-IDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAK 182
           GA +  + +  LD+S ++   + + F  +GN+   K          G   V+  +  +  
Sbjct: 1   GADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK----PGAAMVEMADGYAVD 56

Query: 183 SAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFN----------------------- 219
            AI  LN   +  +++ V    +       +                             
Sbjct: 57  RAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAK 116

Query: 220 --------NVYVKNLSETTTEDDLKKIFGEFGIITSTAV-MRDADGKSKCFGFVNFDDPD 270
                    ++  N     TE++  +I  E G+   T+V +     +    G + +D   
Sbjct: 117 NRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKS 176

Query: 271 DAARSVEALNGKKFDDKE 288
           DA  ++  LN  +  +  
Sbjct: 177 DALETLGFLNHYQMKNPN 194

>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 =  109 bits (274), Expect = 4e-28
 Identities = 31/205 (15%), Positives = 61/205 (29%), Gaps = 43/205 (20%)

Query: 39  STSLYVGDLDLS-VNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
           S  L V  LD S +N  +++++F   G V  V+  +        G   V     +   RA
Sbjct: 4   SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRA 58

Query: 98  LDELNFTPLNGKPIRIMYSYRDPTIRKSGAG----------------------------- 128
           +  LN   + G+ + +  S +   +     G                             
Sbjct: 59  ITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNR 118

Query: 129 ------NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESA 181
                  +   N    +  +   +     G      V   S   +    G +++D++  A
Sbjct: 119 IQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDA 178

Query: 182 KSAIDKLNGMLLNDKQVFVGPFLRK 206
              +  LN   + +      P+  K
Sbjct: 179 LETLGFLNHYQMKNPNG-PYPYTLK 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 = 78.2 bits (192), Expect = 7e-17
 Identities = 15/106 (14%), Positives = 36/106 (33%), Gaps = 5/106 (4%)

Query: 323 NLYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
            L V  LD   ++ D++  +F  +G +   K M+       G+  V  +      +A+T 
Sbjct: 6   VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITH 61

Query: 382 MNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPRMPMYPP 427
           +N   +  + + V ++++      +                     
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNR 107

>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 = 62.0 bits (150), Expect = 2e-11
 Identities = 14/113 (12%), Positives = 33/113 (29%)

Query: 3   QVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQ 62
              ++  +        S             +  Q  S  L+  +  L V +   +++ ++
Sbjct: 87  SYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDE 146

Query: 63  MGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY 115
           +G      V            G + +++  +A   L  LN   +        Y
Sbjct: 147 LGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY 199

>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 =  127 bits (322), Expect = 8e-36
 Identities = 26/99 (26%), Positives = 48/99 (48%)

Query: 213 ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDA 272
            +      +++  L+  T E  LK +FG+ G I+   +++D   KS+ F F+ F++P DA
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADA 61

Query: 273 ARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQS 311
             + + +NGK    K   V +A+K   +    +     S
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASS 100

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score =  122 bits (307), Expect = 9e-34
 Identities = 25/108 (23%), Positives = 47/108 (43%), Gaps = 2/108 (1%)

Query: 316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEA 375
            +      L++  L+   ++  LK +F + G I+   +++D    SRG  F+ F    +A
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADA 61

Query: 376 SKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR--PPVGPR 421
             A  +MNGK +  K + V  A++   +    +   +  R   P G  
Sbjct: 62  KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSL 109

>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 = 94.3 bits (235), Expect = 2e-23
 Identities = 24/84 (28%), Positives = 39/84 (46%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
           G +FI  L++  + K L   F   G I    +  D   +SRG+ F+ F+N   AK+A   
Sbjct: 8   GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67

Query: 188 LNGMLLNDKQVFVGPFLRKQERES 211
           +NG  L+ K + V    +   +  
Sbjct: 68  MNGKSLHGKAIKVEQAKKPSFQSG 91

>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 = 73.5 bits (181), Expect = 4e-16
 Identities = 21/90 (23%), Positives = 45/90 (50%), Gaps = 2/90 (2%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              L++G L+   N+  L  +F + G +  V + +D  T +S G+ ++ +    +A  A 
Sbjct: 7   PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAA 65

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAG 128
            ++N   L+GK I++  + + P+ +  G  
Sbjct: 66  KDMNGKSLHGKAIKVEQA-KKPSFQSGGRR 94

>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 =  125 bits (315), Expect = 5e-35
 Identities = 26/95 (27%), Positives = 52/95 (54%), Gaps = 7/95 (7%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            L+V+NL ++++++ L++ FS+FG +   K ++D         F+ F   + A KA+ EM
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEM 65

Query: 383 NGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPP 417
           NGK +  + + +  A+  +++R   +AQ      P
Sbjct: 66  NGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGP 100

>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 =  114 bits (288), Expect = 4e-31
 Identities = 24/101 (23%), Positives = 54/101 (53%), Gaps = 7/101 (6%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPD 270
            ++   +   ++V+NL+ T TE+ L+K F +FG +     ++D       + F++FD+ D
Sbjct: 4   GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERD 56

Query: 271 DAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQS 311
            A +++E +NGK  + +   +  A+   ++  E K + + +
Sbjct: 57  GAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAA 97

>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 = 81.6 bits (202), Expect = 3e-19
 Identities = 20/92 (21%), Positives = 42/92 (45%), Gaps = 8/92 (8%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            +F++NL  ++  + L   FS FG +   K         + Y F+ FD  + A  A++++
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKK-------LKDYAFIHFDERDGAVKAMEEM 65

Query: 189 NGMLLNDKQVFVGPFLRKQERESTADKTRFNN 220
           NG  L  + + +  F +  +++    K +   
Sbjct: 66  NGKDLEGENIEIV-FAKPPDQKRKERKAQRQA 96

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 70.0 bits (172), Expect = 4e-15
 Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
             L+V +L  +V +  L   F+Q G++  V+  +D        Y +++++    A +A++
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAME 63

Query: 100 ELNFTPLNGKPIRI 113
           E+N   L G+ I I
Sbjct: 64  EMNGKDLEGENIEI 77

>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 =  124 bits (314), Expect = 6e-35
 Identities = 23/91 (25%), Positives = 47/91 (51%), Gaps = 3/91 (3%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             +LYVG+L   V +  +  LF+Q+G   S ++  + ++     Y +V +    +A  AL
Sbjct: 15  PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAAL 72

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
             +N   + GK +++ ++   P+ +KSG  +
Sbjct: 73  AAMNGRKILGKEVKVNWA-TTPSSQKSGPSS 102

>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 = 90.0 bits (224), Expect = 3e-22
 Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 1/94 (1%)

Query: 311 SLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFS 370
           S     D  +   LYV NL   +++  + +LFS+ G   SCK++ +    +    FV F 
Sbjct: 5   SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFY 63

Query: 371 TAEEASKALTEMNGKMVVSKPLYVALAQRKEERR 404
              +A+ AL  MNG+ ++ K + V  A     ++
Sbjct: 64  EHRDAAAALAAMNGRKILGKEVKVNWATTPSSQK 97

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 85.0 bits (211), Expect = 2e-20
 Identities = 25/91 (27%), Positives = 42/91 (46%), Gaps = 1/91 (1%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPD 270
              D  +   +YV NLS   TE  + ++F + G   S  ++ +       + FV F +  
Sbjct: 8   MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHR 66

Query: 271 DAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
           DAA ++ A+NG+K   KE  V  A     ++
Sbjct: 67  DAAAALAAMNGRKILGKEVKVNWATTPSSQK 97

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 74.2 bits (183), Expect = 2e-16
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            +++ NL + +    +   FS  G   SCK+ T+    +  Y FV+F     A +A+  +
Sbjct: 17  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAM 75

Query: 189 NGMLLNDKQV 198
           NG  +  K+V
Sbjct: 76  NGRKILGKEV 85

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  121 bits (305), Expect = 1e-33
 Identities = 26/110 (23%), Positives = 53/110 (48%), Gaps = 3/110 (2%)

Query: 291 VGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITS 350
           +G +   +     L  +       T +K +   L+V N+     D  L+++F +FG I  
Sbjct: 1   MGSSHHHHHHSSGLVPRGSH--MNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILD 58

Query: 351 CKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK 400
            +++ +  G S+G GFV F  + +A +A  +++G +V  + + V  A  +
Sbjct: 59  VEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  115 bits (290), Expect = 2e-31
 Identities = 27/97 (27%), Positives = 52/97 (53%), Gaps = 1/97 (1%)

Query: 201 GPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKC 260
              + +    +T +K++   ++V N+     + DL+++FG+FG I    ++ +  G SK 
Sbjct: 12  SGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKG 70

Query: 261 FGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKK 297
           FGFV F++  DA R+ E L+G   + ++  V  A  +
Sbjct: 71  FGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 88.1 bits (219), Expect = 2e-21
 Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 1/84 (1%)

Query: 118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDN 177
              T  KS    + + N+     +  L   F  FG IL  ++  +    S+G+GFV F+N
Sbjct: 20  HMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-RGSKGFGFVTFEN 78

Query: 178 EESAKSAIDKLNGMLLNDKQVFVG 201
              A  A +KL+G ++  +++ V 
Sbjct: 79  SADADRAREKLHGTVVEGRKIEVN 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 = 73.5 bits (181), Expect = 3e-16
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              L+V ++     D  L  +F Q G+++ V +  +   R S G+G+V +  + +A RA 
Sbjct: 29  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAR 86

Query: 99  DELNFTPLNGKPIRI 113
           ++L+ T + G+ I +
Sbjct: 87  EKLHGTVVEGRKIEV 101

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score =  118 bits (297), Expect = 1e-32
 Identities = 23/83 (27%), Positives = 41/83 (49%)

Query: 316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEA 375
           A +     ++V NL+  + ++ L ELF + G +T   + +D  G  +  GFV F   E  
Sbjct: 11  AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESV 70

Query: 376 SKALTEMNGKMVVSKPLYVALAQ 398
           S A+  +NG  +  +P+ V+   
Sbjct: 71  SYAIALLNGIRLYGRPINVSGPS 93

>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 =  109 bits (274), Expect = 3e-29
 Identities = 24/83 (28%), Positives = 40/83 (48%)

Query: 213 ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDA 272
           A +     V+V NL     E+ L ++F + G +T   + +D +GK K FGFV F  P+  
Sbjct: 11  AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESV 70

Query: 273 ARSVEALNGKKFDDKEWYVGKAQ 295
           + ++  LNG +   +   V    
Sbjct: 71  SYAIALLNGIRLYGRPINVSGPS 93

>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 = 90.4 bits (225), Expect = 2e-22
 Identities = 21/79 (26%), Positives = 39/79 (49%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAK 182
           ++     +F+ NL+  +  + L++ F   G +    +  D  G+ + +GFV F + ES  
Sbjct: 12  QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVS 71

Query: 183 SAIDKLNGMLLNDKQVFVG 201
            AI  LNG+ L  + + V 
Sbjct: 72  YAIALLNGIRLYGRPINVS 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 = 89.2 bits (222), Expect = 4e-22
 Identities = 25/90 (27%), Positives = 48/90 (53%), Gaps = 1/90 (1%)

Query: 24  GIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGY 83
           G + + G+  A++    +++VG+L+  V +  LY+LF Q G +  V +C+D    +   +
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSF 59

Query: 84  GYVNYNAAHEATRALDELNFTPLNGKPIRI 113
           G+V +      + A+  LN   L G+PI +
Sbjct: 60  GFVCFKHPESVSYAIALLNGIRLYGRPINV 89

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score =  118 bits (297), Expect = 2e-32
 Identities = 29/96 (30%), Positives = 52/96 (54%), Gaps = 1/96 (1%)

Query: 34  ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
           + +    ++YVG LD  V++  L++LF Q G VV+  + +D  T +  GYG+V + +  +
Sbjct: 10  SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 69

Query: 94  ATRALDELNFTPLNGKPIRIMY-SYRDPTIRKSGAG 128
           A  A+  ++   L GKPIR+   S  +  +    +G
Sbjct: 70  ADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSSG 105

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 87.3 bits (217), Expect = 3e-21
 Identities = 25/92 (27%), Positives = 47/92 (51%), Gaps = 1/92 (1%)

Query: 316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEE 374
           +++ +   +YV  LD+ +S+  L ELF + G + +  + +D   G  +G GFV F + E+
Sbjct: 10  SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 69

Query: 375 ASKALTEMNGKMVVSKPLYVALAQRKEERRAR 406
           A  A+  M+   +  KP+ V  A    +  + 
Sbjct: 70  ADYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101

>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 = 82.3 bits (204), Expect = 2e-19
 Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           VYV  L E  +E  L ++F + G + +T + +D   G+ + +GFV F   +DA  +++ +
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77

Query: 280 NGKKFDDKEWYVGKAQKKYERE 301
           +  K   K   V KA    +  
Sbjct: 78  DMIKLYGKPIRVNKASAHNKNL 99

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 76.1 bits (188), Expect = 3e-17
 Identities = 23/82 (28%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNE 178
           P   ++    +++  LD+ +    L + F   G +++  +  D + GQ +GYGFV+F +E
Sbjct: 8   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67

Query: 179 ESAKSAIDKLNGMLLNDKQVFV 200
           E A  AI  ++ + L  K + V
Sbjct: 68  EDADYAIKIMDMIKLYGKPIRV 89

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score =  113 bits (286), Expect = 6e-31
 Identities = 28/90 (31%), Positives = 43/90 (47%), Gaps = 6/90 (6%)

Query: 323 NLYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKA 378
            +Y+ NL++ I  D+LK+    +FS FG I    V R      RG  FV F     A+ A
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNA 67

Query: 379 LTEMNGKMVVSKPLYVALAQRKEERRARLQ 408
           L  M G     KP+ +  A+   +  A+++
Sbjct: 68  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 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 = 88.4 bits (220), Expect = 9e-22
 Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 6/91 (6%)

Query: 219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
           + +Y+ NL+E   +D+LKK    IF  FG I    V R    K +   FV F +   A  
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS--LKMRGQAFVIFKEVSSATN 66

Query: 275 SVEALNGKKFDDKEWYVGKAQKKYEREMELK 305
           ++ ++ G  F DK   +  A+   +   ++K
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 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 = 78.0 bits (193), Expect = 5e-18
 Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 6/76 (7%)

Query: 129 NIFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
            I+I NL++ I      K+LH  FS FG IL   V+     + RG  FV F    SA +A
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS--LKMRGQAFVIFKEVSSATNA 67

Query: 185 IDKLNGMLLNDKQVFV 200
           +  + G    DK + +
Sbjct: 68  LRSMQGFPFYDKPMRI 83

>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 = 73.0 bits (180), Expect = 3e-16
 Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 7/85 (8%)

Query: 39  STSLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEA 94
           + ++Y+ +L+  +   +L    + +F++ GQ++ + V R L  R   G  +V +     A
Sbjct: 8   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSA 64

Query: 95  TRALDELNFTPLNGKPIRIMYSYRD 119
           T AL  +   P   KP+RI Y+  D
Sbjct: 65  TNALRSMQGFPFYDKPMRIQYAKTD 89

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score =  113 bits (285), Expect = 8e-31
 Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 2/87 (2%)

Query: 215 KTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
           K   N V+V  +     E +++  F  +G +    ++ D  G SK +GFV+F +  D  +
Sbjct: 6   KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65

Query: 275 SVEALNGKKFDDKEWYVGKAQKKYERE 301
            VE  +   F  K+  +G A +K    
Sbjct: 66  IVE--SQINFHGKKLKLGPAIRKQNLS 90

>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 =  109 bits (275), Expect = 2e-29
 Identities = 25/94 (26%), Positives = 49/94 (52%), Gaps = 2/94 (2%)

Query: 124 KSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKS 183
           K     +F+  +D  +D   +   F+ +G++   K+ TD  G S+GYGFV F N+   + 
Sbjct: 6   KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65

Query: 184 AIDKLNGMLLNDKQVFVGPFLRKQERESTADKTR 217
            ++  + +  + K++ +GP +RKQ   +   + R
Sbjct: 66  IVE--SQINFHGKKLKLGPAIRKQNLSTYHVQPR 97

>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 =  108 bits (271), Expect = 9e-29
 Identities = 22/94 (23%), Positives = 44/94 (46%), Gaps = 6/94 (6%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            ++V  +D  + + +++  F+ +G++   K++ D  G+S+G GFV+F    +  K +   
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV--E 68

Query: 383 NGKMVVSKPLYVALAQRKEERRARLQAQFSQMRP 416
           +      K L +  A RK+           Q RP
Sbjct: 69  SQINFHGKKLKLGPAIRKQNL----STYHVQPRP 98

>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 = 62.6 bits (153), Expect = 1e-12
 Identities = 16/75 (21%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             +++VG +D+ ++++++   F + G V  V++  D  T  S GYG+V++    +  + +
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIV 67

Query: 99  DELNFTPLNGKPIRI 113
           +  +    +GK +++
Sbjct: 68  E--SQINFHGKKLKL 80

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score =  108 bits (271), Expect = 6e-29
 Identities = 23/82 (28%), Positives = 44/82 (53%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              ++VGDL   +  + +   F   G++   RV +D++T +S GYG+V++    +A  A+
Sbjct: 6   HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 65

Query: 99  DELNFTPLNGKPIRIMYSYRDP 120
            ++    L G+ IR  ++ R P
Sbjct: 66  QQMGGQWLGGRQIRTNWATRKP 87

>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 = 96.1 bits (240), Expect = 1e-24
 Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           +++V +L   I+   +   F+ FG I+  +V++D   G S+G GFV+F    +A  A+ +
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 382 MNGKMVVSKPLYVALAQRK 400
           M G+ +  + +    A RK
Sbjct: 68  MGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 85.7 bits (213), Expect = 7e-21
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 1/79 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
           +V+V +LS   T   +   F  FG I+   V++D   GKSK +GFV+F +  DA  +++ 
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 279 LNGKKFDDKEWYVGKAQKK 297
           + G+    ++     A +K
Sbjct: 68  MGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 79.1 bits (196), Expect = 1e-18
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           ++F+ +L   I   A+   F+ FG I   +V  D   G+S+GYGFV F N+  A++AI +
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 188 LNGMLLNDKQVFVG 201
           + G  L  +Q+   
Sbjct: 68  MGGQWLGGRQIRTN 81

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score =  108 bits (271), Expect = 1e-28
 Identities = 26/101 (25%), Positives = 51/101 (50%), Gaps = 4/101 (3%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
            +Y++NL    T +++  IFG++G I    V      +++   +V ++D  DA  +V+ L
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHL 67

Query: 280 NGKKFDDKEWYVGKAQ-KKYEREMELKGKFEQSLKETADKF 319
           +G    ++   V      +  ++M+ K K EQ LK   +K+
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQ-LKLLKEKY 107

>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 = 92.8 bits (231), Expect = 4e-23
 Identities = 20/94 (21%), Positives = 48/94 (51%), Gaps = 3/94 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            LY++NL   I+ +++ ++F ++G I   +V   P   +RG+ +V +    +A  A+  +
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDHL 67

Query: 383 NGKMVVSKPLYVALAQ-RKEERRARLQAQFSQMR 415
           +G  V ++ L V      +  ++   + +  Q++
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLK 101

>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 = 83.2 bits (206), Expect = 1e-19
 Identities = 20/90 (22%), Positives = 46/90 (51%), Gaps = 2/90 (2%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            ++I+NL   I  + ++D F  +G I   +V      ++RG  +V +++   AK+A+D L
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHL 67

Query: 189 NGMLLNDKQVFVGPFLRKQERESTADKTRF 218
           +G  ++++ + V  +   +  +    K + 
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDTKKKE 97

>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 = 78.6 bits (194), Expect = 5e-18
 Identities = 22/88 (25%), Positives = 43/88 (48%), Gaps = 3/88 (3%)

Query: 38  VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
           V+  LY+ +L   +   ++YD+F + G +  +RV     TR   G  YV Y    +A  A
Sbjct: 7   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNA 63

Query: 98  LDELNFTPLNGKPIRIMYSYRDPTIRKS 125
           +D L+   ++ + + ++Y   +   +K 
Sbjct: 64  VDHLSGFNVSNRYLVVLYYNANRAFQKM 91

>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 =  108 bits (271), Expect = 1e-28
 Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 1/84 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
            LY+KNL   +++  L  LF+ F       +      G  RG  F+ F   E A +AL  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 382 MNGKMVVSKPLYVALAQRKEERRA 405
           +NG  +  K L +   + K++R +
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQRSS 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 =  100 bits (252), Expect = 6e-26
 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 1/84 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
             +Y+KNLS   TE DL  +F  F       +      G+ +   F+ F + + A +++ 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 278 ALNGKKFDDKEWYVGKAQKKYERE 301
            +NG K   K   +   + K +R 
Sbjct: 86  LVNGYKLYGKILVIEFGKNKKQRS 109

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 85.8 bits (213), Expect = 1e-20
 Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 1/85 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
            +++KNL   +  + L   F+ F       +    + G+ RG  F+ F N+E A  A+  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 188 LNGMLLNDKQVFVGPFLRKQEREST 212
           +NG  L  K + +     K++R S 
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQRSSG 111

>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 = 81.6 bits (202), Expect = 4e-19
 Identities = 18/78 (23%), Positives = 33/78 (42%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           +  LY+ +L   V +  L  LF +  +     +   + T R  G  ++ +     A +AL
Sbjct: 25  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84

Query: 99  DELNFTPLNGKPIRIMYS 116
             +N   L GK + I + 
Sbjct: 85  HLVNGYKLYGKILVIEFG 102

>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 =  106 bits (267), Expect = 2e-28
 Identities = 28/80 (35%), Positives = 48/80 (60%), Gaps = 1/80 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           NL+V +L+ ++ D+ L+  F +F +  S  VM D   G SRG GFV+F++ ++A  A+  
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 382 MNGKMVVSKPLYVALAQRKE 401
           M G+ +  +PL +  A + E
Sbjct: 63  MQGQDLNGRPLRINWAAKLE 82

>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 = 94.5 bits (236), Expect = 5e-24
 Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
            N++V +L+    ++ L+  F +F    S  VM D   G S+ +GFV+F   DDA  +++
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 278 ALNGKKFDDKEWYVGKAQKK 297
           ++ G+  + +   +  A K 
Sbjct: 62  SMQGQDLNGRPLRINWAAKL 81

>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 = 90.6 bits (226), Expect = 1e-22
 Identities = 27/82 (32%), Positives = 49/82 (59%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           + +L+VGDL+++V+D  L + F      +S  V  D+ T  S GYG+V++ +  +A  A+
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60

Query: 99  DELNFTPLNGKPIRIMYSYRDP 120
           D +    LNG+P+RI ++ +  
Sbjct: 61  DSMQGQDLNGRPLRINWAAKLE 82

>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 = 84.9 bits (211), Expect = 1e-20
 Identities = 26/73 (35%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+F+ +L+ ++D++ L + F  F + LS  V  D   G SRGYGFV F +++ A++A+D 
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 188 LNGMLLNDKQVFV 200
           + G  LN + + +
Sbjct: 63  MQGQDLNGRPLRI 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 =  105 bits (263), Expect = 1e-27
 Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           NL++ NL+ + S  +LK   SE        V+    G +R  G+V F +AE+  KAL E+
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-EL 77

Query: 383 NGKMVVSKPLYVALAQRKEERRA 405
            G  V    + +   + ++  R 
Sbjct: 78  TGLKVFGNEIKLEKPKGRDGTRG 100

>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 = 95.8 bits (239), Expect = 2e-24
 Identities = 21/95 (22%), Positives = 44/95 (46%), Gaps = 1/95 (1%)

Query: 207 QERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNF 266
           ++    ++ T   N+++ NL+   +  +LK    E       AV+    G ++ FG+V+F
Sbjct: 6   EDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 65

Query: 267 DDPDDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
           +  +D  +++E L G K    E  + K + +    
Sbjct: 66  ESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDGTR 99

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 77.3 bits (191), Expect = 1e-17
 Identities = 20/99 (20%), Positives = 40/99 (40%), Gaps = 4/99 (4%)

Query: 114 MYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFV 173
           M          +   N+FI NL+ +     L    S         V     G +R +G+V
Sbjct: 4   MLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYV 63

Query: 174 QFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST 212
            F++ E  + A++ L G+ +   ++ +    + + R+ T
Sbjct: 64  DFESAEDLEKALE-LTGLKVFGNEIKLE---KPKGRDGT 98

>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 = 70.0 bits (172), Expect = 4e-15
 Identities = 17/78 (21%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             +L++G+L+ + + ++L    +++     + V  D+ T  +  +GYV++ +A +  +AL
Sbjct: 17  PFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAEDLEKAL 75

Query: 99  DELNFTPLNGKPIRIMYS 116
            EL    + G  I++   
Sbjct: 76  -ELTGLKVFGNEIKLEKP 92

>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 =  103 bits (260), Expect = 3e-27
 Identities = 26/96 (27%), Positives = 50/96 (52%), Gaps = 6/96 (6%)

Query: 32  GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQ-VVSVRVCRDLSTRRSLGYGYVNYNA 90
                 ++ SL++GDL+  ++++ +   F  MG+ V+SV++ R+  T    GY +V +  
Sbjct: 2   SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61

Query: 91  AHEATRALDELNFTPLNG----KPIRIMY-SYRDPT 121
              A + L ++N  PL G    K  ++ Y +Y  P+
Sbjct: 62  LATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPS 97

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 77.0 bits (190), Expect = 1e-17
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 315 TADKFEGLNLYVKNLDDSISDDKLKELFSEFG-TITSCKVMRDP-NGISRGSGFVAFSTA 372
           +       +L++ +L+  + ++ +   F+  G T+ S K++R+   GI  G  FV F+  
Sbjct: 3   SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62

Query: 373 EEASKALTEMNGKMV 387
             A K L ++NGK +
Sbjct: 63  ATAEKCLHKINGKPL 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 = 76.6 bits (189), Expect = 2e-17
 Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFG-NILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID 186
           ++++ +L+  +D   +   F+T G  ++S K+  + L G   GY FV+F +  +A+  + 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 187 KLNGMLLNDKQVFV 200
           K+NG  L       
Sbjct: 71  KINGKPLPGATPAK 84

>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 = 73.9 bits (182), Expect = 2e-16
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDAD-GKSKCFGFVNFDD 268
           S+       ++++ +L     E+ + + F   G  + S  ++R+   G    + FV F D
Sbjct: 2   SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61

Query: 269 PDDAARSVEALNGKKFDDKE 288
              A + +  +NGK      
Sbjct: 62  LATAEKCLHKINGKPLPGAT 81

>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 =  101 bits (255), Expect = 2e-26
 Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 5/83 (6%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            LYV+NL  S S++ +++ F+        +V +      R   FV FS  E+A +A+  +
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKAL 71

Query: 383 NGKMVVSKPLYVALAQRKEERRA 405
           NGK++   P+ V LA+  ++  +
Sbjct: 72  NGKVLDGSPIEVTLAKPVDKDSS 94

>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 = 95.0 bits (237), Expect = 5e-24
 Identities = 25/93 (26%), Positives = 43/93 (46%), Gaps = 7/93 (7%)

Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDP 269
           E T    +   +YV+NL  +T+E+ ++K F          V      K + + FV+F + 
Sbjct: 9   EDTMSSVK--ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVHFSNR 61

Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKKYEREM 302
           +DA  +++ALNGK  D     V  A+   +   
Sbjct: 62  EDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSS 94

>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 = 76.5 bits (189), Expect = 2e-17
 Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 6/87 (6%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            ++++NL  S   + +   F+        +V      + R Y FV F N E A  A+  L
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKAL 71

Query: 189 NGMLLNDKQVFVGPFLRKQERESTADK 215
           NG +L+   + V    +  +++S+   
Sbjct: 72  NGKVLDGSPIEVT-LAKPVDKDSSGPS 97

>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 = 71.5 bits (176), Expect = 1e-15
 Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 9/91 (9%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              LYV +L LS ++  +   FN +      RV      ++   Y +V+++   +A  A+
Sbjct: 15  VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAM 68

Query: 99  DELNFTPLNGKPIRIMYS---YRDPTIRKSG 126
             LN   L+G PI +  +    +D +   SG
Sbjct: 69  KALNGKVLDGSPIEVTLAKPVDKDSSGPSSG 99

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

 Score =  102 bits (255), Expect = 2e-26
 Identities = 14/96 (14%), Positives = 41/96 (42%), Gaps = 1/96 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            +    L+D++ +  LK++  ++G +   +++  P      G   V F++   A + +  
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 382 MNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPP 417
           ++   V+   ++  L  + ++R    +   +    P
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTP 103

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

 Score = 87.8 bits (218), Expect = 3e-21
 Identities = 17/78 (21%), Positives = 32/78 (41%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              +    L+ +V ++ L D+  + G+V  V +     TR+ LG   V + +   A   +
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 99  DELNFTPLNGKPIRIMYS 116
             L+ T + G  I     
Sbjct: 66  KNLHLTSVMGNIIHAQLD 83

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

 Score = 87.1 bits (216), Expect = 4e-21
 Identities = 14/84 (16%), Positives = 27/84 (32%), Gaps = 1/84 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
             V    L++   E  LK +  ++G +    ++      K      V F     A  +V+
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 278 ALNGKKFDDKEWYVGKAQKKYERE 301
            L+         +     K  +R 
Sbjct: 67  NLHLTSVMGNIIHAQLDIKGQQRM 90

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

 Score = 86.3 bits (214), Expect = 9e-21
 Identities = 10/85 (11%), Positives = 28/85 (32%), Gaps = 3/85 (3%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
            +    L+ ++    L D    +G +   ++       +  G   V F +   AK  +  
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 188 LNGMLLNDKQVFVG--PFLRKQERE 210
           L+   +    +        +++ + 
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRMKY 92

>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 =  100 bits (251), Expect = 6e-26
 Identities = 27/95 (28%), Positives = 41/95 (43%), Gaps = 7/95 (7%)

Query: 311 SLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFS 370
           S  E     +G  LYV   D  ++   L+  FS FG I    +        R   FV + 
Sbjct: 5   SSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYE 57

Query: 371 TAEEASKALTEMNGKMVVSKPLYVALAQRKEERRA 405
             E A +A+ E+NG  V S  L V +A+++    +
Sbjct: 58  KMESADQAVAELNGTQVESVQLKVNIARKQPMLDS 92

>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 = 78.9 bits (195), Expect = 3e-18
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 7/83 (8%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N +YV       T   L+  F  FG I   ++        +   FV ++  + A ++V  
Sbjct: 16  NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAE 68

Query: 279 LNGKKFDDKEWYVGKAQKKYERE 301
           LNG + +  +  V  A+K+   +
Sbjct: 69  LNGTQVESVQLKVNIARKQPMLD 91

>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 = 77.7 bits (192), Expect = 6e-18
 Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 7/83 (8%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            +++   D  +    L   FS FGNI+   +        R   FV ++  ESA  A+ +L
Sbjct: 17  TLYVYGED--MTPTLLRGAFSPFGNIIDLSM-----DPPRNCAFVTYEKMESADQAVAEL 69

Query: 189 NGMLLNDKQVFVGPFLRKQERES 211
           NG  +   Q+ V    ++   +S
Sbjct: 70  NGTQVESVQLKVNIARKQPMLDS 92

>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 = 64.6 bits (158), Expect = 3e-13
 Identities = 18/90 (20%), Positives = 36/90 (40%), Gaps = 9/90 (10%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
            +LYV   D  +  + L   F+  G ++ + +             +V Y     A +A+ 
Sbjct: 16  NTLYVYGED--MTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVA 67

Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
           ELN T +    +++  + R   +  SG  +
Sbjct: 68  ELNGTQVESVQLKVNIA-RKQPMLDSGPSS 96

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score =  100 bits (251), Expect = 7e-26
 Identities = 26/102 (25%), Positives = 49/102 (48%), Gaps = 1/102 (0%)

Query: 317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEA 375
           D     +++V +L   I+ + +K  F+ FG I+  +V++D   G S+G GFV+F    +A
Sbjct: 11  DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70

Query: 376 SKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPP 417
             A+ +M G+ +  + +    A RK           ++   P
Sbjct: 71  ENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGP 112

>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 = 98.2 bits (245), Expect = 5e-25
 Identities = 25/91 (27%), Positives = 46/91 (50%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              ++VGDL   +    +   F   G++   RV +D++T +S GYG+V++    +A  A+
Sbjct: 15  HFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 74

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
            ++    L G+ IR  ++ R P   KS   +
Sbjct: 75  QQMGGQWLGGRQIRTNWATRKPPAPKSTYES 105

>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 = 87.8 bits (218), Expect = 3e-21
 Identities = 28/101 (27%), Positives = 52/101 (51%), Gaps = 4/101 (3%)

Query: 201 GPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSK 259
           G      +++ T++     +V+V +LS   T +D+K  F  FG I+   V++D   GKSK
Sbjct: 1   GSSGSSGQKKDTSNHF---HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSK 57

Query: 260 CFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
            +GFV+F +  DA  +++ + G+    ++     A +K   
Sbjct: 58  GYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPA 98

>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 = 82.8 bits (205), Expect = 2e-19
 Identities = 27/97 (27%), Positives = 47/97 (48%), Gaps = 1/97 (1%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKS 183
           S   ++F+ +L   I  + +   F+ FG I   +V  D   G+S+GYGFV F N+  A++
Sbjct: 13  SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 72

Query: 184 AIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNN 220
           AI ++ G  L  +Q+      RK     +  ++    
Sbjct: 73  AIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQ 109

>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 =  100 bits (250), Expect = 8e-26
 Identities = 24/96 (25%), Positives = 47/96 (48%), Gaps = 1/96 (1%)

Query: 311 SLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFS 370
           S   +  K     L+V N+     D  L+++F +FG I   +++ +  G S+G GFV F 
Sbjct: 5   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFE 63

Query: 371 TAEEASKALTEMNGKMVVSKPLYVALAQRKEERRAR 406
            + +A +A  +++G +V  + + V  A  +    + 
Sbjct: 64  NSADADRAREKLHGTVVEGRKIEVNNATARVMTNSG 99

>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 = 99.7 bits (249), Expect = 1e-25
 Identities = 26/93 (27%), Positives = 48/93 (51%), Gaps = 1/93 (1%)

Query: 209 RESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDD 268
             ++  K+    ++V N+     + DL+++FG+FG I    ++ +  G SK FGFV F++
Sbjct: 6   SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFEN 64

Query: 269 PDDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
             DA R+ E L+G   + ++  V  A  +    
Sbjct: 65  SADADRAREKLHGTVVEGRKIEVNNATARVMTN 97

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 89.3 bits (222), Expect = 7e-22
 Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 1/95 (1%)

Query: 118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDN 177
              +  KS    + + N+     +  L   F  FG IL  ++  +    S+G+GFV F+N
Sbjct: 6   SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-RGSKGFGFVTFEN 64

Query: 178 EESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST 212
              A  A +KL+G ++  +++ V     +    S 
Sbjct: 65  SADADRAREKLHGTVVEGRKIEVNNATARVMTNSG 99

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 72.7 bits (179), Expect = 4e-16
 Identities = 22/91 (24%), Positives = 45/91 (49%), Gaps = 3/91 (3%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              L+V ++     D  L  +F Q G+++ V +  +   R S G+G+V +  + +A RA 
Sbjct: 15  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAR 72

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
           ++L+ T + G+ I +  +     +  SG  +
Sbjct: 73  EKLHGTVVEGRKIEVNNA-TARVMTNSGPSS 102

>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 =  102 bits (255), Expect = 4e-25
 Identities = 34/201 (16%), Positives = 65/201 (32%), Gaps = 17/201 (8%)

Query: 261 FGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFE 320
           +G  +  D  D   S  A NG   +D+++         +   +                +
Sbjct: 12  YGGHDQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAA----PNVVYTYTGK 67

Query: 321 GLNLYVKNLDDSISDDKLKELFSEFGT--ITSCKVMRDP-NGISRGSGFVAFSTAEEASK 377
            + LY+ NL    +D+ L E     G   I   K   +  NG S+G   V   +   + K
Sbjct: 68  RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 127

Query: 378 ALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR----------PPVGPRMPMYPP 427
            +  +  + +  +   V    ++   +  +Q++ +             PP G     +P 
Sbjct: 128 LMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQ 187

Query: 428 VAPGLGQQLFYGQGPPIIPPQ 448
              G G+      G    P  
Sbjct: 188 GGRGRGRFPGAVPGGDRFPGP 208

>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 = 87.9 bits (217), Expect = 5e-20
 Identities = 19/98 (19%), Positives = 43/98 (43%), Gaps = 3/98 (3%)

Query: 213 ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGI--ITSTAVMRD-ADGKSKCFGFVNFDDP 269
               +   +Y+ NL+  TT++DL +     G+  I       + A+G+SK F  V     
Sbjct: 63  TYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSE 122

Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGK 307
             + + ++ L  ++   +   V    K++  + E++ +
Sbjct: 123 ASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSR 160

>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 = 76.7 bits (188), Expect = 4e-16
 Identities = 18/121 (14%), Positives = 44/121 (36%), Gaps = 4/121 (3%)

Query: 2   AQVQVQPQAPVAVAAQPSPATNGIANNGG--VGDARQFVSTSLYVGDLDLSVNDSQLYDL 59
           A     P+    +   P    + +       V         +LY+G+L     D  L + 
Sbjct: 29  ANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEA 88

Query: 60  FNQMG--QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY 117
            + +G   ++ ++   + +  +S G+  V   +   + + +D L    L+G+   +    
Sbjct: 89  VHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVN 148

Query: 118 R 118
           +
Sbjct: 149 K 149

>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 = 73.6 bits (180), Expect = 4e-15
 Identities = 21/92 (22%), Positives = 40/92 (43%), Gaps = 3/92 (3%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFG--NILSCKVATDSL-GQSRGYGFVQFDNEESAKSAI 185
            ++I NL     ++ L +   + G  +IL  K   +   GQS+G+  V   +E S+K  +
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 186 DKLNGMLLNDKQVFVGPFLRKQERESTADKTR 217
           D L    L+ +   V P  ++   +      +
Sbjct: 130 DLLPKRELHGQNPVVTPVNKQFLSQFEMQSRK 161

>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 = 99.9 bits (249), Expect = 4e-25
 Identities = 25/91 (27%), Positives = 47/91 (51%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S +LYVG+L     + Q+Y+LF++ G +  + +  D   + + G+ +V Y +  +A  A+
Sbjct: 39  SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
             +N T L+ + IR  +       R+ G G 
Sbjct: 99  RYINGTRLDDRIIRTDWDAGFKEGRQYGRGR 129

>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 = 79.8 bits (197), Expect = 5e-18
 Identities = 27/120 (22%), Positives = 52/120 (43%), Gaps = 7/120 (5%)

Query: 286 DKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEF 345
             + YV  +Q + +       + E+ LK++        LYV NL    +++++ ELFS+ 
Sbjct: 10  RSDSYVELSQYRDQHFRGDNEEQEKLLKKSC------TLYVGNLSFYTTEEQIYELFSKS 63

Query: 346 GTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERR 404
           G I    +  D     + G  FV + +  +A  A+  +NG  +  + +        +E R
Sbjct: 64  GDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGR 123

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 77.9 bits (192), Expect = 2e-17
 Identities = 24/98 (24%), Positives = 39/98 (39%), Gaps = 1/98 (1%)

Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGF 263
           R    E      +   +YV NLS  TTE+ + ++F + G I    +  D     +  F F
Sbjct: 26  RGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCF 85

Query: 264 VNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
           V +    DA  ++  +NG + DD+           E  
Sbjct: 86  VEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGR 123

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 72.5 bits (178), Expect = 2e-15
 Identities = 16/86 (18%), Positives = 40/86 (46%), Gaps = 1/86 (1%)

Query: 116 SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQ 174
              +       +  +++ NL      + +++ FS  G+I    +  D +   + G+ FV+
Sbjct: 28  DNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVE 87

Query: 175 FDNEESAKSAIDKLNGMLLNDKQVFV 200
           + +   A++A+  +NG  L+D+ +  
Sbjct: 88  YYSRADAENAMRYINGTRLDDRIIRT 113

>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 = 96.8 bits (242), Expect = 7e-25
 Identities = 19/86 (22%), Positives = 43/86 (50%), Gaps = 2/86 (2%)

Query: 217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD--GKSKCFGFVNFDDPDDAAR 274
           +   V++  L+   T+D + +IF  +G I    +  +      SK + +V F++PD+A +
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 275 SVEALNGKKFDDKEWYVGKAQKKYER 300
           +++ ++G + D +E         + R
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAPWPR 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 = 89.5 bits (223), Expect = 3e-22
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN--GISRGSGFVAFSTAEEASKALT 380
            +++  L  +++ D + E+FS +G I    +  +     +S+G  +V F   +EA KAL 
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 381 EMNGKMVVSKPLYVALAQRKEER 403
            M+G  +  + +          R
Sbjct: 66  HMDGGQIDGQEITATAVLAPWPR 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 = 80.7 bits (200), Expect = 5e-19
 Identities = 18/83 (21%), Positives = 42/83 (50%), Gaps = 2/83 (2%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL--GQSRGYGFVQFDNEESAKSAID 186
            + I  L +++    + + FST+G I    +  + +    S+GY +V+F+N + A+ A+ 
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 187 KLNGMLLNDKQVFVGPFLRKQER 209
            ++G  ++ +++     L    R
Sbjct: 66  HMDGGQIDGQEITATAVLAPWPR 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 = 71.0 bits (175), Expect = 1e-15
 Identities = 17/76 (22%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRD-LSTRRSLGYGYVNYNAAHEATRA 97
            T +++G L  +V    + ++F+  G++  + +  + +    S GY YV +    EA +A
Sbjct: 4   PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63

Query: 98  LDELNFTPLNGKPIRI 113
           L  ++   ++G+ I  
Sbjct: 64  LKHMDGGQIDGQEITA 79

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 95.7 bits (239), Expect = 2e-24
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
            +Y++ L   TT+ DL K+   +G I ST  + D    K K +GFV+FD P  A ++V A
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 279 LNGKKFDDKEWYVGKAQ 295
           L       +        
Sbjct: 67  LKASGVQAQMAKQSGPS 83

>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 = 94.5 bits (236), Expect = 5e-24
 Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 1/80 (1%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKA 378
               LY++ L    +D  L +L   +G I S K + D      +G GFV F +   A KA
Sbjct: 4   GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63

Query: 379 LTEMNGKMVVSKPLYVALAQ 398
           +T +    V ++    +   
Sbjct: 64  VTALKASGVQAQMAKQSGPS 83

>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 = 88.4 bits (220), Expect = 8e-22
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKS 183
           SG+  ++I+ L     ++ L      +G I+S K   D    + +GYGFV FD+  +A+ 
Sbjct: 3   SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62

Query: 184 AIDKLNGMLLNDKQVFV 200
           A+  L    +  +    
Sbjct: 63  AVTALKASGVQAQMAKQ 79

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 76.8 bits (190), Expect = 9e-18
 Identities = 19/74 (25%), Positives = 37/74 (50%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S+ LY+  L     D  L  L    G++VS +   D +T +  GYG+V++++   A +A+
Sbjct: 5   SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64

Query: 99  DELNFTPLNGKPIR 112
             L  + +  +  +
Sbjct: 65  TALKASGVQAQMAK 78

>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 = 98.0 bits (244), Expect = 3e-24
 Identities = 26/135 (19%), Positives = 54/135 (40%), Gaps = 6/135 (4%)

Query: 175 FDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTR-----FNNVYVKNLSET 229
              +E AK    +  G   N ++        + E +   +           ++V ++ E 
Sbjct: 24  VRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEE 83

Query: 230 TTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKE 288
             ED++++ F ++G I +  +  D   G SK +  V ++    A  + EALNG +   + 
Sbjct: 84  AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT 143

Query: 289 WYVGKAQKKYEREME 303
             V     K  + ++
Sbjct: 144 IQVDWCFVKGPKRVK 158

>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 = 91.0 bits (226), Expect = 9e-22
 Identities = 31/154 (20%), Positives = 67/154 (43%), Gaps = 19/154 (12%)

Query: 265 NFDDPDDAARSVEAL-----------NGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLK 313
            F+  +D  + +  L            G   + +E      + + E + EL+   ++S+ 
Sbjct: 12  EFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSV- 70

Query: 314 ETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTA 372
                 EG  L+V ++ +   +D+++E F ++G I +  +  D   G S+G   V + T 
Sbjct: 71  ------EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124

Query: 373 EEASKALTEMNGKMVVSKPLYVALAQRKEERRAR 406
           ++A  A   +NG  ++ + + V     K  +R +
Sbjct: 125 KQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVK 158

>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 = 77.6 bits (191), Expect = 4e-17
 Identities = 19/96 (19%), Positives = 41/96 (42%), Gaps = 1/96 (1%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESA 181
           R      +F+ ++ +      + + F  +G I +  +  D   G S+GY  V+++  + A
Sbjct: 68  RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQA 127

Query: 182 KSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTR 217
            +A + LNG  +  + + V     K  +     + R
Sbjct: 128 LAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKR 163

>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 = 76.4 bits (188), Expect = 1e-16
 Identities = 21/101 (20%), Positives = 41/101 (40%), Gaps = 1/101 (0%)

Query: 27  NNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYV 86
           +    G  R      L+V  +     + ++ + F   G++ ++ +  D  T  S GY  V
Sbjct: 60  DELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 119

Query: 87  NYNAAHEATRALDELNFTPLNGKPIRIMYS-YRDPTIRKSG 126
            Y    +A  A + LN   + G+ I++ +   + P   K  
Sbjct: 120 EYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKS 160

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 94.8 bits (236), Expect = 7e-24
 Identities = 22/96 (22%), Positives = 44/96 (45%), Gaps = 8/96 (8%)

Query: 317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEAS 376
           +  +  ++Y+K      + D +KE   + G + + ++ R  +   +GS FV F + E A 
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66

Query: 377 KALTEMNGK------MVVSKPLYVALAQRKEERRAR 406
           K +     K      +++ K  Y   A++ EER+  
Sbjct: 67  KFVETPGQKYKETDLLILFKDDYF--AKKNEERKQN 100

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 92.5 bits (230), Expect = 4e-23
 Identities = 21/97 (21%), Positives = 42/97 (43%), Gaps = 1/97 (1%)

Query: 209 RESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDD 268
           R    +  +  +VY+K      T DD+K+   + G + +  + R      K   FV FD 
Sbjct: 2   RWILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDS 61

Query: 269 PDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELK 305
            + A + VE   G+K+ + +  +      + ++ E +
Sbjct: 62  IESAKKFVE-TPGQKYKETDLLILFKDDYFAKKNEER 97

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 66.3 bits (162), Expect = 8e-14
 Identities = 17/90 (18%), Positives = 36/90 (40%), Gaps = 4/90 (4%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +++IK          + +     G +L+ ++        +G  FV FD+ ESAK  + + 
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ET 71

Query: 189 NGMLLNDKQVFVGP---FLRKQERESTADK 215
            G    +  + +     +  K+  E   +K
Sbjct: 72  PGQKYKETDLLILFKDDYFAKKNEERKQNK 101

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 55.9 bits (135), Expect = 4e-10
 Identities = 11/80 (13%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 35  RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEA 94
               + S+Y+           + +     GQV+++++ R    +   G  +V +++   A
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESA 65

Query: 95  TRALDELNFTPLNGKPIRIM 114
            + + E          + I+
Sbjct: 66  KKFV-ETPGQKYKETDLLIL 84

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

 Score = 95.0 bits (236), Expect = 1e-23
 Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 6/88 (6%)

Query: 323 NLYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKA 378
            + + N++  +  +KL+     L S  G I    V    +  + G  ++ F+T E A   
Sbjct: 31  VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDD--NSGKAYIVFATQESAQAF 88

Query: 379 LTEMNGKMVVSKPLYVALAQRKEERRAR 406
           +    G      PL +  ++  + + A 
Sbjct: 89  VEAFQGYPFQGNPLVITFSETPQSQVAE 116

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

 Score = 77.2 bits (190), Expect = 2e-17
 Identities = 16/112 (14%), Positives = 32/112 (28%), Gaps = 7/112 (6%)

Query: 207 QERESTADKTRFNNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFG 262
               +         V + N++    ++ L+     +    G I    V       +    
Sbjct: 18  DLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLS--DDNSGKA 75

Query: 263 FVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKE 314
           ++ F   + A   VEA  G  F      +  ++    +  E  G  E     
Sbjct: 76  YIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAE-DGSLEHHHHH 126

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

 Score = 74.2 bits (182), Expect = 3e-16
 Identities = 18/109 (16%), Positives = 39/109 (35%), Gaps = 7/109 (6%)

Query: 15  AAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQL----YDLFNQMGQVVSVR 70
           AA      +  + + G        S  + + +++  V   +L    Y L +  G ++ + 
Sbjct: 5   AAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIV 64

Query: 71  VCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRD 119
           V     +  + G  Y+ +     A   ++     P  G P+ I +S   
Sbjct: 65  VDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETP 110

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

 Score = 72.2 bits (177), Expect = 1e-15
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 129 NIFIKNLDKSIDN----KALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
            + I N++  +        L+   S+ G+IL   V       + G  ++ F  +ESA++ 
Sbjct: 31  VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLS--DDNSGKAYIVFATQESAQAF 88

Query: 185 IDKLNGMLLNDKQVFV 200
           ++   G       + +
Sbjct: 89  VEAFQGYPFQGNPLVI 104

>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 = 93.9 bits (234), Expect = 1e-23
 Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 5/84 (5%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            L+V NL   I+++++++LF ++G      + +D     +G GF+   T   A  A  E+
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVEL 71

Query: 383 NGKMVVSKPLYVALAQRKEERRAR 406
           +   +  K L V  A       + 
Sbjct: 72  DNMPLRGKQLRVRFACHSASLTSG 95

>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 = 86.9 bits (216), Expect = 4e-21
 Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAA 273
             T+ + ++V NL    TE++++K+F ++G      + +D     K FGF+  +    A 
Sbjct: 11  TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAE 65

Query: 274 RSVEALNGKKFDDKEWYVGKAQKKYERE 301
            +   L+      K+  V  A       
Sbjct: 66  IAKVELDNMPLRGKQLRVRFACHSASLT 93

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 76.9 bits (190), Expect = 1e-17
 Identities = 19/92 (20%), Positives = 35/92 (38%), Gaps = 5/92 (5%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAK 182
             +    +F+ NL   I  + +   F  +G      +  D     +G+GF++ +    A+
Sbjct: 11  TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAE 65

Query: 183 SAIDKLNGMLLNDKQVFVGPFLRKQERESTAD 214
            A  +L+ M L  KQ+ V          S   
Sbjct: 66  IAKVELDNMPLRGKQLRVRFACHSASLTSGPS 97

>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 = 72.7 bits (179), Expect = 5e-16
 Identities = 25/102 (24%), Positives = 48/102 (47%), Gaps = 8/102 (7%)

Query: 26  ANNGGVGDARQFV-STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYG 84
            ++G  G  + F   + L+VG+L   + + ++  LF + G+   V + +D   +   G+G
Sbjct: 1   GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD---K---GFG 54

Query: 85  YVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSG 126
           ++       A  A  EL+  PL GK +R+ ++        SG
Sbjct: 55  FIRLETRTLAEIAKVELDNMPLRGKQLRVRFA-CHSASLTSG 95

>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 = 94.0 bits (234), Expect = 3e-23
 Identities = 29/88 (32%), Positives = 47/88 (53%), Gaps = 1/88 (1%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKA 378
              NL V  +  ++ + +L++LF  +G I S K++ D     SRG GFV F +   A +A
Sbjct: 41  VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100

Query: 379 LTEMNGKMVVSKPLYVALAQRKEERRAR 406
           +  +NG  +++K L VALA    +R   
Sbjct: 101 IAGLNGFNILNKRLKVALAASGHQRPGI 128

>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 = 91.7 bits (228), Expect = 2e-22
 Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 1/83 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
            N+ V  +  T  E  L+++F  +G I S  ++ D +  +S+ +GFV F     A +++ 
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102

Query: 278 ALNGKKFDDKEWYVGKAQKKYER 300
            LNG    +K   V  A   ++R
Sbjct: 103 GLNGFNILNKRLKVALAASGHQR 125

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 91.0 bits (226), Expect = 4e-22
 Identities = 37/142 (26%), Positives = 60/142 (42%), Gaps = 7/142 (4%)

Query: 83  YGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNK 142
              V+    +  T  L +L       + I       +P + +    N+ +  +  ++D  
Sbjct: 4   IPLVSQYDPYGQTAQLQQLQ--QQQQQHIPPTQMNPEPDVLR----NLMVNYIPTTVDEV 57

Query: 143 ALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVG 201
            L   F  +G I S K+  D    QSRGYGFV+F +  SA+ AI  LNG  + +K++ V 
Sbjct: 58  QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117

Query: 202 PFLRKQERESTADKTRFNNVYV 223
                 +R   A      N Y+
Sbjct: 118 LAASGHQRPGIAGAVGDGNGYL 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 = 87.1 bits (216), Expect = 1e-20
 Identities = 34/139 (24%), Positives = 58/139 (41%), Gaps = 7/139 (5%)

Query: 1   MAQV-QVQPQAPVAVAAQPSPATNGIANNGGVGDARQF--VSTSLYVGDLDLSVNDSQLY 57
           M+Q+  V    P    AQ          +           V  +L V  +  +V++ QL 
Sbjct: 1   MSQIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLR 60

Query: 58  DLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY-- 115
            LF + G + SV++  D  TR+S GYG+V + +   A +A+  LN   +  K +++    
Sbjct: 61  QLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA 120

Query: 116 --SYRDPTIRKSGAGNIFI 132
               R       G GN ++
Sbjct: 121 SGHQRPGIAGAVGDGNGYL 139

>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 = 92.7 bits (231), Expect = 3e-23
 Identities = 26/85 (30%), Positives = 39/85 (45%), Gaps = 1/85 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            LYV  L + + D  L   F  FG IT  ++  D      RG  FV F  AE+A+ A+  
Sbjct: 14  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73

Query: 382 MNGKMVVSKPLYVALAQRKEERRAR 406
           MN   +  + + V LA+    + + 
Sbjct: 74  MNESELFGRTIRVNLAKPMRIKESG 98

>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 = 89.6 bits (223), Expect = 5e-22
 Identities = 25/94 (26%), Positives = 42/94 (44%), Gaps = 1/94 (1%)

Query: 209 RESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFD 267
             S+   T    +YV  L+E   +  L   F  FG IT   +  D +  K + F FV F+
Sbjct: 3   SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 62

Query: 268 DPDDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
             +DAA +++ +N  +   +   V  A+    +E
Sbjct: 63  LAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKE 96

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 78.8 bits (195), Expect = 3e-18
 Identities = 29/103 (28%), Positives = 51/103 (49%), Gaps = 3/103 (2%)

Query: 26  ANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGY 85
            ++G  G A       LYVG L   V+D  L+  F   G +  +++  D  T +  G+ +
Sbjct: 1   GSSGSSGMATT--KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAF 58

Query: 86  VNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAG 128
           V +  A +A  A+D +N + L G+ IR+  + +   I++SG  
Sbjct: 59  VEFELAEDAAAAIDNMNESELFGRTIRVNLA-KPMRIKESGPS 100

>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 = 78.4 bits (194), Expect = 5e-18
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
            +++  L + +D+K LH  F  FG+I   ++  D    + RG+ FV+F+  E A +AID 
Sbjct: 14  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73

Query: 188 LNGMLLNDKQVFV 200
           +N   L  + + V
Sbjct: 74  MNESELFGRTIRV 86

>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 = 92.8 bits (231), Expect = 4e-23
 Identities = 20/113 (17%), Positives = 45/113 (39%), Gaps = 12/113 (10%)

Query: 21  ATNGIANNGGVGDARQFVS------TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRD 74
            ++G + N         V+       ++Y G +   + D  +   F+  GQ++ +RV  +
Sbjct: 1   GSSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60

Query: 75  LSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGA 127
                  GY +V ++    A  A+  +N T + G  ++  +    P +    +
Sbjct: 61  K------GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPS 107

>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 = 86.2 bits (214), Expect = 9e-21
 Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 5/87 (5%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            +Y   +   ++D  +++ FS FG I   +V  +     +G  FV FST E A+ A+  +
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSV 81

Query: 383 NGKMVVSKPLYVALAQRKEERRARLQA 409
           NG  +    +     +   +  +   +
Sbjct: 82  NGTTIEGHVVKCYWGKESPDMTSGPSS 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 = 74.7 bits (184), Expect = 1e-16
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 5/69 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             VY   ++   T+  +++ F  FG I    V  +     K + FV F   + AA ++ +
Sbjct: 26  CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVS 80

Query: 279 LNGKKFDDK 287
           +NG   +  
Sbjct: 81  VNGTTIEGH 89

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

 Score = 73.5 bits (181), Expect = 3e-16
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            ++   +   + ++ +  TFS FG I+  +V  +     +GY FV+F   ESA  AI  +
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSV 81

Query: 189 NGMLLNDKQVFVG 201
           NG  +    V   
Sbjct: 82  NGTTIEGHVVKCY 94

>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 = 91.5 bits (228), Expect = 9e-23
 Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 1/83 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
             + V NLSE T E DL+++F  FG I+   + +D   G+SK F F++F   +DAAR++ 
Sbjct: 16  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75

Query: 278 ALNGKKFDDKEWYVGKAQKKYER 300
            ++G  +D     V  A+     
Sbjct: 76  GVSGFGYDHLILNVEWAKPSTNS 98

>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 = 90.4 bits (225), Expect = 3e-22
 Identities = 23/88 (26%), Positives = 42/88 (47%), Gaps = 1/88 (1%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKA 378
           +   + V NL +   +  L+ELF  FG+I+   + +D   G S+G  F++F   E+A++A
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73

Query: 379 LTEMNGKMVVSKPLYVALAQRKEERRAR 406
           +  ++G       L V  A+        
Sbjct: 74  IAGVSGFGYDHLILNVEWAKPSTNSGPS 101

>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 = 78.0 bits (193), Expect = 6e-18
 Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNE 178
           P  R      I + NL +      L + F  FG+I    +A D   GQS+G+ F+ F   
Sbjct: 8   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67

Query: 179 ESAKSAIDKLNGMLLNDKQVFV 200
           E A  AI  ++G   +   + V
Sbjct: 68  EDAARAIAGVSGFGYDHLILNV 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 = 76.9 bits (190), Expect = 1e-17
 Identities = 16/102 (15%), Positives = 48/102 (47%), Gaps = 1/102 (0%)

Query: 26  ANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGY 85
           ++     + R   + ++ V +L     ++ L +LF   G +  + + +D +T +S G+ +
Sbjct: 2   SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61

Query: 86  VNYNAAHEATRALDELNFTPLNGKPIRIMYS-YRDPTIRKSG 126
           ++++   +A RA+  ++    +   + + ++     +   SG
Sbjct: 62  ISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103

>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 = 92.2 bits (229), Expect = 2e-22
 Identities = 32/142 (22%), Positives = 51/142 (35%), Gaps = 6/142 (4%)

Query: 266 FDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLY 325
             D   A +  +        D EW    A K          +         D     +L 
Sbjct: 20  AVDAATAEKVFKQYANDNGVDGEWTYDDATKT-----FTVTEGSHHHHHHMDVEGMTSLK 74

Query: 326 VKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEMNG 384
           V NL    S D L+ +F ++G +    + RD     SRG  FV F    +A  A+  M+G
Sbjct: 75  VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134

Query: 385 KMVVSKPLYVALAQRKEERRAR 406
            ++  + L V +A+      + 
Sbjct: 135 AVLDGRELRVQMARYGRPPDSH 156

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 87.2 bits (216), Expect = 1e-20
 Identities = 29/137 (21%), Positives = 51/137 (37%), Gaps = 5/137 (3%)

Query: 172 FVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRF----NNVYVKNLS 227
            V     E         NG+                E               ++ V NL+
Sbjct: 20  AVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT 79

Query: 228 ETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFDD 286
             T+ D L+++F ++G +    + RD    +S+ F FV F D  DA  +++A++G   D 
Sbjct: 80  YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG 139

Query: 287 KEWYVGKAQKKYEREME 303
           +E  V  A+     +  
Sbjct: 140 RELRVQMARYGRPPDSH 156

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 76.4 bits (188), Expect = 1e-16
 Identities = 26/106 (24%), Positives = 49/106 (46%), Gaps = 2/106 (1%)

Query: 8   PQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVV 67
            +     A +    T G  ++    D      TSL V +L    +   L  +F + G+V 
Sbjct: 41  GEWTYDDATKTFTVTEGSHHHHHHMDVE--GMTSLKVDNLTYRTSPDTLRRVFEKYGRVG 98

Query: 68  SVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI 113
            V + RD  T+ S G+ +V ++   +A  A+D ++   L+G+ +R+
Sbjct: 99  DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 144

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 73.3 bits (180), Expect = 1e-15
 Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKS 183
            G  ++ + NL        L   F  +G +    +  D    +SRG+ FV+F ++  A+ 
Sbjct: 68  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127

Query: 184 AIDKLNGMLLNDKQVFV 200
           A+D ++G +L+ +++ V
Sbjct: 128 AMDAMDGAVLDGRELRV 144

>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 = 89.3 bits (222), Expect = 6e-22
 Identities = 30/81 (37%), Positives = 48/81 (59%), Gaps = 1/81 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
            LYV +L  +I++D L+ +F  FG I S ++M D   G S+G GF+ FS +E A KAL +
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87

Query: 382 MNGKMVVSKPLYVALAQRKEE 402
           +NG  +  +P+ V     + +
Sbjct: 88  LNGFELAGRPMKVGHVTERTD 108

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 88.1 bits (219), Expect = 2e-21
 Identities = 31/108 (28%), Positives = 51/108 (47%), Gaps = 8/108 (7%)

Query: 200 VGPFLRKQERESTADKTRFN-------NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMR 252
           +G         + A              +YV +L    TED L+ IF  FG I S  +M 
Sbjct: 1   MGHHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMM 60

Query: 253 DAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYE 299
           D++ G+SK +GF+ F D + A +++E LNG +   +   VG   ++ +
Sbjct: 61  DSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 77.0 bits (190), Expect = 2e-17
 Identities = 30/98 (30%), Positives = 52/98 (53%), Gaps = 3/98 (3%)

Query: 16  AQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDL 75
              S     +ANN   G A       LYVG L  ++ +  L  +F   G++ S+++  D 
Sbjct: 6   HHHSHMAAAMANNLQKGSA---GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDS 62

Query: 76  STRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI 113
            T RS GYG++ ++ +  A +AL++LN   L G+P+++
Sbjct: 63  ETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 76.6 bits (189), Expect = 2e-17
 Identities = 28/78 (35%), Positives = 45/78 (57%), Gaps = 1/78 (1%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKS 183
           +G   +++ +L  +I    L   F  FG I S ++  DS  G+S+GYGF+ F + E AK 
Sbjct: 24  AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKK 83

Query: 184 AIDKLNGMLLNDKQVFVG 201
           A+++LNG  L  + + VG
Sbjct: 84  ALEQLNGFELAGRPMKVG 101

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 88.5 bits (220), Expect = 1e-21
 Identities = 18/84 (21%), Positives = 42/84 (50%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           E   L++  L  S + ++L+E+    GT+   +++ +  G  +G  +V +    +AS+A+
Sbjct: 16  EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAV 75

Query: 380 TEMNGKMVVSKPLYVALAQRKEER 403
            +M+G  +    + VA++      
Sbjct: 76  MKMDGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 86.9 bits (216), Expect = 4e-21
 Identities = 13/79 (16%), Positives = 38/79 (48%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           + +++  L  + T+++L++I    G +    ++ +  GK K   +V +++   A+++V  
Sbjct: 18  HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMK 77

Query: 279 LNGKKFDDKEWYVGKAQKK 297
           ++G    +    V  +   
Sbjct: 78  MDGMTIKENIIKVAISNSG 96

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 81.2 bits (201), Expect = 4e-19
 Identities = 18/72 (25%), Positives = 37/72 (51%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            +FI  L  S   + L +     G +   ++ T+  G+ +G  +V+++NE  A  A+ K+
Sbjct: 19  KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKM 78

Query: 189 NGMLLNDKQVFV 200
           +GM + +  + V
Sbjct: 79  DGMTIKENIIKV 90

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 72.7 bits (179), Expect = 4e-16
 Identities = 16/90 (17%), Positives = 38/90 (42%), Gaps = 1/90 (1%)

Query: 27  NNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYV 86
           ++G    +       L++  L  S    +L ++    G V  +R+  +    +  G  YV
Sbjct: 5   SSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYV 63

Query: 87  NYNAAHEATRALDELNFTPLNGKPIRIMYS 116
            Y    +A++A+ +++   +    I++  S
Sbjct: 64  EYENESQASQAVMKMDGMTIKENIIKVAIS 93

>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 = 88.5 bits (220), Expect = 1e-21
 Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 1/85 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            L+V  L    ++  L+++FS++G I+   V++D     SRG GFV F   ++A  A+  
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73

Query: 382 MNGKMVVSKPLYVALAQRKEERRAR 406
           MNGK V  + + V  A +  + R+ 
Sbjct: 74  MNGKSVDGRQIRVDQAGKSSDNRSG 98

>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 = 88.1 bits (219), Expect = 2e-21
 Identities = 28/83 (33%), Positives = 50/83 (60%), Gaps = 1/83 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
             ++V  LS  T E  L+++F ++G I+   V++D +  +S+ FGFV F++ DDA  ++ 
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72

Query: 278 ALNGKKFDDKEWYVGKAQKKYER 300
           A+NGK  D ++  V +A K  + 
Sbjct: 73  AMNGKSVDGRQIRVDQAGKSSDN 95

>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 = 79.2 bits (196), Expect = 2e-18
 Identities = 26/86 (30%), Positives = 44/86 (51%), Gaps = 1/86 (1%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID 186
           G +F+  L    + ++L   FS +G I    V  D    +SRG+GFV F+N + AK A+ 
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72

Query: 187 KLNGMLLNDKQVFVGPFLRKQEREST 212
            +NG  ++ +Q+ V    +  +  S 
Sbjct: 73  AMNGKSVDGRQIRVDQAGKSSDNRSG 98

>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 = 75.7 bits (187), Expect = 4e-17
 Identities = 25/98 (25%), Positives = 45/98 (45%), Gaps = 1/98 (1%)

Query: 32  GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
                     L+VG L    N+  L  +F++ GQ+  V V +D  T+RS G+G+V +   
Sbjct: 5   SSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENI 64

Query: 92  HEATRALDELNFTPLNGKPIRIMYSY-RDPTIRKSGAG 128
            +A  A+  +N   ++G+ IR+  +           +G
Sbjct: 65  DDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSSG 102

>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 = 87.2 bits (217), Expect = 3e-21
 Identities = 28/85 (32%), Positives = 50/85 (58%), Gaps = 1/85 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            LYV +L  +I++D L+ +F  FG I +  +M+D + G S+G GF+ FS +E A +AL +
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 382 MNGKMVVSKPLYVALAQRKEERRAR 406
           +NG  +  +P+ V     + +  + 
Sbjct: 67  LNGFELAGRPMRVGHVTERLDGGSG 91

>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 = 86.8 bits (216), Expect = 3e-21
 Identities = 30/83 (36%), Positives = 49/83 (59%), Gaps = 1/83 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
           + +YV +L    TED L+ IF  FG I +  +M+D+D G+SK +GF+ F D + A R++E
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 278 ALNGKKFDDKEWYVGKAQKKYER 300
            LNG +   +   VG   ++ + 
Sbjct: 66  QLNGFELAGRPMRVGHVTERLDG 88

>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 = 78.7 bits (195), Expect = 3e-18
 Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 1/88 (1%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKS 183
           SG+  +++ +L  +I    L   F  FG I +  +  DS  G+S+GYGF+ F + E A+ 
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 184 AIDKLNGMLLNDKQVFVGPFLRKQERES 211
           A+++LNG  L  + + VG    + +  S
Sbjct: 63  ALEQLNGFELAGRPMRVGHVTERLDGGS 90

>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 = 78.0 bits (193), Expect = 6e-18
 Identities = 26/75 (34%), Positives = 47/75 (62%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S+ LYVG L  ++ +  L  +F   G++ ++ + +D  T RS GYG++ ++ +  A RAL
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64

Query: 99  DELNFTPLNGKPIRI 113
           ++LN   L G+P+R+
Sbjct: 65  EQLNGFELAGRPMRV 79

>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 = 87.4 bits (217), Expect = 4e-21
 Identities = 23/99 (23%), Positives = 46/99 (46%), Gaps = 3/99 (3%)

Query: 311 SLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN--GISRGSGFVA 368
           S  +   K     + V+N+    +  +++ELFS FG + + ++ +     G  RG GFV 
Sbjct: 5   SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64

Query: 369 FSTAEEASKALTEM-NGKMVVSKPLYVALAQRKEERRAR 406
           F T ++A KA   + +   +  + L +  A  +   ++ 
Sbjct: 65  FITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSG 103

>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 = 83.5 bits (207), Expect = 7e-20
 Identities = 17/94 (18%), Positives = 40/94 (42%), Gaps = 3/94 (3%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD--GKSKCFGFVNFDD 268
               K   + + V+N+     + +++++F  FG + +  + +     G  + FGFV+F  
Sbjct: 8   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67

Query: 269 PDDAARSVEAL-NGKKFDDKEWYVGKAQKKYERE 301
             DA ++  AL +      +   +  A  +   +
Sbjct: 68  KQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 73.9 bits (182), Expect = 2e-16
 Identities = 21/96 (21%), Positives = 44/96 (45%), Gaps = 3/96 (3%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD--SLGQSRGYGFVQFDNEES 180
           +K     I ++N+    + + + + FSTFG + + ++       G  RG+GFV F  ++ 
Sbjct: 11  KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70

Query: 181 AKSAIDKL-NGMLLNDKQVFVGPFLRKQERESTADK 215
           AK A + L +   L  +++ +     +   +S    
Sbjct: 71  AKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106

>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 = 72.7 bits (179), Expect = 6e-16
 Identities = 18/91 (19%), Positives = 50/91 (54%), Gaps = 2/91 (2%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDL-STRRSLGYGYVNYNAAHEATRA 97
           ++ + V ++    N  ++ +LF+  G++ +VR+ + +  T    G+G+V++    +A +A
Sbjct: 15  TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74

Query: 98  LDEL-NFTPLNGKPIRIMYSYRDPTIRKSGA 127
            + L + T L G+ + + ++  + T++   +
Sbjct: 75  FNALCHSTHLYGRRLVLEWADSEVTVQSGPS 105

>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 = 87.0 bits (216), Expect = 5e-21
 Identities = 27/104 (25%), Positives = 47/104 (45%), Gaps = 7/104 (6%)

Query: 310 QSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVA 368
            S    +D  EG  ++++NL     ++ L E+  +FG +   +V+  P+   S+G  F  
Sbjct: 4   GSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQ 63

Query: 369 FSTAEEASKALTEMN------GKMVVSKPLYVALAQRKEERRAR 406
           F T E A K L   +      G  +  + L V LA  ++E  + 
Sbjct: 64  FMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 107

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 80.9 bits (200), Expect = 8e-19
 Identities = 24/103 (23%), Positives = 42/103 (40%), Gaps = 7/103 (6%)

Query: 206 KQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFV 264
                  +D T    V+++NLS  + E+ L ++  +FG +    V+   D   SK   F 
Sbjct: 3   SGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 62

Query: 265 NFDDPDDAARSVEALN------GKKFDDKEWYVGKAQKKYERE 301
            F   + A + + A +      G K D ++  V  A  + E  
Sbjct: 63  QFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 105

>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 = 73.9 bits (182), Expect = 2e-16
 Identities = 22/94 (23%), Positives = 42/94 (44%), Gaps = 7/94 (7%)

Query: 127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAI 185
              +FI+NL    + +AL +    FG++   +V        S+G  F QF  +E+A+  +
Sbjct: 15  GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74

Query: 186 DKLN------GMLLNDKQVFVGPFLRKQERESTA 213
              +      G+ L+ +Q+ V   + + E  S  
Sbjct: 75  AAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGP 108

>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 = 69.3 bits (170), Expect = 9e-15
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 7/97 (7%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             ++++ +L     +  L ++  Q G +  VRV     T  S G  +  +     A + L
Sbjct: 15  GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74

Query: 99  DELNFTP------LNGKPIRIMYSY-RDPTIRKSGAG 128
              +         L+G+ +++  +  RD       +G
Sbjct: 75  AAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSSG 111

>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 = 86.5 bits (215), Expect = 5e-21
 Identities = 25/82 (30%), Positives = 46/82 (56%), Gaps = 1/82 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           ++V+NLS T++E+DL+K+F  +G ++      D+   K K F FV F  P+ A ++   +
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 280 NGKKFDDKEWYVGKAQKKYERE 301
           +G+ F  +  +V  +  K E  
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEAS 92

>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 = 83.4 bits (207), Expect = 6e-20
 Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           L+V+NL  + S++ L++LFS +G ++      D      +G  FV F   E A KA  E+
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70

Query: 383 NGKMVVSKPLYVALAQRKEERRAR 406
           +G++   + L+V  +  K+E    
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEASQS 94

>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 = 78.0 bits (193), Expect = 5e-18
 Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 1/95 (1%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESA 181
             SG+G +F++NL  +   + L   FS +G +       DSL  + +G+ FV F   E A
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 182 KSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKT 216
             A  +++G +   + + V P   K+E   +   +
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>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 = 76.1 bits (188), Expect = 3e-17
 Identities = 20/98 (20%), Positives = 43/98 (43%)

Query: 32  GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
           G +    S  L+V +L  + ++  L  LF+  G +  +    D  T++  G+ +V +   
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 92  HEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
             A +A  E++     G+ + ++ S       +SG  +
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>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 = 86.6 bits (215), Expect = 6e-21
 Identities = 21/91 (23%), Positives = 45/91 (49%), Gaps = 4/91 (4%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKA 378
           + + L++  +  ++ +  LK LF EFG I    V++D   G+ +G  F+ +   E A KA
Sbjct: 12  DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71

Query: 379 LTEMNGKMVV---SKPLYVALAQRKEERRAR 406
            + ++ +  +   ++P+ V  A  +    + 
Sbjct: 72  QSALHEQKTLPGMNRPIQVKPADSESRGGSG 102

>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 = 78.5 bits (194), Expect = 5e-18
 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEA 278
            +++  +     E DLK +F EFG I    V++D   G  K   F+ + + + A ++  A
Sbjct: 15  KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74

Query: 279 LNGKK 283
           L+ +K
Sbjct: 75  LHEQK 79

>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 = 74.3 bits (183), Expect = 1e-16
 Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 116 SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQ 174
           S     ++   A  +FI  + +++D K L   F  FG I    V  D   G  +G  F+ 
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

Query: 175 FDNEESAKSAIDKLNGM 191
           +   ESA  A   L+  
Sbjct: 62  YCERESALKAQSALHEQ 78

>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 = 65.0 bits (159), Expect = 3e-13
 Identities = 21/105 (20%), Positives = 45/105 (42%), Gaps = 6/105 (5%)

Query: 28  NGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVN 87
           + G    +   +  L++G +  ++++  L  LF + G++  + V +D  T    G  ++ 
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

Query: 88  YNAAHEATRALDELN---FTPLNGKPIRIMYS---YRDPTIRKSG 126
           Y     A +A   L+     P   +PI++  +    R  +   SG
Sbjct: 62  YCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSGPSSG 106

>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 = 86.1 bits (214), Expect = 6e-21
 Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSV 276
              + V  LS  TTE DL+++F ++G I   +++ D    +S+ F FV F++ DDA  + 
Sbjct: 15  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74

Query: 277 EALNGKKFDDKEWYVGKAQ 295
           E  NG + D +   V    
Sbjct: 75  ERANGMELDGRRIRVSGPS 93

>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 = 83.0 bits (206), Expect = 9e-20
 Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            L V  L    ++  L+E+FS++G I    ++ D     SRG  FV F   ++A +A   
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76

Query: 382 MNGKMVVSKPLYVALAQR 399
            NG  +  + + V+    
Sbjct: 77  ANGMELDGRRIRVSGPSS 94

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 77.6 bits (192), Expect = 7e-18
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
            + +  L      + L + FS +G I    +  D    +SRG+ FV F+N + AK A ++
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76

Query: 188 LNGMLLNDKQVFV 200
            NGM L+ +++ V
Sbjct: 77  ANGMELDGRRIRV 89

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 77.6 bits (192), Expect = 8e-18
 Identities = 21/78 (26%), Positives = 38/78 (48%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           +  L V  L L   +  L ++F++ G +  V +  D  +RRS G+ +V +    +A  A 
Sbjct: 15  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74

Query: 99  DELNFTPLNGKPIRIMYS 116
           +  N   L+G+ IR+   
Sbjct: 75  ERANGMELDGRRIRVSGP 92

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 86.0 bits (213), Expect = 8e-21
 Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 2/85 (2%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
               L ++N+   +  + L  L  ++G + SC+ +   +        V +S+ ++A +AL
Sbjct: 14  RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS--ETAVVNVTYSSKDQARQAL 71

Query: 380 TEMNGKMVVSKPLYVALAQRKEERR 404
            ++NG  + +  L VA    +   +
Sbjct: 72  DKLNGFQLENFTLKVAYIPDEMAAQ 96

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 77.5 bits (191), Expect = 8e-18
 Identities = 15/92 (16%), Positives = 38/92 (41%), Gaps = 4/92 (4%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITS-TAVMRDADGKSKCFGFVNFDDP 269
           S   + R   + ++N+      + L  +  ++G++ S   V  D++        V +   
Sbjct: 8   SVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV---VNVTYSSK 64

Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
           D A ++++ LNG + ++    V     +   +
Sbjct: 65  DQARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 72.1 bits (177), Expect = 6e-16
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 2/78 (2%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAK 182
           ++     + I+N+   +  + L      +G + SC+              V + +++ A+
Sbjct: 11  KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT--DSETAVVNVTYSSKDQAR 68

Query: 183 SAIDKLNGMLLNDKQVFV 200
            A+DKLNG  L +  + V
Sbjct: 69  QALDKLNGFQLENFTLKV 86

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 64.4 bits (157), Expect = 3e-13
 Identities = 21/91 (23%), Positives = 39/91 (42%), Gaps = 4/91 (4%)

Query: 26  ANNGGVGDA-RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYG 84
            ++G  G   ++     L + ++   +    L  L  Q G V S   C  ++T       
Sbjct: 1   GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVES---CEQVNTDSETAVV 57

Query: 85  YVNYNAAHEATRALDELNFTPLNGKPIRIMY 115
            V Y++  +A +ALD+LN   L    +++ Y
Sbjct: 58  NVTYSSKDQARQALDKLNGFQLENFTLKVAY 88

>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 = 86.7 bits (215), Expect = 1e-20
 Identities = 27/94 (28%), Positives = 47/94 (50%), Gaps = 1/94 (1%)

Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGF 263
             +   + A+      + V  LS  TTE DL+++F ++G I   +++ D    +S+ F F
Sbjct: 33  GSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 92

Query: 264 VNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKK 297
           V F++ DDA  + E  NG + D +   V  +  K
Sbjct: 93  VYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 82.5 bits (204), Expect = 3e-19
 Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            L V  L    ++  L+E+FS++G I    ++ D     SRG  FV F   ++A +A   
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107

Query: 382 MNGKMVVSKPLYVALAQRK 400
            NG  +  + + V  +  K
Sbjct: 108 ANGMELDGRRIRVDFSITK 126

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 80.5 bits (199), Expect = 2e-18
 Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 1/86 (1%)

Query: 116 SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQ 174
            +            + +  L      + L + FS +G I    +  D    +SRG+ FV 
Sbjct: 35  RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 94

Query: 175 FDNEESAKSAIDKLNGMLLNDKQVFV 200
           F+N + AK A ++ NGM L+ +++ V
Sbjct: 95  FENVDDAKEAKERANGMELDGRRIRV 120

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 79.4 bits (196), Expect = 5e-18
 Identities = 22/78 (28%), Positives = 40/78 (51%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           +  L V  L L   +  L ++F++ G +  V +  D  +RRS G+ +V +    +A  A 
Sbjct: 46  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 105

Query: 99  DELNFTPLNGKPIRIMYS 116
           +  N   L+G+ IR+ +S
Sbjct: 106 ERANGMELDGRRIRVDFS 123

>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 = 85.4 bits (212), Expect = 1e-20
 Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 1/85 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            L V NL    S D L+ +F ++G +    + R+P+    RG  FV F    +A  A   
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74

Query: 382 MNGKMVVSKPLYVALAQRKEERRAR 406
           M+G  +  + L V +A+      + 
Sbjct: 75  MDGAELDGRELRVQVARYGRRDLSG 99

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 85.0 bits (211), Expect = 2e-20
 Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 1/89 (1%)

Query: 213 ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDD 271
            D      + V NL+  T+ D L+++F ++G +    + R+      + F FV F D  D
Sbjct: 8   PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67

Query: 272 AARSVEALNGKKFDDKEWYVGKAQKKYER 300
           A  +  A++G + D +E  V  A+     
Sbjct: 68  AQDAEAAMDGAELDGRELRVQVARYGRRD 96

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 75.0 bits (185), Expect = 7e-17
 Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 1/86 (1%)

Query: 116 SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQ 174
           S         G   + + NL       +L   F  +G +    +  +      RG+ FV+
Sbjct: 2   SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61

Query: 175 FDNEESAKSAIDKLNGMLLNDKQVFV 200
           F +   A+ A   ++G  L+ +++ V
Sbjct: 62  FHDRRDAQDAEAAMDGAELDGRELRV 87

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 75.0 bits (185), Expect = 8e-17
 Identities = 19/91 (20%), Positives = 42/91 (46%), Gaps = 1/91 (1%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             +L V +L    +   L  +F + G+V  V + R+  T+   G+ +V ++   +A  A 
Sbjct: 13  MITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAE 72

Query: 99  DELNFTPLNGKPIRIMYS-YRDPTIRKSGAG 128
             ++   L+G+ +R+  + Y    +    +G
Sbjct: 73  AAMDGAELDGRELRVQVARYGRRDLSGPSSG 103

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 86.3 bits (214), Expect = 2e-20
 Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 1/85 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           +L V NL    S D L+ +F ++G +    + RD     SRG  FV F    +A  A+  
Sbjct: 49  SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108

Query: 382 MNGKMVVSKPLYVALAQRKEERRAR 406
           M+G ++  + L V +A+      + 
Sbjct: 109 MDGAVLDGRELRVQMARYGRPPDSH 133

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 84.8 bits (210), Expect = 6e-20
 Identities = 25/94 (26%), Positives = 45/94 (47%), Gaps = 1/94 (1%)

Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGF 263
                    D     ++ V NL+  T+ D L+++F ++G +    + RD    +S+ F F
Sbjct: 34  SMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAF 93

Query: 264 VNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKK 297
           V F D  DA  +++A++G   D +E  V  A+  
Sbjct: 94  VRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 127

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 75.9 bits (187), Expect = 7e-17
 Identities = 24/106 (22%), Positives = 47/106 (44%)

Query: 8   PQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVV 67
           P+     +          + + G         TSL V +L    +   L  +F + G+V 
Sbjct: 16  PRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVG 75

Query: 68  SVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI 113
            V + RD  T+ S G+ +V ++   +A  A+D ++   L+G+ +R+
Sbjct: 76  DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 74.0 bits (182), Expect = 4e-16
 Identities = 23/94 (24%), Positives = 44/94 (46%), Gaps = 1/94 (1%)

Query: 108 GKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQ 166
            +  R   SY  P     G  ++ + NL        L   F  +G +    +  D    +
Sbjct: 28  QQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE 87

Query: 167 SRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
           SRG+ FV+F ++  A+ A+D ++G +L+ +++ V
Sbjct: 88  SRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121

>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 = 85.0 bits (211), Expect = 2e-20
 Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
           + VYV NL  + T +DL +IF ++G +    +M+D D  KSK   F+ F D D A     
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76

Query: 278 ALNGKKFDDKEWYVGKA 294
           A+N K+   +      A
Sbjct: 77  AINNKQLFGRVIKASIA 93

>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 = 79.2 bits (196), Expect = 2e-18
 Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            +YV NL  S++++ L  +FS++G +    +M+D +   S+G  F+ F   + A      
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77

Query: 382 MNGKMVVSKPLYVALA 397
           +N K +  + +  ++A
Sbjct: 78  INNKQLFGRVIKASIA 93

>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 = 78.4 bits (194), Expect = 3e-18
 Identities = 23/90 (25%), Positives = 46/90 (51%)

Query: 24  GIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGY 83
           G + + G+        +++YV +L  S+ ++ LY +F++ G+VV V + +D  TR+S G 
Sbjct: 1   GSSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGV 60

Query: 84  GYVNYNAAHEATRALDELNFTPLNGKPIRI 113
            ++ +     A      +N   L G+ I+ 
Sbjct: 61  AFILFLDKDSAQNCTRAINNKQLFGRVIKA 90

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 75.7 bits (187), Expect = 3e-17
 Identities = 17/73 (23%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
            +++ NL  S+ N  L+  FS +G ++   +  D    +S+G  F+ F +++SA++    
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77

Query: 188 LNGMLLNDKQVFV 200
           +N   L  + +  
Sbjct: 78  INNKQLFGRVIKA 90

>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 = 85.9 bits (213), Expect = 2e-20
 Identities = 25/120 (20%), Positives = 56/120 (46%), Gaps = 7/120 (5%)

Query: 309 EQSLKETADKF------EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GIS 361
             S+++  D+       EG  L+V  + +  +++ + + F+E+G I +  +  D   G  
Sbjct: 4   YDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 63

Query: 362 RGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPR 421
           +G   V + T +EA  A+  +NG+ ++ +P+ V     +   + + +    + R P   R
Sbjct: 64  KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPDRRR 123

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 82.8 bits (205), Expect = 3e-19
 Identities = 21/94 (22%), Positives = 42/94 (44%), Gaps = 1/94 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
             ++V  + E  TE+D+   F E+G I +  +  D   G  K +  V ++   +A  ++E
Sbjct: 23  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82

Query: 278 ALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQS 311
            LNG+    +   V     +   + + +G   +S
Sbjct: 83  GLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRS 116

>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 = 76.6 bits (189), Expect = 4e-17
 Identities = 26/104 (25%), Positives = 43/104 (41%), Gaps = 1/104 (0%)

Query: 27  NNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYV 86
           +    G  R      L+V  +     +  ++D F + G++ ++ +  D  T    GY  V
Sbjct: 10  DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 69

Query: 87  NYNAAHEATRALDELNFTPLNGKPIRIMYS-YRDPTIRKSGAGN 129
            Y    EA  A++ LN   L G+PI + +   R P   K   G 
Sbjct: 70  EYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGR 113

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 74.7 bits (184), Expect = 2e-16
 Identities = 18/73 (24%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
            +F+  + +    + +HD F+ +G I +  +  D   G  +GY  V+++  + A++A++ 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 188 LNGMLLNDKQVFV 200
           LNG  L  + + V
Sbjct: 84  LNGQDLMGQPISV 96

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 86.4 bits (214), Expect = 2e-20
 Identities = 26/76 (34%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            LYV  L + + D  L   F  FG IT  ++  D      RG  FV F  AE+A+ A+  
Sbjct: 65  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124

Query: 382 MNGKMVVSKPLYVALA 397
           MN   +  + + V LA
Sbjct: 125 MNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 85.6 bits (212), Expect = 4e-20
 Identities = 27/110 (24%), Positives = 45/110 (40%), Gaps = 4/110 (3%)

Query: 4   VQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQM 63
             V               + G   +GG           LYVG L   V+D  L+  F   
Sbjct: 32  ESVAYTCVNCTERHVDGGSGGSGGSGGSAT----TKRVLYVGGLAEEVDDKVLHAAFIPF 87

Query: 64  GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI 113
           G +  +++  D  T +  G+ +V +  A +A  A+D +N + L G+ IR+
Sbjct: 88  GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 137

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 83.7 bits (207), Expect = 2e-19
 Identities = 31/125 (24%), Positives = 54/125 (43%), Gaps = 16/125 (12%)

Query: 92  HEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAG---------------NIFIKNLD 136
           H     L +  +  L+  P  + Y+  + T R    G                +++  L 
Sbjct: 13  HSKCENLSDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLA 72

Query: 137 KSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKLNGMLLND 195
           + +D+K LH  F  FG+I   ++  D    + RG+ FV+F+  E A +AID +N   L  
Sbjct: 73  EEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG 132

Query: 196 KQVFV 200
           + + V
Sbjct: 133 RTIRV 137

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 83.3 bits (206), Expect = 2e-19
 Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 1/85 (1%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDP 269
           S    T    +YV  L+E   +  L   F  FG IT   +  D +  K + F FV F+  
Sbjct: 56  SGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 115

Query: 270 DDAARSVEALNGKKFDDKEWYVGKA 294
           +DAA +++ +N  +   +   V  A
Sbjct: 116 EDAAAAIDNMNESELFGRTIRVNLA 140

>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 = 84.1 bits (209), Expect = 2e-20
 Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
            LYV  L + + D  L   F  FG IT  ++  D      RG  FV F  AE+A+ A+  
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68

Query: 382 MNGKMVVSKPLYVALAQ 398
           MN   +  + + V LA+
Sbjct: 69  MNESELFGRTIRVNLAK 85

>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 = 82.2 bits (204), Expect = 1e-19
 Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
             +YV  L+E   +  L   F  FG IT   +  D +  K + F FV F+  +DAA +++
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 278 ALNGKKFDDKEWYVGKAQ 295
            +N  +   +   V  A+
Sbjct: 68  NMNESELFGRTIRVNLAK 85

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 79.5 bits (197), Expect = 1e-18
 Identities = 23/75 (30%), Positives = 39/75 (52%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              LYVG L   V+D  L+  F   G +  +++  D  T +  G+ +V +  A +A  A+
Sbjct: 7   KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66

Query: 99  DELNFTPLNGKPIRI 113
           D +N + L G+ IR+
Sbjct: 67  DNMNESELFGRTIRV 81

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 76.0 bits (188), Expect = 2e-17
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
            +++  L + +D+K LH  F  FG+I   ++  D    + RG+ FV+F+  E A +AID 
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68

Query: 188 LNGMLLNDKQVFV 200
           +N   L  + + V
Sbjct: 69  MNESELFGRTIRV 81

>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 = 84.2 bits (209), Expect = 3e-20
 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 1/85 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
            VY+ ++    TE+ +  +    G + +  +M D   G+SK + F+ F D + +A +V  
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 279 LNGKKFDDKEWYVGKAQKKYEREME 303
           LNG +   +    G +       + 
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVS 88

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 80.4 bits (199), Expect = 8e-19
 Identities = 20/87 (22%), Positives = 44/87 (50%), Gaps = 1/87 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            +Y+ ++    +++++ +L S  G + + K+M DP  G S+G  F+ F   E ++ A+  
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 382 MNGKMVVSKPLYVALAQRKEERRARLQ 408
           +NG  + S+ L    +   +     L+
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVSLE 90

>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 = 78.0 bits (193), Expect = 5e-18
 Identities = 20/93 (21%), Positives = 44/93 (47%), Gaps = 1/93 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
            +++ ++      + + D  S  G +++ K+  D   G+S+GY F++F + ES+ SA+  
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 188 LNGMLLNDKQVFVGPFLRKQERESTADKTRFNN 220
           LNG  L  + +  G          + +    ++
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVSLEHHHHHH 96

>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 = 76.5 bits (189), Expect = 2e-17
 Identities = 18/75 (24%), Positives = 38/75 (50%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S  +Y+G +     + Q+ DL + +G V+++++  D  T RS GY ++ +     +  A+
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 99  DELNFTPLNGKPIRI 113
             LN   L  + ++ 
Sbjct: 62  RNLNGYQLGSRFLKC 76

>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 = 83.5 bits (207), Expect = 9e-20
 Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           ++V ++ E   ED++++ F ++G I +  +  D   G SK +  V ++    A  + EAL
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88

Query: 280 NGKKFDDKEWYVGKAQKKYER 300
           NG +   +   V     K  +
Sbjct: 89  NGAEIMGQTIQVDWCFVKGPK 109

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 81.2 bits (201), Expect = 6e-19
 Identities = 22/86 (25%), Positives = 44/86 (51%), Gaps = 1/86 (1%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKA 378
           EG  L+V ++ +   +D+++E F ++G I +  +  D   G S+G   V + T ++A  A
Sbjct: 25  EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84

Query: 379 LTEMNGKMVVSKPLYVALAQRKEERR 404
              +NG  ++ + + V     K  +R
Sbjct: 85  KEALNGAEIMGQTIQVDWCFVKGPKR 110

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 72.7 bits (179), Expect = 6e-16
 Identities = 19/84 (22%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 119 DPTIRKSGAGN-IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFD 176
           +P  ++S  G  +F+ ++ +      + + F  +G I +  +  D   G S+GY  V+++
Sbjct: 17  EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 76

Query: 177 NEESAKSAIDKLNGMLLNDKQVFV 200
             + A +A + LNG  +  + + V
Sbjct: 77  THKQALAAKEALNGAEIMGQTIQV 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 = 72.7 bits (179), Expect = 6e-16
 Identities = 19/82 (23%), Positives = 36/82 (43%)

Query: 32  GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
           G  R      L+V  +     + ++ + F   G++ ++ +  D  T  S GY  V Y   
Sbjct: 19  GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78

Query: 92  HEATRALDELNFTPLNGKPIRI 113
            +A  A + LN   + G+ I++
Sbjct: 79  KQALAAKEALNGAEIMGQTIQV 100

>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 = 82.6 bits (205), Expect = 9e-20
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGT--ITSCKVMRDP-NGISRGSGFVAFSTAEEASKA 378
           + LY+ NL    +D+ L E     G   I   K   +  NG S+G   V   +   + K 
Sbjct: 2   IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61

Query: 379 LTEMNGKMVVSKPLYVALAQRKEERRAR 406
           +  +  + +  +   V  + + E     
Sbjct: 62  MDLLPKRELHGQNPVVTPSNKLEHHHHH 89

>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 = 78.4 bits (194), Expect = 3e-18
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 3/84 (3%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGI--ITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSV 276
            +Y+ NL+  TT++DL +     G+  I       +   G+SK F  V       + + +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 277 EALNGKKFDDKEWYVGKAQKKYER 300
           + L  ++   +   V  + K    
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 = 72.6 bits (179), Expect = 3e-16
 Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 3/86 (3%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFG--NILSCKVATD-SLGQSRGYGFVQFDNEESAKSAI 185
            ++I NL     ++ L +   + G  +IL  K   + + GQS+G+  V   +E S+K  +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 186 DKLNGMLLNDKQVFVGPFLRKQERES 211
           D L    L+ +   V P  + +    
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLEHHHH 88

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 67.6 bits (166), Expect = 2e-14
 Identities = 14/75 (18%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMG--QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           +LY+G+L     D  L +  + +G   ++ ++   + +  +S G+  V   +   + + +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 99  DELNFTPLNGKPIRI 113
           D L    L+G+   +
Sbjct: 63  DLLPKRELHGQNPVV 77

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 82.3 bits (204), Expect = 1e-19
 Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 6/84 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N +Y+ NLS   T DDL+++FG+  +  +  V          + FV++ D + A R++E 
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIET 63

Query: 279 LNGK-KFDDKEWYVGKAQKKYERE 301
           L+GK +   K   V  +  K  R 
Sbjct: 64  LSGKVELHGKIMEVDYSVSKKLRS 87

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 76.5 bits (189), Expect = 2e-17
 Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 6/83 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LY+ NL  +++ D L++LF +     + +V+        G  FV +     A +A+  ++
Sbjct: 11  LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLS 65

Query: 384 GKMVVS-KPLYVALAQRKEERRA 405
           GK+ +  K + V  +  K+ R +
Sbjct: 66  GKVELHGKIMEVDYSVSKKLRSS 88

>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 = 70.0 bits (172), Expect = 3e-15
 Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 6/88 (6%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           SG   ++I NL  ++    L   F      L+ +V         GY FV + ++  A  A
Sbjct: 6   SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRA 60

Query: 185 IDKLNGML-LNDKQVFVGPFLRKQERES 211
           I+ L+G + L+ K + V   + K+ R S
Sbjct: 61  IETLSGKVELHGKIMEVDYSVSKKLRSS 88

>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 = 62.7 bits (153), Expect = 1e-12
 Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 8/89 (8%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
             LY+G+L  +V    L  LF      ++ +           GY +V+Y   + A RA++
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNWAIRAIE 62

Query: 100 ELN-FTPLNGKPIRIMYSYRDPTIRKSGA 127
            L+    L+GK + + YS     +R SG 
Sbjct: 63  TLSGKVELHGKIMEVDYS-VSKKLRSSGP 90

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 82.7 bits (205), Expect = 1e-19
 Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 1/80 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
             ++V  + E  TE+D+   F E+G I +  +  D   G  K +  V ++   +A  ++E
Sbjct: 24  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 278 ALNGKKFDDKEWYVGKAQKK 297
            LNG+    +   V     +
Sbjct: 84  GLNGQDLMGQPISVDWCFVR 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 79.2 bits (196), Expect = 3e-18
 Identities = 22/99 (22%), Positives = 49/99 (49%), Gaps = 7/99 (7%)

Query: 309 EQSLKETADKF------EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GIS 361
             S+++  D+       EG  L+V  + +  +++ + + F+E+G I +  +  D   G  
Sbjct: 5   YDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 64

Query: 362 RGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK 400
           +G   V + T +EA  A+  +NG+ ++ +P+ V     +
Sbjct: 65  KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 75.0 bits (185), Expect = 9e-17
 Identities = 18/73 (24%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
            +F+  + +    + +HD F+ +G I +  +  D   G  +GY  V+++  + A++A++ 
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 188 LNGMLLNDKQVFV 200
           LNG  L  + + V
Sbjct: 85  LNGQDLMGQPISV 97

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 74.6 bits (184), Expect = 1e-16
 Identities = 22/87 (25%), Positives = 38/87 (43%)

Query: 27  NNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYV 86
           +    G  R      L+V  +     +  ++D F + G++ ++ +  D  T    GY  V
Sbjct: 11  DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 70

Query: 87  NYNAAHEATRALDELNFTPLNGKPIRI 113
            Y    EA  A++ LN   L G+PI +
Sbjct: 71  EYETYKEAQAAMEGLNGQDLMGQPISV 97

>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 = 82.2 bits (203), Expect = 3e-19
 Identities = 19/88 (21%), Positives = 32/88 (36%), Gaps = 6/88 (6%)

Query: 211 STADKTRFNNV-YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDP 269
           S+    R   V   KNL   T   ++++ F  FG +    +      +      V F +P
Sbjct: 2   SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-----PEGGITAIVEFLEP 56

Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKK 297
            +A ++   L   KF     Y+  A   
Sbjct: 57  LEARKAFRHLAYSKFHHVPLYLEWAPIG 84

>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 = 70.6 bits (173), Expect = 3e-15
 Identities = 18/77 (23%), Positives = 28/77 (36%), Gaps = 5/77 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           +  KNL       +++E FS FG++    +          +  V F    EA KA   + 
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLA 67

Query: 384 GKMVVSKPLYVALAQRK 400
                  PLY+  A   
Sbjct: 68  YSKFHHVPLYLEWAPIG 84

>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 = 60.6 bits (147), Expect = 1e-11
 Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 5/71 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           I  KNL        + +TFS FG++    +      +      V+F     A+ A   L 
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLA 67

Query: 190 GMLLNDKQVFV 200
               +   +++
Sbjct: 68  YSKFHHVPLYL 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 = 54.0 bits (130), Expect = 2e-09
 Identities = 11/75 (14%), Positives = 28/75 (37%), Gaps = 6/75 (8%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
            T +   +L      +++ + F++ G +  V +              V +    EA +A 
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAF 63

Query: 99  DELNFTPLNGKPIRI 113
             L ++  +  P+ +
Sbjct: 64  RHLAYSKFHHVPLYL 78

>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 = 83.4 bits (206), Expect = 3e-19
 Identities = 30/126 (23%), Positives = 48/126 (38%), Gaps = 7/126 (5%)

Query: 172 FVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTT 231
           F Q+ N+          +                   R+S     +   VYV NL     
Sbjct: 30  FKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCK---VYVGNLGNNGN 86

Query: 232 EDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYV 291
           + +L++ FG +G + S  V R+       F FV F+DP DAA +V  L+G+        V
Sbjct: 87  KTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRV 142

Query: 292 GKAQKK 297
             +  +
Sbjct: 143 ELSNGE 148

>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 = 82.2 bits (203), Expect = 8e-19
 Identities = 31/148 (20%), Positives = 56/148 (37%), Gaps = 8/148 (5%)

Query: 257 KSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETA 316
             K        D   A +  +        D EW    A K +              +++ 
Sbjct: 11  TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSC 70

Query: 317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEAS 376
                  +YV NL ++ +  +L+  F  +G + S  V R+P     G  FV F    +A+
Sbjct: 71  PL--DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP----PGFAFVEFEDPRDAA 124

Query: 377 KALTEMNGKMVVSKPLYVALAQRKEERR 404
            A+ E++G+ +    + V L+    E+R
Sbjct: 125 DAVRELDGRTLCGCRVRVELS--NGEKR 150

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 66.8 bits (163), Expect = 2e-13
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 9/87 (10%)

Query: 114 MYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFV 173
           M+    P   K     +++ NL  + +   L   F  +G + S  VA +      G+ FV
Sbjct: 65  MHRDSCPLDCK-----VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP----PGFAFV 115

Query: 174 QFDNEESAKSAIDKLNGMLLNDKQVFV 200
           +F++   A  A+ +L+G  L   +V V
Sbjct: 116 EFEDPRDAADAVRELDGRTLCGCRVRV 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 = 57.2 bits (138), Expect = 4e-10
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              +YVG+L  + N ++L   F   G + SV V      R   G+ +V +    +A  A+
Sbjct: 73  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAV 127

Query: 99  DELNFTPLNGKPIRI 113
            EL+   L G  +R+
Sbjct: 128 RELDGRTLCGCRVRV 142

>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 = 81.2 bits (201), Expect = 5e-19
 Identities = 18/84 (21%), Positives = 41/84 (48%), Gaps = 3/84 (3%)

Query: 218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
              + + NLS + TE+ L+++F +   I    V ++ +GKSK + F+ F   +DA  ++ 
Sbjct: 15  SKTLVLSNLSYSATEETLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDAKEALN 71

Query: 278 ALNGKKFDDKEWYVGKAQKKYERE 301
           + N ++ + +   +     +    
Sbjct: 72  SCNKREIEGRAIRLELQGPRGSPN 95

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 80.4 bits (199), Expect = 9e-19
 Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 3/83 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L + NL  S +++ L+E+F +   I   KV ++ NG S+G  F+ F++ E+A +AL   N
Sbjct: 18  LVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74

Query: 384 GKMVVSKPLYVALAQRKEERRAR 406
            + +  + + + L   +    + 
Sbjct: 75  KREIEGRAIRLELQGPRGSPNSG 97

>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 = 70.8 bits (174), Expect = 2e-15
 Identities = 20/94 (21%), Positives = 39/94 (41%), Gaps = 3/94 (3%)

Query: 119 DPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNE 178
             +     +  + + NL  S   + L + F     I   KV  +  G+S+GY F++F + 
Sbjct: 7   GNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASF 63

Query: 179 ESAKSAIDKLNGMLLNDKQVFVGPFLRKQEREST 212
           E AK A++  N   +  + + +     +    S 
Sbjct: 64  EDAKEALNSCNKREIEGRAIRLELQGPRGSPNSG 97

>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 = 63.8 bits (156), Expect = 6e-13
 Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 5/95 (5%)

Query: 32  GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
                  S +L + +L  S  +  L ++F +   +            +S GY ++ + + 
Sbjct: 8   NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYAFIEFASF 63

Query: 92  HEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSG 126
            +A  AL+  N   + G+ IR+           SG
Sbjct: 64  EDAKEALNSCNKREIEGRAIRLELQ-GPRGSPNSG 97

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 83.0 bits (205), Expect = 5e-19
 Identities = 22/102 (21%), Positives = 42/102 (41%), Gaps = 5/102 (4%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGT--ITSCKVMRDP-NGISRGSGFVAFSTAEEASKAL 379
            +YV +     +D +L ++    G   +   K   +  NG S+G   V  ++     K L
Sbjct: 57  AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116

Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPR 421
             + GK++  + + V  A R+   +   QA+  +      PR
Sbjct: 117 ELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRE--CVRVPR 156

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 82.7 bits (204), Expect = 7e-19
 Identities = 20/107 (18%), Positives = 45/107 (42%), Gaps = 3/107 (2%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGI--ITSTAVMRDAD-GKSKCFGFVNFD 267
            +  + R   VYV + S  TT+  L ++    G+  +       +   G+SK +  V   
Sbjct: 48  YSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVA 107

Query: 268 DPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKE 314
             +   + +E L GK  + ++  V  A ++   + E + +  + ++ 
Sbjct: 108 SENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRECVRV 154

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 76.1 bits (187), Expect = 1e-16
 Identities = 24/112 (21%), Positives = 44/112 (39%), Gaps = 3/112 (2%)

Query: 8   PQAPVAVAAQPSPATNGIANNGG-VGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMG-- 64
            + P  V  +PSP  N             +    ++YVG       D QL  +   +G  
Sbjct: 23  MEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVY 82

Query: 65  QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS 116
            VV ++   + +  +S GY  V   + +   + L+ L    LNG+ + +  +
Sbjct: 83  DVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA 134

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 72.3 bits (177), Expect = 3e-15
 Identities = 18/79 (22%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFG--NILSCKVATDSL-GQSRGYGFVQFDNEESA 181
           +    +++ +      ++ L     + G  +++  K A +   GQS+GY  V   +E S 
Sbjct: 53  NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSV 112

Query: 182 KSAIDKLNGMLLNDKQVFV 200
              ++ L G +LN ++V V
Sbjct: 113 HKLLELLPGKVLNGEKVDV 131

>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 = 81.1 bits (201), Expect = 5e-19
 Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 1/84 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
            +V+V N+    TE+ LK IF E G + S  ++ D + GK K +GF  + D + A  ++ 
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 278 ALNGKKFDDKEWYVGKAQKKYERE 301
            LNG++F  +   V  A  +  +E
Sbjct: 69  NLNGREFSGRALRVDNAASEKNKE 92

>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 = 79.6 bits (197), Expect = 2e-18
 Identities = 24/106 (22%), Positives = 49/106 (46%), Gaps = 3/106 (2%)

Query: 314 ETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTA 372
           + A      +++V N+    ++++LK++FSE G + S +++ D   G  +G GF  +   
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60

Query: 373 EEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPV 418
           E A  A+  +NG+    + L V  A  ++ +            P +
Sbjct: 61  ETALSAMRNLNGREFSGRALRVDNAASEKNKEEL--KSLGTGAPVI 104

>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 = 74.2 bits (183), Expect = 1e-16
 Identities = 24/75 (32%), Positives = 41/75 (54%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             S++VG++     + QL D+F+++G VVS R+  D  T +  GYG+  Y     A  A+
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67

Query: 99  DELNFTPLNGKPIRI 113
             LN    +G+ +R+
Sbjct: 68  RNLNGREFSGRALRV 82

>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 = 71.1 bits (175), Expect = 2e-15
 Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 2/73 (2%)

Query: 119 DPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDN 177
           DP + +S   ++F+ N+      + L D FS  G ++S ++  D   G+ +GYGF ++ +
Sbjct: 1   DPAVDRSLR-SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 178 EESAKSAIDKLNG 190
           +E+A SA+  LNG
Sbjct: 60  QETALSAMRNLNG 72

>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 = 79.9 bits (198), Expect = 8e-19
 Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
           N+YV NL  + T + +K++F +FG + +  ++ D +  K K FGFV   + +  + ++  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 279 LNGKKFDDKEWYVGKAQKKYERE 301
           L+   F  +   V +A  K   E
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLE 84

>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 = 79.5 bits (197), Expect = 1e-18
 Identities = 25/85 (29%), Positives = 45/85 (52%), Gaps = 2/85 (2%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           N+YV NL  S + +++KELFS+FG + + K++ D      +G GFV     E  S+A+ +
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 382 MNGKMVVSKPLYVALAQRKEERRAR 406
           ++    + + + V  A  K+     
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEHH 86

>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 = 68.7 bits (169), Expect = 8e-15
 Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           ++YVG+L  S    Q+ +LF+Q G+V +V++  D  T++  G+G+V        + A+ +
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAIAK 61

Query: 101 LNFTPLNGKPIRI 113
           L+ T   G+ IR+
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 = 67.6 bits (166), Expect = 2e-14
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 5/92 (5%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           NI++ NL  S  ++ + + FS FG + + K+  D    + +G+GFV+   E     AI K
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61

Query: 188 LNGMLLNDKQVFVGPFLRKQERESTADKTRFN 219
           L+      + + V        ++S       +
Sbjct: 62  LDNTDFMGRTIRVT---EANPKKSLEHHHHHH 90

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 80.9 bits (200), Expect = 1e-18
 Identities = 25/97 (25%), Positives = 44/97 (45%), Gaps = 9/97 (9%)

Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTA--------VMRDAD-GKSKCFGFV 264
           D +  N ++V+ L E  T + +   F + GII +          +  D + GK K    V
Sbjct: 3   DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62

Query: 265 NFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
           +FDDP  A  +++  +GK+F      V  A ++ +  
Sbjct: 63  SFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFN 99

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 73.2 bits (180), Expect = 5e-16
 Identities = 18/90 (20%), Positives = 39/90 (43%), Gaps = 9/90 (10%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITS--------CKVMRDP-NGISRGSGFVAFSTAE 373
            ++V+ L ++++ + + + F + G I +          +  D   G  +G   V+F    
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 374 EASKALTEMNGKMVVSKPLYVALAQRKEER 403
            A  A+   +GK     P+ V+ A R+ + 
Sbjct: 69  SAKAAIDWFDGKEFSGNPIKVSFATRRADF 98

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 68.2 bits (167), Expect = 3e-14
 Identities = 25/104 (24%), Positives = 44/104 (42%), Gaps = 9/104 (8%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILS--------CKVATDSL-GQSRGYGFV 173
             S    IF++ L +++  +++ D F   G I +          + TD   G+ +G   V
Sbjct: 3   DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62

Query: 174 QFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTR 217
            FD+  SAK+AID  +G   +   + V    R+ +        R
Sbjct: 63  SFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGR 106

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 62.0 bits (151), Expect = 4e-12
 Identities = 19/99 (19%), Positives = 41/99 (41%), Gaps = 8/99 (8%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQV--------VSVRVCRDLSTRRSLGYGYVNYNA 90
           + +++V  L  +V    + D F Q+G +          + +  D  T +  G   V+++ 
Sbjct: 7   NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 66

Query: 91  AHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
              A  A+D  +    +G PI++ ++ R     + G   
Sbjct: 67  PPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNG 105

>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 = 80.0 bits (198), Expect = 1e-18
 Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 4/84 (4%)

Query: 218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSV 276
              ++VK LSE TTE+ LK+ F          ++ D + G SK FGFV+F+  +DA  + 
Sbjct: 15  SKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71

Query: 277 EALNGKKFDDKEWYVGKAQKKYER 300
           EA+   + D  +  +  A+ K E 
Sbjct: 72  EAMEDGEIDGNKVTLDWAKPKGEG 95

>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 = 75.0 bits (185), Expect = 7e-17
 Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 4/85 (4%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            L+VK L +  +++ LKE F         +++ D   G S+G GFV F++ E+A  A   
Sbjct: 17  TLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73

Query: 382 MNGKMVVSKPLYVALAQRKEERRAR 406
           M    +    + +  A+ K E  + 
Sbjct: 74  MEDGEIDGNKVTLDWAKPKGEGGSG 98

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 71.5 bits (176), Expect = 1e-15
 Identities = 20/88 (22%), Positives = 40/88 (45%), Gaps = 3/88 (3%)

Query: 26  ANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGY 85
           ++     +AR   S +L+V  L     +  L + F      V  R+  D  T  S G+G+
Sbjct: 2   SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGF 58

Query: 86  VNYNAAHEATRALDELNFTPLNGKPIRI 113
           V++N+  +A  A + +    ++G  + +
Sbjct: 59  VDFNSEEDAKAAKEAMEDGEIDGNKVTL 86

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 70.4 bits (173), Expect = 3e-15
 Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 4/84 (4%)

Query: 118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFD 176
             P  R   +  +F+K L +    + L ++F      +  ++ TD   G S+G+GFV F+
Sbjct: 6   SGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFN 62

Query: 177 NEESAKSAIDKLNGMLLNDKQVFV 200
           +EE AK+A + +    ++  +V +
Sbjct: 63  SEEDAKAAKEAMEDGEIDGNKVTL 86

>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 = 80.5 bits (199), Expect = 1e-18
 Identities = 26/105 (24%), Positives = 46/105 (43%), Gaps = 9/105 (8%)

Query: 206 KQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTA--------VMRDAD-G 256
                   + +  + +YV+ L+++ T DDL   F + G++            +  D + G
Sbjct: 3   SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 62

Query: 257 KSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
           K K    V+++DP  A  +VE  +GK F   +  V  A+KK    
Sbjct: 63  KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107

>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 = 76.7 bits (189), Expect = 3e-17
 Identities = 23/107 (21%), Positives = 44/107 (41%), Gaps = 9/107 (8%)

Query: 309 EQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITS--------CKVMRDP-NG 359
             S  +  +  +   +YV+ L+DS++ D L + F + G +            +  D   G
Sbjct: 3   SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 62

Query: 360 ISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRAR 406
             +G   V++     A  A+   +GK      L V+LA++K    + 
Sbjct: 63  KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSG 109

>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 = 65.5 bits (160), Expect = 2e-13
 Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 9/103 (8%)

Query: 118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILS--------CKVATDSL-GQSR 168
                  S    I+++ L+ S+    L D F   G +            +  D   G+ +
Sbjct: 6   SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPK 65

Query: 169 GYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
           G   V +++  +AK+A++  +G      ++ V    +K    S
Sbjct: 66  GDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 108

>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 = 60.1 bits (146), Expect = 2e-11
 Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 8/83 (9%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQV--------VSVRVCRDLSTRRSLGYGYVNYNA 90
           ++++YV  L+ SV    L D F Q G V          + +  D  T +  G   V+Y  
Sbjct: 15  NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74

Query: 91  AHEATRALDELNFTPLNGKPIRI 113
              A  A++  +     G  +++
Sbjct: 75  PPTAKAAVEWFDGKDFQGSKLKV 97

>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 = 80.4 bits (199), Expect = 1e-18
 Identities = 19/99 (19%), Positives = 44/99 (44%), Gaps = 2/99 (2%)

Query: 309 EQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFV 367
           E     + ++ +   ++   L   I    L++ FS  G +   +++ D N   S+G  +V
Sbjct: 13  EPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV 72

Query: 368 AFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRAR 406
            F   +    A+  + G+ ++  P+ V  +Q ++ R + 
Sbjct: 73  EFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNRLSG 110

>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 = 72.7 bits (179), Expect = 7e-16
 Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 2/98 (2%)

Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGF 263
           R+     + ++     V+   L+      DL+  F   G +    ++ D +  +SK   +
Sbjct: 12  REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 71

Query: 264 VNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
           V F +   +      L G++       V  +Q +  R 
Sbjct: 72  VEFCEI-QSVPLAIGLTGQRLLGVPIIVQASQAEKNRL 108

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 71.6 bits (176), Expect = 1e-15
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           + +++   L   +    L D F+ +G+V  VR+  D ++RRS G  YV +        A+
Sbjct: 25  ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 84

Query: 99  DELNFTPLNGKPIRIMYS 116
             L    L G PI +  S
Sbjct: 85  -GLTGQRLLGVPIIVQAS 101

>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 = 70.0 bits (172), Expect = 5e-15
 Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 2/98 (2%)

Query: 118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFD 176
            + +  +  A  +F   L   I  + L D FS  G +   ++ +D    +S+G  +V+F 
Sbjct: 16  DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 75

Query: 177 NEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTAD 214
             +S   AI  L G  L    + V     ++ R S   
Sbjct: 76  EIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNRLSGPS 112

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 79.6 bits (197), Expect = 2e-18
 Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 4/81 (4%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
            VYV NL     + +L++ F  +G + +  + R+       F FV F+DP DA  +V  L
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 280 NGKKFDDKEWYVGKAQKKYER 300
           +GK        V  +     R
Sbjct: 58  DGKVICGSRVRVELSTGMPRR 78

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 72.3 bits (178), Expect = 7e-16
 Identities = 24/96 (25%), Positives = 41/96 (42%), Gaps = 11/96 (11%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
           + +YV NL       +L+  FS +G + +  + R+P     G  FV F    +A  A+  
Sbjct: 1   MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP----PGFAFVEFEDPRDAEDAVRG 56

Query: 382 MNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPP 417
           ++GK++    + V L+     R           RPP
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRSRF-------DRPP 85

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 64.6 bits (158), Expect = 4e-13
 Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            +++ NL        L   FS +G + +  +A +      G+ FV+F++   A+ A+  L
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP----PGFAFVEFEDPRDAEDAVRGL 57

Query: 189 NGMLLNDKQVFV 200
           +G ++   +V V
Sbjct: 58  DGKVICGSRVRV 69

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 5/73 (6%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
            +YVG+L       +L   F+  G + +V +      R   G+ +V +    +A  A+  
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRG 56

Query: 101 LNFTPLNGKPIRI 113
           L+   + G  +R+
Sbjct: 57  LDGKVICGSRVRV 69

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 78.9 bits (195), Expect = 2e-18
 Identities = 15/85 (17%), Positives = 36/85 (42%), Gaps = 7/85 (8%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGI--ITSTAVMRDAD-GKSKCFGFVNFDDPDDAARS 275
           + + ++N++  T  D +      +    + +  +++D    +++ F FV      DA++ 
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 276 VEALNGK----KFDDKEWYVGKAQK 296
           ++ L       K D K   V  A+ 
Sbjct: 70  LQILQSLHPPLKIDGKTIGVDFAKS 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 74.7 bits (184), Expect = 8e-17
 Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 7/84 (8%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGT--ITSCKVMRDPN-GISRGSGFVAFSTAEEASKAL 379
            + ++N+      D +    S + +  + + ++++D     +RG  FV  S+A +AS+ L
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 380 TEMNGKMVVS----KPLYVALAQR 399
             +           K + V  A+ 
Sbjct: 71  QILQSLHPPLKIDGKTIGVDFAKS 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 72.0 bits (177), Expect = 7e-16
 Identities = 14/79 (17%), Positives = 33/79 (41%), Gaps = 7/79 (8%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGN--ILSCKVATDSL-GQSRGYGFVQFDNEESAKSAI 185
            I ++N+       ++    S + +  + + ++  D    Q+RG+ FVQ  +   A   +
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 186 DKLNGM----LLNDKQVFV 200
             L  +     ++ K + V
Sbjct: 71  QILQSLHPPLKIDGKTIGV 89

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 71.6 bits (176), Expect = 1e-15
 Identities = 14/92 (15%), Positives = 41/92 (44%), Gaps = 6/92 (6%)

Query: 31  VGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQ--VVSVRVCRDLSTRRSLGYGYVNY 88
           +G        ++ + ++        +    +      V ++R+ +D  T+++ G+ +V  
Sbjct: 1   MGHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQL 60

Query: 89  NAAHEATRALDELN----FTPLNGKPIRIMYS 116
           ++A +A++ L  L        ++GK I + ++
Sbjct: 61  SSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>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 = 78.8 bits (195), Expect = 2e-18
 Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 7/83 (8%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             ++V N+S T T  +L+  F E+G +    +++D       + FV+ +  +DA  ++  
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRG 63

Query: 279 LNGKKFDDKEWYVGKAQKKYERE 301
           L+  +F  K  +V  +  +    
Sbjct: 64  LDNTEFQGKRMHVQLSTSRLRTA 86

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 76.9 bits (190), Expect = 1e-17
 Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 7/84 (8%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            L+V N+  + ++ +L+  F E+G +  C +++D         FV    AE+A +A+  +
Sbjct: 12  KLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY-------AFVHMERAEDAVEAIRGL 64

Query: 383 NGKMVVSKPLYVALAQRKEERRAR 406
           +      K ++V L+  +    + 
Sbjct: 65  DNTEFQGKRMHVQLSTSRLRTASG 88

>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 = 64.6 bits (158), Expect = 3e-13
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 7/78 (8%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAK 182
               +  + + N+  +  N+ L   F  +G ++ C +        + Y FV  +  E A 
Sbjct: 6   SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAV 58

Query: 183 SAIDKLNGMLLNDKQVFV 200
            AI  L+      K++ V
Sbjct: 59  EAIRGLDNTEFQGKRMHV 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 = 58.4 bits (142), Expect = 4e-11
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 8/75 (10%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           ST L+VG++  +  + +L   F + G V+   + +         Y +V+   A +A  A+
Sbjct: 10  STKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAI 61

Query: 99  DELNFTPLNGKPIRI 113
             L+ T   GK + +
Sbjct: 62  RGLDNTEFQGKRMHV 76

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 78.1 bits (193), Expect = 4e-18
 Identities = 22/93 (23%), Positives = 42/93 (45%), Gaps = 4/93 (4%)

Query: 313 KETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTA 372
             +        L  KNL  +I++D+LKE+F +   I   +++   +G S+G  ++ F + 
Sbjct: 8   CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI---RLVSQ-DGKSKGIAYIEFKSE 63

Query: 373 EEASKALTEMNGKMVVSKPLYVALAQRKEERRA 405
            +A K L E  G  +  + + +     K   R 
Sbjct: 64  ADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 77.7 bits (192), Expect = 8e-18
 Identities = 27/94 (28%), Positives = 43/94 (45%), Gaps = 5/94 (5%)

Query: 208 ERESTADKTR-FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNF 266
           E   T+ K R    +  KNLS   TED+LK++F +   I     +   DGKSK   ++ F
Sbjct: 5   EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI----RLVSQDGKSKGIAYIEF 60

Query: 267 DDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
               DA +++E   G + D +   +    +K   
Sbjct: 61  KSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94

>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 = 66.1 bits (162), Expect = 8e-14
 Identities = 13/78 (16%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           + +L   +L  ++ + +L ++F    ++  V         +S G  Y+ + +  +A + L
Sbjct: 16  ARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNL 70

Query: 99  DELNFTPLNGKPIRIMYS 116
           +E     ++G+ + + Y+
Sbjct: 71  EEKQGAEIDGRSVSLYYT 88

>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 = 65.7 bits (161), Expect = 1e-13
 Identities = 16/81 (19%), Positives = 38/81 (46%), Gaps = 4/81 (4%)

Query: 120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEE 179
            + +   A  +  KNL  +I    L + F     I   ++ +   G+S+G  +++F +E 
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI---RLVSQD-GKSKGIAYIEFKSEA 64

Query: 180 SAKSAIDKLNGMLLNDKQVFV 200
            A+  +++  G  ++ + V +
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSL 85

>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 = 78.5 bits (194), Expect = 5e-18
 Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 2/75 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV NL       D++ +F ++G I    +          F FV F+DP DA  +V   +
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRD 82

Query: 281 GKKFDDKEWYVGKAQ 295
           G  +D     V   +
Sbjct: 83  GYDYDGYRLRVEFPR 97

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 70.8 bits (174), Expect = 2e-15
 Identities = 17/83 (20%), Positives = 30/83 (36%), Gaps = 2/83 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           +YV NL   I    ++++F ++G I    +     G      FV F    +A  A+   +
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG--PPFAFVEFEDPRDAEDAVYGRD 82

Query: 384 GKMVVSKPLYVALAQRKEERRAR 406
           G       L V   +      + 
Sbjct: 83  GYDYDGYRLRVEFPRSGRGTGSG 105

>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 = 64.3 bits (157), Expect = 6e-13
 Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           I++ NL   I  K + D F  +G I    +          + FV+F++   A+ A+   +
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRD 82

Query: 190 GMLLNDKQVFV 200
           G   +  ++ V
Sbjct: 83  GYDYDGYRLRV 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 = 58.1 bits (141), Expect = 7e-11
 Identities = 15/90 (16%), Positives = 36/90 (40%), Gaps = 3/90 (3%)

Query: 24  GIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGY 83
           G++  G +          +YVG+L   +    + D+F + G +  + +      R    +
Sbjct: 7   GMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPF 63

Query: 84  GYVNYNAAHEATRALDELNFTPLNGKPIRI 113
            +V +    +A  A+   +    +G  +R+
Sbjct: 64  AFVEFEDPRDAEDAVYGRDGYDYDGYRLRV 93

>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 = 77.6 bits (192), Expect = 6e-18
 Identities = 15/81 (18%), Positives = 38/81 (46%), Gaps = 7/81 (8%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
            +++ NL    TE +++ +F ++G +    ++++       +GFV+ +D   A  ++  L
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN-------YGFVHIEDKTAAEDAIRNL 62

Query: 280 NGKKFDDKEWYVGKAQKKYER 300
           +  K       V  ++ K + 
Sbjct: 63  HHYKLHGVNINVEASKNKSKA 83

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 76.1 bits (188), Expect = 2e-17
 Identities = 14/84 (16%), Positives = 36/84 (42%), Gaps = 7/84 (8%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            L++ NL    ++ +++ LF ++G +  C ++       +  GFV       A  A+  +
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNL 62

Query: 383 NGKMVVSKPLYVALAQRKEERRAR 406
           +   +    + V  ++ K +  + 
Sbjct: 63  HHYKLHGVNINVEASKNKSKASSG 86

>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 = 66.8 bits (164), Expect = 3e-14
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           SG   +FI NL +    + +   F  +G +L C +        + YGFV  +++ +A+ A
Sbjct: 6   SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDA 58

Query: 185 IDKLNGMLLNDKQVFV 200
           I  L+   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 = 57.6 bits (140), Expect = 7e-11
 Identities = 21/98 (21%), Positives = 42/98 (42%), Gaps = 9/98 (9%)

Query: 32  GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
           G +       L++G+L     + ++  LF Q G+V+   + +         YG+V+    
Sbjct: 1   GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIEDK 52

Query: 92  HEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
             A  A+  L+   L+G  I +  S ++ +   SG  +
Sbjct: 53  TAAEDAIRNLHHYKLHGVNINVEAS-KNKSKASSGPSS 89

>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 = 78.2 bits (193), Expect = 8e-18
 Identities = 19/113 (16%), Positives = 42/113 (37%), Gaps = 2/113 (1%)

Query: 295 QKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVM 354
             K       +G  +    E   + +  ++YV N+D   +   L+  FS  G+I    ++
Sbjct: 10  HSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITIL 69

Query: 355 RDPN-GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRAR 406
            D   G  +G  ++ F+       A+  M+  +   + + V   +      + 
Sbjct: 70  CDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMPGISS 121

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 72.1 bits (177), Expect = 1e-15
 Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 2/79 (2%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
           +VYV N+   +T  DL+  F   G I    ++ D   G  K + ++ F +  ++  +  A
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAER-NSVDAAVA 96

Query: 279 LNGKKFDDKEWYVGKAQKK 297
           ++   F  +   V   +  
Sbjct: 97  MDETVFRGRTIKVLPKRTN 115

>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 = 68.6 bits (168), Expect = 3e-14
 Identities = 18/90 (20%), Positives = 40/90 (44%), Gaps = 2/90 (2%)

Query: 127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAI 185
             ++++ N+D     + L   FS+ G+I    +  D   G  +GY +++F    S  +A+
Sbjct: 36  KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95

Query: 186 DKLNGMLLNDKQVFVGPFLRKQERESTADK 215
             ++  +   + + V P        S+ D+
Sbjct: 96  -AMDETVFRGRTIKVLPKRTNMPGISSTDR 124

>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 = 68.2 bits (167), Expect = 3e-14
 Identities = 23/113 (20%), Positives = 42/113 (37%), Gaps = 6/113 (5%)

Query: 2   AQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFN 61
             +Q       A A    P     A      D R     S+YVG++D       L   F+
Sbjct: 4   PCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKR-----SVYVGNVDYGSTAQDLEAHFS 58

Query: 62  QMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM 114
             G +  + +  D  +    GY Y+ +   +    A+  ++ T   G+ I+++
Sbjct: 59  SCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVL 110

>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 = 77.3 bits (191), Expect = 1e-17
 Identities = 24/87 (27%), Positives = 36/87 (41%), Gaps = 10/87 (11%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           ++V  L    +D  L++ F  FG I    V+ D   G SRG GFV  +    A +A  + 
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79

Query: 383 N----GKMVVSKPLYVALAQRKEERRA 405
           N    G+          LA    + R+
Sbjct: 80  NPIIDGRKANVN-----LAYLGAKPRS 101

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 77.3 bits (191), Expect = 2e-17
 Identities = 28/99 (28%), Positives = 41/99 (41%), Gaps = 2/99 (2%)

Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDD 268
             +   T F  ++V  L   TT+  L+K F  FG I    V+ D   GKS+ +GFV   D
Sbjct: 9   HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 68

Query: 269 PDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGK 307
              A R+ +  N    D ++  V  A    +      G 
Sbjct: 69  RAAAERACKDPN-PIIDGRKANVNLAYLGAKPRSLQTGF 106

>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 = 68.1 bits (167), Expect = 3e-14
 Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 7/86 (8%)

Query: 116 SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQ 174
           S +D T  K     IF+  L     + +L   F  FG+I    V TD   G+SRGYGFV 
Sbjct: 11  SQKDTTFTK-----IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 65

Query: 175 FDNEESAKSAIDKLNGMLLNDKQVFV 200
             +  +A+ A    N + ++ ++  V
Sbjct: 66  MADRAAAERACKDPNPI-IDGRKANV 90

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 58.8 bits (143), Expect = 4e-11
 Identities = 23/87 (26%), Positives = 36/87 (41%), Gaps = 1/87 (1%)

Query: 26  ANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGY 85
            ++G  G  +    T ++VG L     D+ L   F   G +    V  D  T +S GYG+
Sbjct: 4   GSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGF 63

Query: 86  VNYNAAHEATRALDELNFTPLNGKPIR 112
           V       A RA  + N   ++G+   
Sbjct: 64  VTMADRAAAERACKDPNPI-IDGRKAN 89

>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 = 76.1 bits (188), Expect = 2e-17
 Identities = 21/92 (22%), Positives = 42/92 (45%), Gaps = 10/92 (10%)

Query: 209 RESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDD 268
             S+ +  +   ++V N+S   T  +L+ +F   G +    V++D       + FV+ + 
Sbjct: 3   SGSSGNTWK---IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEK 52

Query: 269 PDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
             DA  ++  LNGK+   K   V  + K  ++
Sbjct: 53  EADAKAAIAQLNGKEVKGKRINVELSTKGQKK 84

>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 = 75.7 bits (187), Expect = 3e-17
 Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++V N+  + +  +L+ LF   G +  C V++D         FV      +A  A+ ++N
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVKDY-------AFVHMEKEADAKAAIAQLN 64

Query: 384 GKMVVSKPLYVALAQRKEERRA 405
           GK V  K + V L+ + +++  
Sbjct: 65  GKEVKGKRINVELSTKGQKKSG 86

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 65.7 bits (161), Expect = 1e-13
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 7/78 (8%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAK 182
                  IF+ N+  +  ++ L   F   G ++ C V        + Y FV  + E  AK
Sbjct: 5   SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAK 57

Query: 183 SAIDKLNGMLLNDKQVFV 200
           +AI +LNG  +  K++ V
Sbjct: 58  AAIAQLNGKEVKGKRINV 75

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 57.2 bits (139), Expect = 9e-11
 Identities = 19/90 (21%), Positives = 39/90 (43%), Gaps = 8/90 (8%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           +  ++VG++  +    +L  LF + G+V+   V +         Y +V+     +A  A+
Sbjct: 9   TWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAI 60

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAG 128
            +LN   + GK I +  S +        +G
Sbjct: 61  AQLNGKEVKGKRINVELSTKGQKKSGPSSG 90

>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 = 76.2 bits (188), Expect = 2e-17
 Identities = 16/87 (18%), Positives = 37/87 (42%), Gaps = 1/87 (1%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMR-DADGKSKCFGFVNFDDP 269
           S++ K     + V+N+  T + D++   F  + +I  +  ++ +  G       V F+  
Sbjct: 8   SSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67

Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQK 296
           D+A  +V  LN +    ++  +     
Sbjct: 68  DEATAAVIDLNDRPIGSRKVKLSGPSS 94

>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 = 70.0 bits (172), Expect = 4e-15
 Identities = 16/75 (21%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMR-DPNGISRGSGFVAFSTAEEASKALTEM 382
           + V+N+  ++S D++ + F  +  I     ++ +  G+  G   VAF + +EA+ A+ ++
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77

Query: 383 NGKMVVSKPLYVALA 397
           N + + S+ + ++  
Sbjct: 78  NDRPIGSRKVKLSGP 92

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 60.4 bits (147), Expect = 8e-12
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 124 KSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSC-KVATDSLGQSRGYGFVQFDNEESAK 182
           K G   I ++N+  ++    + D F  +  I     +  +  G   G   V F++ + A 
Sbjct: 12  KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71

Query: 183 SAIDKLNGMLLNDKQVFV 200
           +A+  LN   +  ++V +
Sbjct: 72  AAVIDLNDRPIGSRKVKL 89

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 57.7 bits (140), Expect = 7e-11
 Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVV-SVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
            T + V ++  +V+  ++ D F     +  SV +  +       G   V + +  EAT A
Sbjct: 15  PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAA 73

Query: 98  LDELNFTPLNGKPIRIMYS 116
           + +LN  P+  + +++   
Sbjct: 74  VIDLNDRPIGSRKVKLSGP 92

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

 Score = 76.2 bits (188), Expect = 3e-17
 Identities = 21/80 (26%), Positives = 31/80 (38%), Gaps = 11/80 (13%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
             Y+ N+    TE DL  +F  FG I       +     K   F+ +D  + AA  + AL
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDTHEQAAVCIVAL 83

Query: 280 NGKKFDDKE----WYVGKAQ 295
               F  +     W  GK +
Sbjct: 84  ANFPFQGRNLRTGW--GKER 101

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

 Score = 76.2 bits (188), Expect = 3e-17
 Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 5/70 (7%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
             Y+ N+    ++  L  LF  FG I   K   +     +G  F+ + T E+A+  +  +
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDTHEQAAVCIVAL 83

Query: 383 NGKMVVSKPL 392
                  + L
Sbjct: 84  ANFPFQGRNL 93

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

 Score = 75.8 bits (187), Expect = 4e-17
 Identities = 22/98 (22%), Positives = 34/98 (34%), Gaps = 7/98 (7%)

Query: 106 LNGKPIRIMYSYRDPTIRKSGAGN--IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS 163
             G P ++     D  IR +       +I N+        L   F  FG IL  K   + 
Sbjct: 4   TIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE- 62

Query: 164 LGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVG 201
               +G  F+++D  E A   I  L       + +  G
Sbjct: 63  ----KGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG 96

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

 Score = 73.9 bits (182), Expect = 2e-16
 Identities = 20/114 (17%), Positives = 39/114 (34%), Gaps = 23/114 (20%)

Query: 2   AQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFN 61
              QV PQA   +     P                   T+ Y+G++     ++ L  LF 
Sbjct: 7   LPPQVNPQAVDHIIRSAPPR-----------------VTTAYIGNIPHFATEADLIPLFQ 49

Query: 62  QMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY 115
             G ++  +   +       G  ++ Y+   +A   +  L   P  G+ +R  +
Sbjct: 50  NFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW 97

>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 = 76.1 bits (188), Expect = 3e-17
 Identities = 19/92 (20%), Positives = 46/92 (50%), Gaps = 2/92 (2%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDP 269
           S +  ++ N ++V  +     E +L++ F +FG++T   ++ DA+  + + FGF+ F+D 
Sbjct: 3   SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62

Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
             +      ++      K+  V +A+ +  + 
Sbjct: 63  -QSVDQAVNMHFHDIMGKKVEVKRAEPRDSKS 93

>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 = 74.2 bits (183), Expect = 1e-16
 Identities = 18/84 (21%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           ++V  +  +  + +L+E F +FG +T   ++ D      RG GF+ F   +   +A+  M
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71

Query: 383 NGKMVVSKPLYVALAQRKEERRAR 406
           +   ++ K + V  A+ ++ + + 
Sbjct: 72  HFHDIMGKKVEVKRAEPRDSKSSG 95

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 64.1 bits (157), Expect = 4e-13
 Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           IF+  +  +     L + F  FG +    +  D+   + RG+GF+ F++E+S   A+  +
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71

Query: 189 NGMLLNDKQVFVGPFLRKQERES 211
           +   +  K+V V     +  + S
Sbjct: 72  HFHDIMGKKVEVKRAEPRDSKSS 94

>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 = 17/84 (20%), Positives = 40/84 (47%), Gaps = 1/84 (1%)

Query: 30  GVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYN 89
           G   +    S  ++VG +  +  +++L + F + G V  V +  D   +R  G+G++ + 
Sbjct: 1   GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60

Query: 90  AAHEATRALDELNFTPLNGKPIRI 113
                 +A+  ++F  + GK + +
Sbjct: 61  DEQSVDQAV-NMHFHDIMGKKVEV 83

>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 = 75.8 bits (187), Expect = 3e-17
 Identities = 17/79 (21%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVM-RDPNGISRGSGFVAFSTAEEASKALTEM 382
           + V+N+  ++S D++ + F  +  I     +  +  G+  G   VAF + +EA+ A+ ++
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77

Query: 383 NGKMVVSKPLYVALAQRKE 401
           N + + S+ + + L     
Sbjct: 78  NDRPIGSRKVKLVLGSGPS 96

>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 = 73.9 bits (182), Expect = 2e-16
 Identities = 15/88 (17%), Positives = 36/88 (40%), Gaps = 1/88 (1%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVM-RDADGKSKCFGFVNFDDP 269
           +++ K     + V+N+  T + D++   F  + +I  +  +  +  G       V F+  
Sbjct: 8   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67

Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKK 297
           D+A  +V  LN +    ++  +      
Sbjct: 68  DEATAAVIDLNDRPIGSRKVKLVLGSGP 95

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 62.3 bits (152), Expect = 2e-12
 Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNI-LSCKVATDSLGQSRGYGFVQFDNE 178
            +  K G   I ++N+  ++    + D F  +  I  S  +  +  G   G   V F++ 
Sbjct: 8   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67

Query: 179 ESAKSAIDKLNGMLLNDKQVFV 200
           + A +A+  LN   +  ++V +
Sbjct: 68  DEATAAVIDLNDRPIGSRKVKL 89

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 16/79 (20%), Positives = 36/79 (45%), Gaps = 2/79 (2%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVV-SVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
            T + V ++  +V+  ++ D F     +  SV +  +       G   V + +  EAT A
Sbjct: 15  PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAA 73

Query: 98  LDELNFTPLNGKPIRIMYS 116
           + +LN  P+  + ++++  
Sbjct: 74  VIDLNDRPIGSRKVKLVLG 92

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 75.2 bits (186), Expect = 4e-17
 Identities = 15/77 (19%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           ++YV N+D   + ++L+  F   G++    ++ D   G  +G  ++ FS  E    +L  
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66

Query: 382 MNGKMVVSKPLYVALAQ 398
           ++  +   + + V   +
Sbjct: 67  LDESLFRGRQIKVIPKR 83

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 72.5 bits (179), Expect = 3e-16
 Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 2/79 (2%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
           ++YV N+    T ++L+  F   G +    ++ D   G  K F ++ F D  ++ R+  A
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLA 66

Query: 279 LNGKKFDDKEWYVGKAQKK 297
           L+   F  ++  V   +  
Sbjct: 67  LDESLFRGRQIKVIPKRTN 85

>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 = 69.5 bits (171), Expect = 4e-15
 Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           + S+YVG++D      +L   F+  G V  V +  D  +    G+ Y+ ++       +L
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65

Query: 99  DELNFTPLNGKPIRIMY 115
             L+ +   G+ I+++ 
Sbjct: 66  -ALDESLFRGRQIKVIP 81

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 67.2 bits (165), Expect = 3e-14
 Identities = 17/75 (22%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAI 185
           A +I++ N+D     + L   F   G++    +  D   G  +G+ +++F ++ES ++++
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65

Query: 186 DKLNGMLLNDKQVFV 200
             L+  L   +Q+ V
Sbjct: 66  -ALDESLFRGRQIKV 79

>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 = 74.6 bits (184), Expect = 9e-17
 Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 9/86 (10%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           L V  L    ++  LKE FS FG +   +V +D   G S+G GFV F+  E   K +++ 
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77

Query: 383 ---NGKMVVSKPLYVALAQRKEERRA 405
              +G+    K     L   K+ + +
Sbjct: 78  HMIDGRWCDCK-----LPNSKQSQDS 98

>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 = 71.1 bits (175), Expect = 2e-15
 Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 9/85 (10%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA- 278
           + V  L   TTE DLK+ F  FG +    V +D   G SK FGFV F + +   + +   
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77

Query: 279 --LNGKKFDDKEWYVGKAQKKYERE 301
             ++G+  D K         K  ++
Sbjct: 78  HMIDGRWCDCK-----LPNSKQSQD 97

>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 = 64.6 bits (158), Expect = 4e-13
 Identities = 21/86 (24%), Positives = 41/86 (47%), Gaps = 3/86 (3%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID 186
            ++ +  L      + L + FSTFG +L  +V  D   G S+G+GFV+F   E+    + 
Sbjct: 16  SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75

Query: 187 KLNGMLLNDKQVFVGPFLRKQEREST 212
           + +  +++ +         KQ ++S 
Sbjct: 76  QRH--MIDGRWCDCKLPNSKQSQDSG 99

>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 = 51.1 bits (123), Expect = 2e-08
 Identities = 22/89 (24%), Positives = 41/89 (46%), Gaps = 3/89 (3%)

Query: 26  ANNGGVGDARQFVSTS-LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYG 84
            ++G  G  R    TS L V  L     +  L + F+  G+V+ V+V +DL T  S G+G
Sbjct: 1   GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60

Query: 85  YVNYNAAHEATRALDELNFTPLNGKPIRI 113
           +V +       + + + +   ++G+    
Sbjct: 61  FVRFTEYETQVKVMSQRHM--IDGRWCDC 87

>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 = 74.3 bits (183), Expect = 1e-16
 Identities = 24/96 (25%), Positives = 40/96 (41%), Gaps = 9/96 (9%)

Query: 208 ERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTA--------VMRDAD-GKS 258
                   +  N ++V+ L E  T + +   F + GII +          +  D + GK 
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 259 KCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA 294
           K    V+FDDP  A  +++  +GK+F      V  A
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 66.6 bits (163), Expect = 6e-14
 Identities = 23/92 (25%), Positives = 40/92 (43%), Gaps = 9/92 (9%)

Query: 118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILS--------CKVATDSL-GQSR 168
                  S    IF++ L +++  +++ D F   G I +          + TD   G+ +
Sbjct: 4   HHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLK 63

Query: 169 GYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
           G   V FD+  SAK+AID  +G   +   + V
Sbjct: 64  GEATVSFDDPPSAKAAIDWFDGKEFSGNPIKV 95

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 65.8 bits (161), Expect = 1e-13
 Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 9/84 (10%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITS--------CKVMRDP-NGISRGSGFVAFSTAE 373
            ++V+ L ++++ + + + F + G I +          +  D   G  +G   V+F    
Sbjct: 15  TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74

Query: 374 EASKALTEMNGKMVVSKPLYVALA 397
            A  A+   +GK     P+ V+ A
Sbjct: 75  SAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 61.9 bits (151), Expect = 2e-12
 Identities = 17/83 (20%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVS--------VRVCRDLSTRRSLGYGYVNYNA 90
           + +++V  L  +V    + D F Q+G + +        + +  D  T +  G   V+++ 
Sbjct: 13  NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 72

Query: 91  AHEATRALDELNFTPLNGKPIRI 113
              A  A+D  +    +G PI++
Sbjct: 73  PPSAKAAIDWFDGKEFSGNPIKV 95

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 74.4 bits (183), Expect = 1e-16
 Identities = 23/93 (24%), Positives = 45/93 (48%), Gaps = 10/93 (10%)

Query: 201 GPFLRKQERESTADKTRFNNVYVKNLSETTTE------DDLKKIFGEFGIITSTAVMRDA 254
           G  L+ + +E+       + + V N+ +   +      + + KIF +FG IT+     + 
Sbjct: 1   GDVLKDRPQEADGID---SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN-DFYPEE 56

Query: 255 DGKSKCFGFVNFDDPDDAARSVEALNGKKFDDK 287
           DGK+K + F+ +  P  A  +V+  +G K D +
Sbjct: 57  DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 59.0 bits (143), Expect = 3e-11
 Identities = 18/96 (18%), Positives = 36/96 (37%), Gaps = 7/96 (7%)

Query: 120 PTIRKSGAGNIFIKNL------DKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFV 173
           P         I + N+              +H  FS FG I +     +  G+++GY F+
Sbjct: 8   PQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEED-GKTKGYIFL 66

Query: 174 QFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQER 209
           ++ +   A  A+   +G  L+ +  F        ++
Sbjct: 67  EYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFDK 102

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 58.2 bits (141), Expect = 6e-11
 Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 313 KETADKFEGLNLYVKNLDDSISD------DKLKELFSEFGTITSCKVMRDPNGISRGSGF 366
           +          + V N+     D      + + ++FS+FG IT+     + +G ++G  F
Sbjct: 7   RPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIF 65

Query: 367 VAFSTAEEASKALTEMNGK 385
           + +++   A  A+   +G 
Sbjct: 66  LEYASPAHAVDAVKNADGY 84

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 11/67 (16%), Positives = 30/67 (44%), Gaps = 2/67 (2%)

Query: 43  YVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN 102
            VG   L    + ++ +F++ G++ +     +    ++ GY ++ Y +   A  A+   +
Sbjct: 25  QVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNAD 82

Query: 103 FTPLNGK 109
              L+ +
Sbjct: 83  GYKLDKQ 89

>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 = 74.8 bits (183), Expect = 4e-16
 Identities = 22/113 (19%), Positives = 45/113 (39%), Gaps = 6/113 (5%)

Query: 87  NYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGNIF---IKNLDKSIDNKA 143
           +++    A  AL  +N        +    +  D  +  +G   +    ++NL   +    
Sbjct: 3   HHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDV 62

Query: 144 LHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDK 196
           LH  FS FG +L     T +   ++    +Q+ +  SA+ A   L+G  + + 
Sbjct: 63  LHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNA 112

>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 = 57.4 bits (138), Expect = 4e-10
 Identities = 20/115 (17%), Positives = 44/115 (38%), Gaps = 4/115 (3%)

Query: 174 QFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTED 233
              +  SA++A+  +N +   +  +            + A ++    + V+NL    T D
Sbjct: 3   HHHHHGSAQAALQAVNSVQSGNLALAASAAAV-DAGMAMAGQSPVLRIIVENLFYPVTLD 61

Query: 234 DLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKE 288
            L +IF +FG +         +        + + DP  A  +  +L+G+   +  
Sbjct: 62  VLHQIFSKFGTVLKIITFTKNNQFQ---ALLQYADPVSAQHAKLSLDGQNIYNAC 113

>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 = 54.3 bits (130), Expect = 5e-09
 Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
           L + V+NL   ++ D L ++FS+FGT+         N        + ++    A  A   
Sbjct: 47  LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLS 103

Query: 382 MNGKMV 387
           ++G+ +
Sbjct: 104 LDGQNI 109

>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 = 41.6 bits (97), Expect = 1e-04
 Identities = 22/117 (18%), Positives = 41/117 (35%), Gaps = 7/117 (5%)

Query: 2   AQVQVQPQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFN 61
           AQ  +Q    V        A+    + G     +  V   + V +L   V    L+ +F+
Sbjct: 10  AQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPV-LRIIVENLFYPVTLDVLHQIFS 68

Query: 62  QMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKP--IRIMYS 116
           + G V+ +       T+ +     + Y     A  A   L+   +      +RI +S
Sbjct: 69  KFGTVLKIITF----TKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 121

>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 = 73.1 bits (180), Expect = 4e-16
 Identities = 27/87 (31%), Positives = 45/87 (51%), Gaps = 10/87 (11%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALT-- 380
           L++  L    +++ L+  + ++G +T C VMRDP    SRG GFV FS+  E   A+   
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89

Query: 381 --EMNGKMVVSKPLYVALAQRKEERRA 405
              ++G++V  K      A  +EE  +
Sbjct: 90  PHSIDGRVVEPKR-----AVAREESGS 111

>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 = 68.5 bits (168), Expect = 2e-14
 Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 5/84 (5%)

Query: 209 RESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFD 267
                +K +F  +++  LS  TTE+ L+  + ++G +T   VMRD    +S+ FGFV F 
Sbjct: 18  ERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS 77

Query: 268 DPDDAARSVEA----LNGKKFDDK 287
              +   ++ A    ++G+  + K
Sbjct: 78  SMAEVDAAMAARPHSIDGRVVEPK 101

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 59.2 bits (144), Expect = 4e-11
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 5/66 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAID-- 186
           +FI  L      ++L + +  +G +  C V  D    +SRG+GFV F +     +A+   
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89

Query: 187 --KLNG 190
              ++G
Sbjct: 90  PHSIDG 95

>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 = 46.5 bits (111), Expect = 9e-07
 Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L++G L     +  L + + Q G++    V RD +++RS G+G+V +++  E   A+   
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AA 88

Query: 102 NFTPLNGKPIR 112
               ++G+ + 
Sbjct: 89  RPHSIDGRVVE 99

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 71.8 bits (177), Expect = 4e-16
 Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALT-- 380
           +++  L    + + L+E F +FG +  C VMRDP    SRG GFV F       K L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 381 --EMNGKMVVSK 390
             E++ K +  K
Sbjct: 63  RHELDSKTIDPK 74

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 68.3 bits (168), Expect = 9e-15
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA- 278
           +++  LS  TT++ L++ FG+FG +    VMRD    +S+ FGFV F D     + +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 279 ---LNGKKFDDK 287
              L+ K  D K
Sbjct: 63  RHELDSKTIDPK 74

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 59.8 bits (146), Expect = 8e-12
 Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           +FI  L      + L + F  FG +  C V  D L  +SRG+GFV F ++      +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 189 NGMLLNDKQV 198
           +   L+ K +
Sbjct: 62  SRHELDSKTI 71

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 47.9 bits (115), Expect = 1e-07
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           +++G L        L + F Q G+V    V RD  T+RS G+G+V +       + L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 102 NFTPLNGKPIR 112
           +   L+ K I 
Sbjct: 62  SRHELDSKTID 72

>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 = 72.7 bits (179), Expect = 5e-16
 Identities = 12/67 (17%), Positives = 25/67 (37%), Gaps = 5/67 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             ++V  L   T+   L + F  FG I +   ++        F ++ ++  D A  +   
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAK 72

Query: 279 LNGKKFD 285
           + G    
Sbjct: 73  MRGFPLG 79

>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 = 70.7 bits (174), Expect = 2e-15
 Identities = 16/80 (20%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            L+V  L  + S   L   F  FG+I +   ++          ++ + + + A  A  +M
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKM 73

Query: 383 NGKMV--VSKPLYVALAQRK 400
            G  +    + L V  A+  
Sbjct: 74  RGFPLGGPDRRLRVDFAKSG 93

>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 = 70.3 bits (173), Expect = 2e-15
 Identities = 19/88 (21%), Positives = 39/88 (44%), Gaps = 11/88 (12%)

Query: 107 NGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ 166
           +G   +I Y   +PT R      +++  L  +    AL   F  FG+I +          
Sbjct: 3   SGSSGKIGYGKANPTTR------LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG---- 52

Query: 167 SRGYGFVQFDNEESAKSAIDKLNGMLLN 194
              + ++Q+++ ++A++A  K+ G  L 
Sbjct: 53  -DSFAYIQYESLDAAQAACAKMRGFPLG 79

>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 = 64.6 bits (158), Expect = 3e-13
 Identities = 19/97 (19%), Positives = 45/97 (46%), Gaps = 8/97 (8%)

Query: 27  NNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYV 86
           ++G +G  +   +T L+VG L  + + + L   F++ G + ++         +   + Y+
Sbjct: 5   SSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH------VKGDSFAYI 58

Query: 87  NYNAAHEATRALDELNFTPLNG--KPIRIMYSYRDPT 121
            Y +   A  A  ++   PL G  + +R+ ++   P+
Sbjct: 59  QYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS 95

>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 = 71.8 bits (177), Expect = 6e-16
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           ++V  L    S   LK+ F++FG +  C +  DPN G SRG GF+ F  A    K L + 
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 383 ----NGKMV 387
               +G+++
Sbjct: 74  EHRLDGRVI 82

>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 = 66.8 bits (164), Expect = 4e-14
 Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 5/82 (6%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDP 269
           ++ ++     ++V  LS  T++ DLK  F +FG +    +  D + G+S+ FGF+ F D 
Sbjct: 4   ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA 63

Query: 270 DDAARSVEA----LNGKKFDDK 287
               + ++     L+G+  D K
Sbjct: 64  ASVEKVLDQKEHRLDGRVIDPK 85

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 60.3 bits (147), Expect = 6e-12
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           +F+  L      K L D F+ FG ++ C +  D   G+SRG+GF+ F +  S +  +D+ 
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 189 NGMLLNDKQV 198
               L+ + +
Sbjct: 74  EHR-LDGRVI 82

>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 = 49.5 bits (119), Expect = 4e-08
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VG L    +   L D F + G+VV   +  D +T RS G+G++ +  A    + LD+ 
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 102 NFTPLNGKPIR 112
               L+G+ I 
Sbjct: 74  EHR-LDGRVID 83

>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 = 72.1 bits (177), Expect = 8e-16
 Identities = 22/94 (23%), Positives = 35/94 (37%), Gaps = 6/94 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           + V  L  S S   LK+   E G +    V RD      G+G V F   E+ + A+ +++
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD 71

Query: 384 GKMVVSKPLYVALAQRKEERRARLQAQFSQMRPP 417
                S     A  + K +         S+   P
Sbjct: 72  NTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGP 105

>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 = 69.8 bits (171), Expect = 6e-15
 Identities = 22/83 (26%), Positives = 30/83 (36%), Gaps = 6/83 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N V V  L  + +  DLK    E G +    V RD        G V F   +D   +V  
Sbjct: 16  NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRK 69

Query: 279 LNGKKFDDKEWYVGKAQKKYERE 301
           L+  KF   E      + K +  
Sbjct: 70  LDNTKFRSHEGETAYIRVKVDGP 92

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 64.0 bits (156), Expect = 5e-13
 Identities = 15/71 (21%), Positives = 25/71 (35%), Gaps = 6/71 (8%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + +  L  S   + L D     G++    V  D      G G V+F  +E    A+ KL+
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD 71

Query: 190 GMLLNDKQVFV 200
                  +   
Sbjct: 72  NTKFRSHEGET 82

>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 = 55.2 bits (133), Expect = 7e-10
 Identities = 18/74 (24%), Positives = 26/74 (35%), Gaps = 7/74 (9%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           + V  L  S +   L D   + G V    V RD       G G V +    + T A+ +L
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKL 70

Query: 102 NFTPLNGKPIRIMY 115
           + T          Y
Sbjct: 71  DNTKFRSHEGETAY 84

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 71.8 bits (176), Expect = 1e-15
 Identities = 14/89 (15%), Positives = 40/89 (44%), Gaps = 7/89 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT--E 381
           ++++ L   +++ ++  L   FG +T+  +++      +   F+  +T E A+  +    
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 73

Query: 382 MNGKMVVSKPLYVALAQRKEERRARLQAQ 410
               ++  +P+Y+  +  KE +      Q
Sbjct: 74  SVTPVLRGQPIYIQFSNHKELKTDSSPNQ 102

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 59.1 bits (143), Expect = 3e-11
 Identities = 13/95 (13%), Positives = 33/95 (34%), Gaps = 9/95 (9%)

Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFV 264
                  +   +R   ++++ L    TE ++  +   FG +T+  +++      K   F+
Sbjct: 5   HHHHHHGSGVPSR--VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFI 57

Query: 265 NFDDPDDAARSVEAL--NGKKFDDKEWYVGKAQKK 297
             +  + A   V            +  Y+  +  K
Sbjct: 58  EMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK 92

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 52.2 bits (125), Expect = 9e-09
 Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 8/80 (10%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S  +++  L + V + ++  L    G+V ++ + +           ++  N    A   +
Sbjct: 16  SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMV 69

Query: 99  DELNFTP--LNGKPIRIMYS 116
           +        L G+PI I +S
Sbjct: 70  NYYTSVTPVLRGQPIYIQFS 89

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 51.0 bits (122), Expect = 2e-08
 Identities = 14/92 (15%), Positives = 38/92 (41%), Gaps = 10/92 (10%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL- 188
           I I+ L   +    +      FG + +  +        +   F++ + EE+A + ++   
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 73

Query: 189 -NGMLLNDKQVFVGPFLRKQE--RESTADKTR 217
               +L  + +++  F   +E   +S+ ++ R
Sbjct: 74  SVTPVLRGQPIYIQ-FSNHKELKTDSSPNQAR 104

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 71.3 bits (175), Expect = 1e-15
 Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALN 280
            + +      +  L  +F + G + +     D A GK+K F FV     +DA + +++ +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 281 GKKFDDK 287
           GK+ D K
Sbjct: 76  GKRLDLK 82

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 62.8 bits (153), Expect = 1e-12
 Identities = 14/62 (22%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 325 YVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMN 383
            + +    +    L  LFS+ G + + +   D   G ++G  FV   +  +A K +   +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 384 GK 385
           GK
Sbjct: 76  GK 77

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 59.0 bits (143), Expect = 3e-11
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 131 FIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKLN 189
            I +    +  KAL   FS  G +++ +   D   G+++G+ FV+  +   AK  I   +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 190 GMLLNDKQVF 199
           G  L+ K   
Sbjct: 76  GKRLDLKHRL 85

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 57.4 bits (139), Expect = 1e-10
 Identities = 20/92 (21%), Positives = 45/92 (48%), Gaps = 1/92 (1%)

Query: 29  GGVG-DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVN 87
           G +G D    V+ +  +    + V    L  LF++ G+VV++    D +T ++ G+ +V 
Sbjct: 1   GPLGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVE 60

Query: 88  YNAAHEATRALDELNFTPLNGKPIRIMYSYRD 119
             + ++A + +   +   L+ K    +Y+ +D
Sbjct: 61  CGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKD 92

>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 = 70.8 bits (174), Expect = 2e-15
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 11/87 (12%)

Query: 116 SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQF 175
           S  D TI       +++  L  +I    L + F  FG I +  V        +   F+QF
Sbjct: 6   SGEDKTIT-----TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQF 55

Query: 176 DNEESAKSAIDK-LNGMLLNDKQVFVG 201
              ++A+ A +K  N +++N +++ V 
Sbjct: 56  ATRQAAEVAAEKSFNKLIVNGRRLNVK 82

>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 = 70.0 bits (172), Expect = 2e-15
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            LYV  L D+I++  L+  F +FG I +  V++      +   F+ F+T + A  A  + 
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKS 68

Query: 383 -NGKMVVSKPLYV 394
            N  +V  + L V
Sbjct: 69  FNKLIVNGRRLNV 81

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 66.5 bits (163), Expect = 4e-14
 Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 6/70 (8%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA- 278
            +YV  L +T TE DL+  F +FG I +  V++      +   F+ F     A  + E  
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKS 68

Query: 279 LNGKKFDDKE 288
            N    + + 
Sbjct: 69  FNKLIVNGRR 78

>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 = 64.6 bits (158), Expect = 2e-13
 Identities = 16/77 (20%), Positives = 37/77 (48%), Gaps = 7/77 (9%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+LYVG L  ++ ++ L + F Q G++ ++ V +           ++ +     A  A +
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAE 66

Query: 100 E-LNFTPLNGKPIRIMY 115
           +  N   +NG+ + + +
Sbjct: 67  KSFNKLIVNGRRLNVKW 83

>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 = 70.2 bits (173), Expect = 2e-15
 Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA- 278
           ++V  LS  T E+ +++ FG FG + S  +  D    K + F F+ F + +   + +E  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 279 ---LNGKKFDDK 287
              +   K + K
Sbjct: 62  YHNVGLSKCEIK 73

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 66.4 bits (163), Expect = 3e-14
 Identities = 15/69 (21%), Positives = 27/69 (39%), Gaps = 5/69 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALT-- 380
           ++V  L     ++K++E F  FG + S ++  D      RG  F+ F   E   K +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 381 --EMNGKMV 387
              +     
Sbjct: 62  YHNVGLSKC 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 = 58.7 bits (143), Expect = 2e-11
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 2/70 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           IF+  L      + + + F  FG + S ++  D+   + RG+ F+ F  EE  K  ++K 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 189 NGMLLNDKQV 198
               +   + 
Sbjct: 61  KYHNVGLSKC 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 = 44.4 bits (106), Expect = 2e-06
 Identities = 12/72 (16%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VG L     + ++ + F   G+V S+ +  D  T +  G+ ++ +       + + E 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60

Query: 102 NFTPLNGKPIRI 113
            +  +      I
Sbjct: 61  KYHNVGLSKCEI 72

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 71.1 bits (175), Expect = 2e-15
 Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 10/87 (11%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALT-- 380
           L+V  LD S + + L+  FS++G +  C +M+D     SRG GFV F         L   
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78

Query: 381 --EMNGKMVVSKPLYVALAQRKEERRA 405
              ++G+ +  KP        +  + +
Sbjct: 79  PHTLDGRNIDPKP-----CTPRGMQPS 100

>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 = 68.8 bits (169), Expect = 1e-14
 Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 5/83 (6%)

Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDD 268
            + +       ++V  L  +TT++ L+  F ++G +    +M+D    +S+ FGFV F D
Sbjct: 8   MNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67

Query: 269 PDDAARSVEA----LNGKKFDDK 287
           P+     + +    L+G+  D K
Sbjct: 68  PNCVGTVLASRPHTLDGRNIDPK 90

>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 = 59.2 bits (144), Expect = 3e-11
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           +F+  LD S   + L   FS +G ++ C +  D    QSRG+GFV+F +     + +   
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL-AS 77

Query: 189 NGMLLNDKQV 198
               L+ + +
Sbjct: 78  RPHTLDGRNI 87

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 50.3 bits (121), Expect = 4e-08
 Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 1/89 (1%)

Query: 24  GIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGY 83
           G + + G+ ++       L+VG LD S     L   F+Q G+VV   + +D +T +S G+
Sbjct: 1   GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGF 60

Query: 84  GYVNYNAAHEATRALDELNFTPLNGKPIR 112
           G+V +   +     L       L+G+ I 
Sbjct: 61  GFVKFKDPNCVGTVL-ASRPHTLDGRNID 88

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 69.8 bits (172), Expect = 2e-15
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA- 278
           ++V  LS  TT +D+K  F +FG +    +M D    + + FGFV F+  D   +  E  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 279 ---LNGKKFDDK 287
              +N K  + K
Sbjct: 62  FHEINNKMVECK 73

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 68.3 bits (168), Expect = 9e-15
 Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALT-- 380
           ++V  L  + + + +K  F +FG +    +M D      RG GFV F + +   K     
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 381 --EMNGKMV 387
             E+N KMV
Sbjct: 62  FHEINNKMV 70

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 62.1 bits (152), Expect = 1e-12
 Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           IF+  L  +   + +   F  FG +    +  D    + RG+GFV F++E+  +    ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 189 NGMLLNDKQV 198
           +   +N+K V
Sbjct: 61  HFHEINNKMV 70

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 49.0 bits (118), Expect = 4e-08
 Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VG L ++     +   F Q G+V    +  D +T R  G+G+V + +     +   E+
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 102 NFTPLNGKPIRI 113
           +F  +N K +  
Sbjct: 61  HFHEINNKMVEC 72

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 70.1 bits (172), Expect = 2e-15
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 219 NNVYVKNLSETTTE------DDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDA 272
           + + V N+ +   +      + + KIF +FG IT+     + DGK+K + F+ +  P  A
Sbjct: 2   SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN-DFYPEEDGKTKGYIFLEYASPAHA 60

Query: 273 ARSVEALNGKKFDDK 287
             +V+  +G K D +
Sbjct: 61  VDAVKNADGYKLDKQ 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 59.7 bits (145), Expect = 9e-12
 Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 7/76 (9%)

Query: 130 IFIKNL------DKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKS 183
           I + N+              +H  FS FG I +     +  G+++GY F+++ +   A  
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEED-GKTKGYIFLEYASPAHAVD 62

Query: 184 AIDKLNGMLLNDKQVF 199
           A+   +G  L+ +  F
Sbjct: 63  AVKNADGYKLDKQHTF 78

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 58.2 bits (141), Expect = 3e-11
 Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 337 KLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGK 385
            + ++FS+FG IT+     + +G ++G  F+ +++   A  A+   +G 
Sbjct: 23  VIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGY 70

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 44.3 bits (105), Expect = 3e-06
 Identities = 8/56 (14%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 54  SQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK 109
           + ++ +F++ G++ +     +    ++ GY ++ Y +   A  A+   +   L+ +
Sbjct: 22  NVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75

>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 = 70.8 bits (174), Expect = 3e-15
 Identities = 25/85 (29%), Positives = 39/85 (45%), Gaps = 10/85 (11%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALT-- 380
           +++  L    + + L+E F +FG +  C VMRDP    SRG GFV F       K L   
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87

Query: 381 --EMNGKMVVSKPLYVALAQRKEER 403
             E++ K +  K     +A  +  +
Sbjct: 88  RHELDSKTIDPK-----VAFPRRAQ 107

>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 = 66.9 bits (164), Expect = 7e-14
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA- 278
           +++  LS  TT++ L++ FG+FG +    VMRD    +S+ FGFV F D     + +   
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87

Query: 279 ---LNGKKFDDK 287
              L+ K  D K
Sbjct: 88  RHELDSKTIDPK 99

>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 = 63.8 bits (156), Expect = 8e-13
 Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 7/95 (7%)

Query: 105 PLNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL 164
             +   +    S+   +  K     +FI  L      + L + F  FG +  C V  D L
Sbjct: 8   HHHSSGLVPRGSHMGSSGCK-----MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL 62

Query: 165 -GQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQV 198
             +SRG+GFV F ++      +   +   L+ K +
Sbjct: 63  TKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTI 96

>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 = 47.3 bits (113), Expect = 5e-07
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           +++G L        L + F Q G+V    V RD  T+RS G+G+V +       + L   
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 86

Query: 102 NFTPLNGKPIRI 113
           +   L+ K I  
Sbjct: 87  SRHELDSKTIDP 98

>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 = 70.6 bits (173), Expect = 4e-15
 Identities = 23/98 (23%), Positives = 36/98 (36%), Gaps = 6/98 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           + V  L  S S   LK+   E G +    V RD      G+G V F   E+ + A+ +++
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD 72

Query: 384 GKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPR 421
                S     A  + K +         S+ R     R
Sbjct: 73  NTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSR 110

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 67.9 bits (166), Expect = 3e-14
 Identities = 22/83 (26%), Positives = 30/83 (36%), Gaps = 6/83 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N V V  L  + +  DLK    E G +    V RD        G V F   +D   +V  
Sbjct: 17  NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRK 70

Query: 279 LNGKKFDDKEWYVGKAQKKYERE 301
           L+  KF   E      + K +  
Sbjct: 71  LDNTKFRSHEGETAYIRVKVDGP 93

>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 = 62.5 bits (152), Expect = 3e-12
 Identities = 15/71 (21%), Positives = 25/71 (35%), Gaps = 6/71 (8%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + +  L  S   + L D     G++    V  D      G G V+F  +E    A+ KL+
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD 72

Query: 190 GMLLNDKQVFV 200
                  +   
Sbjct: 73  NTKFRSHEGET 83

>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 = 53.3 bits (128), Expect = 4e-09
 Identities = 18/74 (24%), Positives = 26/74 (35%), Gaps = 7/74 (9%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           + V  L  S +   L D   + G V    V RD       G G V +    + T A+ +L
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKL 71

Query: 102 NFTPLNGKPIRIMY 115
           + T          Y
Sbjct: 72  DNTKFRSHEGETAY 85

>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 = 69.8 bits (171), Expect = 6e-15
 Identities = 11/92 (11%), Positives = 32/92 (34%), Gaps = 5/92 (5%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGT-ITSCKVMRDPN--GISRGSGFVAFSTAEEASKALT 380
           L++  +      +++ E  ++    +    V         +RG  FV + +   A+ A  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 381 EMNGK--MVVSKPLYVALAQRKEERRARLQAQ 410
           ++      +    + V  A+ + +    +   
Sbjct: 71  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 102

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 67.5 bits (165), Expect = 4e-14
 Identities = 11/92 (11%), Positives = 35/92 (38%), Gaps = 5/92 (5%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDAD--GKSKCFGFVNFDDPDDAARSVE 277
           +++  + +    +++ +   +    +    V   A    K++ F FV ++    AA +  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 278 ALNGKKF--DDKEWYVGKAQKKYEREMELKGK 307
            L   +      +  V  A+ + + + ++   
Sbjct: 71  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 102

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 57.9 bits (140), Expect = 1e-10
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFG-NILSCKVATDS--LGQSRGYGFVQFDNEESAKSAID 186
           +FI  + K    + + +  +     +L   V   +    ++RG+ FV++++  +A  A  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 187 KLN--GMLLNDKQVFV 200
           KL    + L   Q+ V
Sbjct: 71  KLMPGRIQLWGHQIAV 86

>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 = 52.9 bits (127), Expect = 6e-09
 Identities = 16/88 (18%), Positives = 34/88 (38%), Gaps = 9/88 (10%)

Query: 38  VSTS-----LYVGDLDLSVNDSQLYDLFNQMGQVV-SVRVCRDL-STRRSLGYGYVNYNA 90
            S S     L++G +       ++ +   ++ + V  V V        ++ G+ +V Y +
Sbjct: 2   SSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61

Query: 91  AHEATRALDELN--FTPLNGKPIRIMYS 116
              A  A  +L      L G  I + ++
Sbjct: 62  HRAAAMARRKLMPGRIQLWGHQIAVDWA 89

>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 = 68.8 bits (169), Expect = 7e-15
 Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 6/92 (6%)

Query: 209 RESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDD 268
           R S       + V+V   +E  T ++L++ F ++G +    + +      + F FV F D
Sbjct: 2   RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFAD 57

Query: 269 PDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
              A                 ++  A+ K+ +
Sbjct: 58  DKVAQSLCG--EDLIIKGISVHISNAEPKHNK 87

>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 = 64.6 bits (158), Expect = 2e-13
 Identities = 14/84 (16%), Positives = 35/84 (41%), Gaps = 12/84 (14%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM- 382
           ++V    + ++ ++L++ F ++G +    + +      R   FV F+  + A     E  
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQSLCGEDL 69

Query: 383 --NGKMVVSKPLYVALAQRKEERR 404
              G  V     +++ A+ K  + 
Sbjct: 70  IIKGISV-----HISNAEPKHNKL 88

>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 = 55.7 bits (135), Expect = 3e-10
 Identities = 12/82 (14%), Positives = 32/82 (39%), Gaps = 6/82 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+    + +  + L   F  +G ++   +        R + FV F +++ A+S   +  
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQSLCGEDL 69

Query: 190 GMLLNDKQVFVGPFLRKQERES 211
             ++    V +     K  + +
Sbjct: 70  --IIKGISVHISNAEPKHNKLN 89

>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 = 40.3 bits (95), Expect = 9e-05
 Identities = 14/82 (17%), Positives = 27/82 (32%), Gaps = 7/82 (8%)

Query: 32  GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA 91
                   + ++VG     +   +L   F Q G+VV V +      +    + +V +   
Sbjct: 4   SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFADD 58

Query: 92  HEATRALDELNFTPLNGKPIRI 113
             A     E     + G  + I
Sbjct: 59  KVAQSLCGEDLI--IKGISVHI 78

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 68.8 bits (169), Expect = 1e-14
 Identities = 18/84 (21%), Positives = 41/84 (48%), Gaps = 3/84 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
            YV NL  +     +  +F +   I S +++RD +    +G  +V F   +   +AL   
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TY 75

Query: 383 NGKMVVSKPLYVALAQRKEERRAR 406
           +G ++  + L V +A+ +++ ++ 
Sbjct: 76  DGALLGDRSLRVDIAEGRKQDKSG 99

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 67.3 bits (165), Expect = 4e-14
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
            YV NL   T + D+  IF +  I  S  ++RD D  K K F +V FD+  D+ +     
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLSI-RSVRLVRDKDTDKFKGFCYVEFDE-VDSLKEALTY 75

Query: 280 NGKKFDDKEWYVGKAQKKYERE 301
           +G    D+   V  A+ + + +
Sbjct: 76  DGALLGDRSLRVDIAEGRKQDK 97

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 60.7 bits (148), Expect = 7e-12
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             + YVG+L  +     +  +F  +  + SVR+ RD  T +  G+ YV ++       AL
Sbjct: 15  PYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73

Query: 99  DELNFTPLNGKPIRIMYS 116
              +   L  + +R+  +
Sbjct: 74  -TYDGALLGDRSLRVDIA 90

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 58.4 bits (142), Expect = 4e-11
 Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL 188
            ++ NL  +     +   F     I S ++  D    + +G+ +V+FD  +S K A+   
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TY 75

Query: 189 NGMLLNDKQVFV 200
           +G LL D+ + V
Sbjct: 76  DGALLGDRSLRV 87

>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 = 69.0 bits (169), Expect = 1e-14
 Identities = 18/108 (16%), Positives = 38/108 (35%), Gaps = 2/108 (1%)

Query: 311 SLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTI-TSCKVMRDPNGISRGSGFVAF 369
           S  E       +  ++ N+  SI+   + +          +  V+ D NG   G   V F
Sbjct: 5   SSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQF 64

Query: 370 STAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPP 417
              ++A K+   ++ K +  +  +V +   ++ R             P
Sbjct: 65  KNEDDARKSE-RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGP 111

>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 = 66.7 bits (163), Expect = 9e-14
 Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTA-VMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
            ++ N+  + T+ D+ +      +  +   V+ D +G+      V F + DDA +  E L
Sbjct: 18  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK-SERL 76

Query: 280 NGKKFDDKEWYVGKAQKKYEREME 303
           + KK + +E +V     +  RE+E
Sbjct: 77  HRKKLNGREAFVHVVTLEDMREIE 100

>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 = 59.0 bits (143), Expect = 5e-11
 Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 2/89 (2%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNIL-SCKVATDSLGQSRGYGFVQFDNEESA 181
             S      I N+  SI    +            +  V  D+ GQ  G   VQF NE+ A
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

Query: 182 KSAIDKLNGMLLNDKQVFVGPFLRKQERE 210
           + +  +L+   LN ++ FV     +  RE
Sbjct: 71  RKSE-RLHRKKLNGREAFVHVVTLEDMRE 98

>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 = 49.4 bits (118), Expect = 1e-07
 Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 3/83 (3%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVV-SVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
               ++ ++  S+    +      +     +V V  D +  + LG   V +    +A ++
Sbjct: 15  KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD-NNGQGLGQALVQFKNEDDARKS 73

Query: 98  LDELNFTPLNGKPIRIMYSYRDP 120
              L+   LNG+   +     + 
Sbjct: 74  E-RLHRKKLNGREAFVHVVTLED 95

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 67.9 bits (166), Expect = 2e-14
 Identities = 19/97 (19%), Positives = 33/97 (34%), Gaps = 4/97 (4%)

Query: 201 GPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKC 260
                              +VYV NL       DLK+   E G +     +R      + 
Sbjct: 2   SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP----LRLTWQGPRR 57

Query: 261 FGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKK 297
             F+++ D   A ++V  L G +       V  A+++
Sbjct: 58  RAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 58.3 bits (141), Expect = 5e-11
 Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 4/81 (4%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           ++YV NL        LK    E G++      + P    R   F+ +  +  A +A++ +
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGP----RRRAFLHYPDSAAAQQAVSCL 76

Query: 383 NGKMVVSKPLYVALAQRKEER 403
            G  + +  L VALA+++ ++
Sbjct: 77  QGLRLGTDTLRVALARQQRDK 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 52.5 bits (126), Expect = 5e-09
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 5/75 (6%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           +  +YVG+L      S L     ++G  V +R+    + +      +++Y  +  A +A+
Sbjct: 19  AADVYVGNLPRDARVSDLKRALRELG-SVPLRL----TWQGPRRRAFLHYPDSAAAQQAV 73

Query: 99  DELNFTPLNGKPIRI 113
             L    L    +R+
Sbjct: 74  SCLQGLRLGTDTLRV 88

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 52.1 bits (125), Expect = 8e-09
 Identities = 12/72 (16%), Positives = 28/72 (38%), Gaps = 4/72 (5%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           ++++ NL +      L       G  +  ++        R   F+ + +  +A+ A+  L
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELG-SVPLRLTWQG---PRRRAFLHYPDSAAAQQAVSCL 76

Query: 189 NGMLLNDKQVFV 200
            G+ L    + V
Sbjct: 77  QGLRLGTDTLRV 88

>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 = 68.8 bits (168), Expect = 2e-14
 Identities = 14/89 (15%), Positives = 40/89 (44%), Gaps = 7/89 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT--E 381
           ++++ L   +++ ++  L   FG +T+  +++      +   F+  +T E A+  +    
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 88

Query: 382 MNGKMVVSKPLYVALAQRKEERRARLQAQ 410
               ++  +P+Y+  +  KE +      Q
Sbjct: 89  SVTPVLRGQPIYIQFSNHKELKTDSSPNQ 117

>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 = 58.8 bits (142), Expect = 5e-11
 Identities = 12/81 (14%), Positives = 30/81 (37%), Gaps = 7/81 (8%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE- 277
             ++++ L    TE ++  +   FG +T+  +++      K   F+  +  + A   V  
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNY 86

Query: 278 -ALNGKKFDDKEWYVGKAQKK 297
                     +  Y+  +  K
Sbjct: 87  YTSVTPVLRGQPIYIQFSNHK 107

>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 = 53.4 bits (128), Expect = 4e-09
 Identities = 16/109 (14%), Positives = 37/109 (33%), Gaps = 8/109 (7%)

Query: 10  APVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSV 69
                    S       ++ G   +    S  +++  L + V + ++  L    G+V ++
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNL 61

Query: 70  RVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTP--LNGKPIRIMYS 116
            + +           ++  N    A   ++        L G+PI I +S
Sbjct: 62  LMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS 104

>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 = 51.5 bits (123), Expect = 2e-08
 Identities = 14/92 (15%), Positives = 39/92 (42%), Gaps = 10/92 (10%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID--K 187
           I I+ L   +    +      FG + +       + + +   F++ + EE+A + ++   
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLL-----MLKGKNQAFIEMNTEEAANTMVNYYT 88

Query: 188 LNGMLLNDKQVFVGPFLRKQE--RESTADKTR 217
               +L  + +++  F   +E   +S+ ++ R
Sbjct: 89  SVTPVLRGQPIYIQ-FSNHKELKTDSSPNQAR 119

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

 Score = 67.6 bits (166), Expect = 3e-14
 Identities = 19/92 (20%), Positives = 40/92 (43%), Gaps = 11/92 (11%)

Query: 207 QERESTADKTRFNNVYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVN 265
            E  +   K+R   +++ NL  +  +++DL +IF  +G I    +          FGF+ 
Sbjct: 2   TEMHNIPPKSR---LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA-------FGFIQ 51

Query: 266 FDDPDDAARSVEALNGKKFDDKEWYVGKAQKK 297
           FD+P     ++E  + +    K+  +  +   
Sbjct: 52  FDNPQSVRDAIECESQEMNFGKKLILEVSSSN 83

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

 Score = 62.2 bits (152), Expect = 2e-12
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 8/72 (11%)

Query: 130 IFIKNLD-KSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +FI NL  K++  + L   FS +G+I+   +          +GF+QFDN +S + AI+  
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECE 65

Query: 189 NGMLLNDKQVFV 200
           +  +   K++ +
Sbjct: 66  SQEMNFGKKLIL 77

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

 Score = 61.1 bits (149), Expect = 4e-12
 Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 8/84 (9%)

Query: 324 LYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           L++ NL   ++S + L  +FS +G I    +           GF+ F   +    A+   
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIECE 65

Query: 383 NGKMVVSKPLYVALAQRKEERRAR 406
           + +M   K L + ++      +  
Sbjct: 66  SQEMNFGKKLILEVSSSNARPQFD 89

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

 Score = 48.7 bits (117), Expect = 1e-07
 Identities = 14/92 (15%), Positives = 39/92 (42%), Gaps = 10/92 (10%)

Query: 39  STSLYVGDLDL-SVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
            + L++G+L L +V+   L+ +F+  G ++ + +           +G++ ++       A
Sbjct: 10  KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDA 61

Query: 98  LDELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
           ++  +     GK + +  S       +   G+
Sbjct: 62  IECESQEMNFGKKLILEVS-SSNARPQFDHGD 92

>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 = 67.3 bits (165), Expect = 4e-14
 Identities = 17/83 (20%), Positives = 43/83 (51%), Gaps = 4/83 (4%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN--GISRGSGFVAFSTAEEASKALTE 381
            ++ NL   ++++ +KE F     I++ ++ R+P+     +G G+  F   +    AL  
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 382 MNGKMVVSKPLYVALAQRKEERR 404
           +N + + +K + V +A + +++ 
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKD 98

>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 = 66.9 bits (164), Expect = 5e-14
 Identities = 18/82 (21%), Positives = 37/82 (45%), Gaps = 2/82 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
            ++ NL    TE+ +K+ F    I         ++  + K FG+  F+D D    ++ +L
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SL 76

Query: 280 NGKKFDDKEWYVGKAQKKYERE 301
           N +   +K   V  A +  +++
Sbjct: 77  NEESLGNKRIRVDVADQAQDKD 98

>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 = 58.4 bits (142), Expect = 4e-11
 Identities = 16/73 (21%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL--GQSRGYGFVQFDNEESAKSAIDK 187
            F+ NL   +  +++ + F     I + ++  +     + +G+G+ +F++ +S  SA+  
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 188 LNGMLLNDKQVFV 200
           LN   L +K++ 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 = 56.5 bits (137), Expect = 2e-10
 Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTR-RSLGYGYVNYNAAHEATRA 97
             + ++G+L   V +  + + F  +  + +VR+ R+ S   R  G+GY  +        A
Sbjct: 15  PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73

Query: 98  LDELNFTPLNGKPIRIMYS 116
           L  LN   L  K IR+  +
Sbjct: 74  L-SLNEESLGNKRIRVDVA 91

>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 = 67.2 bits (164), Expect = 5e-14
 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 219 NNVYVKNLSETTTEDDL---KKIFGEFGIITSTAVMRDADGK----SKCFGFVNFDDPDD 271
           N V+V  LS+   + ++    + FG+FG I    +                +V +   +D
Sbjct: 16  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 272 AARSVEALNGKKFDDK 287
           A R+++ +N    D +
Sbjct: 76  ALRAIQCVNNVVVDGR 91

>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 = 62.2 bits (151), Expect = 3e-12
 Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 7/84 (8%)

Query: 324 LYVKNLDDSISDD---KLKELFSEFGTITSCKVMRDPNG----ISRGSGFVAFSTAEEAS 376
           ++V  L   ++D    K  E F +FG I    +    +         S +V +  +E+A 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 377 KALTEMNGKMVVSKPLYVALAQRK 400
           +A+  +N  +V  + L  +L   K
Sbjct: 78  RAIQCVNNVVVDGRTLKASLGTTK 101

>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 = 60.6 bits (147), Expect = 1e-11
 Identities = 16/97 (16%), Positives = 38/97 (39%), Gaps = 6/97 (6%)

Query: 26  ANNGGVGDARQFVSTSLYVGDLDLSVNDSQL---YDLFNQMGQVVSVRVCRDLST---RR 79
           ++       R      ++V  L   + D ++    + F + G++  V +    S    + 
Sbjct: 2   SSGSSGASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQG 61

Query: 80  SLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS 116
                YV Y  + +A RA+  +N   ++G+ ++    
Sbjct: 62  PSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLG 98

>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 = 56.8 bits (137), Expect = 2e-10
 Identities = 12/78 (15%), Positives = 30/78 (38%), Gaps = 7/78 (8%)

Query: 130 IFIKNLDKSIDNKAL---HDTFSTFGNILSCKVATDSLG----QSRGYGFVQFDNEESAK 182
           +F+  L + + +  +    + F  FG I    +   +            +V +   E A 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 183 SAIDKLNGMLLNDKQVFV 200
            AI  +N ++++ + +  
Sbjct: 78  RAIQCVNNVVVDGRTLKA 95

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 66.1 bits (162), Expect = 8e-14
 Identities = 16/81 (19%), Positives = 42/81 (51%), Gaps = 4/81 (4%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN--GISRGSGFVAFSTAEEASKALTE 381
            ++ NL   ++++ +KE F     I++ ++ R+P+     +G G+  F   +    AL  
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 79

Query: 382 MNGKMVVSKPLYVALAQRKEE 402
           +N + + ++ + V +A + ++
Sbjct: 80  LNEESLGNRRIRVDVADQAQD 100

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 65.7 bits (161), Expect = 1e-13
 Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 2/78 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVM-RDADGKSKCFGFVNFDDPDDAARSVEAL 279
            ++ NL    TE+ +K+ F    I             + K FG+  F+D D    ++  L
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-L 80

Query: 280 NGKKFDDKEWYVGKAQKK 297
           N +   ++   V  A + 
Sbjct: 81  NEESLGNRRIRVDVADQA 98

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 58.0 bits (141), Expect = 6e-11
 Identities = 15/73 (20%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDS--LGQSRGYGFVQFDNEESAKSAIDK 187
            F+ NL   +  +++ + F     I + ++  +     + +G+G+ +F++ +S  SA+  
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 79

Query: 188 LNGMLLNDKQVFV 200
           LN   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 = 57.6 bits (140), Expect = 8e-11
 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 3/76 (3%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTR-RSLGYGYVNYNAAHEATRA 97
             + ++G+L   V +  + + F  +  + +VR+ R+ S   R  G+GY  +        A
Sbjct: 19  PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 77

Query: 98  LDELNFTPLNGKPIRI 113
           L  LN   L  + IR+
Sbjct: 78  L-SLNEESLGNRRIRV 92

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 66.0 bits (161), Expect = 1e-13
 Identities = 14/80 (17%), Positives = 37/80 (46%), Gaps = 7/80 (8%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT--E 381
           L+++ L   +++ ++  L   FG +T+  +++      +   F+  +T E A   +    
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYS 72

Query: 382 MNGKMVVSKPLYVALAQRKE 401
                + ++P+Y+  +  KE
Sbjct: 73  AVTPHLRNQPIYIQYSNHKE 92

>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 = 57.9 bits (140), Expect = 8e-11
 Identities = 12/79 (15%), Positives = 31/79 (39%), Gaps = 7/79 (8%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE--A 278
           ++++ L    TE ++  +   FG +T+  +++      K   F+     + A   V   +
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYS 72

Query: 279 LNGKKFDDKEWYVGKAQKK 297
                  ++  Y+  +  K
Sbjct: 73  AVTPHLRNQPIYIQYSNHK 91

>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 = 50.6 bits (121), Expect = 2e-08
 Identities = 9/73 (12%), Positives = 29/73 (39%), Gaps = 7/73 (9%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID--K 187
           + I+ L   +    +      FG + +  +      + +   F++   EE+A + ++   
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILM-----LKGKNQAFLELATEEAAITMVNYYS 72

Query: 188 LNGMLLNDKQVFV 200
                L ++ +++
Sbjct: 73  AVTPHLRNQPIYI 85

>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 = 48.3 bits (115), Expect = 2e-07
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 8/80 (10%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S  L++  L   V ++++  L    G+V ++ + +           ++       A   +
Sbjct: 15  SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMV 68

Query: 99  DELNFTP--LNGKPIRIMYS 116
           +  +     L  +PI I YS
Sbjct: 69  NYYSAVTPHLRNQPIYIQYS 88

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 65.8 bits (161), Expect = 1e-13
 Identities = 15/81 (18%), Positives = 27/81 (33%), Gaps = 5/81 (6%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           +V+V           L + F  FG + S  + +D       F  V   D   A  +V + 
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD----KGVFAIVEMGDV-GAREAVLSQ 64

Query: 280 NGKKFDDKEWYVGKAQKKYER 300
           +          V   ++K  +
Sbjct: 65  SQHSLGGHRLRVRPREQKEFQ 85

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 61.2 bits (149), Expect = 4e-12
 Identities = 14/84 (16%), Positives = 27/84 (32%), Gaps = 5/84 (5%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           +++V      +   +L E F  FG + S  + +D          V           L   
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVF----AIVEMGDVGAREAVL-SQ 64

Query: 383 NGKMVVSKPLYVALAQRKEERRAR 406
           +   +    L V   ++KE +   
Sbjct: 65  SQHSLGGHRLRVRPREQKEFQSPA 88

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 15/93 (16%), Positives = 39/93 (41%), Gaps = 5/93 (5%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           SG  ++F+    + +D+  L + F  FG + S  +  D       +  V+  +  + ++ 
Sbjct: 6   SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD----KGVFAIVEMGDVGAREAV 61

Query: 185 IDKLNGMLLNDKQVFVGPFLRKQERESTADKTR 217
           +   +   L   ++ V P  +K+ +   +   +
Sbjct: 62  L-SQSQHSLGGHRLRVRPREQKEFQSPASKSPK 93

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 43.5 bits (103), Expect = 8e-06
 Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 6/73 (8%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           S++V      V+ +QL + F   G V SV + +D        +  V           L  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGAREAVL-S 63

Query: 101 LNFTPLNGKPIRI 113
            +   L G  +R+
Sbjct: 64  QSQHSLGGHRLRV 76

>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 = 65.5 bits (160), Expect = 1e-13
 Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 6/77 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           + VKNL    +  ++ +L  ++  +  C V       ++ + FV     E+A  A+   +
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-----DRNKRTAFVTLLNGEQAQNAIQMFH 61

Query: 384 GKMVVSKPLYVALAQRK 400
                 K L V L    
Sbjct: 62  QYSFRGKDLIVQLQPTD 78

>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 = 65.1 bits (159), Expect = 2e-13
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 6/76 (7%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           SG+  I +KNL +  + + +HD    +  +  C V      +++   FV   N E A++A
Sbjct: 3   SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-----DRNKRTAFVTLLNGEQAQNA 56

Query: 185 IDKLNGMLLNDKQVFV 200
           I   +      K + V
Sbjct: 57  IQMFHQYSFRGKDLIV 72

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 63.6 bits (155), Expect = 5e-13
 Identities = 11/79 (13%), Positives = 30/79 (37%), Gaps = 6/79 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           + + VKNL + +   ++  +  ++ +            ++K   FV   + + A  +++ 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYV------DRNKRTAFVTLLNGEQAQNAIQM 59

Query: 279 LNGKKFDDKEWYVGKAQKK 297
            +   F  K+  V      
Sbjct: 60  FHQYSFRGKDLIVQLQPTD 78

>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 = 55.5 bits (134), Expect = 4e-10
 Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S+ + V +L    N  +++DL         ++ C      R+    +V      +A  A+
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYD----LKYCY---VDRNKRTAFVTLLNGEQAQNAI 57

Query: 99  DELNFTPLNGKPIRIMYSYRD 119
              +     GK + +     D
Sbjct: 58  QMFHQYSFRGKDLIVQLQPTD 78

>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 = 64.9 bits (159), Expect = 2e-13
 Identities = 16/80 (20%), Positives = 31/80 (38%), Gaps = 6/80 (7%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           V+V   +   TED+L++ F ++G +    + +      + F FV F D   A        
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--E 61

Query: 281 GKKFDDKEWYVGKAQKKYER 300
                    ++  A+ K+  
Sbjct: 62  DLIIKGISVHISNAEPKHNS 81

>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 = 63.4 bits (155), Expect = 6e-13
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 12/83 (14%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM- 382
           ++V      +++D+L+E FS++G +    + +      R   FV F+  + A     E  
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGEDL 63

Query: 383 --NGKMVVSKPLYVALAQRKEER 403
              G  V     +++ A+ K   
Sbjct: 64  IIKGISV-----HISNAEPKHNS 81

>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 = 56.1 bits (136), Expect = 2e-10
 Identities = 13/63 (20%), Positives = 29/63 (46%), Gaps = 4/63 (6%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           SG+  +F+      +    L + FS +G+++   +        R + FV F +++ A+S 
Sbjct: 3   SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF----RAFAFVTFADDQIAQSL 58

Query: 185 IDK 187
             +
Sbjct: 59  CGE 61

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 7/72 (9%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VG     + + +L + F+Q G V+ V +      +    + +V +     A     E 
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQSLCGED 62

Query: 102 NFTPLNGKPIRI 113
               + G  + I
Sbjct: 63  LI--IKGISVHI 72

>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 = 65.5 bits (160), Expect = 2e-13
 Identities = 21/106 (19%), Positives = 46/106 (43%), Gaps = 8/106 (7%)

Query: 302 MELKGKFEQSLKETADKFEGLNLYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGI 360
           M LK +      +   K     +++ NL+   +    ++ +FS++G +  C        +
Sbjct: 8   MSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCS-------V 60

Query: 361 SRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRAR 406
            +G  FV +S    A  A+   NG+++  + L + +A   +  R+ 
Sbjct: 61  HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSG 106

>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 = 64.7 bits (158), Expect = 4e-13
 Identities = 27/99 (27%), Positives = 48/99 (48%), Gaps = 15/99 (15%)

Query: 107 NGKPIRIMYSY----RDPTIRKSGAGNIFIKNLDKSIDNKA-LHDTFSTFGNILSCKVAT 161
           +G  +++  S      DP    S    +FI NL+ ++  K+ +   FS +G +  C V  
Sbjct: 6   SGMSLKLQASNVTNKNDPKSINS---RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-- 60

Query: 162 DSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
                 +GY FVQ+ NE  A++A+   NG +L  + + +
Sbjct: 61  -----HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDI 94

>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 = 62.8 bits (153), Expect = 2e-12
 Identities = 17/86 (19%), Positives = 37/86 (43%), Gaps = 9/86 (10%)

Query: 204 LRKQERESTADKTRFNN-VYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCF 261
           L+     +  D    N+ V++ NL+     + D++ IF ++G +   +V +        +
Sbjct: 12  LQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG-------Y 64

Query: 262 GFVNFDDPDDAARSVEALNGKKFDDK 287
            FV + +   A  +V   NG+    +
Sbjct: 65  AFVQYSNERHARAAVLGENGRVLAGQ 90

>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 = 52.8 bits (127), Expect = 6e-09
 Identities = 21/93 (22%), Positives = 45/93 (48%), Gaps = 10/93 (10%)

Query: 38  VSTSLYVGDLDLS-VNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
           +++ +++G+L+ + V  S +  +F++ G+V    V +        GY +V Y+    A  
Sbjct: 26  INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARA 77

Query: 97  ALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
           A+   N   L G+ + I  +  +P   +SG  +
Sbjct: 78  AVLGENGRVLAGQTLDINMA-GEPKPDRSGPSS 109

>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 = 65.2 bits (159), Expect = 2e-13
 Identities = 19/101 (18%), Positives = 47/101 (46%), Gaps = 2/101 (1%)

Query: 306 GKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSG 365
           G    S K      + L + V  +  S  ++ +++ F     + +  +++D  G + G+G
Sbjct: 1   GSSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNG 59

Query: 366 FVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRAR 406
            V F + ++  +AL + N  +++ + + V+ A  ++   A 
Sbjct: 60  LVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATERQWVAAG 99

>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 = 58.6 bits (142), Expect = 6e-11
 Identities = 19/91 (20%), Positives = 36/91 (39%), Gaps = 5/91 (5%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           V V  +  +  E+D++  F    +  +  +++D  G++   G V F  P D   +++  N
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGLRV-DAVHLLKDHVGRNNGNGLVKFLSPQDTFEALK-RN 76

Query: 281 GKKFDDKEWYVGKAQKKYEREMELKGKFEQS 311
                 +   V  A    ER+    G    S
Sbjct: 77  RMLMIQRYVEVSPAT---ERQWVAAGGHITS 104

>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 = 52.1 bits (125), Expect = 8e-09
 Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 2/97 (2%)

Query: 120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEE 179
           P         + +  +  S     + D F     + +  +  D +G++ G G V+F + +
Sbjct: 9   PLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQ 67

Query: 180 SAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTADKT 216
               A+ + N ML+  + V V P   +Q   +    T
Sbjct: 68  DTFEALKR-NRMLMIQRYVEVSPATERQWVAAGGHIT 103

>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 = 50.9 bits (122), Expect = 2e-08
 Identities = 17/103 (16%), Positives = 41/103 (39%), Gaps = 3/103 (2%)

Query: 24  GIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGY 83
           G + + G           + V  +  S  ++ + D F+ + +V +V + +D   R + G 
Sbjct: 1   GSSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNN-GN 58

Query: 84  GYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSG 126
           G V + +  +   AL + N   +  + + +  +     +   G
Sbjct: 59  GLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATERQWVAAGG 100

>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 = 64.8 bits (158), Expect = 2e-13
 Identities = 16/90 (17%), Positives = 32/90 (35%), Gaps = 7/90 (7%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            ++V+ L +S+ +  L E   +FGTI    +M       +    V F   + A + +T  
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFA 71

Query: 383 --NGKMVVSKPLYVALAQRKEERRARLQAQ 410
                 +  +  +   +  K   R      
Sbjct: 72  ADVPVYIAGQQAFFNYSTSKRITRPGNSGP 101

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 59.8 bits (145), Expect = 2e-11
 Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 5/66 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             V+V+ L E+  E DL +   +FG I    +M       K    V F++ D A   V  
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTF 70

Query: 279 LNGKKF 284
                 
Sbjct: 71  AADVPV 76

>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 = 56.0 bits (135), Expect = 3e-10
 Identities = 14/74 (18%), Positives = 29/74 (39%), Gaps = 7/74 (9%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID-- 186
            + ++ L +S+    L +    FG I    +        +    V+F+N +SAK  +   
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFA 71

Query: 187 KLNGMLLNDKQVFV 200
               + +  +Q F 
Sbjct: 72  ADVPVYIAGQQAFF 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 = 53.3 bits (128), Expect = 3e-09
 Identities = 16/92 (17%), Positives = 29/92 (31%), Gaps = 8/92 (8%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S  ++V  L  SV ++ L +   + G +  V +              V +     A   +
Sbjct: 15  SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECV 68

Query: 99  DELNFTP--LNGKPIRIMYSYRDPTIRKSGAG 128
                 P  + G+     YS      R   +G
Sbjct: 69  TFAADVPVYIAGQQAFFNYSTSKRITRPGNSG 100

>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 = 64.6 bits (158), Expect = 3e-13
 Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 8/68 (11%)

Query: 221 VYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           +++ NL  +  +++DL +IF  +G I    +          FGF+ FD+P     ++E  
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA-------FGFIQFDNPQSVRDAIEXE 77

Query: 280 NGKKFDDK 287
           + +    K
Sbjct: 78  SQEMNFGK 85

>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 = 60.4 bits (147), Expect = 8e-12
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 8/72 (11%)

Query: 130 IFIKNLD-KSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +FI NL  K++  + L   FS +G+I+   +          +GF+QFDN +S + AI+  
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXE 77

Query: 189 NGMLLNDKQVFV 200
           +  +   K++ +
Sbjct: 78  SQEMNFGKKLIL 89

>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 = 59.3 bits (144), Expect = 2e-11
 Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 10/82 (12%)

Query: 324 LYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           L++ NL   ++S + L  +FS +G I    +           GF+ F   +    A+   
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIEXE 77

Query: 383 NGKMVVSKPLYVALAQRKEERR 404
           + +M   K L + ++      R
Sbjct: 78  SQEMNFGKKLILEVS--SSNAR 97

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 48.5 bits (116), Expect = 1e-07
 Identities = 13/80 (16%), Positives = 37/80 (46%), Gaps = 9/80 (11%)

Query: 38  VSTSLYVGDLDL-SVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
           + + L++G+L L +V+   L+ +F+  G ++ + +           +G++ ++       
Sbjct: 21  MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRD 72

Query: 97  ALDELNFTPLNGKPIRIMYS 116
           A++  +     GK + +  S
Sbjct: 73  AIEXESQEMNFGKKLILEVS 92

>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 = 66.8 bits (162), Expect = 5e-13
 Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 9/86 (10%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           ++Y+K      + D +KE   + G + + ++ R  +   +GS FV F + E A K +   
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 170

Query: 383 NGK------MVVSKPLYVALAQRKEE 402
             K      +++ K  Y A   +K E
Sbjct: 171 GQKYKETDLLILFKDDYFA---KKNE 193

>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 = 66.4 bits (161), Expect = 6e-13
 Identities = 20/87 (22%), Positives = 39/87 (44%), Gaps = 1/87 (1%)

Query: 217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSV 276
           +  +VY+K      T DD+K+   + G + +  + R      K   FV FD  + A + V
Sbjct: 108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV 167

Query: 277 EALNGKKFDDKEWYVGKAQKKYEREME 303
           E   G+K+ + +  +      + ++ E
Sbjct: 168 ETP-GQKYKETDLLILFKDDYFAKKNE 193

>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 = 51.4 bits (122), Expect = 9e-08
 Identities = 19/103 (18%), Positives = 38/103 (36%), Gaps = 5/103 (4%)

Query: 110 PIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRG 169
           P + +    D         +++IK          + +     G +L+ ++        +G
Sbjct: 92  PSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG 151

Query: 170 YGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGP----FLRKQE 208
             FV FD+ ESAK  ++   G    +  + +      F +K E
Sbjct: 152 SIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDYFAKKNE 193

>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 = 44.1 bits (103), Expect = 2e-05
 Identities = 10/80 (12%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 35  RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEA 94
               + S+Y+           + +     GQV+++++ R    +   G  +V +++   A
Sbjct: 105 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESA 163

Query: 95  TRALDELNFTPLNGKPIRIM 114
            + ++           + I+
Sbjct: 164 KKFVETPGQK-YKETDLLIL 182

>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 = 65.2 bits (159), Expect = 6e-13
 Identities = 21/114 (18%), Positives = 42/114 (36%), Gaps = 5/114 (4%)

Query: 306 GKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSG 365
           G+     + T     G  ++++ L    +++ +   FS         +   P+G   G  
Sbjct: 31  GRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEA 89

Query: 366 FVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVG 419
            V F+T EEA  A+   +   +  + + + L            A  SQ+   +G
Sbjct: 90  DVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGASNG---AYSSQVMQGMG 139

>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 = 58.3 bits (141), Expect = 1e-10
 Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 2/80 (2%)

Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFV 264
              + E T   T  + V+++ L    TE+D+   F     +    +    DG+      V
Sbjct: 33  GSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPDGRVTGEADV 91

Query: 265 NFDDPDDAARSVEALNGKKF 284
            F   ++A  ++   +    
Sbjct: 92  EFATHEEAVAAMS-KDRANM 110

>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 = 51.8 bits (124), Expect = 2e-08
 Identities = 13/94 (13%), Positives = 36/94 (38%), Gaps = 2/94 (2%)

Query: 107 NGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ 166
            G+ +       + T++ +    + ++ L        +++ FS     +   +     G+
Sbjct: 26  GGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGR 84

Query: 167 SRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
             G   V+F   E A +A+ K +   +  + + +
Sbjct: 85  VTGEADVEFATHEEAVAAMSK-DRANMQHRYIEL 117

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 46.4 bits (110), Expect = 2e-06
 Identities = 14/110 (12%), Positives = 36/110 (32%), Gaps = 3/110 (2%)

Query: 14  VAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCR 73
           +A+       G  +       +      +++  L     ++ +Y+ F+ +   V V +  
Sbjct: 21  MASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEI 79

Query: 74  DLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIR 123
               R + G   V +    EA  A+   +   +  + I +  +       
Sbjct: 80  GPDGRVT-GEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGASN 127

>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 = 64.5 bits (157), Expect = 6e-13
 Identities = 19/109 (17%), Positives = 42/109 (38%), Gaps = 3/109 (2%)

Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVM-RDADGKSKCFGF 263
            ++   S +       VY+K L        +   F +  I+  +  +    +GK+   GF
Sbjct: 12  GQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGF 71

Query: 264 VNFDDPDDAARSVEALNGKKFDDKEWYVGKA-QKKYEREMELKGKFEQS 311
           V F +  D   ++   + +   ++   V    +K    ++++  K  QS
Sbjct: 72  VEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQS 119

>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 = 62.5 bits (152), Expect = 3e-12
 Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 3/98 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSC-KVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           +Y+K L     +  + + F +   +     +   PNG + G GFV F    +   AL   
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CR 86

Query: 383 NGKMVVSKPLYVALAQRKE-ERRARLQAQFSQMRPPVG 419
           + + + ++ + V    +K    +  +  +  Q  P  G
Sbjct: 87  HKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGPSSG 124

>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 = 54.1 bits (130), Expect = 3e-09
 Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSC-KVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +++K L    +NK + D F     +     +A    G++ G GFV+F NE   K+A+ + 
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR- 86

Query: 189 NGMLLNDKQVFVGPFLRKQERE 210
           +   + ++ + V P  +K   E
Sbjct: 87  HKQYMGNRFIQVHPITKKGMLE 108

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 45.6 bits (108), Expect = 3e-06
 Identities = 15/98 (15%), Positives = 37/98 (37%), Gaps = 10/98 (10%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVV-SVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
              +Y+  L     +  + D F ++  V  S+ +    + + + G G+V +    +   A
Sbjct: 25  GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT-GEGFVEFRNEADYKAA 83

Query: 98  LDELNFTPLNGKPIRI-------MYSYRDPTIRKSGAG 128
           L   +   +  + I++       M    D   ++  +G
Sbjct: 84  L-CRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSG 120

>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 = 64.1 bits (156), Expect = 8e-13
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVM-RDPNGISRGSGFVAFSTAEEASKALTEM 382
           + ++ L    + +++ + FS    + +   +  DP G   G  FV F++ E A KAL   
Sbjct: 45  VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL-GK 103

Query: 383 NGKMVVSKPLYVALAQRKEERR 404
           + + +  + + V  + ++E R 
Sbjct: 104 HKERIGHRYIEVFKSSQEEVRS 125

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 59.9 bits (145), Expect = 3e-11
 Identities = 14/83 (16%), Positives = 35/83 (42%), Gaps = 2/83 (2%)

Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVM-RDADGKSKCFGF 263
           +     ++AD      V ++ L    T++++ + F    I+ +   +  D +GK     F
Sbjct: 29  QMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAF 88

Query: 264 VNFDDPDDAARSVEALNGKKFDD 286
           V F   + A +++   + ++   
Sbjct: 89  VQFASQELAEKALG-KHKERIGH 110

>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 = 50.3 bits (120), Expect = 6e-08
 Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSC-KVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           + ++ L      + +   FS    + +   +  D  G+  G  FVQF ++E A+ A+ K 
Sbjct: 45  VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK- 103

Query: 189 NGMLLNDKQVFV 200
           +   +  + + V
Sbjct: 104 HKERIGHRYIEV 115

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 49.1 bits (117), Expect = 2e-07
 Identities = 16/110 (14%), Positives = 36/110 (32%), Gaps = 3/110 (2%)

Query: 8   PQAPVAVAAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQV- 66
               V   +  +  T G     G   A       + +  L       ++   F+ +  V 
Sbjct: 11  SSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVP 70

Query: 67  VSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS 116
             + +  D   + + G  +V + +   A +AL   +   +  + I +  S
Sbjct: 71  NGITLPVDPEGKIT-GEAFVQFASQELAEKAL-GKHKERIGHRYIEVFKS 118

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

 Score = 62.9 bits (153), Expect = 1e-12
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++++ L D + +  L E   EFG I+   VM       +    V F     A  A+    
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAA 78

Query: 384 GKMVV--SKPLYVALAQRKE 401
              +     P +V  +  ++
Sbjct: 79  DNQIYIAGHPAFVNYSTSQK 98

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

 Score = 60.2 bits (146), Expect = 1e-11
 Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 5/66 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             V+++ L +   E DL +   EFG I+   VM       K    V F+D   A  +V  
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNY 76

Query: 279 LNGKKF 284
               + 
Sbjct: 77  AADNQI 82

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

 Score = 55.5 bits (134), Expect = 5e-10
 Identities = 13/73 (17%), Positives = 25/73 (34%), Gaps = 7/73 (9%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + I+ L   +    L +    FG I    V        +    V+F++   A +A++   
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAA 78

Query: 190 GM--LLNDKQVFV 200
                +     FV
Sbjct: 79  DNQIYIAGHPAFV 91

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

 Score = 51.7 bits (124), Expect = 1e-08
 Identities = 14/80 (17%), Positives = 27/80 (33%), Gaps = 8/80 (10%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S  +++  L   V ++ L +   + G +  V V              V +     A  A+
Sbjct: 21  SPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAV 74

Query: 99  DELNFTP--LNGKPIRIMYS 116
           +        + G P  + YS
Sbjct: 75  NYAADNQIYIAGHPAFVNYS 94

>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 = 68.3 bits (166), Expect = 1e-12
 Identities = 20/96 (20%), Positives = 40/96 (41%), Gaps = 5/96 (5%)

Query: 218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSV 276
           F  ++V  ++  TTE  L++ F  +G I    ++     GK + + F+ ++   D   + 
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161

Query: 277 EALNGKKFDD----KEWYVGKAQKKYEREMELKGKF 308
           +  +GKK D      +   G+  K +       G  
Sbjct: 162 KHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLG 197

>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 = 62.6 bits (151), Expect = 1e-10
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 119 DPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDN 177
           DP  +      +F+  ++       L   F  +G I    +      G+ RGY F+++++
Sbjct: 94  DPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEH 153

Query: 178 EESAKSAIDKLNGMLLNDKQVFV 200
           E    SA    +G  ++ ++V V
Sbjct: 154 ERDMHSAYKHADGKKIDGRRVLV 176

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 61.0 bits (147), Expect = 3e-10
 Identities = 17/107 (15%), Positives = 42/107 (39%), Gaps = 12/107 (11%)

Query: 293 KAQKKYEREMELKGKFEQSLKETADKFEGLN-----------LYVKNLDDSISDDKLKEL 341
           + ++   +  E   + +Q ++     ++  N           L+V  ++   ++ KL+  
Sbjct: 63  REERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRRE 122

Query: 342 FSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMV 387
           F  +G I    ++    +G  RG  F+ +    +   A    +GK +
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKI 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 = 53.3 bits (127), Expect = 9e-08
 Identities = 11/79 (13%), Positives = 31/79 (39%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +L+V  ++    +S+L   F   G +  + +     + +  GY ++ Y    +   A   
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163

Query: 101 LNFTPLNGKPIRIMYSYRD 119
            +   ++G+ + +      
Sbjct: 164 ADGKKIDGRRVLVDVERGR 182

>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 = 62.1 bits (151), Expect = 3e-12
 Identities = 19/83 (22%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVM-RDPNGISRGSGFVAFSTAEEASKALTEM 382
           + ++ L    S +++ + FS    + +   +  D  G S G  FV F++ E A KAL + 
Sbjct: 18  VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KK 76

Query: 383 NGKMVVSKPLYVALAQRKEERRA 405
           + + +  + + +  + R E R +
Sbjct: 77  HKERIGHRYIEIFKSSRAEVRTS 99

>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 = 57.4 bits (139), Expect = 1e-10
 Identities = 12/81 (14%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 208 ERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVM-RDADGKSKCFGFVNF 266
              ++ D      V ++ L    +++++ + F    I+ +   +  D  G+S    FV F
Sbjct: 5   SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF 64

Query: 267 DDPDDAARSVEALNGKKFDDK 287
              + A ++++  + ++   +
Sbjct: 65  ASQEIAEKALK-KHKERIGHR 84

>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 = 47.8 bits (114), Expect = 3e-07
 Identities = 15/72 (20%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSC-KVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           + ++ L      + +   FS    + +   +  D  G+S G  FVQF ++E A+ A+ K 
Sbjct: 18  VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK- 76

Query: 189 NGMLLNDKQVFV 200
           +   +  + + +
Sbjct: 77  HKERIGHRYIEI 88

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 42.0 bits (99), Expect = 3e-05
 Identities = 17/92 (18%), Positives = 37/92 (40%), Gaps = 4/92 (4%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQV-VSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
              + +  L    +  ++   F+ +  V   + +  D   R + G  +V + +   A +A
Sbjct: 15  DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRST-GEAFVQFASQEIAEKA 73

Query: 98  LDELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
           L + +   +  + I I  S R   +R SG  +
Sbjct: 74  L-KKHKERIGHRYIEIFKSSRAE-VRTSGPSS 103

>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 = 61.5 bits (149), Expect = 6e-12
 Identities = 19/89 (21%), Positives = 39/89 (43%), Gaps = 12/89 (13%)

Query: 323 NLYVKN--LDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
           +L V N  L + +S ++L  +  + G + +  +  +     +   F  + T EE+ +A  
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYV 81

Query: 381 EMNGKMVV-----SKPLYVALAQRKEERR 404
            +NGK VV        LY+   ++ +   
Sbjct: 82  TLNGKEVVDDLGQKITLYLNFVEKVQWSG 110

>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 = 59.9 bits (145), Expect = 2e-11
 Identities = 18/98 (18%), Positives = 40/98 (40%), Gaps = 10/98 (10%)

Query: 204 LRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGF 263
           LR +  E+ +  T+   V    L    + + L  +  + G++ +  +  +     K + F
Sbjct: 13  LRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSF 67

Query: 264 VNFDDPDDAARSVEALNGKKFDDKE-----WYVGKAQK 296
             +   +++ R+   LNGK+  D        Y+   +K
Sbjct: 68  ARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 105

>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 = 55.3 bits (133), Expect = 8e-10
 Identities = 13/77 (16%), Positives = 26/77 (33%), Gaps = 7/77 (9%)

Query: 129 NIFIKN--LDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID 186
           ++ + N  L   +    L       G + +  +  +     + Y F ++   E +K A  
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYV 81

Query: 187 KLNGMLLNDKQVFVGPF 203
            LNG  + D        
Sbjct: 82  TLNGKEVVDDLGQKITL 98

>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 = 45.7 bits (108), Expect = 2e-06
 Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 9/85 (10%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S  +  G L   V+ +QL  +  + G V ++ +  +        Y +  Y    E+ RA 
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAY 80

Query: 99  DELN---FTPLNGKPIRIMYSYRDP 120
             LN        G+ I +  ++ + 
Sbjct: 81  VTLNGKEVVDDLGQKITLYLNFVEK 105

>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 = 60.0 bits (146), Expect = 9e-12
 Identities = 14/78 (17%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           + ++    ++++  + E  +      + +++R+ +G   G  FV FS  EE  +AL + N
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQAL-KCN 70

Query: 384 GKMVVSKPLYVALAQRKE 401
            + +  + + V   +   
Sbjct: 71  REYMGGRYIEVFREKSGP 88

>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 = 56.2 bits (136), Expect = 2e-10
 Identities = 10/64 (15%), Positives = 30/64 (46%), Gaps = 2/64 (3%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           V ++      TE ++ +       + +  ++R+A G    + FV+F + ++  ++++  N
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CN 70

Query: 281 GKKF 284
            +  
Sbjct: 71  REYM 74

>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 = 52.7 bits (127), Expect = 4e-09
 Identities = 14/71 (19%), Positives = 32/71 (45%), Gaps = 2/71 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + ++    ++  K + +  +     ++ ++  ++ G   GY FV F NEE  K A+   N
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKC-N 70

Query: 190 GMLLNDKQVFV 200
              +  + + V
Sbjct: 71  REYMGGRYIEV 81

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 14/83 (16%), Positives = 38/83 (45%), Gaps = 3/83 (3%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             ++ +     +V +  + +    +   V++R+ R+    ++ GY +V+++   E  +AL
Sbjct: 10  CHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKT-GYIFVDFSNEEEVKQAL 67

Query: 99  DELNFTPLNGKPIRIMYSYRDPT 121
            + N   + G+ I +      P+
Sbjct: 68  -KCNREYMGGRYIEVFREKSGPS 89

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 60.6 bits (147), Expect = 1e-11
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 2/71 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           I +KNL +    + L D        L    ++ +     G G ++F +EE    A+++LN
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENS--LETTFSSVNTRDFDGTGALEFPSEEILVEALERLN 88

Query: 190 GMLLNDKQVFV 200
            +      + V
Sbjct: 89  NIEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 59.8 bits (145), Expect = 2e-11
 Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             + +KNL E  +  DLK +  E  + T+ +            G + F   +    ++E 
Sbjct: 29  YRITMKNLPEGCSWQDLKDLARENSLETTFS--SVNTRDFDGTGALEFPSEEILVEALER 86

Query: 279 LNGKKFDDKEWYV 291
           LN  +F      V
Sbjct: 87  LNNIEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 57.9 bits (140), Expect = 8e-11
 Identities = 18/83 (21%), Positives = 29/83 (34%), Gaps = 3/83 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           + +KNL +  S   LK+L  E                  G+G + F + E   +AL  +N
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLE--TTFSSVNTRDFDGTGALEFPSEEILVEALERLN 88

Query: 384 GKMVVSKPLYVALA-QRKEERRA 405
                   + V         RR+
Sbjct: 89  NIEFRGSVITVERDDNPPPIRRS 111

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 54.1 bits (130), Expect = 2e-09
 Identities = 18/84 (21%), Positives = 31/84 (36%), Gaps = 3/84 (3%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           + + +L    +   L DL  +            ++TR   G G + + +      AL+ L
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLET---TFSSVNTRDFDGTGALEFPSEEILVEALERL 87

Query: 102 NFTPLNGKPIRIMYSYRDPTIRKS 125
           N     G  I +      P IR+S
Sbjct: 88  NNIEFRGSVITVERDDNPPPIRRS 111

>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 = 59.4 bits (144), Expect = 2e-11
 Identities = 16/90 (17%), Positives = 38/90 (42%), Gaps = 11/90 (12%)

Query: 29  GGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRV-----CRDLSTRRSLGY 83
           G +G AR      LYVG++   + +  + D FN   ++  +          +   +   +
Sbjct: 1   GPLGSAR-----RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNF 55

Query: 84  GYVNYNAAHEATRALDELNFTPLNGKPIRI 113
            ++ + +  E T+A+   +     G+ ++I
Sbjct: 56  AFLEFRSVDETTQAM-AFDGIIFQGQSLKI 84

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 54.0 bits (130), Expect = 1e-09
 Identities = 15/73 (20%), Positives = 29/73 (39%), Gaps = 7/73 (9%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITST------AVMRDADGKSKCFGFVNFDDPDDAAR 274
           +YV N+    TE+ +   F     +          V+     + K F F+ F   D+  +
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 275 SVEALNGKKFDDK 287
           ++ A +G  F  +
Sbjct: 69  AM-AFDGIIFQGQ 80

>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 = 53.2 bits (128), Expect = 2e-09
 Identities = 13/77 (16%), Positives = 33/77 (42%), Gaps = 7/77 (9%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCK------VMRDPNGISRGSGFVAFSTAEEASK 377
           LYV N+   I+++ + + F+    +          V+       +   F+ F + +E ++
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 378 ALTEMNGKMVVSKPLYV 394
           A+   +G +   + L +
Sbjct: 69  AM-AFDGIIFQGQSLKI 84

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 51.7 bits (124), Expect = 8e-09
 Identities = 11/78 (14%), Positives = 33/78 (42%), Gaps = 7/78 (8%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCK------VATDSLGQSRGYGFVQFDNEESAKS 183
           +++ N+   I  +A+ D F+    +          V    + Q + + F++F + +    
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 184 AIDKLNGMLLNDKQVFVG 201
           A+   +G++   + + + 
Sbjct: 69  AM-AFDGIIFQGQSLKIR 85

>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 = 58.9 bits (143), Expect = 3e-11
 Identities = 13/82 (15%), Positives = 32/82 (39%), Gaps = 2/82 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++++ L    +++ +   FS         +   P+G   G   V F+T E+A  A+   +
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKD 75

Query: 384 GKMVVSKPLYVALAQRKEERRA 405
              +  + + + L        +
Sbjct: 76  KANMQHRYVELFLNSTAGTSGS 97

>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 = 57.0 bits (138), Expect = 1e-10
 Identities = 14/77 (18%), Positives = 28/77 (36%), Gaps = 2/77 (2%)

Query: 208 ERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFD 267
              S+   T  + V+++ L    TE+D+   F     +    +    DG+      V F 
Sbjct: 5   SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFA 63

Query: 268 DPDDAARSVEALNGKKF 284
             +DA  ++   +    
Sbjct: 64  THEDAVAAMA-KDKANM 79

>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 = 48.9 bits (117), Expect = 1e-07
 Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 2/71 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + ++ L        +++ FS   N +   +     G+  G   V+F   E A +A+ K +
Sbjct: 18  VHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK-D 75

Query: 190 GMLLNDKQVFV 200
              +  + V +
Sbjct: 76  KANMQHRYVEL 86

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 11/92 (11%), Positives = 33/92 (35%), Gaps = 7/92 (7%)

Query: 29  GGVGDARQFV----STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYG 84
           G  G +           +++  L     ++ +Y+ F+ +   + V +      R + G  
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVT-GEA 58

Query: 85  YVNYNAAHEATRALDELNFTPLNGKPIRIMYS 116
            V +    +A  A+   +   +  + + +  +
Sbjct: 59  DVEFATHEDAVAAM-AKDKANMQHRYVELFLN 89

>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 = 62.2 bits (150), Expect = 2e-10
 Identities = 63/509 (12%), Positives = 132/509 (25%), Gaps = 151/509 (29%)

Query: 40  TSLYVGDLDLSVNDSQLY--------DLFNQ------------------MG----QVVSV 69
           T +Y+   D   ND+Q++          + +                  +       V++
Sbjct: 109 TRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVAL 168

Query: 70  RVCRDLSTRRSLGYG--YVNYNAAHEATRALDELN-----FTPLNGKPIRIMYSYRDPTI 122
            VC     +  + +   ++N    +     L+ L        P          + +    
Sbjct: 169 DVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIH 228

Query: 123 RKSGAGNIFIKN---------LDKSIDNKALHDTFSTFGNILSCKV--------ATDSLG 165
                    +K+         L    + KA  + F+     LSCK+         TD L 
Sbjct: 229 SIQAELRRLLKSKPYENCLLVLLNVQNAKAW-NAFN-----LSCKILLTTRFKQVTDFLS 282

Query: 166 QSRGYGFVQ------FDNEESAKSAIDKLNGMLLND--KQVF-VGPFL------RKQERE 210
            +                +E  KS + K       D  ++V    P          ++  
Sbjct: 283 AATTTHISLDHHSMTLTPDEV-KSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGL 341

Query: 211 STADKTRFNNVYVKNLSETT-------TEDDLKKIFGEFGIITSTAVMRDADGKSKCFGF 263
           +T D   + +V    L+             + +K+F    +                F  
Sbjct: 342 ATWD--NWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV----------------F-- 381

Query: 264 VNFDDPDDA---ARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQ-SLKETADKF 319
                P  A      +  +         W+           M +  K  + SL E   K 
Sbjct: 382 -----PPSAHIPTILLSLI---------WF----DVIKSDVMVVVNKLHKYSLVEKQPKE 423

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMR--DPNGIS--RGSGFVAFSTAEEA 375
             +++    L+  +  +    L      +    + +  D + +       +         
Sbjct: 424 STISIPSIYLELKVKLENEYALHRSI--VDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHL 481

Query: 376 SKALTEMNGKMVVSKPLYVALA--QRKEERRARLQAQFSQMRPPVGPRMPMYPPVAPGLG 433
                E   +M + + +++     ++K             +R            +   L 
Sbjct: 482 KNI--EHPERMTLFRMVFLDFRFLEQK-------------IR-HDSTAWNASGSILNTLQ 525

Query: 434 QQLFYGQGPPIIPPQVIYSFLLIDYFNAL 462
           Q  FY     I      Y  L+    + L
Sbjct: 526 QLKFYKP--YICDNDPKYERLVNAILDFL 552

>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 = 54.1 bits (129), Expect = 8e-08
 Identities = 58/388 (14%), Positives = 105/388 (27%), Gaps = 152/388 (39%)

Query: 115 YSYRD--PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGF 172
           Y Y+D       +     F+ N D         D      +ILS +     +        
Sbjct: 16  YQYKDILSVFEDA-----FVDNFD-------CKDVQDMPKSILSKEEIDHII-------- 55

Query: 173 VQFDNEESAKSAIDKLNGMLLNDK----QVFVG-------PFL----RKQERESTADKTR 217
                 + A S   +L   LL+ +    Q FV         FL    + ++R+ +     
Sbjct: 56  ----MSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRM 111

Query: 218 F----------NNVYVK-NLSETTTEDDLKK------------IFGEFGIITST---AVM 251
           +          N V+ K N+S       L++            I G  G   +     V 
Sbjct: 112 YIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVC 171

Query: 252 RDADGKSKCFGF----VNF---DDPDDAARSVEAL------NGKKFDDK----EWYVGKA 294
                + K   F    +N    + P+     ++ L      N     D     +  +   
Sbjct: 172 LSYKVQCK-MDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSI 230

Query: 295 QKKYEREMELKGKFEQSL--------KETADKFEGLNLYVKNL----DDSISD------- 335
           Q +  R ++ K  +E  L         +  + F   NL  K L       ++D       
Sbjct: 231 QAELRRLLKSK-PYENCLLVLLNVQNAKAWNAF---NLSCKILLTTRFKQVTDFLSAATT 286

Query: 336 --------------DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
                         D++K L  ++     C+    P                E       
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKY---LDCRPQDLP---------------REVLTTN-- 326

Query: 382 MNGKMVVSKPLYVAL-AQRKEERRARLQ 408
                    P  +++ A+   +  A   
Sbjct: 327 ---------PRRLSIIAESIRDGLATWD 345

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 55.8 bits (134), Expect = 8e-10
 Identities = 16/100 (16%), Positives = 36/100 (36%), Gaps = 4/100 (4%)

Query: 309 EQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEF---GTITSCKVMRDPNGISRGSG 365
             S+    +  EG  + ++ L  S S + ++   S+            +    G   G  
Sbjct: 32  RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEA 91

Query: 366 FVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRA 405
           FV   + ++   AL + + + +  + + V  + R E    
Sbjct: 92  FVELGSEDDVKMAL-KKDRESMGHRYIEVFKSHRTEMDWV 130

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 48.5 bits (115), Expect = 3e-07
 Identities = 10/84 (11%), Positives = 28/84 (33%), Gaps = 4/84 (4%)

Query: 206 KQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMR---DADGKSKCFG 262
           +       +      V ++ L  + + +D++    +  I    A +      +G+     
Sbjct: 32  RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEA 91

Query: 263 FVNFDDPDDAARSVEALNGKKFDD 286
           FV     DD   +++  + +    
Sbjct: 92  FVELGSEDDVKMALK-KDRESMGH 114

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 43.5 bits (102), Expect = 2e-05
 Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 4/74 (5%)

Query: 130 IFIKNLDKSIDNKALHDTFSTF---GNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID 186
           + ++ L  S   + + +  S                  G+  G  FV+  +E+  K A+ 
Sbjct: 47  VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK 106

Query: 187 KLNGMLLNDKQVFV 200
           K +   +  + + V
Sbjct: 107 K-DRESMGHRYIEV 119

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 15/94 (15%), Positives = 33/94 (35%), Gaps = 8/94 (8%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQM---GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEAT 95
              + +  L  S +   + +  +          V        R+S G  +V   +  +  
Sbjct: 44  GFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQS-GEAFVELGSEDDVK 102

Query: 96  RALDELNFTPLNGKPIRIMYSYR---DPTIRKSG 126
            AL + +   +  + I +  S+R   D  ++ SG
Sbjct: 103 MAL-KKDRESMGHRYIEVFKSHRTEMDWVLKHSG 135

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 54.6 bits (131), Expect = 1e-09
 Identities = 17/93 (18%), Positives = 39/93 (41%), Gaps = 6/93 (6%)

Query: 315 TADKFEGLNLYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFS 370
           +     G ++ V N+D  +S  +L++     F+  G + S ++    +   +    V   
Sbjct: 3   SGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQME 60

Query: 371 TAEEASKALTEMNGKMVVSKPLYVALAQRKEER 403
             ++A  A+  ++   + SK + V+LA      
Sbjct: 61  NLQDAIGAVNSLHRYKIGSKKILVSLATGASGP 93

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 6/76 (7%)

Query: 129 NIFIKNLDKSIDNK----ALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           ++ + N+D  +  K     L + F+  G + S +++  +  Q      VQ +N + A  A
Sbjct: 11  DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQ--LKAVVQMENLQDAIGA 68

Query: 185 IDKLNGMLLNDKQVFV 200
           ++ L+   +  K++ V
Sbjct: 69  VNSLHRYKIGSKKILV 84

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 6/86 (6%)

Query: 220 NVYVKNLSETTTEDDLKKI----FGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARS 275
           +V V N+    +  +L+++    F   G + S  +    D + K    V  ++  DA  +
Sbjct: 11  DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKA--VVQMENLQDAIGA 68

Query: 276 VEALNGKKFDDKEWYVGKAQKKYERE 301
           V +L+  K   K+  V  A       
Sbjct: 69  VNSLHRYKIGSKKILVSLATGASGPS 94

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 16/89 (17%), Positives = 35/89 (39%), Gaps = 8/89 (8%)

Query: 42  LYVGDLDLSVNDSQ----LYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
           + V ++D  ++  +    L + F + G+V SV +      +       V      +A  A
Sbjct: 12  VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQ---LKAVVQMENLQDAIGA 68

Query: 98  LDELNFTPLNGKPIRIMYSYRDPTIRKSG 126
           ++ L+   +  K I +  +    +   SG
Sbjct: 69  VNSLHRYKIGSKKILVSLA-TGASGPSSG 96

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 55.3 bits (133), Expect = 1e-09
 Identities = 18/100 (18%), Positives = 40/100 (40%), Gaps = 6/100 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTIT----SCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           + ++ L  + + +++   F +   IT        +  P+G   G  FV F+  E A  AL
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85

Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVG 419
              +  ++  + + +  +   E ++   +   S   P  G
Sbjct: 86  -RKHKDLLGKRYIELFRSTAAEVQQVLNRFS-SASGPSSG 123

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 54.1 bits (130), Expect = 2e-09
 Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 5/81 (6%)

Query: 208 ERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTA----VMRDADGKSKCFGF 263
           E      K     V ++ L  T T +++   FG+   IT        +   DG+     F
Sbjct: 13  EVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAF 72

Query: 264 VNFDDPDDAARSVEALNGKKF 284
           V F   + A  ++   +    
Sbjct: 73  VLFACEEYAQNALR-KHKDLL 92

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 44.1 bits (104), Expect = 8e-06
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 5/75 (6%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNIL----SCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
           + ++ L  +   + +   F     I          T   G+  G  FV F  EE A++A+
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85

Query: 186 DKLNGMLLNDKQVFV 200
            K +  LL  + + +
Sbjct: 86  RK-HKDLLGKRYIEL 99

>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 = 54.5 bits (131), Expect = 2e-09
 Identities = 16/101 (15%), Positives = 37/101 (36%), Gaps = 4/101 (3%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEF---GTITSCKVMRDPNGISRGSGFVAFSTAEEAS 376
           EG  + ++ L  S S + ++   S+      +     +    G   G  FV   + ++  
Sbjct: 16  EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVK 75

Query: 377 KALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPP 417
            AL + + + +  + + V  + R E       +  +    P
Sbjct: 76  LAL-KKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGP 115

>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 = 51.8 bits (124), Expect = 1e-08
 Identities = 10/67 (14%), Positives = 27/67 (40%), Gaps = 4/67 (5%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMR---DADGKSKCFGFVNFDDPDDAARSVE 277
           V ++ L  + + +D++    +  I    A +      +G+     FV  +  DD   +++
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79

Query: 278 ALNGKKF 284
             + +  
Sbjct: 80  -KDRESM 85

>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 = 46.8 bits (111), Expect = 9e-07
 Identities = 14/94 (14%), Positives = 35/94 (37%), Gaps = 5/94 (5%)

Query: 130 IFIKNLDKSIDNKALHDTFSTF---GNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID 186
           + ++ L  S   + + +  S       +          G+  G  FV+ ++E+  K A+ 
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79

Query: 187 KLNGMLLNDKQVFVGPFLRKQERESTADKTRFNN 220
           K +   +  + + V     + E +     +  N+
Sbjct: 80  K-DRESMGHRYIEVFK-SHRTEMDWVLKHSGPNS 111

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 52.3 bits (125), Expect = 9e-09
 Identities = 13/84 (15%), Positives = 28/84 (33%), Gaps = 6/84 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD---GKSKCFGFVNFDDPDDAARS 275
             V+V  L     ED++   F  FG +      +         K + F+ F +       
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQA- 67

Query: 276 VEALNGKKFDDKEWYVGKAQKKYE 299
              ++    +D + Y+  +    +
Sbjct: 68  --LIDACLEEDGKLYLCVSSPTIK 89

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 48.1 bits (114), Expect = 3e-07
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 3/61 (4%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD---SLGQSRGYGFVQFDNEESAKSAID 186
           +F+  L   ID   +  +F  FG ++          S    +GY F+ F  E S ++ ID
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 187 K 187
            
Sbjct: 71  A 71

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 46.1 bits (109), Expect = 1e-06
 Identities = 14/98 (14%), Positives = 30/98 (30%), Gaps = 12/98 (12%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN---GISRGSGFVAFSTAEEASKALT 380
           ++V  L   I +D++   F  FG +      +  +      +G  F+ F         + 
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 381 EMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPV 418
                    K      +   +++         Q+RP  
Sbjct: 71  --ACLEEDGKLYLCVSSPTIKDKPV-------QIRPWN 99

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 52.7 bits (126), Expect = 9e-09
 Identities = 18/92 (19%), Positives = 37/92 (40%), Gaps = 6/92 (6%)

Query: 107 NGKPIRIMYSYRDPTIRKSGAGNI---FIKNLDKSIDNKALHDTFSTFGNILSCKVATDS 163
               +    +  D  +  +G   +    ++NL   +    LH  FS FG +L     T +
Sbjct: 5   GNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN 64

Query: 164 LGQSRGYGFVQFDNEESAKSAIDKLNGMLLND 195
              ++    +Q+ +  SA+ A   L+G  + +
Sbjct: 65  ---NQFQALLQYADPVSAQHAKLSLDGQNIYN 93

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 51.2 bits (122), Expect = 3e-08
 Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 3/66 (4%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           + V+NL    T D L +IF +FG +            ++    + + DP  A  +  +L+
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLD 87

Query: 281 GKKFDD 286
           G+   +
Sbjct: 88  GQNIYN 93

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 50.8 bits (121), Expect = 5e-08
 Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
           L + V+NL   ++ D L ++FS+FGT+         N        + ++    A  A   
Sbjct: 29  LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLS 85

Query: 382 MNGKMV 387
           ++G+ +
Sbjct: 86  LDGQNI 91

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 41.2 bits (96), Expect = 1e-04
 Identities = 20/104 (19%), Positives = 40/104 (38%), Gaps = 6/104 (5%)

Query: 15  AAQPSPATNGIANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRD 74
           +   + A +  A + G+  A Q     + V +L   V    L+ +F++ G V+ +     
Sbjct: 4   SGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF-- 61

Query: 75  LSTRRSLGYGYVNYNAAHEATRALDELNFTPL--NGKPIRIMYS 116
             T+ +     + Y     A  A   L+   +      +RI +S
Sbjct: 62  --TKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 103

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

 Score = 54.4 bits (130), Expect = 1e-08
 Identities = 19/103 (18%), Positives = 40/103 (38%), Gaps = 17/103 (16%)

Query: 323 NLYVKNLDDSIS---------DDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAE 373
            LYV  +D +++         + +++ +FS  G I   + +      S+  GFV F    
Sbjct: 136 TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQA 190

Query: 374 EASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRP 416
            A  A   M+ + ++         +R+      L  +++   P
Sbjct: 191 NAEFAKEAMSNQTLLLPSDKEWDDRREGT---GLLVKWANEDP 230

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

 Score = 52.5 bits (125), Expect = 7e-08
 Identities = 15/90 (16%), Positives = 36/90 (40%), Gaps = 14/90 (15%)

Query: 129 NIFIKNLDKSIDNKA---------LHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEE 179
            +++  +D ++++K          +   FS  G+I   +       +S+  GFV+F  + 
Sbjct: 136 TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-----ESKNCGFVKFKYQA 190

Query: 180 SAKSAIDKLNGMLLNDKQVFVGPFLRKQER 209
           +A+ A + ++   L           R+   
Sbjct: 191 NAEFAKEAMSNQTLLLPSDKEWDDRREGTG 220

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

 Score = 49.8 bits (118), Expect = 5e-07
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 5/82 (6%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             +  K+L     E  ++ +F   G I     +     +SK  GFV F    +A  + EA
Sbjct: 144 GALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-----ESKNCGFVKFKYQANAEFAKEA 198

Query: 279 LNGKKFDDKEWYVGKAQKKYER 300
           ++ +            +++   
Sbjct: 199 MSNQTLLLPSDKEWDDRREGTG 220

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

 Score = 45.9 bits (108), Expect = 1e-05
 Identities = 23/115 (20%), Positives = 49/115 (42%), Gaps = 28/115 (24%)

Query: 27  NNGGVGDARQFVSTSLYVGDLDLSVN---------DSQLYDLFNQMGQVVSVRVCRDLST 77
           + GG+G  R+  + +LYVG +D ++N         +S++  +F+++G +  +R       
Sbjct: 123 DMGGIGSFRKK-NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV----- 176

Query: 78  RRSLGYGYVNYNAAHEATRALDELNFTPL------------NGKPIRIMYSYRDP 120
             S   G+V +     A  A + ++   L             G  + + ++  DP
Sbjct: 177 -ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDP 230

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 51.4 bits (123), Expect = 1e-08
 Identities = 10/60 (16%), Positives = 24/60 (40%), Gaps = 3/60 (5%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMR---DADGKSKCFGFVNFDDPDDAARSVE 277
           +  + L  + T +D+   F +  I      +    + DGK +    +  +   D  +++E
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE 73

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 51.4 bits (123), Expect = 2e-08
 Identities = 13/90 (14%), Positives = 32/90 (35%), Gaps = 4/90 (4%)

Query: 324 LYVKNLDDSISDDKLKELFSEF---GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT 380
           +  + L  S + + +   FS+            + + +G  RG   +   + ++  KAL 
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL- 72

Query: 381 EMNGKMVVSKPLYVALAQRKEERRARLQAQ 410
           E +   +  + + V     ++        Q
Sbjct: 73  EKHRMYMGQRYVEVYEINNEDVDALMKSLQ 102

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 4/74 (5%)

Query: 130 IFIKNLDKSIDNKALHDTFSTF---GNILSCKVATDSLGQSRGYGFVQFDNEESAKSAID 186
           I  + L  S   + + + FS               +  G+ RG   ++ ++E+  + A++
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE 73

Query: 187 KLNGMLLNDKQVFV 200
           K + M +  + V V
Sbjct: 74  K-HRMYMGQRYVEV 86

>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 = 51.0 bits (122), Expect = 2e-08
 Identities = 14/66 (21%), Positives = 31/66 (46%)

Query: 331 DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSK 390
           D   ++   E+  ++G +    V  +      G+ +V F   E+A KA+ ++N +    +
Sbjct: 37  DEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96

Query: 391 PLYVAL 396
           P++  L
Sbjct: 97  PIHAEL 102

>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 = 47.9 bits (114), Expect = 3e-07
 Identities = 11/56 (19%), Positives = 25/56 (44%)

Query: 232 EDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDK 287
           E+   ++  ++G +    V  +         +V F   +DA ++V  LN + F+ +
Sbjct: 41  EEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96

>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 = 44.5 bits (105), Expect = 4e-06
 Identities = 12/50 (24%), Positives = 21/50 (42%)

Query: 151 FGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
           +G +    V  +      G  +V+F  EE A+ A+  LN    N + +  
Sbjct: 51  YGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100

>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 = 38.7 bits (90), Expect = 4e-04
 Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 11/71 (15%)

Query: 53  DSQLYDLFNQM----GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN---FTP 105
           D    ++F +M    G+V  + VC +      +G  YV +    +A +A+ +LN   F  
Sbjct: 37  DEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWF-- 93

Query: 106 LNGKPIRIMYS 116
            NG+PI    S
Sbjct: 94  -NGQPIHAELS 103

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 51.1 bits (122), Expect = 2e-08
 Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 8/82 (9%)

Query: 324 LYVKNL-DDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT-- 380
           +++ NL     SD  + +L   +G I +  +MR      +   F+   T E+A   +   
Sbjct: 28  IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----MKSQAFIEMETREDAMAMVDHC 82

Query: 381 EMNGKMVVSKPLYVALAQRKEE 402
                    + + V L+++ ++
Sbjct: 83  LKKALWFQGRCVKVDLSEKYKK 104

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 46.1 bits (109), Expect = 1e-06
 Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 221 VYVKNL-SETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE-- 277
           +++ NL     ++  + K+   +G I +  +M     + K   F+  +  +DA   V+  
Sbjct: 28  IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-----RMKSQAFIEMETREDAMAMVDHC 82

Query: 278 ALNGKKFDDKEWYVGKAQKKYE 299
                 F  +   V  ++K  +
Sbjct: 83  LKKALWFQGRCVKVDLSEKYKK 104

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 46.6 bits (110), Expect = 1e-06
 Identities = 12/68 (17%), Positives = 24/68 (35%), Gaps = 4/68 (5%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + I+N    I    L+   +  G +    +   +         V+F++   A+ A   LN
Sbjct: 28  LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN----GIQAMVEFESVLCAQKAKAALN 83

Query: 190 GMLLNDKQ 197
           G  +    
Sbjct: 84  GADIYAGC 91

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 43.5 bits (102), Expect = 1e-05
 Identities = 13/83 (15%), Positives = 27/83 (32%), Gaps = 4/83 (4%)

Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFV 264
           R    +  +   +   + ++N     T D L  +    G +    + +    +      V
Sbjct: 12  RPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQ----AMV 67

Query: 265 NFDDPDDAARSVEALNGKKFDDK 287
            F+    A ++  ALNG      
Sbjct: 68  EFESVLCAQKAKAALNGADIYAG 90

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 42.7 bits (100), Expect = 3e-05
 Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 6/82 (7%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
           L L ++N    I+ D L  + +  G +    + +     +     V F +   A KA   
Sbjct: 26  LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR----NGIQAMVEFESVLCAQKAKAA 81

Query: 382 MNGKMVVSK--PLYVALAQRKE 401
           +NG  + +    L +  A+   
Sbjct: 82  LNGADIYAGCCTLKIEYARPTR 103

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 5/81 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L +KNL   I    L+ L  + G + S         +++G     ++T EEA+KA   +N
Sbjct: 10  LLLKNLTAQIDGPTLRTLCMQHGPLVSFHP-----YLNQGIALCKYTTREEANKAQMALN 64

Query: 384 GKMVVSKPLYVALAQRKEERR 404
             ++ +  ++       E + 
Sbjct: 65  NCVLANTTIFAESPSENEVQS 85

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 44.4 bits (105), Expect = 4e-06
 Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 3/59 (5%)

Query: 232 EDDLKKIFGEFGIITSTAVMRDADGKS---KCFGFVNFDDPDDAARSVEALNGKKFDDK 287
            +D++    ++G++ S  + R  DG         FV F    D  ++++ L G+KF ++
Sbjct: 29  VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANR 87

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 14/61 (22%), Positives = 31/61 (50%), Gaps = 6/61 (9%)

Query: 330 DDSISDDKLKELFSE---FGTITSCKVMRDPNGIS---RGSGFVAFSTAEEASKALTEMN 383
           DD   ++ ++++  E   +G + S ++ R  +G+     G  FV F++  +  KA+  + 
Sbjct: 21  DDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLT 80

Query: 384 G 384
           G
Sbjct: 81  G 81

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 40.9 bits (96), Expect = 8e-05
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 3/63 (4%)

Query: 144 LHDTFSTFGNILSCKVATDSLGQS---RGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
           + D  S +G + S ++     G      G  FV+F +    + A+  L G    ++ V  
Sbjct: 32  VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 91

Query: 201 GPF 203
              
Sbjct: 92  KYC 94

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 96

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 16/79 (20%), Positives = 27/79 (34%), Gaps = 4/79 (5%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LYV NL  +     +             KV+     I+  S  + F   + A +A   M 
Sbjct: 12  LYVYNLPANKDGKSVSNRLRRLSDNCGGKVLS----ITGCSAILRFINQDSAERAQKRME 67

Query: 384 GKMVVSKPLYVALAQRKEE 402
            + V    + V+   +  E
Sbjct: 68  NEDVFGNRIIVSFTPKNRE 86

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 6/61 (9%)

Query: 329 LDDSISDDKLKELFSEFGTITSCKVMRDPNGISR-----GSGFVAFSTAEEASKALTEMN 383
           +DD +  + + E   +FG +    + ++  G           FV FS A E  KA+  +N
Sbjct: 34  IDDDLEGE-VTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN 92

Query: 384 G 384
           G
Sbjct: 93  G 93

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 13/61 (21%), Positives = 30/61 (49%), Gaps = 5/61 (8%)

Query: 232 EDDLKKIFGEFGIITSTAVMRDADGKSKCFG-----FVNFDDPDDAARSVEALNGKKFDD 286
           E ++ +  G+FG +    + ++  G+ +        FV F    +  ++++ALNG+ F  
Sbjct: 39  EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG 98

Query: 287 K 287
           +
Sbjct: 99  R 99

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 41.4 bits (97), Expect = 4e-05
 Identities = 9/61 (14%), Positives = 23/61 (37%), Gaps = 6/61 (9%)

Query: 221 VYVKNL-SETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           V++ +          L ++   FG+I++  ++           F+     +DA  +V+  
Sbjct: 18  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-----NKINEAFIEMATTEDAQAAVDYY 72

Query: 280 N 280
            
Sbjct: 73  T 73

>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 Length = 104

 Score = 41.1 bits (96), Expect = 6e-05
 Identities = 16/101 (15%), Positives = 33/101 (32%), Gaps = 10/101 (9%)

Query: 323 NLYVKNLDDSI-SDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASK 377
            L     +D + S+ + +     LF  +   T+ +  +     S     + FS    A+ 
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAAD 61

Query: 378 ALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPV 418
           A   ++    + K + +  AQ      + L         P 
Sbjct: 62  ARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSGPS 102

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 41.1 bits (96), Expect = 6e-05
 Identities = 15/71 (21%), Positives = 26/71 (36%), Gaps = 6/71 (8%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE--- 277
           V V+ L     ++ L   F          V+     +  C G + F +P DA R +    
Sbjct: 11  VEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ--RLGCGGVLTFREPADAERVLAQAD 68

Query: 278 -ALNGKKFDDK 287
             L+G +   +
Sbjct: 69  HELHGAQLSLR 79

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 5/57 (8%)

Query: 232 EDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDK 287
           +DD+ +   + G +    V ++ A G      +V       A  +V AL+G+ F  K
Sbjct: 31  KDDVIEECNKHGGVIHIYVDKNSAQGN----VYVKCPSIAAAIAAVNALHGRWFAGK 83

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 4/57 (7%)

Query: 328 NLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNG 384
             D  I DD + E  ++ G +    V ++    ++G+ +V   +   A  A+  ++G
Sbjct: 25  GWDTEIKDD-VIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHG 77

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 38.9 bits (91), Expect = 5e-04
 Identities = 10/51 (19%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 148 FSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQV 198
            +  G ++   V  +S   ++G  +V+  +  +A +A++ L+G     K +
Sbjct: 38  CNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWFAGKMI 85

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 14/59 (23%), Positives = 28/59 (47%), Gaps = 3/59 (5%)

Query: 329 LDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSG--FVAFSTAEEASKALTEMNGK 385
           +D+ +  +  KE   ++G +  C +   P      +   F+ F   E A KA+ ++NG+
Sbjct: 22  VDEDLEVE-TKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGR 79

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 4/57 (7%)

Query: 328 NLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNG 384
            + + I +D L+   S+FG I    +         G   V+F   EEA   +  ++G
Sbjct: 34  LVLNEIRED-LRVECSKFGQIRKLLLFDRH---PDGVASVSFRDPEEADYCIQTLDG 86

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 38.1 bits (89), Expect = 7e-04
 Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 5/57 (8%)

Query: 232 EDDLKKIFGEFGIITSTAVM-RDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDK 287
            +DL+    +FG I    +  R  DG       V+F DP++A   ++ L+G+ F  +
Sbjct: 40  REDLRVECSKFGQIRKLLLFDRHPDGV----ASVSFRDPEEADYCIQTLDGRWFGGR 92

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	467
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.98
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.97
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.97
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.97
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.97
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.97
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.97
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.97
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.97
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.96
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.96
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.96
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.96
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.96
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.96
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.96
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.95
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.95
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.95
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.94
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.87
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.86
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.85
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.85
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.84
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.84
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.84
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.82
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.82
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.81
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.81
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.81
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.81
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.81
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.81
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.8
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.8
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.8
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.8
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.8
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.8
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.8
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.8
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.8
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.8
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.79
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.79
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.79
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.79
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.79
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.79
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.79
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.79
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.79
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.79
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.79
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.79
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.79
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.79
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.79
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.79
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.79
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.78
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.78
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.78
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.78
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.78
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.78
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.78
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.78
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.78
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.78
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.78
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.78
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.78
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.78
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.78
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.78
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.78
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.78
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.78
2div_A	99	TRNA selenocysteine associated protein; structural	99.77
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.77
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.77
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.77
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.77
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.77
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.77
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.77
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.77
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.77
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.77
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.77
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.77
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.77
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.77
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.77
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.77
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.77
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.77
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.77
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.77
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.77
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.77
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.77
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.76
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.76
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.76
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.76
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.76
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.76
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.76
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.76
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.76
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.76
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.76
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.76
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.76
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.76
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.76
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.76
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.76
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.76
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.76
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.76
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.76
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.76
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.76
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.76
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.76
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.76
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.76
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.76
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.76
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.76
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.76
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.76
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.75
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.75
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.75
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.75
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.75
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.75
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.75
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.75
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.75
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.75
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.75
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.75
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.75
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.75
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.75
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.75
2div_A	99	TRNA selenocysteine associated protein; structural	99.75
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.75
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.75
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.75
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.74
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.74
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.74
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.74
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.74
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.74
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.74
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.74
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.74
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.74
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.74
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.74
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.74
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.74
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.74
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.74
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.73
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.73
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.73
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.73
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.73
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.73
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.73
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.73
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.73
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.73
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.73
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.73
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.73
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.73
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.73
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.73
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.73
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.73
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.73
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.73
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.73
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.73
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.73
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.73
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.73
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.73
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.73
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.72
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.72
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.72
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.72
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.72
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.72
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.72
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.72
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.72
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.72
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.72
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.72
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.72
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.72
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.72
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	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
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.72
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.72
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.71
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.71
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.71
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.71
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.71
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.71
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.71
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.71
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.71
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.71
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.71
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.71
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.71
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.71
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.71
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.71
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.71
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.71
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.7
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.7
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.7
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.7
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.7
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.7
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.7
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.7
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.7
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.7
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.7
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.7
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.7
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.7
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.7
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.7
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.69
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.69
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.69
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.69
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.69
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.69
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.69
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.69
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.69
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.69
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.69
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.69
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.69
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.69
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.69
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.69
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.69
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.68
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.68
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.68
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.68
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.68
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.68
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.68
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.68
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.68
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.67
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.5
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.67
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.67
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.67
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.67
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.67
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.67
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.67
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.67
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.66
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.66
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.66
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.66
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.66
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.66
1x5p_A	97	Negative elongation factor E; structure genomics,	99.66
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.66
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.66
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.66
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.66
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.66
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.66
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.47
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.65
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.65
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.65
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.65
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.65
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.65
1x5p_A	97	Negative elongation factor E; structure genomics,	99.65
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.64
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.64
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.64
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.64
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.64
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.63
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.63
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.63
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.62
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.62
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.62
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.62
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.62
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.62
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.61
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.61
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.6
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.59
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.59
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.59
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.59
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.57
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.57
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.56
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.56
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.56
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.54
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.52
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.52
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.52
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.51
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.5
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.47
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.45
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.44
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.42
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.42
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.36
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.32
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.31
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.29
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.19
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.12
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.1
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.02
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.97
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.85
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.8
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.78
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.59
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.32
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.96
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.86
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.81
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.75
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.7
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.67
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.35
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.31
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.22
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.18
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.05
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.88
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.62
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.6
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.23
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.84
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.7
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	89.54
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	88.92
3iot_A	449	Maltose-binding protein, huntingtin fusion protei;	82.62

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=100.00  E-value=1.2e-45  Score=337.91  Aligned_cols=253  Identities=21%  Similarity=0.291  Sum_probs=225.5

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .++++|||+|||+++++++|+++|+.|| |.++.+      ++++|||||+|.+.++|.+|++.+++..+.|+.++|.++
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~   92 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ   92 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEec
Confidence            3579999999999999999999999999 999988      346689999999999999999999999999999999986


Q ss_pred             ccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCccCC
Q 012257          117 YRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLND  195 (467)
Q Consensus       117 ~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g  195 (467)
                      .        ...+|||+|||.++++++|+++|+.||.|..+.+..+ .+|.++|+|||+|.+.++|..|++.++|..+.|
T Consensus        93 ~--------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g  164 (284)
T 3smz_A           93 P--------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP  164 (284)
T ss_dssp             C--------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             C--------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            4        3368999999999999999999999999999999988 689999999999999999999999999999999


Q ss_pred             eeeEecccccccccccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHH
Q 012257          196 KQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARS  275 (467)
Q Consensus       196 ~~~~v~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a  275 (467)
                      +.|.+.++......                                                                  
T Consensus       165 ~~i~v~~a~~~~~~------------------------------------------------------------------  178 (284)
T 3smz_A          165 RTLYVHWTDAGQLT------------------------------------------------------------------  178 (284)
T ss_dssp             EECEEEECCGGGCC------------------------------------------------------------------
T ss_pred             cEEEEEECCCCCCC------------------------------------------------------------------
Confidence            99999765332100                                                                  


Q ss_pred             HHHhCCCccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCC-CHHHHHHhhccCCceeEEEEe
Q 012257          276 VEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSI-SDDKLKELFSEFGTITSCKVM  354 (467)
Q Consensus       276 ~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~-~~~~l~~~F~~~G~v~~v~i~  354 (467)
                                                              ......++|||+|||..+ ++++|+++|+.||.|.++++.
T Consensus       179 ----------------------------------------~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~  218 (284)
T 3smz_A          179 ----------------------------------------PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLA  218 (284)
T ss_dssp             ----------------------------------------TTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEE
T ss_pred             ----------------------------------------cccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEE
Confidence                                                    000234579999999995 999999999999999999999


Q ss_pred             eCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhhHHHHHHHHhh
Q 012257          355 RDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERRARLQAQ  410 (467)
Q Consensus       355 ~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~  410 (467)
                      .+.+|.++|+|||+|.+.++|.+|+..|||..++|+.|+|+|++++..++....++
T Consensus       219 ~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~  274 (284)
T 3smz_A          219 CGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAAL  274 (284)
T ss_dssp             ECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSCHHHHHHHH
T ss_pred             ECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCcccchhhhh
Confidence            99999999999999999999999999999999999999999998877665544443

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

Probab=100.00  E-value=2.2e-45  Score=337.53  Aligned_cols=256  Identities=20%  Similarity=0.376  Sum_probs=213.7

Q ss_pred             CCCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCc
Q 012257           30 GVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK  109 (467)
Q Consensus        30 ~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  109 (467)
                      .....+.+++++|||+|||+++++++|+++|+.||.|.+|++.++..+  ++|||||+|.+.++|.+|++ +++..+.|+
T Consensus        32 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~-~~~~~~~g~  108 (292)
T 2ghp_A           32 NEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQN  108 (292)
T ss_dssp             ----------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTE
T ss_pred             ccccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHH-hCCcEeCCc
Confidence            335566778999999999999999999999999999999999998744  57999999999999999996 899999999


Q ss_pred             eeeeeecccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcC-CeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHh
Q 012257          110 PIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFG-NILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL  188 (467)
Q Consensus       110 ~~~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g-~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l  188 (467)
                      .+.|.++         ..++|||+|||..+++++|+++|+.|| .|..+.+..+..|.++|||||+|.+.++|..|++.|
T Consensus       109 ~i~v~~~---------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l  179 (292)
T 2ghp_A          109 EIIVSHL---------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL  179 (292)
T ss_dssp             ECEEEEC---------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHH
T ss_pred             EEEEEEC---------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHh
Confidence            9999876         356899999999999999999999999 999999999877889999999999999999999999


Q ss_pred             cCCccCCeeeEecccccccccccccccccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCC
Q 012257          189 NGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDD  268 (467)
Q Consensus       189 ~~~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~  268 (467)
                      +|..+.|+.|.+.++.........                                                        
T Consensus       180 ~g~~~~g~~l~v~~a~~~~~~~~~--------------------------------------------------------  203 (292)
T 2ghp_A          180 NGLKIEGYTLVTKVSNPLEKSKRT--------------------------------------------------------  203 (292)
T ss_dssp             TTCEETTEECEEEECCCC--------------------------------------------------------------
T ss_pred             CCCEeCCcEEEEEECCCCcccccc--------------------------------------------------------
Confidence            999999999999765432110000                                                        


Q ss_pred             HHHHHHHHHHhCCCccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCC-CCHHHHHHhhccCCc
Q 012257          269 PDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDS-ISDDKLKELFSEFGT  347 (467)
Q Consensus       269 ~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~-~~~~~l~~~F~~~G~  347 (467)
                                                                    .......++|||+|||.. +++++|+++|++||.
T Consensus       204 ----------------------------------------------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~  237 (292)
T 2ghp_A          204 ----------------------------------------------DSATLEGREIMIRNLSTELLDENLLRESFEGFGS  237 (292)
T ss_dssp             -------------------------------------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSC
T ss_pred             ----------------------------------------------cccCCCCceEEEECCCcccCCHHHHHHHHhccCC
Confidence                                                          001224558999999999 999999999999999


Q ss_pred             eeEEEEeeCCC--CCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          348 ITSCKVMRDPN--GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       348 v~~v~i~~~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      |.+|+++.+..  |.++|||||+|.+.++|.+|+ .|||..|+|+.|.|+|++++
T Consensus       238 v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          238 IEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             EEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             eeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            99999999887  999999999999999999999 99999999999999999864

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=5e-35  Score=254.69  Aligned_cols=171  Identities=61%  Similarity=1.054  Sum_probs=158.4

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .++++|||+|||++++|++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|.+|++.+++..+.|+.+++.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCe
Q 012257          117 YRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDK  196 (467)
Q Consensus       117 ~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~  196 (467)
                      ............+|||+|||..+++++|+++|+.||.|.++.++.+.. .++|||||+|.+.++|.+|++.|+|..+.|+
T Consensus        93 ~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~-~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~  171 (213)
T 4f02_A           93 QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDR  171 (213)
T ss_dssp             CCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             cccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCC-CCceEEEEEeCCHHHHHHHHHHhCCCEECCE
Confidence            877666666778999999999999999999999999999999998753 3799999999999999999999999999999


Q ss_pred             eeEecccccccc
Q 012257          197 QVFVGPFLRKQE  208 (467)
Q Consensus       197 ~~~v~~~~~~~~  208 (467)
                      .|.|.++..+..
T Consensus       172 ~i~V~~a~~~~~  183 (213)
T 4f02_A          172 KVFVGRFKSRKE  183 (213)
T ss_dssp             ECEEEECCCHHH
T ss_pred             EEEEEEcCCCcc
Confidence            999988766543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.4e-32  Score=230.44  Aligned_cols=164  Identities=28%  Similarity=0.556  Sum_probs=154.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecccC
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRD  119 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~  119 (467)
                      |+|||+|||+++++++|+++|+.||.|.+|++.+++ .++++|||||+|.+.++|.+|++.+++..+.|+.++|.++...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            689999999999999999999999999999999997 4779999999999999999999999999999999999999877


Q ss_pred             cccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeee
Q 012257          120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQV  198 (467)
Q Consensus       120 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~  198 (467)
                      .........+|+|+|||..+++++|+++|+.||.|..+.+..+ .+|.++|+|||+|.+.++|.+|++.|+|..+.|+.|
T Consensus        80 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  159 (166)
T 3md3_A           80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL  159 (166)
T ss_dssp             CCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Confidence            7777777889999999999999999999999999999999998 788999999999999999999999999999999999


Q ss_pred             Eecccc
Q 012257          199 FVGPFL  204 (467)
Q Consensus       199 ~v~~~~  204 (467)
                      .|.++.
T Consensus       160 ~v~~a~  165 (166)
T 3md3_A          160 RINWAA  165 (166)
T ss_dssp             EEEESC
T ss_pred             EEEecC
Confidence            997753

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=1.7e-32  Score=238.62  Aligned_cols=174  Identities=35%  Similarity=0.527  Sum_probs=155.7

Q ss_pred             cccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccc
Q 012257          217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQ  295 (467)
Q Consensus       217 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~  295 (467)
                      ..++|||+|||..+++++|+++|++||.|.++.++.+ .+++++|||||+|.+.++|..|+..+++..+.|+.+.+.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            4478999999999999999999999999999999998 468899999999999999999999999999999999998887


Q ss_pred             cchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHH
Q 012257          296 KKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEA  375 (467)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A  375 (467)
                      ........                ...+|||+|||..+++++|+++|++||.|.+|+|+.+.. .++|||||+|.+.++|
T Consensus        94 ~~~~~~~~----------------~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~-~~~g~~fV~f~~~~~a  156 (213)
T 4f02_A           94 RDPSLRKS----------------GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAA  156 (213)
T ss_dssp             CCTHHHHH----------------CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESSHHHH
T ss_pred             cccccccc----------------ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCC-CCceEEEEEeCCHHHH
Confidence            65433211                234799999999999999999999999999999999864 4799999999999999


Q ss_pred             HHHHHHhCCcEecccceEEehhhhhHHHHHHH
Q 012257          376 SKALTEMNGKMVVSKPLYVALAQRKEERRARL  407 (467)
Q Consensus       376 ~~A~~~l~g~~~~g~~l~v~~~~~~~~~~~~~  407 (467)
                      .+|++.|||..|+|+.|.|++++++.++....
T Consensus       157 ~~Ai~~lng~~~~g~~i~V~~a~~~~~~~~~~  188 (213)
T 4f02_A          157 ERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL  188 (213)
T ss_dssp             HHHHHHHTTCEETTEECEEEECCCHHHHHHHH
T ss_pred             HHHHHHhCCCEECCEEEEEEEcCCCcccchhh
Confidence            99999999999999999999999887655543

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=100.00  E-value=3.8e-32  Score=228.20  Aligned_cols=163  Identities=28%  Similarity=0.527  Sum_probs=151.8

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ++++|||+|||+++++++|+++|+.||.|.+|++.+++.+|+++|||||+|.+.++|++|++.+++..+.|+.++|.++.
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            57999999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             cCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCccCC-
Q 012257          118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLND-  195 (467)
Q Consensus       118 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g-  195 (467)
                      ....  .....+|+|+|||..+++++|+++|+.||.|..+.+..+ .+|.++|+|||+|.+.++|.+|++.|+|..+.| 
T Consensus        82 ~~~~--~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  159 (168)
T 1b7f_A           82 PGGE--SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG  159 (168)
T ss_dssp             CCSS--TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             CCcc--cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCC
Confidence            5433  345678999999999999999999999999999999998 488999999999999999999999999999987 


Q ss_pred             -eeeEecc
Q 012257          196 -KQVFVGP  202 (467)
Q Consensus       196 -~~~~v~~  202 (467)
                       +.|.|.+
T Consensus       160 ~~~l~V~~  167 (168)
T 1b7f_A          160 SQPLSVRL  167 (168)
T ss_dssp             SSCCEEEE
T ss_pred             CeEEEEEe
Confidence             8888754

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=100.00  E-value=5.9e-32  Score=226.89  Aligned_cols=163  Identities=32%  Similarity=0.552  Sum_probs=150.4

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ++++|||+|||+++++++|+++|+.||.|.+|++.+++.+|+++|||||+|.+.++|.+|++.+++..+.|+.++|.++.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            47899999999999999999999999999999999999899999999999999999999999999999999999999887


Q ss_pred             cCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCe
Q 012257          118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDK  196 (467)
Q Consensus       118 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~  196 (467)
                      ....  .....+|+|+|||..+++++|+++|+.||.|..+.+..+ .+|.++|+|||+|.+.++|.+|++.|+|..+.|+
T Consensus        81 ~~~~--~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  158 (167)
T 1fxl_A           81 PSSA--SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA  158 (167)
T ss_dssp             CCCG--GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             CCcc--cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCC
Confidence            5433  344578999999999999999999999999999999998 5888999999999999999999999999999997


Q ss_pred             e--eEecc
Q 012257          197 Q--VFVGP  202 (467)
Q Consensus       197 ~--~~v~~  202 (467)
                      .  |.+.+
T Consensus       159 ~~~i~v~~  166 (167)
T 1fxl_A          159 TEPITVKF  166 (167)
T ss_dssp             SSCCEEEE
T ss_pred             ccceEEEe
Confidence            6  55543

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=5.2e-32  Score=233.46  Aligned_cols=175  Identities=25%  Similarity=0.436  Sum_probs=151.6

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....++++|||+|||+++++++|+++|+.||.|.+|++++++.+|+++|||||+|.+.++|.+|++. ++..+.|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v   86 (196)
T 1l3k_A            8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEP   86 (196)
T ss_dssp             CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeee
Confidence            3445689999999999999999999999999999999999999999999999999999999999985 888999999999


Q ss_pred             eecccCcccc----cCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHh
Q 012257          114 MYSYRDPTIR----KSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKL  188 (467)
Q Consensus       114 ~~~~~~~~~~----~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l  188 (467)
                      .++.......    .....+|||+|||.++++++|+++|+.||.|..+.+..+ .+|.++|||||+|.+.++|.+|+.. 
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-  165 (196)
T 1l3k_A           87 KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-  165 (196)
T ss_dssp             EECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-
T ss_pred             ecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-
Confidence            9976543322    223478999999999999999999999999999999998 5889999999999999999999986 


Q ss_pred             cCCccCCeeeEecccccccccc
Q 012257          189 NGMLLNDKQVFVGPFLRKQERE  210 (467)
Q Consensus       189 ~~~~~~g~~~~v~~~~~~~~~~  210 (467)
                      ++..+.|+.|.|.++..+....
T Consensus       166 ~~~~~~G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          166 KYHTVNGHNCEVRKALSKQEMA  187 (196)
T ss_dssp             SCCEETTEECEEEECC------
T ss_pred             CCcEECCEEEEEEecCChhHhc
Confidence            7999999999999887765543

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

Probab=100.00  E-value=7.5e-32  Score=236.24  Aligned_cols=171  Identities=22%  Similarity=0.471  Sum_probs=154.2

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .++++|||+|||+++++++|+++|+.||.|.+|++++++.+++++|||||+|.+.++|.+|++.+++..+.|+.|+|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            45789999999999999999999999999999999999989999999999999999999999999999999999999887


Q ss_pred             ccCccc---------ccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHH
Q 012257          117 YRDPTI---------RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAID  186 (467)
Q Consensus       117 ~~~~~~---------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~  186 (467)
                      ......         ......+|||+|||.++++++|+++|+.||.|..+.+..+ .+|.++|+|||+|.+.++|.+|++
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~  185 (216)
T 2qfj_A          106 SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS  185 (216)
T ss_dssp             SCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHH
Confidence            654321         2245579999999999999999999999999999999998 688999999999999999999999


Q ss_pred             HhcCCccCCeeeEeccccccc
Q 012257          187 KLNGMLLNDKQVFVGPFLRKQ  207 (467)
Q Consensus       187 ~l~~~~~~g~~~~v~~~~~~~  207 (467)
                      .|+|..+.|+.|.|.++..+.
T Consensus       186 ~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          186 SMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             HHTTCBCSSSBCEEEECSSCS
T ss_pred             HccCCEeCCcEEEEEEecCCC
Confidence            999999999999998876653

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.98  E-value=3.9e-31  Score=223.67  Aligned_cols=165  Identities=24%  Similarity=0.391  Sum_probs=147.0

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCC--ccccEEEEEecChHHHHHHHHHhCCcccC---Cceee
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTR--RSLGYGYVNYNAAHEATRALDELNFTPLN---GKPIR  112 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~A~~~l~~~~~~---g~~~~  112 (467)
                      ++++|||+|||+++++++|+++|++||.|.+|++.+++.++  +++|||||+|.+.++|++|++.+++..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            47899999999999999999999999999999999999887  89999999999999999999999987765   56677


Q ss_pred             eeecccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCc
Q 012257          113 IMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGML  192 (467)
Q Consensus       113 v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~  192 (467)
                      +.++..... .....++|+|+|||..+++++|+++|+.||.|..+.+..+.+|.++|+|||+|.+.++|.+|++.|+|..
T Consensus        82 ~~~~~~~~~-~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~  160 (175)
T 3nmr_A           82 MKPADSEKN-NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQ  160 (175)
T ss_dssp             EEECGGGCC-SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSC
T ss_pred             Ecccccccc-ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCc
Confidence            766554322 2335678999999999999999999999999999999999889999999999999999999999999987


Q ss_pred             cC---CeeeEeccc
Q 012257          193 LN---DKQVFVGPF  203 (467)
Q Consensus       193 ~~---g~~~~v~~~  203 (467)
                      +.   ++.|.|.++
T Consensus       161 ~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          161 TMEGCSSPMVVKFA  174 (175)
T ss_dssp             CCTTCSSCCEEEEC
T ss_pred             ccCCCCCCeEEEec
Confidence            65   388888654

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.97  E-value=7.1e-32  Score=226.26  Aligned_cols=165  Identities=22%  Similarity=0.472  Sum_probs=149.9

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      +++++|||+|||+++++++|+++|+.||.|.+|++.+++.+|+++|||||+|.+.++|.+|++.  +..+.|+.+.+.++
T Consensus         1 k~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~   78 (167)
T 2cjk_A            1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRA   78 (167)
T ss_dssp             CGGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccc
Confidence            4689999999999999999999999999999999999999999999999999999999999984  56789999999887


Q ss_pred             ccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCccCC
Q 012257          117 YRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLND  195 (467)
Q Consensus       117 ~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g  195 (467)
                      .....  ....++|||+|||.++++++|+++|+.||.|.++.+..+ .+|.++|+|||+|.+.++|.+|++ +++..+.|
T Consensus        79 ~~~~~--~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g  155 (167)
T 2cjk_A           79 IPRDE--QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKD  155 (167)
T ss_dssp             CCHHH--HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSS
T ss_pred             cchhh--ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCC
Confidence            54332  234568999999999999999999999999999999988 679999999999999999999998 89999999


Q ss_pred             eeeEecccccc
Q 012257          196 KQVFVGPFLRK  206 (467)
Q Consensus       196 ~~~~v~~~~~~  206 (467)
                      +.|.|.++.++
T Consensus       156 ~~i~V~~a~pk  166 (167)
T 2cjk_A          156 RKIEIKRAEPR  166 (167)
T ss_dssp             SCEEEEECCCC
T ss_pred             eEEEEeecCCC
Confidence            99999877543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.97  E-value=6.2e-31  Score=220.38  Aligned_cols=164  Identities=31%  Similarity=0.524  Sum_probs=151.0

Q ss_pred             cceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccch
Q 012257          219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKY  298 (467)
Q Consensus       219 ~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~  298 (467)
                      ++|||+|||..+++++|+++|+.||.|.++.+..+..++++|+|||+|.+.++|..|+..+++..+.|+.+.+.++....
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            46999999999999999999999999999999999888899999999999999999999999999999999998886532


Q ss_pred             HHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHH
Q 012257          299 EREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASK  377 (467)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~  377 (467)
                      .                .......+|||+|||..+++++|+++|++||.|.++++..+. +|.++|+|||+|.+.++|.+
T Consensus        81 ~----------------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~  144 (166)
T 3md3_A           81 Q----------------SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN  144 (166)
T ss_dssp             C----------------CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHH
T ss_pred             C----------------CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHH
Confidence            1                223456789999999999999999999999999999999984 78899999999999999999


Q ss_pred             HHHHhCCcEecccceEEehhh
Q 012257          378 ALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       378 A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      |++.|||..++|+.|+|+|++
T Consensus       145 A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          145 AMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             HHHHHTTCEETTEECEEEESC
T ss_pred             HHHHhCCCccCCcEEEEEecC
Confidence            999999999999999999986

>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=99.97  E-value=4.9e-30  Score=215.16  Aligned_cols=162  Identities=33%  Similarity=0.621  Sum_probs=148.9

Q ss_pred             ccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccccc
Q 012257          218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQK  296 (467)
Q Consensus       218 ~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~-~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~  296 (467)
                      .++|||+|||..+++++|+++|+.||.|.++.+..+. ++.++|+|||+|.+.++|..|+..+++..+.|+.+.+.++..
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            3689999999999999999999999999999999986 789999999999999999999999999999999999988875


Q ss_pred             chHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHH
Q 012257          297 KYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEA  375 (467)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A  375 (467)
                      ...                  .....+|||+|||..+++++|+++|++||.|.++++..+. +|.++|+|||+|.+.++|
T Consensus        82 ~~~------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A  143 (167)
T 1fxl_A           82 SSA------------------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA  143 (167)
T ss_dssp             CCG------------------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHH
T ss_pred             Ccc------------------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHH
Confidence            321                  1245689999999999999999999999999999999987 788999999999999999


Q ss_pred             HHHHHHhCCcEecccc--eEEehh
Q 012257          376 SKALTEMNGKMVVSKP--LYVALA  397 (467)
Q Consensus       376 ~~A~~~l~g~~~~g~~--l~v~~~  397 (467)
                      .+|++.|||..+.|+.  |+|+||
T Consensus       144 ~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          144 EEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHhcCCccCCCccceEEEeC
Confidence            9999999999999975  888875

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

Probab=99.97  E-value=5.8e-30  Score=224.21  Aligned_cols=177  Identities=27%  Similarity=0.432  Sum_probs=153.1

Q ss_pred             cccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECC-CCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccc
Q 012257          217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDA-DGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQ  295 (467)
Q Consensus       217 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~-~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~  295 (467)
                      ..++|||+|||.++++++|+++|+.||.|.++.+..+. ++.++|||||+|.+.++|..|+..+++..+.|+.+.+.++.
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            34789999999999999999999999999999998874 78899999999999999999999999999999999998887


Q ss_pred             cchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHH
Q 012257          296 KKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEE  374 (467)
Q Consensus       296 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~  374 (467)
                      ............       .......++|||+|||..+++++|+++|++||.|.+|++..+. +|.++|+|||+|.+.++
T Consensus       107 ~~~~~~~~~~~~-------~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~  179 (216)
T 2qfj_A          107 NIGQAQPIIDQL-------AEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQS  179 (216)
T ss_dssp             CCGGGHHHHHHH-------HHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHH
T ss_pred             Cccccchhhhhh-------hcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHH
Confidence            654332211111       1122355789999999999999999999999999999999986 78899999999999999


Q ss_pred             HHHHHHHhCCcEecccceEEehhhhh
Q 012257          375 ASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       375 A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      |.+|++.|||..|+|+.|+|.|+.+.
T Consensus       180 A~~A~~~l~g~~~~g~~i~V~~a~~~  205 (216)
T 2qfj_A          180 SQDAVSSMNLFDLGGQYLRVGKAVTP  205 (216)
T ss_dssp             HHHHHHHHTTCBCSSSBCEEEECSSC
T ss_pred             HHHHHHHccCCEeCCcEEEEEEecCC
Confidence            99999999999999999999998743

>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=99.97  E-value=6.8e-30  Score=220.18  Aligned_cols=177  Identities=23%  Similarity=0.426  Sum_probs=148.6

Q ss_pred             cccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcc
Q 012257          215 KTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGK  293 (467)
Q Consensus       215 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~  293 (467)
                      ....++|||+|||..+++++|+++|+.||.|.++.+..+ .++.++|||||+|.+.++|..|+.. ++..+.|+.+.+.+
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~   88 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKR   88 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeec
Confidence            345688999999999999999999999999999999998 4588999999999999999999985 89999999999998


Q ss_pred             cccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCH
Q 012257          294 AQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTA  372 (467)
Q Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~  372 (467)
                      +........            .......++|||+|||..+++++|+++|+.||.|.+|++..+. +|.++|||||+|.+.
T Consensus        89 ~~~~~~~~~------------~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~  156 (196)
T 1l3k_A           89 AVSREDSQR------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH  156 (196)
T ss_dssp             CCC-----------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             ccCcccccc------------cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCH
Confidence            876432211            1122355789999999999999999999999999999999986 788999999999999


Q ss_pred             HHHHHHHHHhCCcEecccceEEehhhhhHHHHH
Q 012257          373 EEASKALTEMNGKMVVSKPLYVALAQRKEERRA  405 (467)
Q Consensus       373 ~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~~  405 (467)
                      ++|.+|+.. +|..++|+.|.|+++.++.+...
T Consensus       157 ~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          157 DSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             HHHHHHHHC-SCCEETTEECEEEECC-------
T ss_pred             HHHHHHHHh-CCcEECCEEEEEEecCChhHhcc
Confidence            999999986 89999999999999998876544

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.97  E-value=3.7e-31  Score=223.62  Aligned_cols=167  Identities=19%  Similarity=0.307  Sum_probs=148.9

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....++++|||+|||.++++++|+++|+.||.+.. .++.+..+++++|||||+|.+.++|.+|++ +++..+.|+.|+|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v   85 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKL   85 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEE
Confidence            44567899999999999999999999999997766 344455678899999999999999999995 9999999999999


Q ss_pred             eecccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCcc
Q 012257          114 MYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLL  193 (467)
Q Consensus       114 ~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~  193 (467)
                      .++............+|||+|||..+++++|+++|+.||.|..+    ..+|.++|+|||+|.+.++|.+|++.|+|..+
T Consensus        86 ~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  161 (175)
T 1fje_B           86 EKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI  161 (175)
T ss_dssp             ECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEE
T ss_pred             ecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            99987766666778899999999999999999999999988665    66778999999999999999999999999999


Q ss_pred             CCeeeEecccccc
Q 012257          194 NDKQVFVGPFLRK  206 (467)
Q Consensus       194 ~g~~~~v~~~~~~  206 (467)
                      .|+.|.|.++.++
T Consensus       162 ~g~~i~v~~a~~k  174 (175)
T 1fje_B          162 DGRSVSLYYTGEK  174 (175)
T ss_dssp             TTEEEEEEECSSC
T ss_pred             CCeEEEEEecCCC
Confidence            9999999877543

>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=99.97  E-value=4e-30  Score=215.83  Aligned_cols=162  Identities=34%  Similarity=0.574  Sum_probs=149.8

Q ss_pred             ccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccccc
Q 012257          218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQK  296 (467)
Q Consensus       218 ~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~  296 (467)
                      .++|+|+|||..+++++|+++|+.||.|.++.+..+ .++.++|+|||+|.+.++|..|+..+++..+.|+.+.+.++..
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   82 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   82 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCC
Confidence            478999999999999999999999999999999887 4688999999999999999999999999999999999998875


Q ss_pred             chHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHH
Q 012257          297 KYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEA  375 (467)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A  375 (467)
                      ...                  ....++|||+|||..+++++|+++|++||.|.++++.++. +|.++|+|||+|.+.++|
T Consensus        83 ~~~------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A  144 (168)
T 1b7f_A           83 GGE------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA  144 (168)
T ss_dssp             CSS------------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHH
T ss_pred             Ccc------------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHH
Confidence            421                  2345689999999999999999999999999999999987 888999999999999999


Q ss_pred             HHHHHHhCCcEecc--cceEEehh
Q 012257          376 SKALTEMNGKMVVS--KPLYVALA  397 (467)
Q Consensus       376 ~~A~~~l~g~~~~g--~~l~v~~~  397 (467)
                      .+|++.|||..+.|  ++|+|+||
T Consensus       145 ~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          145 QEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHhcCCEecCCCeEEEEEeC
Confidence            99999999999987  99999986

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.97  E-value=1.4e-29  Score=213.30  Aligned_cols=158  Identities=24%  Similarity=0.515  Sum_probs=143.5

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcC----C-------CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcc
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQM----G-------QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTP  105 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~----G-------~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~  105 (467)
                      +++++|||+|||+++++++|+++|++|    |       .|.++.+.+      ++|||||+|.+.++|.+|+ .+++..
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~   74 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGII   74 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcE
Confidence            468999999999999999999999999    6       778877754      3589999999999999999 799999


Q ss_pred             cCCceeeeeecccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHH
Q 012257          106 LNGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSA  184 (467)
Q Consensus       106 ~~g~~~~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a  184 (467)
                      +.|+.++|.++.....  .....+|+|+|||..+++++|+++|+.||.|..+.+..+ .+|.++|+|||+|.+.++|.+|
T Consensus        75 ~~g~~i~v~~~~~~~~--~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A  152 (172)
T 2g4b_A           75 FQGQSLKIRRPHDYQP--LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA  152 (172)
T ss_dssp             ETTEECEEECCSSCCC--CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHH
T ss_pred             ecCceeeecCCcccCC--CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHH
Confidence            9999999998754432  344689999999999999999999999999999999999 5899999999999999999999


Q ss_pred             HHHhcCCccCCeeeEeccc
Q 012257          185 IDKLNGMLLNDKQVFVGPF  203 (467)
Q Consensus       185 ~~~l~~~~~~g~~~~v~~~  203 (467)
                      ++.|+|..+.|+.|.|.++
T Consensus       153 ~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          153 IAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             HHHHTTCEETTEECEEEEC
T ss_pred             HHHcCCCEECCeEEEEEeC
Confidence            9999999999999999765

>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=99.97  E-value=1.5e-29  Score=213.91  Aligned_cols=164  Identities=27%  Similarity=0.513  Sum_probs=144.8

Q ss_pred             ccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCC---CceeEEEEEeCCHHHHHHHHHHhCCCccC---CceEEE
Q 012257          218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG---KSKCFGFVNFDDPDDAARSVEALNGKKFD---DKEWYV  291 (467)
Q Consensus       218 ~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~---~~~g~afv~f~~~~~a~~a~~~l~~~~~~---~~~l~~  291 (467)
                      .++|||+|||..+++++|+++|++||.|.++.+..+..+   +++|||||+|.+.++|..|+..+++..+.   ++.+.+
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~   82 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQM   82 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEE
Confidence            478999999999999999999999999999999988655   78999999999999999999999998775   456666


Q ss_pred             cccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCC
Q 012257          292 GKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFST  371 (467)
Q Consensus       292 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~  371 (467)
                      .++....                 ......++|||+|||..+++++|+++|++||.|.++++..+.+|.++|||||+|.+
T Consensus        83 ~~~~~~~-----------------~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~  145 (175)
T 3nmr_A           83 KPADSEK-----------------NNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTT  145 (175)
T ss_dssp             EECGGGC-----------------CSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESS
T ss_pred             ccccccc-----------------cccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECC
Confidence            5554321                 11234568999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhCCcEec---ccceEEehhh
Q 012257          372 AEEASKALTEMNGKMVV---SKPLYVALAQ  398 (467)
Q Consensus       372 ~~~A~~A~~~l~g~~~~---g~~l~v~~~~  398 (467)
                      .++|.+|++.|||..+.   |++|+|+||.
T Consensus       146 ~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          146 RAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             HHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            99999999999998876   4999999974

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.97  E-value=2.3e-29  Score=229.80  Aligned_cols=172  Identities=20%  Similarity=0.304  Sum_probs=158.5

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ..++|||+|||+++++++|+++|+.||.|.++.+..++.+|+++|||||+|.+.++|.+|++.+++..+.|+.|+|.++.
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            45899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCcccc-cCCCccEEEcCCCCcC-CHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCC
Q 012257          118 RDPTIR-KSGAGNIFIKNLDKSI-DNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLND  195 (467)
Q Consensus       118 ~~~~~~-~~~~~~l~v~nlp~~~-t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g  195 (467)
                      ...... .....+|+|+|||..+ ++++|+++|+.||.|.++.+..+.+|.++|+|||+|.+.++|.+|+..|+|..+.|
T Consensus       174 ~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  253 (284)
T 3smz_A          174 AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGG  253 (284)
T ss_dssp             GGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCC
Confidence            654332 2456789999999995 99999999999999999999999889999999999999999999999999999999


Q ss_pred             eeeEeccccccccc
Q 012257          196 KQVFVGPFLRKQER  209 (467)
Q Consensus       196 ~~~~v~~~~~~~~~  209 (467)
                      +.|.|.++.++...
T Consensus       254 ~~l~v~~a~~~~~~  267 (284)
T 3smz_A          254 SHLRVSFCAPGPPG  267 (284)
T ss_dssp             EECEEEECCSSSCH
T ss_pred             eEEEEEEecCCCcc
Confidence            99999988766543

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.97  E-value=1.9e-29  Score=216.57  Aligned_cols=155  Identities=18%  Similarity=0.266  Sum_probs=135.3

Q ss_pred             CccCeEEEcCCC-CCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           37 FVSTSLYVGDLD-LSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        37 ~~~~~l~v~nLp-~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      .++++|||+||| .++++++|+++|+.||.|.+|++++++     +|||||+|.+.++|++|++.|++..+.|+.|+|.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            357899999999 899999999999999999999998763     58999999999999999999999999999999998


Q ss_pred             cccCcccc-----------------------------------cCCCccEEEcCCCCcCCHHHHHHHHhhcCCe--EEEE
Q 012257          116 SYRDPTIR-----------------------------------KSGAGNIFIKNLDKSIDNKALHDTFSTFGNI--LSCK  158 (467)
Q Consensus       116 ~~~~~~~~-----------------------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v--~~~~  158 (467)
                      +.......                                   .....+|||+|||..+++++|+++|+.||.|  .+++
T Consensus        77 s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~  156 (205)
T 3tyt_A           77 SKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVK  156 (205)
T ss_dssp             CSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEE
T ss_pred             ccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEE
Confidence            75321100                                   0123469999999999999999999999999  8898


Q ss_pred             EeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCee
Q 012257          159 VATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQ  197 (467)
Q Consensus       159 ~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~  197 (467)
                      +..+. +.++|+|||+|.+.++|..|+..|||..+.|..
T Consensus       157 ~~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~  194 (205)
T 3tyt_A          157 VFSGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPN  194 (205)
T ss_dssp             ECSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSS
T ss_pred             EEcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCC
Confidence            88765 445699999999999999999999999988773

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.97  E-value=3.8e-29  Score=215.87  Aligned_cols=163  Identities=23%  Similarity=0.492  Sum_probs=143.5

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcC----C-------CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcc
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQM----G-------QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTP  105 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~----G-------~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~  105 (467)
                      +.+++|||+|||+++++++|+++|+.|    |       .|.++.+.      +++|||||+|.+.++|++|+ .+++..
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al-~l~g~~   74 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGII   74 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHG-GGTTEE
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHH-HhcCCE
Confidence            568999999999999999999999999    5       66666653      45689999999999999999 799999


Q ss_pred             cCCceeeeeecccCccc------------------ccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCC
Q 012257          106 LNGKPIRIMYSYRDPTI------------------RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQ  166 (467)
Q Consensus       106 ~~g~~~~v~~~~~~~~~------------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~  166 (467)
                      +.|+.|+|.++......                  .....++|||+|||..+++++|+++|+.||.|..+.+..+ .+|.
T Consensus        75 ~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~  154 (198)
T 2yh0_A           75 FQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGL  154 (198)
T ss_dssp             ETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCS
T ss_pred             EcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCC
Confidence            99999999987654211                  1245579999999999999999999999999999999998 5899


Q ss_pred             ceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEecccccc
Q 012257          167 SRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRK  206 (467)
Q Consensus       167 ~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~  206 (467)
                      ++|+|||+|.+.++|..|++.|+|..+.|+.|.|.++..+
T Consensus       155 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  194 (198)
T 2yh0_A          155 SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG  194 (198)
T ss_dssp             EEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             cceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            9999999999999999999999999999999999887554

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.96  E-value=8e-29  Score=225.98  Aligned_cols=162  Identities=24%  Similarity=0.431  Sum_probs=143.8

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHH----HHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCce
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLY----DLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKP  110 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~----~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  110 (467)
                      ..+++++|||+|||+++++++|+    ++|+.||.|.+|++.+   +++++|||||+|.+.++|.+|++.+++..+.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            34668999999999999999966    8999999999999885   6778999999999999999999999999999999


Q ss_pred             eeeeecccCcc---------------------------------------------------------------------
Q 012257          111 IRIMYSYRDPT---------------------------------------------------------------------  121 (467)
Q Consensus       111 ~~v~~~~~~~~---------------------------------------------------------------------  121 (467)
                      |+|.++.....                                                                     
T Consensus        82 l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  161 (282)
T 3pgw_A           82 MRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQP  161 (282)
T ss_pred             EEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCC
Confidence            99998755332                                                                     


Q ss_pred             ----------------------------------------cccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEee
Q 012257          122 ----------------------------------------IRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVAT  161 (467)
Q Consensus       122 ----------------------------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~  161 (467)
                                                              ......++|||+|||..+++++|+++|+.||.|.++.+..
T Consensus       162 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~  241 (282)
T 3pgw_A          162 PYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP  241 (282)
T ss_pred             CCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEec
Confidence                                                    0111346799999999999999999999999999999986


Q ss_pred             CCCCCceeEEEEEeCCHHHHHHHHHHhcCCccC-CeeeEeccc
Q 012257          162 DSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLN-DKQVFVGPF  203 (467)
Q Consensus       162 ~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~-g~~~~v~~~  203 (467)
                      +    .+|+|||+|.+.++|.+|++.|+|..+. |+.|.|.++
T Consensus       242 ~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a  280 (282)
T 3pgw_A          242 G----RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFA  280 (282)
T ss_pred             C----CCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEe
Confidence            4    2589999999999999999999999999 999999775

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.96  E-value=1.1e-29  Score=213.00  Aligned_cols=162  Identities=27%  Similarity=0.508  Sum_probs=146.1

Q ss_pred             ccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccccc
Q 012257          218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQK  296 (467)
Q Consensus       218 ~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~  296 (467)
                      .++|||+|||.++++++|+++|+.||.|.++.+..+ .++.++|||||+|.+.++|..|+..  +..+.|+.+.+.++..
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccccc
Confidence            478999999999999999999999999999999888 4688999999999999999999984  5688899998887765


Q ss_pred             chHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHH
Q 012257          297 KYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEA  375 (467)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A  375 (467)
                      .....                  ...+|||+|||..+++++|+++|++||.|.++++..+. +|.++|+|||+|.+.++|
T Consensus        81 ~~~~~------------------~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a  142 (167)
T 2cjk_A           81 RDEQD------------------KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV  142 (167)
T ss_dssp             HHHHH------------------HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHH
T ss_pred             hhhcc------------------CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHH
Confidence            43211                  24579999999999999999999999999999999986 789999999999999999


Q ss_pred             HHHHHHhCCcEecccceEEehhhhh
Q 012257          376 SKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       376 ~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      .+|++ ++|..++|+.|.|+|+.++
T Consensus       143 ~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          143 DRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             HHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             HHHHh-CCCEEeCCeEEEEeecCCC
Confidence            99998 8999999999999999764

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.96  E-value=1e-28  Score=217.42  Aligned_cols=162  Identities=23%  Similarity=0.279  Sum_probs=142.9

Q ss_pred             CCCccCeEEEcCCCC-CCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           35 RQFVSTSLYVGDLDL-SVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~-~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ...++++|||+|||+ ++++++|+++|+.||.|.+|++.+++     +|||||+|.+.++|++|++.+++..+.|+.|+|
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v  104 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345689999999999 99999999999999999999999876     479999999999999999999999999999999


Q ss_pred             eecccCcccc---------------------------------cCCCccEEEcCCCCcCCHHHHHHHHhhcC-CeEEEEE
Q 012257          114 MYSYRDPTIR---------------------------------KSGAGNIFIKNLDKSIDNKALHDTFSTFG-NILSCKV  159 (467)
Q Consensus       114 ~~~~~~~~~~---------------------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~g-~v~~~~~  159 (467)
                      .++.......                                 .....+|||+|||..+++++|+++|+.|| .|..+.+
T Consensus       105 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i  184 (229)
T 2adc_A          105 TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF  184 (229)
T ss_dssp             ECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEE
T ss_pred             EEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEE
Confidence            9876431100                                 11246799999999999999999999999 9999998


Q ss_pred             eeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccC-CeeeEeccccc
Q 012257          160 ATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLN-DKQVFVGPFLR  205 (467)
Q Consensus       160 ~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~-g~~~~v~~~~~  205 (467)
                      ..+    .+++|||+|.+.++|.+|++.|+|..+. |+.|.+.++..
T Consensus       185 ~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          185 FQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             CSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             EEC----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            653    4689999999999999999999999999 99999987643

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.96  E-value=4.4e-28  Score=217.67  Aligned_cols=161  Identities=28%  Similarity=0.512  Sum_probs=144.9

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      .....++++|||+|||+++++++|+++|+.||.|.+|++.++      +|||||+|.+.++|.+|++.+++..+.|+.|+
T Consensus        16 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~   89 (261)
T 3sde_A           16 EKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLR   89 (261)
T ss_dssp             CCSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeE
Confidence            334456899999999999999999999999999999999654      47999999999999999999999999999999


Q ss_pred             eeecccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhc-CC
Q 012257          113 IMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN-GM  191 (467)
Q Consensus       113 v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~-~~  191 (467)
                      |.++..        ..+|||+|||..+++++|+++|+.||.|..+.+..+.+|.++|+|||+|.+.++|..|+..|+ +.
T Consensus        90 v~~a~~--------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~  161 (261)
T 3sde_A           90 IRFATH--------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGA  161 (261)
T ss_dssp             EEECCC--------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSC
T ss_pred             eeeccc--------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCe
Confidence            998853        468999999999999999999999999999999999899999999999999999999999995 44


Q ss_pred             ccC---CeeeEeccccccc
Q 012257          192 LLN---DKQVFVGPFLRKQ  207 (467)
Q Consensus       192 ~~~---g~~~~v~~~~~~~  207 (467)
                      .+.   ++.+.|.++....
T Consensus       162 ~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          162 FLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             EESSSSCCBCEEEECCCEE
T ss_pred             EEecCCCceEEEeeccccC
Confidence            444   8999998776543

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

Probab=99.96  E-value=1.3e-28  Score=225.66  Aligned_cols=167  Identities=20%  Similarity=0.343  Sum_probs=145.4

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCC-CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMG-QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G-~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ..++|||+|||+++++++|+++|+.|| .|.+|.+.+++. +.++|||||+|.+.++|.+|++.|++..+.|+.|+|.++
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            479999999999999999999999999 999999998875 788999999999999999999999999999999999998


Q ss_pred             ccCccc-----ccCCCccEEEcCCCCc-CCHHHHHHHHhhcCCeEEEEEeeCCC--CCceeEEEEEeCCHHHHHHHHHHh
Q 012257          117 YRDPTI-----RKSGAGNIFIKNLDKS-IDNKALHDTFSTFGNILSCKVATDSL--GQSRGYGFVQFDNEESAKSAIDKL  188 (467)
Q Consensus       117 ~~~~~~-----~~~~~~~l~v~nlp~~-~t~~~l~~~f~~~g~v~~~~~~~~~~--g~~~~~afV~f~~~~~A~~a~~~l  188 (467)
                      ......     ......+|||+|||.. +++++|+++|+.||.|..+.+..+..  |.++|+|||+|.+.++|.+|+ .|
T Consensus       195 ~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l  273 (292)
T 2ghp_A          195 NPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QM  273 (292)
T ss_dssp             CCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GG
T ss_pred             CCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-Hh
Confidence            655432     2235678999999999 99999999999999999999998865  899999999999999999999 99


Q ss_pred             cCCccCCeeeEecccccc
Q 012257          189 NGMLLNDKQVFVGPFLRK  206 (467)
Q Consensus       189 ~~~~~~g~~~~v~~~~~~  206 (467)
                      +|..+.|+.|.|.++..+
T Consensus       274 ~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          274 NRSLLGNREISVSLADKK  291 (292)
T ss_dssp             TTEEETTEEEEEEECCCC
T ss_pred             cCCEECCcEEEEEEecCC
Confidence            999999999999887653

>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=99.96  E-value=1.1e-28  Score=211.69  Aligned_cols=175  Identities=18%  Similarity=0.226  Sum_probs=140.8

Q ss_pred             ccceeecCCC-ccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccccc
Q 012257          218 FNNVYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQK  296 (467)
Q Consensus       218 ~~~l~v~nlp-~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~  296 (467)
                      .++|||+||+ ..+++++|+++|+.||.|.++.++.+    .+|+|||+|.+.++|..|+..|+|..+.|+.|.+.++..
T Consensus         4 ~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~   79 (205)
T 3tyt_A            4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQ   79 (205)
T ss_dssp             CSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccC
Confidence            4689999999 89999999999999999999998764    368999999999999999999999999999999998864


Q ss_pred             chHHHHH---h-hhh-----hhhh----------hhccccCCCCceEEEecCCCCCCHHHHHHhhccCCce--eEEEEee
Q 012257          297 KYEREME---L-KGK-----FEQS----------LKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTI--TSCKVMR  355 (467)
Q Consensus       297 ~~~~~~~---~-~~~-----~~~~----------~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v--~~v~i~~  355 (467)
                      .......   . ...     ....          ........++.+|||+|||+.+++++|+++|++||.|  .++++..
T Consensus        80 ~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~  159 (205)
T 3tyt_A           80 PAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFS  159 (205)
T ss_dssp             SCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECS
T ss_pred             CccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEc
Confidence            3210000   0 000     0000          0000112456789999999999999999999999999  8999988


Q ss_pred             CCCCCccceEEEEcCCHHHHHHHHHHhCCcEeccc----ceEEehh
Q 012257          356 DPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSK----PLYVALA  397 (467)
Q Consensus       356 ~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~----~l~v~~~  397 (467)
                      +. +.++|+|||+|.+.++|.+|+..|||..+.|+    ++.|+|+
T Consensus       160 ~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          160 GK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            76 55579999999999999999999999999876    5666654

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.96  E-value=2.3e-28  Score=205.93  Aligned_cols=156  Identities=23%  Similarity=0.464  Sum_probs=140.9

Q ss_pred             ccceeecCCCccCCHHHHHHhhccc----C-------CeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCC
Q 012257          218 FNNVYVKNLSETTTEDDLKKIFGEF----G-------IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDD  286 (467)
Q Consensus       218 ~~~l~v~nlp~~~~~~~l~~~f~~~----g-------~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~  286 (467)
                      .++|||+|||..+++++|+++|++|    |       .|.++.+..     ++|+|||+|.+.++|..|+ .+++..+.|
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~-----~~g~afV~f~~~~~A~~A~-~~~~~~~~g   77 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ-----DKNFAFLEFRSVDETTQAM-AFDGIIFQG   77 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET-----TTTEEEEEESSHHHHHHHG-GGTTCEETT
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC-----CCCEEEEEeCCHHHHHHHH-HhCCcEecC
Confidence            4789999999999999999999999    6       677766653     4789999999999999999 899999999


Q ss_pred             ceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceE
Q 012257          287 KEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSG  365 (467)
Q Consensus       287 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~a  365 (467)
                      +.+.+.++....                  ......+|||+|||..+++++|+++|++||.|.++++..+. +|.++|+|
T Consensus        78 ~~i~v~~~~~~~------------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~a  139 (172)
T 2g4b_A           78 QSLKIRRPHDYQ------------------PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA  139 (172)
T ss_dssp             EECEEECCSSCC------------------CCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEE
T ss_pred             ceeeecCCcccC------------------CCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEE
Confidence            999998865431                  11235689999999999999999999999999999999996 89999999


Q ss_pred             EEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          366 FVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       366 fV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ||+|.+.++|.+|++.|||..++|+.|.|+||
T Consensus       140 fV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          140 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             EEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             EEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            99999999999999999999999999999987

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

Probab=99.96  E-value=2.4e-28  Score=210.62  Aligned_cols=159  Identities=24%  Similarity=0.292  Sum_probs=140.9

Q ss_pred             ccCeEEEcCCCC-CCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           38 VSTSLYVGDLDL-SVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        38 ~~~~l~v~nLp~-~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .+++|||+|||+ ++++++|+++|+.||.|.+|++.+++     +|||||+|.+.++|++|++.|++..+.|+.|+|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            368999999999 99999999999999999999998875     479999999999999999999999999999999987


Q ss_pred             ccCcccc---------------------------------cCCCccEEEcCCCCcCCHHHHHHHHhhcC-CeEEEEEeeC
Q 012257          117 YRDPTIR---------------------------------KSGAGNIFIKNLDKSIDNKALHDTFSTFG-NILSCKVATD  162 (467)
Q Consensus       117 ~~~~~~~---------------------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~g-~v~~~~~~~~  162 (467)
                      .......                                 .....+|+|+|||..+++++|+++|+.|| .|.++.+..+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~  156 (198)
T 1qm9_A           77 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK  156 (198)
T ss_dssp             CCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST
T ss_pred             cCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC
Confidence            6431100                                 11256799999999999999999999999 9999998764


Q ss_pred             CCCCceeEEEEEeCCHHHHHHHHHHhcCCccC-CeeeEeccccc
Q 012257          163 SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLN-DKQVFVGPFLR  205 (467)
Q Consensus       163 ~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~-g~~~~v~~~~~  205 (467)
                          .+|+|||+|.+.++|..|+..|+|..+. |+.|.+.++..
T Consensus       157 ----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          157 ----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             ----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             ----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence                4789999999999999999999999999 99999877643

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.96  E-value=8.8e-28  Score=219.06  Aligned_cols=177  Identities=23%  Similarity=0.395  Sum_probs=146.9

Q ss_pred             ccccceeecCCCccCCHHHHH----HhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEE
Q 012257          216 TRFNNVYVKNLSETTTEDDLK----KIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYV  291 (467)
Q Consensus       216 ~~~~~l~v~nlp~~~~~~~l~----~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~  291 (467)
                      ...++|||+|||..+++++|+    ++|+.||.|.++.+..  +++++|||||+|.+.++|..|+..+++..+.|+.+.+
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            345789999999999999976    8999999999998875  6778999999999999999999999999999999999


Q ss_pred             cccccchHHHHHhhhhhhhh------------------------------------------------------------
Q 012257          292 GKAQKKYEREMELKGKFEQS------------------------------------------------------------  311 (467)
Q Consensus       292 ~~~~~~~~~~~~~~~~~~~~------------------------------------------------------------  311 (467)
                      .++.................                                                            
T Consensus        85 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  164 (282)
T 3pgw_A           85 QYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYM  164 (282)
T ss_pred             EEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCC
Confidence            99865442111100000000                                                            


Q ss_pred             ---------------------------------hhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCC
Q 012257          312 ---------------------------------LKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN  358 (467)
Q Consensus       312 ---------------------------------~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~  358 (467)
                                                       ..........++|||+|||..+++++|+++|++||.|.+|++..+. 
T Consensus       165 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-  243 (282)
T 3pgw_A          165 PPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-  243 (282)
T ss_pred             CCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-
Confidence                                             0000223356789999999999999999999999999999999763 


Q ss_pred             CCccceEEEEcCCHHHHHHHHHHhCCcEec-ccceEEehhh
Q 012257          359 GISRGSGFVAFSTAEEASKALTEMNGKMVV-SKPLYVALAQ  398 (467)
Q Consensus       359 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~v~~~~  398 (467)
                         +|+|||+|.+.++|.+|++.|||..++ |+.|+|+|++
T Consensus       244 ---~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          244 ---HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             ---CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence               579999999999999999999999999 9999999986

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.96  E-value=5e-29  Score=210.48  Aligned_cols=165  Identities=25%  Similarity=0.393  Sum_probs=142.8

Q ss_pred             cccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccc
Q 012257          215 KTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA  294 (467)
Q Consensus       215 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~  294 (467)
                      ....++|||+|||..+++++|+++|..||.+..+.+....++.++|||||+|.+.++|..|++ +++..+.|+.+.+.++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecC
Confidence            345588999999999999999999999987666333333556789999999999999999995 9999999999999998


Q ss_pred             ccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHH
Q 012257          295 QKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEE  374 (467)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~  374 (467)
                      .....                ......++|||+|||..+++++|+++|++||.|..+    ..++.++|+|||+|.+.++
T Consensus        89 ~~~~~----------------~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~  148 (175)
T 1fje_B           89 KGRDS----------------KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEAD  148 (175)
T ss_dssp             CCSSC----------------STTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHH
T ss_pred             CCccc----------------cccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHH
Confidence            76421                112245689999999999999999999999998766    5678899999999999999


Q ss_pred             HHHHHHHhCCcEecccceEEehhhhh
Q 012257          375 ASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       375 A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      |.+|++.|||..++|+.|+|+|++++
T Consensus       149 A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          149 AEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHHHHHHhCCCEECCeEEEEEecCCC
Confidence            99999999999999999999999764

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.95  E-value=6.1e-28  Score=208.30  Aligned_cols=177  Identities=21%  Similarity=0.394  Sum_probs=145.9

Q ss_pred             ccceeecCCCccCCHHHHHHhhccc----C-------CeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCC
Q 012257          218 FNNVYVKNLSETTTEDDLKKIFGEF----G-------IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDD  286 (467)
Q Consensus       218 ~~~l~v~nlp~~~~~~~l~~~f~~~----g-------~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~  286 (467)
                      .++|||+|||..+++++|+++|+.|    |       .|.++.+.     .++|||||+|.+.++|..|+ .+++..+.|
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~-----~~~g~afV~F~~~~~A~~Al-~l~g~~~~g   77 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-----QDKNFAFLEFRSVDETTQAM-AFDGIIFQG   77 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE-----TTTTEEEEEESCSHHHHHHG-GGTTEEETT
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec-----CCCCEEEEEeCCHHHHHHHH-HhcCCEEcC
Confidence            4789999999999999999999999    5       56665553     45889999999999999999 899999999


Q ss_pred             ceEEEcccccchHHHHHhhh--hhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccc
Q 012257          287 KEWYVGKAQKKYEREMELKG--KFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRG  363 (467)
Q Consensus       287 ~~l~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g  363 (467)
                      +.+.+.++............  ...............++|||+|||..+++++|+++|++||.|.++++..+. +|.++|
T Consensus        78 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g  157 (198)
T 2yh0_A           78 QSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG  157 (198)
T ss_dssp             EEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEE
T ss_pred             ceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcce
Confidence            99999988654211000000  000000111223567899999999999999999999999999999999996 889999


Q ss_pred             eEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          364 SGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       364 ~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      ||||+|.+.++|.+|++.|||..++|+.|+|+|+++.
T Consensus       158 ~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  194 (198)
T 2yh0_A          158 YAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG  194 (198)
T ss_dssp             EEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             EEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            9999999999999999999999999999999999764

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.95  E-value=2e-27  Score=209.03  Aligned_cols=177  Identities=21%  Similarity=0.302  Sum_probs=145.4

Q ss_pred             ccccceeecCCCc-cCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccc
Q 012257          216 TRFNNVYVKNLSE-TTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA  294 (467)
Q Consensus       216 ~~~~~l~v~nlp~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~  294 (467)
                      ...++|||+|||. .+++++|+++|+.||.|.++.+..+.    +|||||+|.+.++|..|+..+++..+.|+.+.+.++
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  107 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS  107 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            4457899999999 99999999999999999999998764    679999999999999999999999999999999988


Q ss_pred             ccchHHH-------HHhhhhhh----------hhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCC-ceeEEEEeeC
Q 012257          295 QKKYERE-------MELKGKFE----------QSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFG-TITSCKVMRD  356 (467)
Q Consensus       295 ~~~~~~~-------~~~~~~~~----------~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G-~v~~v~i~~~  356 (467)
                      .......       ........          ..........+.++|||+|||..+++++|+++|++|| .|.++++..+
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~  187 (229)
T 2adc_A          108 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK  187 (229)
T ss_dssp             SCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS
T ss_pred             cCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC
Confidence            6431100       00000000          0000011124568999999999999999999999999 9999999764


Q ss_pred             CCCCccceEEEEcCCHHHHHHHHHHhCCcEec-ccceEEehhhhh
Q 012257          357 PNGISRGSGFVAFSTAEEASKALTEMNGKMVV-SKPLYVALAQRK  400 (467)
Q Consensus       357 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~v~~~~~~  400 (467)
                          .+|+|||+|.+.++|.+|++.|||..++ |+.|+|+|+++.
T Consensus       188 ----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          188 ----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             ----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             ----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence                3679999999999999999999999999 999999998753

>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=99.95  E-value=8.5e-27  Score=209.25  Aligned_cols=157  Identities=29%  Similarity=0.501  Sum_probs=143.5

Q ss_pred             cccccceeecCCCccCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccc
Q 012257          215 KTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKA  294 (467)
Q Consensus       215 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~  294 (467)
                      ....++|||+|||.++++++|+++|+.||.|..+.+..     ++|||||+|.+.++|..|+..+++..+.|+.+.+.++
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~-----~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-----DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            34557899999999999999999999999999999864     3789999999999999999999999999999999887


Q ss_pred             ccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHH
Q 012257          295 QKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEE  374 (467)
Q Consensus       295 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~  374 (467)
                      ..                        ..+|||+|||..+++++|+++|+.||.|.+|+++.+.+|.++|||||+|.+.++
T Consensus        94 ~~------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~  149 (261)
T 3sde_A           94 TH------------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPP  149 (261)
T ss_dssp             CC------------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHH
T ss_pred             cc------------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHH
Confidence            53                        347999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhC-CcEec---ccceEEehhhhh
Q 012257          375 ASKALTEMN-GKMVV---SKPLYVALAQRK  400 (467)
Q Consensus       375 A~~A~~~l~-g~~~~---g~~l~v~~~~~~  400 (467)
                      |.+|+..|| +..+.   +++|.|.++...
T Consensus       150 A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          150 ARKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             HHHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             HHHHHHHhcCCeEEecCCCceEEEeecccc
Confidence            999999995 55554   999999998754

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

Probab=99.94  E-value=2.1e-27  Score=204.62  Aligned_cols=174  Identities=22%  Similarity=0.307  Sum_probs=143.3

Q ss_pred             ccceeecCCCc-cCCHHHHHHhhcccCCeeEEEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccccc
Q 012257          218 FNNVYVKNLSE-TTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQK  296 (467)
Q Consensus       218 ~~~l~v~nlp~-~~~~~~l~~~f~~~g~v~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~  296 (467)
                      .++|||+|||. .+++++|+++|+.||.|.++.+..+.    +|+|||+|.+.++|..|+..+++..+.|+.+.+.++..
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~   78 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   78 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecC
Confidence            36899999999 99999999999999999999988753    67999999999999999999999999999999998865


Q ss_pred             chHHHHHhh----h---hhh----------hhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCC-ceeEEEEeeCCC
Q 012257          297 KYEREMELK----G---KFE----------QSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFG-TITSCKVMRDPN  358 (467)
Q Consensus       297 ~~~~~~~~~----~---~~~----------~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G-~v~~v~i~~~~~  358 (467)
                      .........    .   ...          ..........+.++|||+|||..+++++|+++|++|| .|.++++..+  
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~--  156 (198)
T 1qm9_A           79 QNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK--  156 (198)
T ss_dssp             CSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST--
T ss_pred             CCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC--
Confidence            321100000    0   000          0000001123578999999999999999999999999 9999999775  


Q ss_pred             CCccceEEEEcCCHHHHHHHHHHhCCcEec-ccceEEehhhh
Q 012257          359 GISRGSGFVAFSTAEEASKALTEMNGKMVV-SKPLYVALAQR  399 (467)
Q Consensus       359 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~v~~~~~  399 (467)
                        .+|+|||+|.+.++|.+|+..|||..++ |+.|+|+|+++
T Consensus       157 --~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          157 --DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             --TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             --CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence              2689999999999999999999999999 99999999875

>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=99.87  E-value=4.1e-22  Score=154.35  Aligned_cols=104  Identities=28%  Similarity=0.475  Sum_probs=74.9

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      .+++|||+|||++++|++|+++|+.||.|.+|+|.+++  +.++|||||+|.+.++|++|++.|++..+.|+.|+|.++.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            36789999999999999999999999999999999986  4588999999999999999999999999999999999876


Q ss_pred             cCccc------ccCCCccEEEcCCCCcCCHHH
Q 012257          118 RDPTI------RKSGAGNIFIKNLDKSIDNKA  143 (467)
Q Consensus       118 ~~~~~------~~~~~~~l~v~nlp~~~t~~~  143 (467)
                      .....      .....++|||+|||+++|++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           82 SRKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CCCC----------------------------
T ss_pred             CccccccccccccCCCCceEeCCCCCCccccc
Confidence            54332      122345799999999998764

>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=99.86  E-value=1e-21  Score=162.09  Aligned_cols=147  Identities=22%  Similarity=0.286  Sum_probs=110.0

Q ss_pred             EEEEECCCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEe
Q 012257          248 TAVMRDADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVK  327 (467)
Q Consensus       248 ~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~  327 (467)
                      +.++.+.. +++|||||+|.+.++|.+|+..+++....+..+...........     .................+|||+
T Consensus         3 ~kl~ln~~-~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~l~v~   76 (158)
T 2kn4_A            3 YKLILNGK-TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTV-----TEGSHHHHHHMDVEGMTSLKVD   76 (158)
T ss_dssp             EEEEEECS-SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEE-----ECCCCCSSCCCCCCBCCEEEEE
T ss_pred             EEEEecCc-cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccc-----cccccccccccCCCCCCEEEEe
Confidence            34444433 57999999999999999999887754333333322211110000     0000011112223456799999


Q ss_pred             cCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          328 NLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       328 nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      |||..+++++|+++|++||.|.+|++..+. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+|+++.
T Consensus        77 nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  150 (158)
T 2kn4_A           77 NLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG  150 (158)
T ss_dssp             SCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCS
T ss_pred             CCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            999999999999999999999999999986 7899999999999999999999999999999999999999754

>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=99.85  E-value=2.5e-21  Score=145.01  Aligned_cols=81  Identities=40%  Similarity=0.668  Sum_probs=77.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ..+++|||+|||..+|+++|+++|++||.|.+|+++++. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+||
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            456789999999999999999999999999999999986 6899999999999999999999999999999999999999


Q ss_pred             hh
Q 012257          398 QR  399 (467)
Q Consensus       398 ~~  399 (467)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            76

>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=99.85  E-value=3.4e-21  Score=144.29  Aligned_cols=82  Identities=38%  Similarity=0.609  Sum_probs=78.3

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ...++|||+|||++++|++|+++|++||.|.+|++.+|+.+|+++|||||+|.+.++|++|++.|++..+.|+.|+|.++
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            45689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cc
Q 012257          117 YR  118 (467)
Q Consensus       117 ~~  118 (467)
                      .+
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            53

>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=99.84  E-value=1.7e-20  Score=154.83  Aligned_cols=138  Identities=17%  Similarity=0.270  Sum_probs=109.7

Q ss_pred             EEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcc-cCCce------eeeeeccc----CcccccCCCccEEEcCCC
Q 012257           68 SVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTP-LNGKP------IRIMYSYR----DPTIRKSGAGNIFIKNLD  136 (467)
Q Consensus        68 ~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~-~~g~~------~~v~~~~~----~~~~~~~~~~~l~v~nlp  136 (467)
                      ++++..+..  +++|||||+|.+.++|++|++.+++.. +.|..      ........    ..........+|||+|||
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~   79 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT   79 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCC
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCC
Confidence            466777654  588999999999999999998876432 22211      11111111    111122346799999999


Q ss_pred             CcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEeccccccc
Q 012257          137 KSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQ  207 (467)
Q Consensus       137 ~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~~  207 (467)
                      .++++++|+++|+.||.|.++.+..+ .+|.++|||||+|.+.++|..|++.|+|..+.|+.|.|.++....
T Consensus        80 ~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           80 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             TTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             CCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            99999999999999999999999998 689999999999999999999999999999999999998876543

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

Probab=99.84  E-value=3.9e-20  Score=141.25  Aligned_cols=92  Identities=14%  Similarity=0.271  Sum_probs=83.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      .+.++|||+|||+.+++++|+++|++||.|.+|+|+.+. +|+++|||||+|.+.++|.+|++.|||..++|+.|+|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            456789999999999999999999999999999999987 5899999999999999999999999999999999999999


Q ss_pred             hhhHHHHHHHHhh
Q 012257          398 QRKEERRARLQAQ  410 (467)
Q Consensus       398 ~~~~~~~~~~~~~  410 (467)
                      .....+.......
T Consensus        84 ~~~~~~~~~~~~~   96 (110)
T 3s8s_A           84 IKGQQRMKYYELI   96 (110)
T ss_dssp             STTHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHh
Confidence            8777665544443

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.84  E-value=3e-21  Score=157.59  Aligned_cols=138  Identities=21%  Similarity=0.307  Sum_probs=112.8

Q ss_pred             CCceeEEEEEeCCHHHHHHHHHHh-CCCccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCC
Q 012257          256 GKSKCFGFVNFDDPDDAARSVEAL-NGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSIS  334 (467)
Q Consensus       256 ~~~~g~afv~f~~~~~a~~a~~~l-~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~  334 (467)
                      ...+|+++++|.+.++|.+|+..+ ++..++| .+.+.++.........  ................++|||+|||..++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~--~~~~~~~~~~~~~~~~~~l~V~nl~~~~t   86 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEG--SHHHHHHMHRDSCPLDCKVYVGNLGNNGN   86 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECS--SSSCCCCSCSSSSTTSCEEEEESCCSCCS
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccc--cccccccccccCCCCCCEEEEeCCCCCCC
Confidence            356889999999999999999999 9999999 9999887653211000  00000111223345678999999999999


Q ss_pred             HHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          335 DDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       335 ~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      +++|+++|++||.|.+|+++.+    ++|||||+|.+.++|.+|+..|||..++|+.|+|+|++++
T Consensus        87 ~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           87 KTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             CHHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            9999999999999999999887    5789999999999999999999999999999999998764

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

Probab=99.82  E-value=6.8e-20  Score=139.89  Aligned_cols=83  Identities=20%  Similarity=0.324  Sum_probs=79.0

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .+.++|||+|||++++|++|+++|++||.|.+|+|++|+.+++++|||||+|.+.++|++|++.||+..+.|+.|+|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ccC
Q 012257          117 YRD  119 (467)
Q Consensus       117 ~~~  119 (467)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.82  E-value=8.3e-21  Score=139.99  Aligned_cols=83  Identities=22%  Similarity=0.379  Sum_probs=76.8

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCC-CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhC-CcccCCceeeeeec
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMG-QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN-FTPLNGKPIRIMYS  116 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G-~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~-~~~~~g~~~~v~~~  116 (467)
                      |++|||+|||++++|++|+++|+.|| .|.+|++++|+.+|+++|||||+|.+.++|++|++.++ +..+.|+.|+|.++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            57999999999999999999999999 89999999999999999999999999999999998774 56799999999998


Q ss_pred             ccCcc
Q 012257          117 YRDPT  121 (467)
Q Consensus       117 ~~~~~  121 (467)
                      .+.+.
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            76544

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.81  E-value=4.3e-19  Score=142.82  Aligned_cols=88  Identities=27%  Similarity=0.429  Sum_probs=82.0

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....+.++|||+|||.++++++|+++|+.||.|.+|++.+++.+++++|||||+|.+.++|.+|++.|++..+.|+.|+|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34456899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccCcc
Q 012257          114 MYSYRDPT  121 (467)
Q Consensus       114 ~~~~~~~~  121 (467)
                      .++.....
T Consensus       117 ~~a~~~~~  124 (139)
T 1u6f_A          117 ALAASGHQ  124 (139)
T ss_dssp             EESSCCCC
T ss_pred             EECCCCCC
Confidence            99876544

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.81  E-value=3.2e-20  Score=137.10  Aligned_cols=84  Identities=15%  Similarity=0.321  Sum_probs=77.2

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCC--CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCc----ccCC
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMG--QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFT----PLNG  108 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G--~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~----~~~g  108 (467)
                      ......+|||+|||+++++++|+++|++||  .|.+|++.+|+.+|+++|||||+|.+.++|++|++.|++.    .++|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            445678999999999999999999999999  4779999999999999999999999999999999999886    4899


Q ss_pred             ceeeeeeccc
Q 012257          109 KPIRIMYSYR  118 (467)
Q Consensus       109 ~~~~v~~~~~  118 (467)
                      +.|+|.++..
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999998863

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.81  E-value=8.1e-20  Score=148.73  Aligned_cols=82  Identities=23%  Similarity=0.372  Sum_probs=76.6

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCC--CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMG--QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G--~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ...++|||+|||+++++++|+++|+.||  .|.+|+++.|+.+|+++|||||+|.+.++|++|++.|++..|.|+.|+|.
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            3568999999999999999999999999  99999999999999999999999999999999999999999999999999


Q ss_pred             eccc
Q 012257          115 YSYR  118 (467)
Q Consensus       115 ~~~~  118 (467)
                      ++..
T Consensus       133 ~a~~  136 (156)
T 3n9u_C          133 PATR  136 (156)
T ss_dssp             ECCH
T ss_pred             EcCC
Confidence            8753

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.81  E-value=2.6e-19  Score=139.66  Aligned_cols=85  Identities=21%  Similarity=0.328  Sum_probs=79.5

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      ......+.++|||+|||+++++++|+++|++||.|.+|++.+++.+++++|||||+|.+.++|++|++.|++..+.|+.|
T Consensus        33 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l  112 (118)
T 2khc_A           33 KQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRL  112 (118)
T ss_dssp             SSCCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34445668999999999999999999999999999999999999899999999999999999999999999999999999


Q ss_pred             eeeec
Q 012257          112 RIMYS  116 (467)
Q Consensus       112 ~v~~~  116 (467)
                      +|.++
T Consensus       113 ~V~~a  117 (118)
T 2khc_A          113 KVQLK  117 (118)
T ss_dssp             CEEEC
T ss_pred             EEEec
Confidence            99876

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.81  E-value=1.6e-19  Score=147.31  Aligned_cols=124  Identities=19%  Similarity=0.248  Sum_probs=108.9

Q ss_pred             CccccEEEEEecChHHHHHHHHHh-CCcccCCceeeeeecccC--------------cccccCCCccEEEcCCCCcCCHH
Q 012257           78 RRSLGYGYVNYNAAHEATRALDEL-NFTPLNGKPIRIMYSYRD--------------PTIRKSGAGNIFIKNLDKSIDNK  142 (467)
Q Consensus        78 ~~~~g~afV~f~~~~~A~~A~~~l-~~~~~~g~~~~v~~~~~~--------------~~~~~~~~~~l~v~nlp~~~t~~  142 (467)
                      ..-+|+++|+|.+.++|++|++.+ ++..+.| .+++.++...              ........++|||+|||.+++++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~   88 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKT   88 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCH
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHH
Confidence            356799999999999999999999 9999999 9999876542              12233456799999999999999


Q ss_pred             HHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEecccccc
Q 012257          143 ALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRK  206 (467)
Q Consensus       143 ~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~~  206 (467)
                      +|+++|+.||.|.++.+..+    ++|||||+|.+.++|..|+..|+|..+.|+.|.|.++..+
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            99999999999999999875    6899999999999999999999999999999999876543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=2.3e-19  Score=133.85  Aligned_cols=85  Identities=25%  Similarity=0.462  Sum_probs=79.3

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      ......+.++|||+|||+++++++|+++|++||.|.+|.+.+++.+++++|||||+|.+.++|++|++.|++..+.|+.|
T Consensus         9 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   88 (94)
T 2e5h_A            9 SGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVI   88 (94)
T ss_dssp             CCSCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEE
Confidence            33444568999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeec
Q 012257          112 RIMYS  116 (467)
Q Consensus       112 ~v~~~  116 (467)
                      +|.++
T Consensus        89 ~v~~a   93 (94)
T 2e5h_A           89 KASIA   93 (94)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            99886

>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=3.5e-19  Score=133.23  Aligned_cols=87  Identities=25%  Similarity=0.386  Sum_probs=80.9

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      ......++++|||+|||+++++++|+++|++||.|.+|.+.+++.+++++|||||+|.+.++|++|++.|++..+.|+.|
T Consensus         8 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (95)
T 2cqc_A            8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI   87 (95)
T ss_dssp             CCCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34445668999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeeccc
Q 012257          112 RIMYSYR  118 (467)
Q Consensus       112 ~v~~~~~  118 (467)
                      +|.++..
T Consensus        88 ~v~~a~~   94 (95)
T 2cqc_A           88 RVSGPSS   94 (95)
T ss_dssp             EEECCSC
T ss_pred             EEEecCC
Confidence            9998753

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=4.5e-19  Score=133.56  Aligned_cols=88  Identities=18%  Similarity=0.446  Sum_probs=81.3

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....++++|||+|||.++++++|+++|+.||.|.+|.+.+++.+++++|||||+|.+.++|++|++ +++..+.|+.|+|
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V   83 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEV   83 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEE
Confidence            344568999999999999999999999999999999999999999999999999999999999998 9999999999999


Q ss_pred             eecccCccc
Q 012257          114 MYSYRDPTI  122 (467)
Q Consensus       114 ~~~~~~~~~  122 (467)
                      .++......
T Consensus        84 ~~a~~~~~~   92 (99)
T 2dgs_A           84 KRAEPRDSK   92 (99)
T ss_dssp             EECCCCCCC
T ss_pred             EECCCCccc
Confidence            998765443

>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=99.80  E-value=3.8e-19  Score=135.67  Aligned_cols=89  Identities=30%  Similarity=0.527  Sum_probs=82.3

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....+.++|||+|||+++++++|+++|++||.|.+|.+.+++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34456899999999999999999999999999999999999989999999999999999999999999999999999999


Q ss_pred             eecccCccc
Q 012257          114 MYSYRDPTI  122 (467)
Q Consensus       114 ~~~~~~~~~  122 (467)
                      .++......
T Consensus        90 ~~a~~~~~~   98 (105)
T 1x5u_A           90 NKASAHNKN   98 (105)
T ss_dssp             EETTTTSCC
T ss_pred             EECCCCCcC
Confidence            998766443

>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=4.3e-19  Score=133.74  Aligned_cols=87  Identities=20%  Similarity=0.327  Sum_probs=81.8

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..++++|||+|||+++++++|+++|+.||.|.+|.+.+++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|.+
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            45689999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cccCccc
Q 012257          116 SYRDPTI  122 (467)
Q Consensus       116 ~~~~~~~  122 (467)
                      +......
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            8776543

>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=7e-19  Score=132.80  Aligned_cols=89  Identities=18%  Similarity=0.365  Sum_probs=81.8

Q ss_pred             CCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCce
Q 012257           31 VGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKP  110 (467)
Q Consensus        31 ~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  110 (467)
                      .......+.++|||+|||+++++++|+++|+.||.|.+|++..++ +++++|||||+|.+.++|++|++.|++..+.|+.
T Consensus         9 ~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   87 (100)
T 2do4_A            9 FRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENI   87 (100)
T ss_dssp             CCCSSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCE
T ss_pred             cCcccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            344555678999999999999999999999999999999999998 8999999999999999999999999999999999


Q ss_pred             eeeeecccCc
Q 012257          111 IRIMYSYRDP  120 (467)
Q Consensus       111 ~~v~~~~~~~  120 (467)
                      |+|.++...+
T Consensus        88 l~v~~a~~~~   97 (100)
T 2do4_A           88 IKVAISNSGP   97 (100)
T ss_dssp             EEEEECCCCS
T ss_pred             EEEEECCCCC
Confidence            9999987553

>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=99.80  E-value=2.8e-19  Score=131.33  Aligned_cols=83  Identities=27%  Similarity=0.508  Sum_probs=77.0

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .+.++|||+|||.++++++|+++|+.||.|.+|.+.+++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|.++
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            35789999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             ccC
Q 012257          117 YRD  119 (467)
Q Consensus       117 ~~~  119 (467)
                      ..+
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=5e-19  Score=134.37  Aligned_cols=88  Identities=16%  Similarity=0.346  Sum_probs=82.0

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....++++|||+|||+++++++|+++|++||.|.+|.+.+++.+++++|||||+|.+.++|++|++.|++..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (103)
T 2cq0_A           10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNV   89 (103)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            34556899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccCcc
Q 012257          114 MYSYRDPT  121 (467)
Q Consensus       114 ~~~~~~~~  121 (467)
                      .++.....
T Consensus        90 ~~a~~~~~   97 (103)
T 2cq0_A           90 EWAKPSTN   97 (103)
T ss_dssp             EESSCCCC
T ss_pred             EECCCCCC
Confidence            99876543

>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=6.8e-19  Score=131.59  Aligned_cols=85  Identities=31%  Similarity=0.560  Sum_probs=80.4

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .++++|||+|||.++++++|+++|++||.|.+|++.+++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|.++
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            45899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccCcc
Q 012257          117 YRDPT  121 (467)
Q Consensus       117 ~~~~~  121 (467)
                      .....
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            76544

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.80  E-value=8.9e-20  Score=134.68  Aligned_cols=80  Identities=20%  Similarity=0.328  Sum_probs=73.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCc--eeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCc----Eecccce
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGT--ITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGK----MVVSKPL  392 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~--v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~----~~~g~~l  392 (467)
                      ...+|||+|||+.+|+++|+++|++||.  |.+|++++++ +|+++|||||+|.+.++|.+|++.|||.    .++|++|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            4558999999999999999999999995  6789999987 6899999999999999999999999997    5899999


Q ss_pred             EEehhhh
Q 012257          393 YVALAQR  399 (467)
Q Consensus       393 ~v~~~~~  399 (467)
                      .|+||+.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999974

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=4.1e-19  Score=135.72  Aligned_cols=89  Identities=25%  Similarity=0.402  Sum_probs=82.6

Q ss_pred             CCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCce
Q 012257           31 VGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKP  110 (467)
Q Consensus        31 ~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  110 (467)
                      +.+....++++|||+|||+++++++|+++|+.||.|.+|.+.+++.+++++|||||+|.+.++|++|++.|++..+.|+.
T Consensus        15 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   94 (106)
T 1p27_B           15 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP   94 (106)
T ss_dssp             CCBCCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSB
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcE
Confidence            34455567899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeeecccC
Q 012257          111 IRIMYSYRD  119 (467)
Q Consensus       111 ~~v~~~~~~  119 (467)
                      |+|.++...
T Consensus        95 l~V~~a~~~  103 (106)
T 1p27_B           95 ISVDWCFVR  103 (106)
T ss_dssp             CEEEESEES
T ss_pred             EEEEeecCC
Confidence            999998654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=4e-19  Score=134.72  Aligned_cols=89  Identities=27%  Similarity=0.483  Sum_probs=82.3

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....+.++|||+|||+++++++|+++|+.||.|.+|++.+++.+++++|||||+|.+.++|.+|++.|++..+.|+.|+|
T Consensus         7 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   86 (102)
T 1x5s_A            7 GMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   86 (102)
T ss_dssp             CCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            34456899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccCccc
Q 012257          114 MYSYRDPTI  122 (467)
Q Consensus       114 ~~~~~~~~~  122 (467)
                      .++......
T Consensus        87 ~~a~~~~~~   95 (102)
T 1x5s_A           87 DQAGKSSDN   95 (102)
T ss_dssp             EEEECCCCC
T ss_pred             EECCCCCCC
Confidence            998765443

>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=3.3e-19  Score=130.32  Aligned_cols=81  Identities=28%  Similarity=0.518  Sum_probs=77.6

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.+.+++.+++++|||||+|.+.++|.+|++.|++..+.|+.|+|.+
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             c
Q 012257          116 S  116 (467)
Q Consensus       116 ~  116 (467)
                      +
T Consensus        84 a   84 (85)
T 3mdf_A           84 A   84 (85)
T ss_dssp             C
T ss_pred             c
Confidence            6

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.79  E-value=8.6e-19  Score=136.02  Aligned_cols=91  Identities=25%  Similarity=0.490  Sum_probs=83.4

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      ......+.++|||+|||+++++++|+++|+.||.|.+|++.+++.+++++|||||+|.+.++|++|++.|++..|.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (115)
T 2dgo_A            8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI   87 (115)
T ss_dssp             SCCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            33444568999999999999999999999999999999999999899999999999999999999999999999999999


Q ss_pred             eeeecccCccc
Q 012257          112 RIMYSYRDPTI  122 (467)
Q Consensus       112 ~v~~~~~~~~~  122 (467)
                      +|.++......
T Consensus        88 ~V~~a~~~~~~   98 (115)
T 2dgo_A           88 RTNWATRKPPA   98 (115)
T ss_dssp             EEEESSCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99998766543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=5.7e-19  Score=134.09  Aligned_cols=88  Identities=19%  Similarity=0.322  Sum_probs=81.8

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      +....++++|||+|||+++++++|+++|+.||.|.+|.+..++.+++++|||||+|.+.++|++|++.|++..+.|+.|+
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            33445689999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecccCc
Q 012257          113 IMYSYRDP  120 (467)
Q Consensus       113 v~~~~~~~  120 (467)
                      |.++....
T Consensus        87 V~~a~~~~   94 (103)
T 2dnm_A           87 VQVARYGR   94 (103)
T ss_dssp             EEECSSCC
T ss_pred             EEECCcCC
Confidence            99987554

>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=99.79  E-value=3.1e-19  Score=138.06  Aligned_cols=108  Identities=62%  Similarity=1.005  Sum_probs=74.2

Q ss_pred             CCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeCCCCCceeEEEEEeCCHHHHHHHHHHhcCCccCCeeeEeccccc
Q 012257          126 GAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLR  205 (467)
Q Consensus       126 ~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~~~g~~~~~afV~f~~~~~A~~a~~~l~~~~~~g~~~~v~~~~~  205 (467)
                      +.++|||+|||.++++++|+++|+.||.|.+|++..+.. .++|||||+|.+.++|.+|++.|++..+.|+.|.|.++..
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 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC-CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            356899999999999999999999999999999998853 4799999999999999999999999999999999988766


Q ss_pred             ccccccc--cccccccceeecCCCccCCHHH
Q 012257          206 KQEREST--ADKTRFNNVYVKNLSETTTEDD  234 (467)
Q Consensus       206 ~~~~~~~--~~~~~~~~l~v~nlp~~~~~~~  234 (467)
                      +......  ......+++||+|||+.+|++.
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            5443322  2233456899999999988753

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.79  E-value=4e-20  Score=136.34  Aligned_cols=79  Identities=19%  Similarity=0.377  Sum_probs=73.1

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCC-ceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhC-CcEecccceEEehhh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFG-TITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMN-GKMVVSKPLYVALAQ  398 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G-~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~-g~~~~g~~l~v~~~~  398 (467)
                      .+|||+|||..+|+++|+++|++|| .|.+|+++++. +|.++|||||+|.+.++|.+|++.++ +..++|++|+|+|+.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            4799999999999999999999999 89999999886 68999999999999999999999875 567999999999997


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ++
T Consensus        82 ~~   83 (91)
T 2lxi_A           82 PK   83 (91)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.79  E-value=5.7e-19  Score=128.41  Aligned_cols=81  Identities=33%  Similarity=0.625  Sum_probs=77.5

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      +.+|||+|||.++++++|+++|+.||.|.++.+.+++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|.++..
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            46899999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             C
Q 012257          119 D  119 (467)
Q Consensus       119 ~  119 (467)
                      .
T Consensus        81 ~   81 (83)
T 3md1_A           81 L   81 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.79  E-value=1.1e-18  Score=133.13  Aligned_cols=84  Identities=29%  Similarity=0.551  Sum_probs=79.5

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..++++|||+|||.++++++|+++|++||.|.+|.+.+++.+++++|||||+|.+.++|++|++.+++..+.|+.|+|.+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            44579999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccC
Q 012257          116 SYRD  119 (467)
Q Consensus       116 ~~~~  119 (467)
                      +...
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            8654

>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=4.7e-19  Score=132.57  Aligned_cols=84  Identities=24%  Similarity=0.441  Sum_probs=79.6

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ++++|||+|||.++++++|+++|++||.|.+|++.+++.+|+++|||||+|.+.++|++|++.+++..+.|+.|+|.++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            47899999999999999999999999999999999999899999999999999999999999999999999999999987


Q ss_pred             cCcc
Q 012257          118 RDPT  121 (467)
Q Consensus       118 ~~~~  121 (467)
                      ....
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            6543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=9.9e-19  Score=133.88  Aligned_cols=91  Identities=20%  Similarity=0.463  Sum_probs=83.1

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEec-CCCCccccEEEEEecChHHHHHHHHHh-CCcccCCc
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRD-LSTRRSLGYGYVNYNAAHEATRALDEL-NFTPLNGK  109 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~-~~~~~~~g~afV~f~~~~~A~~A~~~l-~~~~~~g~  109 (467)
                      ......++++|||+|||+++++++|+++|+.||.|.+|.+.++ +.+++++|||||+|.+.++|++|++.| ++..+.|+
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~   87 (107)
T 2cph_A            8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR   87 (107)
T ss_dssp             SSCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSC
T ss_pred             ccccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCC
Confidence            3444567899999999999999999999999999999999999 788999999999999999999999999 99999999


Q ss_pred             eeeeeecccCccc
Q 012257          110 PIRIMYSYRDPTI  122 (467)
Q Consensus       110 ~~~v~~~~~~~~~  122 (467)
                      .|+|.++......
T Consensus        88 ~l~v~~a~~~~~~  100 (107)
T 2cph_A           88 RLVLEWADSEVTV  100 (107)
T ss_dssp             BCEEEECCCCCCC
T ss_pred             EEEEEeCCCCCCC
Confidence            9999998766543

>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=99.79  E-value=4.5e-19  Score=139.69  Aligned_cols=88  Identities=26%  Similarity=0.423  Sum_probs=81.9

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      ......++++|||+|||+++++++|+++|++||.|.+|++.+++.+++++|||||+|.+.++|++|++.|++..|.|+.|
T Consensus        39 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l  118 (129)
T 2kxn_B           39 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI  118 (129)
T ss_dssp             CSSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34455678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeecccC
Q 012257          112 RIMYSYRD  119 (467)
Q Consensus       112 ~v~~~~~~  119 (467)
                      +|.++..+
T Consensus       119 ~V~~a~~~  126 (129)
T 2kxn_B          119 RVDFSITK  126 (129)
T ss_dssp             EESCCSSS
T ss_pred             EEEEecCC
Confidence            99998654

>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=99.79  E-value=3.5e-19  Score=138.24  Aligned_cols=104  Identities=21%  Similarity=0.415  Sum_probs=93.0

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .++++|||+|||+++++++|+++|+.||.|.+|.+.++.   .++|||||+|.+.++|.+|++.|++..+.|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECST---TTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCC---CCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            457999999999999999999999999999999998654   45899999999999999999999999999999999998


Q ss_pred             ccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCC
Q 012257          117 YRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN  153 (467)
Q Consensus       117 ~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~  153 (467)
                      ......          .+++...++++|.++|++||-
T Consensus        83 ~~~~~~----------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           83 NANRAF----------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             CHHHHT----------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             cCChhh----------hhhhHhHhHHHHHHHHHHhCC
Confidence            654332          567788899999999999984

>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=99.79  E-value=1.2e-18  Score=135.23  Aligned_cols=89  Identities=22%  Similarity=0.333  Sum_probs=82.0

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....+.++|||+|||+++++++|+++|++||.|.+|++.+++.+++++|||||+|.+.++|++|++.|++..|.|+.|+|
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   99 (115)
T 2cpz_A           20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            33446799999999999999999999999999999999999989999999999999999999999999999999999999


Q ss_pred             eecccCccc
Q 012257          114 MYSYRDPTI  122 (467)
Q Consensus       114 ~~~~~~~~~  122 (467)
                      .++......
T Consensus       100 ~~a~~~~~~  108 (115)
T 2cpz_A          100 QLKRSKNDS  108 (115)
T ss_dssp             ECCCCSCCC
T ss_pred             EEcCCCCcC
Confidence            998766443

>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=4.2e-19  Score=134.59  Aligned_cols=88  Identities=26%  Similarity=0.434  Sum_probs=81.7

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ...+.++|||+|||+++++++|+++|+.||.|.+|.+.+++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCccc
Q 012257          115 YSYRDPTI  122 (467)
Q Consensus       115 ~~~~~~~~  122 (467)
                      ++......
T Consensus        88 ~a~~~~~~   95 (102)
T 2cqb_A           88 LAKPMRIK   95 (102)
T ss_dssp             ECCCCCCC
T ss_pred             eCCCCCCC
Confidence            98765443

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.79  E-value=4.2e-19  Score=125.14  Aligned_cols=77  Identities=23%  Similarity=0.363  Sum_probs=71.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      .+..|+|+||++.+||++|+++|.+||+|.++++..     ++|||||+|.+.++|.+|++.|||..++|+.|+|++|..
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~e   80 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPSE   80 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCCH
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECCH
Confidence            455799999999999999999999999999999976     589999999999999999999999999999999999964


Q ss_pred             hH
Q 012257          400 KE  401 (467)
Q Consensus       400 ~~  401 (467)
                      ..
T Consensus        81 ~~   82 (89)
T 2wbr_A           81 NE   82 (89)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=1.3e-18  Score=132.00  Aligned_cols=90  Identities=28%  Similarity=0.489  Sum_probs=81.8

Q ss_pred             CCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCce
Q 012257           31 VGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKP  110 (467)
Q Consensus        31 ~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  110 (467)
                      .+.....+.++|||+|||+++++++|+++|+.||.|.+|.+..+  ++.++|||||+|.+.++|++|++.|++..+.|+.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   84 (103)
T 2d9p_A            7 GDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP   84 (103)
T ss_dssp             CCCCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSB
T ss_pred             CCccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            34445557899999999999999999999999999999999998  8899999999999999999999999999999999


Q ss_pred             eeeeecccCccc
Q 012257          111 IRIMYSYRDPTI  122 (467)
Q Consensus       111 ~~v~~~~~~~~~  122 (467)
                      |+|.++......
T Consensus        85 l~V~~a~~~~~~   96 (103)
T 2d9p_A           85 LYVALAQRKEER   96 (103)
T ss_dssp             CEEEECSSCCCC
T ss_pred             EEEEEecccccC
Confidence            999998765443

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.79  E-value=9.5e-19  Score=131.72  Aligned_cols=80  Identities=21%  Similarity=0.394  Sum_probs=76.8

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEE--------EEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVS--------VRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG  108 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~--------v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g  108 (467)
                      .+.++|||+|||.++++++|+++|++||.|.+        |++..++.+|+++|||||+|.+.++|++|++.|++..+.|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            45799999999999999999999999999999        9999999999999999999999999999999999999999


Q ss_pred             ceeeeeec
Q 012257          109 KPIRIMYS  116 (467)
Q Consensus       109 ~~~~v~~~  116 (467)
                      +.|+|.++
T Consensus        91 ~~l~V~~A   98 (99)
T 2la6_A           91 NPIKVSFA   98 (99)
T ss_dssp             SBCEEEEC
T ss_pred             cEEEEEec
Confidence            99999876

>2dh8_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=1e-18  Score=133.24  Aligned_cols=91  Identities=24%  Similarity=0.370  Sum_probs=82.9

Q ss_pred             CCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCce
Q 012257           31 VGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKP  110 (467)
Q Consensus        31 ~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  110 (467)
                      .......+.++|||+|||+++++++|+++|+.||.|.+|++.+++.+++++|||||+|.+.++|++|++. ++..|.|+.
T Consensus         8 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~   86 (105)
T 2dh8_A            8 MNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRN   86 (105)
T ss_dssp             CCCCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEE
T ss_pred             CCcCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEE
Confidence            3444556789999999999999999999999999999999999999999999999999999999999997 999999999


Q ss_pred             eeeeecccCccc
Q 012257          111 IRIMYSYRDPTI  122 (467)
Q Consensus       111 ~~v~~~~~~~~~  122 (467)
                      |+|.++......
T Consensus        87 l~V~~a~~~~~~   98 (105)
T 2dh8_A           87 IDPKPCTPRGMQ   98 (105)
T ss_dssp             EBCCCSCCSSCC
T ss_pred             EEEEEccCCCCC
Confidence            999998765443

>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=99.78  E-value=7.3e-19  Score=131.41  Aligned_cols=84  Identities=27%  Similarity=0.540  Sum_probs=77.4

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      +....+.++|||+|||+++++++|+++|+.||.|.+|++.+++. ++++|||||+|.+.++|++|++.|++..+.|+.|+
T Consensus        10 ~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (95)
T 2ywk_A           10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPIN   88 (95)
T ss_dssp             --CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEE
Confidence            34455689999999999999999999999999999999999985 89999999999999999999999999999999999


Q ss_pred             eeecc
Q 012257          113 IMYSY  117 (467)
Q Consensus       113 v~~~~  117 (467)
                      |.++.
T Consensus        89 V~~a~   93 (95)
T 2ywk_A           89 VSGPS   93 (95)
T ss_dssp             EECCC
T ss_pred             EEEcC
Confidence            98875

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=6e-19  Score=132.75  Aligned_cols=85  Identities=20%  Similarity=0.329  Sum_probs=78.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ...++|||+|||..+|+++|+++|++||.|.+|+++.+..|.++|||||+|.+.++|.+|+. ++|..++|+.|.|.++.
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            34568999999999999999999999999999999999889999999999999999999999 89999999999999988


Q ss_pred             hhHHHH
Q 012257          399 RKEERR  404 (467)
Q Consensus       399 ~~~~~~  404 (467)
                      .....+
T Consensus        88 ~~~~~k   93 (103)
T 1s79_A           88 DYFAKK   93 (103)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            765443

>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=99.78  E-value=6.5e-19  Score=129.35  Aligned_cols=81  Identities=28%  Similarity=0.547  Sum_probs=75.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      +.++|||+|||..+++++|+++|++||.|.++++..+. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+|++
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            56689999999999999999999999999999999985 88899999999999999999999999999999999999997


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            64

>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=99.78  E-value=6.1e-19  Score=135.67  Aligned_cols=91  Identities=21%  Similarity=0.356  Sum_probs=83.3

Q ss_pred             CCCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCc
Q 012257           30 GVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK  109 (467)
Q Consensus        30 ~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  109 (467)
                      ...+....++++|||+|||+++++++|+++|+.||.|.+|.+..++.+|+++|||||+|.+.++|.+|++.|++..+.|+
T Consensus        17 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   96 (110)
T 1oo0_B           17 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ   96 (110)
T ss_dssp             -CCBCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            34455567789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeeeecccCc
Q 012257          110 PIRIMYSYRDP  120 (467)
Q Consensus       110 ~~~v~~~~~~~  120 (467)
                      .|+|.++....
T Consensus        97 ~l~V~~a~~~~  107 (110)
T 1oo0_B           97 TIQVDWCFVKG  107 (110)
T ss_dssp             ECEEEESEESS
T ss_pred             EEEEEEcccCC
Confidence            99999986543

>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=99.78  E-value=1.8e-18  Score=133.40  Aligned_cols=88  Identities=16%  Similarity=0.321  Sum_probs=81.7

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhC------CcccC
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN------FTPLN  107 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~------~~~~~  107 (467)
                      ....++++|||+|||+++++++|+++|+.||.|.+|.+.+++.+++++|||||+|.+.++|.+|++.++      +..+.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            344568999999999999999999999999999999999999999999999999999999999999999      99999


Q ss_pred             CceeeeeecccCcc
Q 012257          108 GKPIRIMYSYRDPT  121 (467)
Q Consensus       108 g~~~~v~~~~~~~~  121 (467)
                      |+.|+|.++.....
T Consensus        90 g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           90 GRQLKVDLAVTRDE  103 (111)
T ss_dssp             SCEEEEECCCCCCC
T ss_pred             CEEEEEEECCCCcc
Confidence            99999999876544

>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=99.78  E-value=8.1e-19  Score=127.58  Aligned_cols=79  Identities=34%  Similarity=0.640  Sum_probs=75.3

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      .+|||+|||..+++++|+++|++||.|.++++..+. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+|++++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            579999999999999999999999999999999885 7889999999999999999999999999999999999999864

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=6.8e-19  Score=132.86  Aligned_cols=84  Identities=21%  Similarity=0.443  Sum_probs=79.2

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|++..+.+|.++|||||+|.+.++|.+|++.|||..++|+.|+|.|
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34567789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      ++++
T Consensus        93 a~~~   96 (100)
T 2do4_A           93 SNSG   96 (100)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9765

>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=9.8e-19  Score=131.49  Aligned_cols=86  Identities=23%  Similarity=0.488  Sum_probs=79.6

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCC---CCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLS---TRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~---~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      +.++++|||+|||+++++++|+++|+.||.|.+|.+.+++.   +++++|||||+|.+.++|++|++.|++..+.|+.|+
T Consensus         2 s~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (98)
T 2cpf_A            2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE   81 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            35689999999999999999999999999999999999876   668999999999999999999999999999999999


Q ss_pred             eeecccCcc
Q 012257          113 IMYSYRDPT  121 (467)
Q Consensus       113 v~~~~~~~~  121 (467)
                      |.++.....
T Consensus        82 V~~a~~~~~   90 (98)
T 2cpf_A           82 VRISERATK   90 (98)
T ss_dssp             EECSSCSSC
T ss_pred             EEEccCCCC
Confidence            999876544

>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=99.78  E-value=2.7e-19  Score=132.02  Aligned_cols=80  Identities=23%  Similarity=0.350  Sum_probs=71.3

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCC--ceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFG--TITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G--~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      .+|||+|||..+++++|+++|++||  .|.+++++.+. +|+++|||||+|.+.++|.+|++.|||..++|+.|+|+++.
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            3699999999999999999999999  99999999986 88999999999999999999999999999999999999998


Q ss_pred             hhH
Q 012257          399 RKE  401 (467)
Q Consensus       399 ~~~  401 (467)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.9e-18  Score=134.28  Aligned_cols=90  Identities=26%  Similarity=0.418  Sum_probs=82.3

Q ss_pred             CCCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCc
Q 012257           30 GVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK  109 (467)
Q Consensus        30 ~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  109 (467)
                      ........+.++|||+|||+++++++|+++|++||.|.+|++.+++.+++++|||||+|.+.++|++|++.+++ .|.|+
T Consensus         8 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~   86 (116)
T 2cqd_A            8 MHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGR   86 (116)
T ss_dssp             CCCCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTE
T ss_pred             CCCCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCE
Confidence            34455566789999999999999999999999999999999999999999999999999999999999999998 89999


Q ss_pred             eeeeeecccCc
Q 012257          110 PIRIMYSYRDP  120 (467)
Q Consensus       110 ~~~v~~~~~~~  120 (467)
                      .|+|.++....
T Consensus        87 ~l~V~~a~~~~   97 (116)
T 2cqd_A           87 KANVNLAYLGA   97 (116)
T ss_dssp             ECEEEESTTTC
T ss_pred             EEEEEEcccCC
Confidence            99999986543

>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=99.78  E-value=3.2e-18  Score=130.50  Aligned_cols=86  Identities=20%  Similarity=0.298  Sum_probs=79.5

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC---ceee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG---KPIR  112 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g---~~~~  112 (467)
                      ..++++|||+|||+++++++|+++|+.||.|.+|.+.+++ +++++|||||+|.+.++|++|++.|++..+.|   +.|+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3458999999999999999999999999999999999997 79999999999999999999999999999988   9999


Q ss_pred             eeecccCccc
Q 012257          113 IMYSYRDPTI  122 (467)
Q Consensus       113 v~~~~~~~~~  122 (467)
                      |.++......
T Consensus        91 V~~a~~~~~~  100 (105)
T 2dnh_A           91 VKFADTDKES  100 (105)
T ss_dssp             EEESCSSCCC
T ss_pred             EEECccCccc
Confidence            9998766543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=6.4e-19  Score=132.01  Aligned_cols=85  Identities=26%  Similarity=0.604  Sum_probs=80.2

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEE-EEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSV-RVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v-~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      .++++|||+|||+++++++|+++|+.||.|.+| ++.+++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|.+
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            468999999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             cccCcc
Q 012257          116 SYRDPT  121 (467)
Q Consensus       116 ~~~~~~  121 (467)
                      +.....
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            876544

>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=99.78  E-value=6.6e-19  Score=128.70  Aligned_cols=80  Identities=33%  Similarity=0.481  Sum_probs=75.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeC-CCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      .+.++|||+|||..+++++|+++|++||.|.+++++.+ .++.++|+|||+|.+.++|.+|++.|||..++|+.|+|+|+
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            46679999999999999999999999999999999888 47889999999999999999999999999999999999997


Q ss_pred             h
Q 012257          398 Q  398 (467)
Q Consensus       398 ~  398 (467)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.78  E-value=8.3e-19  Score=131.11  Aligned_cols=82  Identities=27%  Similarity=0.473  Sum_probs=77.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|||+|||..+++++|+++|++||.|.+|++..+.++.++|||||+|.+.++|.+|++.|||..+.|+.|+|+|+
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            34567899999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             hh
Q 012257          398 QR  399 (467)
Q Consensus       398 ~~  399 (467)
                      +.
T Consensus        93 ~~   94 (95)
T 2ywk_A           93 SS   94 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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=99.78  E-value=5.3e-19  Score=146.44  Aligned_cols=141  Identities=19%  Similarity=0.330  Sum_probs=79.4

Q ss_pred             EEeCCHHHHHHHHHHhCCCccC--CceEEEcccccchHHHHHhhh--hhhhhhhccccCCCCceEEEecCCCCCCHHHHH
Q 012257          264 VNFDDPDDAARSVEALNGKKFD--DKEWYVGKAQKKYEREMELKG--KFEQSLKETADKFEGLNLYVKNLDDSISDDKLK  339 (467)
Q Consensus       264 v~f~~~~~a~~a~~~l~~~~~~--~~~l~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~  339 (467)
                      .+|.+.+++..++..+++....  |+.....+.............  ...............++|||+|||..+++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            6788888888888888776554  333333332211100000000  000011122334567789999999999999999


Q ss_pred             HhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhhHHHH
Q 012257          340 ELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEERR  404 (467)
Q Consensus       340 ~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  404 (467)
                      ++|++||.|..|+|+.+. +|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+.+.....
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR  156 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC---
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCCC
Confidence            999999999999999985 88899999999999999999999999999999999999998665443

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=2.4e-18  Score=130.58  Aligned_cols=88  Identities=20%  Similarity=0.365  Sum_probs=80.4

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      ......+.++|||+|||+++++++|+++|+.|| |.+|++.+++.+++++|||||+|.+.++|++|+ .|++..+.|+.|
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   85 (103)
T 2dng_A            8 KELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSL   85 (103)
T ss_dssp             CCCCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEE
Confidence            334455689999999999999999999999997 999999999999999999999999999999999 799999999999


Q ss_pred             eeeecccCcc
Q 012257          112 RIMYSYRDPT  121 (467)
Q Consensus       112 ~v~~~~~~~~  121 (467)
                      +|.++.....
T Consensus        86 ~V~~a~~~~~   95 (103)
T 2dng_A           86 RVDIAEGRKQ   95 (103)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEecCCCC
Confidence            9999876544

>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=99.78  E-value=2.6e-19  Score=132.02  Aligned_cols=81  Identities=19%  Similarity=0.360  Sum_probs=72.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCC--CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMG--QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G--~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      .+|||+|||+++++++|+++|+.||  .|.++++..++.+|+++|||||+|.+.++|++|++.|++..+.|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  99999999999999999999999999999999999999999999999999887


Q ss_pred             cCc
Q 012257          118 RDP  120 (467)
Q Consensus       118 ~~~  120 (467)
                      ..+
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            553

>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=99.78  E-value=4.6e-19  Score=154.25  Aligned_cols=86  Identities=20%  Similarity=0.293  Sum_probs=78.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCC--ceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFG--TITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G--~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ..++|||+||+..+++++|+++|++||  .|++|+|+.+. +|+++|||||+|.+.++|.+||+.|||..|+|+.|+|++
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            456899999999999999999999999  99999999996 899999999999999999999999999999999999999


Q ss_pred             hhhhHHHHH
Q 012257          397 AQRKEERRA  405 (467)
Q Consensus       397 ~~~~~~~~~  405 (467)
                      +++......
T Consensus       147 a~~~~~~~~  155 (229)
T 3q2s_C          147 VNKQFLSQF  155 (229)
T ss_dssp             CCHHHHHHH
T ss_pred             CCCCccchh
Confidence            987765443

>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=1.7e-18  Score=126.96  Aligned_cols=81  Identities=26%  Similarity=0.452  Sum_probs=75.3

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ...+.++|||+|||+++++++|+++|++||.|.+|++.+++.+++++|||||+|.+.++|.+|++ +++..+.|+.|+|.
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999997 57788999999997


Q ss_pred             ec
Q 012257          115 YS  116 (467)
Q Consensus       115 ~~  116 (467)
                      ++
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            64

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.78  E-value=1.9e-18  Score=121.74  Aligned_cols=74  Identities=24%  Similarity=0.256  Sum_probs=69.3

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ..+..|+|+||++.++|++|+++|.+||+|.++++..      ++|||||+|.+.++|.+|++.||+..+.|++|+|.++
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            4588999999999999999999999999999999965      5699999999999999999999999999999999755

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.78  E-value=4.1e-19  Score=133.62  Aligned_cols=83  Identities=20%  Similarity=0.308  Sum_probs=77.8

Q ss_pred             CCceEEEecCCC------CCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecc-cc
Q 012257          320 EGLNLYVKNLDD------SISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVS-KP  391 (467)
Q Consensus       320 ~~~~l~V~nlp~------~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-~~  391 (467)
                      ..++|||+|||.      .+++++|+++|++||.|.+|+++.+. +|+++|||||+|.+.++|.+|++.|||..+.| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            356899999999      99999999999999999999999987 49999999999999999999999999999999 99


Q ss_pred             eEEehhhhhHH
Q 012257          392 LYVALAQRKEE  402 (467)
Q Consensus       392 l~v~~~~~~~~  402 (467)
                      |+|+++.+...
T Consensus        85 l~V~~a~~~~~   95 (100)
T 3ns6_A           85 LFLYTMKDVER   95 (100)
T ss_dssp             CEEEESHHHHH
T ss_pred             EEEEECchhhh
Confidence            99999987654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=131.46  Aligned_cols=85  Identities=27%  Similarity=0.494  Sum_probs=79.6

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeE-EEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCce---
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVV-SVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKP---  110 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~-~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~---  110 (467)
                      ...++++|||+|||+++++++|+++|++||.|. +|++.+++.+++++|||||+|.+.++|++|++.|++..+.|+.   
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   84 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAK   84 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCE
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcce
Confidence            345689999999999999999999999999999 9999999999999999999999999999999999999999999   


Q ss_pred             -eeeeecccC
Q 012257          111 -IRIMYSYRD  119 (467)
Q Consensus       111 -~~v~~~~~~  119 (467)
                       |+|.++...
T Consensus        85 ~l~v~~a~~~   94 (99)
T 2div_A           85 RFKLNYATYS   94 (99)
T ss_dssp             ECCEEETTCC
T ss_pred             eEEEeecCCC
Confidence             999888644

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

Probab=99.77  E-value=6e-19  Score=129.71  Aligned_cols=80  Identities=20%  Similarity=0.328  Sum_probs=72.2

Q ss_pred             ccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcE--ecccceE
Q 012257          316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKM--VVSKPLY  393 (467)
Q Consensus       316 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~--~~g~~l~  393 (467)
                      ....++++|||+|||+.+++++|+++|++||.|.+|++++.     +|+|||+|.+.++|.+|++.|++..  +.|++|+
T Consensus        16 ~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~-----kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~   90 (100)
T 3r27_A           16 HKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAF   90 (100)
T ss_dssp             -CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEE
T ss_pred             ccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEE
Confidence            34457789999999999999999999999999999999863     7899999999999999999999885  7899999


Q ss_pred             Eehhhhh
Q 012257          394 VALAQRK  400 (467)
Q Consensus       394 v~~~~~~  400 (467)
                      |+|++.+
T Consensus        91 V~~S~~k   97 (100)
T 3r27_A           91 VNYSTSQ   97 (100)
T ss_dssp             EEECSCS
T ss_pred             EEecccc
Confidence            9999764

>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=6.2e-19  Score=134.24  Aligned_cols=88  Identities=28%  Similarity=0.506  Sum_probs=81.7

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      +....++++|||+|||+++++++|+++|+.||.|.+|.+.+++.+|+++|||||+|.+.++|++|++.+++..+.|+.|+
T Consensus         2 p~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (104)
T 1p1t_A            2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALR   81 (104)
T ss_dssp             CCSHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBE
T ss_pred             CCcCCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            34455689999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecccCc
Q 012257          113 IMYSYRDP  120 (467)
Q Consensus       113 v~~~~~~~  120 (467)
                      |.++....
T Consensus        82 v~~a~~~~   89 (104)
T 1p1t_A           82 VDNAASEK   89 (104)
T ss_dssp             EEETTCTT
T ss_pred             EEeCCCcc
Confidence            99987543

>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=1.2e-18  Score=131.04  Aligned_cols=81  Identities=14%  Similarity=0.272  Sum_probs=76.0

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..+.++|||+|||+++++++|+++|+.||+|.+|.+.+++. |+++|||||+|.+.++|.+|++ +++..+.|+.|+|.+
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   85 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            45679999999999999999999999999999999999987 9999999999999999999998 899999999999988


Q ss_pred             ccc
Q 012257          116 SYR  118 (467)
Q Consensus       116 ~~~  118 (467)
                      ...
T Consensus        86 ~~~   88 (103)
T 1s79_A           86 KDD   88 (103)
T ss_dssp             HHH
T ss_pred             chH
Confidence            654

>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=99.77  E-value=3.8e-18  Score=129.47  Aligned_cols=87  Identities=22%  Similarity=0.403  Sum_probs=78.6

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....+.++|||+|||+++++++|+++|+.||.|.+|++.+++.+  ++|||||+|.+.++|++|++.|++..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   87 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEE
Confidence            34456899999999999999999999999999999999998543  6899999999999999999999999999999999


Q ss_pred             eecccCccc
Q 012257          114 MYSYRDPTI  122 (467)
Q Consensus       114 ~~~~~~~~~  122 (467)
                      .++......
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cqi_A           88 NWATTPSSQ   96 (103)
T ss_dssp             EECCCTTCC
T ss_pred             EECCCCccc
Confidence            998765443

>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=99.77  E-value=1.6e-18  Score=132.48  Aligned_cols=87  Identities=18%  Similarity=0.375  Sum_probs=80.5

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc---CCcee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL---NGKPI  111 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~---~g~~~  111 (467)
                      ...+.++|||+|||.++++++|+++|++||.|.+|++.+++.+++++|||||+|.+.++|.+|++.|++..+   .|+.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            345689999999999999999999999999999999999999999999999999999999999999999887   89999


Q ss_pred             eeeecccCcc
Q 012257          112 RIMYSYRDPT  121 (467)
Q Consensus       112 ~v~~~~~~~~  121 (467)
                      +|.++.....
T Consensus        89 ~v~~a~~~~~   98 (106)
T 2dgp_A           89 QVKPADSESR   98 (106)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEECCcccc
Confidence            9999876543

>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=2.2e-18  Score=130.96  Aligned_cols=88  Identities=23%  Similarity=0.402  Sum_probs=80.2

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCC-CccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLST-RRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~-~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      +....+.++|||+|||+++++++|+++|+.|| |.+|.+.+++.+ ++++|||||+|.+.++|++|+ .|++..+.|+.|
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            34445679999999999999999999999999 999999999887 999999999999999999999 899999999999


Q ss_pred             eeeecccCccc
Q 012257          112 RIMYSYRDPTI  122 (467)
Q Consensus       112 ~v~~~~~~~~~  122 (467)
                      +|.++......
T Consensus        87 ~V~~a~~~~~~   97 (104)
T 1wi8_A           87 RVDVADQAQDK   97 (104)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99998765443

>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=1.4e-18  Score=129.21  Aligned_cols=81  Identities=17%  Similarity=0.288  Sum_probs=72.6

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCC--cccCCceeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNF--TPLNGKPIRIM  114 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~--~~~~g~~~~v~  114 (467)
                      .++++|||+|||++++|++|+++|++||.|.+|+|+++      +|||||+|.+.++|++|++.+++  ..+.|++|+|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            45899999999999999999999999999999999876      47999999999999999998863  68999999999


Q ss_pred             ecccCcccc
Q 012257          115 YSYRDPTIR  123 (467)
Q Consensus       115 ~~~~~~~~~  123 (467)
                      ++...+...
T Consensus        88 ~A~~~~~~~   96 (105)
T 1sjq_A           88 FSNHKELKT   96 (105)
T ss_dssp             CCSSSSCCC
T ss_pred             EcCCCCCCc
Confidence            987665443

>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=99.77  E-value=1.1e-18  Score=130.45  Aligned_cols=82  Identities=23%  Similarity=0.430  Sum_probs=77.2

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      +++|||+|||..+++++|+++|++||.|.++++..+. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+|+++
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            5689999999999999999999999999999999986 688999999999999999999999999999999999999986


Q ss_pred             hHH
Q 012257          400 KEE  402 (467)
Q Consensus       400 ~~~  402 (467)
                      ...
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            653

>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=6e-19  Score=131.17  Aligned_cols=78  Identities=15%  Similarity=0.373  Sum_probs=71.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCC--cEecccceEEe
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNG--KMVVSKPLYVA  395 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g--~~~~g~~l~v~  395 (467)
                      ..+.++|||+|||+.+++++|+++|++||.|.+|+++++     +|||||+|.+.++|.+|++.|++  ..+.|+.|+|+
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            346678999999999999999999999999999999875     78999999999999999998864  78999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++.+
T Consensus        88 ~A~~~   92 (105)
T 1sjq_A           88 FSNHK   92 (105)
T ss_dssp             CCSSS
T ss_pred             EcCCC
Confidence            99755

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.77  E-value=1e-18  Score=138.66  Aligned_cols=87  Identities=17%  Similarity=0.323  Sum_probs=80.0

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEE--EEEEecCCCCccccEEEEEecChHHHHHHHHHhCCc----c
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVS--VRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFT----P  105 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~--v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~----~  105 (467)
                      .+.....+++|||+|||++++|++|+++|++||.|..  |+|++|+.+|+++|||||+|.+. +|.+|+..|++.    .
T Consensus        16 ~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~   94 (131)
T 2m2b_A           16 EPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT   94 (131)
T ss_dssp             CCCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc
Confidence            3344466899999999999999999999999999977  99999999999999999999999 999999999999    9


Q ss_pred             cCCceeeeeecccC
Q 012257          106 LNGKPIRIMYSYRD  119 (467)
Q Consensus       106 ~~g~~~~v~~~~~~  119 (467)
                      +.|+.|+|.++...
T Consensus        95 ~~gr~l~V~~a~~~  108 (131)
T 2m2b_A           95 IDGKTINVEFAKGS  108 (131)
T ss_dssp             GGGCCCCCEECCCS
T ss_pred             CCCEEEEEEECCCC
Confidence            99999999998654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=5.5e-19  Score=129.02  Aligned_cols=81  Identities=23%  Similarity=0.409  Sum_probs=77.0

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .++++|||+|||+++++++|+++|++||.|.++.+..++.+++++|||||+|.+.++|++|++.|++..+.|+.+++.++
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            46899999999999999999999999999999999999999999999999999999999999999999999999998775


Q ss_pred             c
Q 012257          117 Y  117 (467)
Q Consensus       117 ~  117 (467)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.4e-18  Score=131.93  Aligned_cols=83  Identities=64%  Similarity=1.010  Sum_probs=78.5

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|++..+ ++.++|||||+|.+.++|.+|++.|||..++|+.|+|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4457789999999999999999999999999999999998 889999999999999999999999999999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      ++++
T Consensus        90 a~~~   93 (103)
T 2d9p_A           90 AQRK   93 (103)
T ss_dssp             CSSC
T ss_pred             eccc
Confidence            9865

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.77  E-value=1.9e-19  Score=143.21  Aligned_cols=121  Identities=21%  Similarity=0.290  Sum_probs=78.9

Q ss_pred             EEEEEeCCHHHHHHHHHHhCCCccCCceEEEcccccchHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHH
Q 012257          261 FGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKE  340 (467)
Q Consensus       261 ~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~  340 (467)
                      ++|++|++...+..|+..+++....++... .+..                  ........++|||+|||..+++++|++
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~~-~~~~------------------~~~~~~~~~~l~V~nLp~~~te~~L~~   66 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGSM-SYGR------------------PPPDVEGMTSLKVDNLTYRTSPDTLRR   66 (135)
T ss_dssp             -----------------------------C-CSCC------------------SCSSGGGCCCEEEECCCSSCHHHHHHH
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCCC-CcCC------------------CCCCCCCCCEEEEeCCCCCCCHHHHHH
Confidence            678888899999999998887665443211 1111                  112234567899999999999999999


Q ss_pred             hhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          341 LFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       341 ~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      +|++||.|.+|+++.+. ++.++|||||+|.+.++|.+|++.|||..|.|+.|+|+|+++.
T Consensus        67 ~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~  127 (135)
T 2lea_A           67 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG  127 (135)
T ss_dssp             HHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCC
T ss_pred             HHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            99999999999999886 7889999999999999999999999999999999999999754

>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=99.77  E-value=6.4e-18  Score=128.25  Aligned_cols=88  Identities=22%  Similarity=0.410  Sum_probs=79.1

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      .....+.++|||+|||+++++++|+++|+.||.|.+|++.+++.  .++|||||+|.+.++|++|++.|++..|.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIE   86 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34455689999999999999999999999999999999998864  3889999999999999999999999999999999


Q ss_pred             eeecccCccc
Q 012257          113 IMYSYRDPTI  122 (467)
Q Consensus       113 v~~~~~~~~~  122 (467)
                      |.++......
T Consensus        87 v~~a~~~~~~   96 (103)
T 2cq3_A           87 VNNATARVMT   96 (103)
T ss_dssp             EEECCSSCCC
T ss_pred             EEEcccCCCC
Confidence            9998766443

>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=99.77  E-value=1.7e-18  Score=131.99  Aligned_cols=84  Identities=32%  Similarity=0.589  Sum_probs=78.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecc---cceEE
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVS---KPLYV  394 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g---~~l~v  394 (467)
                      ....++|||+|||..+++++|+++|++||.|.+|++..+.+|.++|||||+|.+.++|.+|++.|||..+.|   +.|+|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            345789999999999999999999999999999999999999999999999999999999999999999988   99999


Q ss_pred             ehhhhhH
Q 012257          395 ALAQRKE  401 (467)
Q Consensus       395 ~~~~~~~  401 (467)
                      .|+++..
T Consensus        92 ~~a~~~~   98 (105)
T 2dnh_A           92 KFADTDK   98 (105)
T ss_dssp             EESCSSC
T ss_pred             EECccCc
Confidence            9998653

>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=99.77  E-value=2.8e-18  Score=132.72  Aligned_cols=84  Identities=23%  Similarity=0.453  Sum_probs=79.0

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..++++|||+|||.++++++|+++|+.||.|.+|.+..++ +++++|||||+|.+.++|++|++.|++..+.|+.|+|.+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3457999999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             cccCc
Q 012257          116 SYRDP  120 (467)
Q Consensus       116 ~~~~~  120 (467)
                      +....
T Consensus        83 a~~~~   87 (116)
T 2fy1_A           83 AKKPS   87 (116)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            87554

>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=99.77  E-value=1.3e-18  Score=131.08  Aligned_cols=84  Identities=29%  Similarity=0.428  Sum_probs=78.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ..+.++|||+|||..+++++|+++|++||.|.+|++..+. ++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.+
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            3466799999999999999999999999999999999987 888999999999999999999999999999999999999


Q ss_pred             hhhhH
Q 012257          397 AQRKE  401 (467)
Q Consensus       397 ~~~~~  401 (467)
                      ++++.
T Consensus        85 a~~~~   89 (99)
T 1whw_A           85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            98663

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

Probab=99.77  E-value=4.3e-18  Score=126.36  Aligned_cols=83  Identities=23%  Similarity=0.335  Sum_probs=77.2

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..+.++|||+|||.++++++|+++|++||.|.+|++.++  +++++|||||+|.+.++|++|++.|++..+.|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            456899999999999999999999999999999999984  788999999999999999999999999999999999999


Q ss_pred             cccCc
Q 012257          116 SYRDP  120 (467)
Q Consensus       116 ~~~~~  120 (467)
                      +....
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            87554

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.9e-18  Score=129.09  Aligned_cols=82  Identities=34%  Similarity=0.609  Sum_probs=77.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ...++|||+|||..+++++|+++|++||.|.+|++..+. ++.++|||||+|.+.++|.+|++.|||..+.|+.|+|+++
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            356789999999999999999999999999999999986 5889999999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      +++
T Consensus        83 ~~~   85 (95)
T 2dnz_A           83 TER   85 (95)
T ss_dssp             SCC
T ss_pred             ccc
Confidence            754

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.77  E-value=8e-19  Score=132.01  Aligned_cols=82  Identities=17%  Similarity=0.244  Sum_probs=77.9

Q ss_pred             ccCeEEEcCCCC------CCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC-ce
Q 012257           38 VSTSLYVGDLDL------SVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG-KP  110 (467)
Q Consensus        38 ~~~~l~v~nLp~------~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g-~~  110 (467)
                      .+++|||+|||.      ++++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|++|++.|++..+.| +.
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            468999999999      99999999999999999999999999999999999999999999999999999999999 99


Q ss_pred             eeeeecccC
Q 012257          111 IRIMYSYRD  119 (467)
Q Consensus       111 ~~v~~~~~~  119 (467)
                      |+|.++.+.
T Consensus        85 l~V~~a~~~   93 (100)
T 3ns6_A           85 LFLYTMKDV   93 (100)
T ss_dssp             CEEEESHHH
T ss_pred             EEEEECchh
Confidence            999987643

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.5e-18  Score=129.37  Aligned_cols=81  Identities=23%  Similarity=0.452  Sum_probs=76.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ....++|||+|||..+++++|+++|++||.|.+|++..+. ++.++|||||+|.+.++|.+|++.|||..++|+.|+|+|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            4566789999999999999999999999999999999987 588899999999999999999999999999999999999


Q ss_pred             hh
Q 012257          397 AQ  398 (467)
Q Consensus       397 ~~  398 (467)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.9e-18  Score=129.18  Aligned_cols=83  Identities=25%  Similarity=0.350  Sum_probs=77.2

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ...+.++|||+|||..+++++|+++|++||.|.+|++..+. ++.++|||||+|.+.++|.+|++.|||..++|+.|+|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS   90 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34466789999999999999999999999999999999987 57899999999999999999999999999999999999


Q ss_pred             hhhh
Q 012257          396 LAQR  399 (467)
Q Consensus       396 ~~~~  399 (467)
                      |++.
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9864

>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=99.77  E-value=1.2e-18  Score=131.07  Aligned_cols=84  Identities=17%  Similarity=0.239  Sum_probs=78.3

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ....++|||+|||+++++++|+++|+.||.|.++.++.++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|.+
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            34578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccC
Q 012257          116 SYRD  119 (467)
Q Consensus       116 ~~~~  119 (467)
                      +...
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            7643

>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=99.76  E-value=7.8e-18  Score=129.16  Aligned_cols=89  Identities=15%  Similarity=0.299  Sum_probs=78.5

Q ss_pred             CCCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCc
Q 012257           30 GVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK  109 (467)
Q Consensus        30 ~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  109 (467)
                      ........+.++|||+|||+++++++|+++|++||.|.+|.+..+   ++++|||||+|.+.++|++|++.|++..+.|+
T Consensus        13 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   89 (109)
T 1x4a_A           13 VIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGY   89 (109)
T ss_dssp             CSSCCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            344455567899999999999999999999999999999999654   45789999999999999999999999999999


Q ss_pred             eeeeeecccCcc
Q 012257          110 PIRIMYSYRDPT  121 (467)
Q Consensus       110 ~~~v~~~~~~~~  121 (467)
                      .|+|.++.....
T Consensus        90 ~l~V~~a~~~~~  101 (109)
T 1x4a_A           90 RLRVEFPRSGRG  101 (109)
T ss_dssp             ECEEECCCCCCC
T ss_pred             EEEEEEcccCCC
Confidence            999999876543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2e-18  Score=131.05  Aligned_cols=84  Identities=27%  Similarity=0.441  Sum_probs=78.8

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ...+.++|||+|||..+++++|+++|++||.|.+|+++.+. ++.++|||||+|.+.++|.+|++.|||..|.|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34567899999999999999999999999999999999986 78999999999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++++
T Consensus        91 ~a~~~   95 (103)
T 2cq0_A           91 WAKPS   95 (103)
T ss_dssp             ESSCC
T ss_pred             ECCCC
Confidence            99755

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=7.7e-18  Score=130.46  Aligned_cols=82  Identities=34%  Similarity=0.582  Sum_probs=77.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|||+|||..+++++|+++|++||.|.+|++..+.++.++|||||+|.+.++|.+|++.|||..|+|+.|+|+++
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            34567899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hh
Q 012257          398 QR  399 (467)
Q Consensus       398 ~~  399 (467)
                      +.
T Consensus        92 ~~   93 (114)
T 2do0_A           92 ER   93 (114)
T ss_dssp             SC
T ss_pred             cc
Confidence            65

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.76  E-value=3.1e-18  Score=139.38  Aligned_cols=85  Identities=21%  Similarity=0.312  Sum_probs=78.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCC--ceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFG--TITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G--~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ..++|||+|||..+++++|+++|+.||  .|.+|+++.+. +|.++|||||+|.+.++|.+|++.|||..|+|+.|+|++
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            456899999999999999999999999  99999999986 799999999999999999999999999999999999999


Q ss_pred             hhhhHHHH
Q 012257          397 AQRKEERR  404 (467)
Q Consensus       397 ~~~~~~~~  404 (467)
                      +.++....
T Consensus       134 a~~~~~~~  141 (156)
T 3n9u_C          134 ATRQNLSQ  141 (156)
T ss_dssp             CCHHHHHH
T ss_pred             cCCCcchh
Confidence            98766544

>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=99.76  E-value=1.9e-18  Score=133.98  Aligned_cols=84  Identities=33%  Similarity=0.531  Sum_probs=78.7

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|++..+. ++.++|||||+|.+.++|.+|++.|||..|+|+.|+|+
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            34466799999999999999999999999999999999987 78999999999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++++
T Consensus       101 ~a~~~  105 (115)
T 2cpz_A          101 LKRSK  105 (115)
T ss_dssp             CCCCS
T ss_pred             EcCCC
Confidence            99765

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=4.4e-18  Score=129.44  Aligned_cols=85  Identities=33%  Similarity=0.481  Sum_probs=79.4

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhc-CCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcc-cCCceeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQ-MGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTP-LNGKPIRI  113 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~-~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~-~~g~~~~v  113 (467)
                      ..++++|||+|||+++++++|+++|+. ||.|.+|.+.+++ +++++|||||+|.+.++|.+|++.|++.. +.|+.|+|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            456799999999999999999999999 9999999999998 99999999999999999999999999999 99999999


Q ss_pred             eecccCcc
Q 012257          114 MYSYRDPT  121 (467)
Q Consensus       114 ~~~~~~~~  121 (467)
                      .++.....
T Consensus        85 ~~a~~~~~   92 (104)
T 2dhg_A           85 SVAIPKAS   92 (104)
T ss_dssp             CBCCCCCS
T ss_pred             EEccCCCc
Confidence            99865543

>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=2.4e-18  Score=133.55  Aligned_cols=86  Identities=17%  Similarity=0.247  Sum_probs=79.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCc---eeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGT---ITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~---v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ...++|||+|||+.+++++|+++|+.||.   |.+|+++.+.+|+++|||||+|.+.++|.+|++ +||..|+|+.|+|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   93 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVF   93 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEE
Confidence            45678999999999999999999999999   899999999889999999999999999999999 99999999999999


Q ss_pred             hhhhhHHHHH
Q 012257          396 LAQRKEERRA  405 (467)
Q Consensus       396 ~~~~~~~~~~  405 (467)
                      ++........
T Consensus        94 ~a~~~~~~~~  103 (118)
T 2db1_A           94 KSHRTEMDWV  103 (118)
T ss_dssp             EECHHHHHHH
T ss_pred             ECCHHHHHHH
Confidence            9987665433

>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=99.76  E-value=1.9e-18  Score=133.71  Aligned_cols=82  Identities=27%  Similarity=0.474  Sum_probs=77.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ...++|||+|||..+++++|+++|++||.|.+|++..+.+|.++|||||+|.+.++|.+|++.|||..++|+.|+|++++
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            45678999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      +.
T Consensus        85 ~~   86 (116)
T 2fy1_A           85 KP   86 (116)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

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

Probab=99.76  E-value=2.4e-18  Score=126.52  Aligned_cols=82  Identities=17%  Similarity=0.205  Sum_probs=71.7

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcc--cCCc
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTP--LNGK  109 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~--~~g~  109 (467)
                      +.....++++|||+|||.++++++|+++|++||.|.+|.++++      +|+|||+|.+.++|.+|++.+++..  +.|+
T Consensus        14 ~~~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr   87 (100)
T 3r27_A           14 DPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGH   87 (100)
T ss_dssp             ---CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTE
T ss_pred             ccccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCc
Confidence            3445567899999999999999999999999999999999853      4799999999999999999998765  7899


Q ss_pred             eeeeeecccC
Q 012257          110 PIRIMYSYRD  119 (467)
Q Consensus       110 ~~~v~~~~~~  119 (467)
                      +|+|.++...
T Consensus        88 ~i~V~~S~~k   97 (100)
T 3r27_A           88 PAFVNYSTSQ   97 (100)
T ss_dssp             EEEEEECSCS
T ss_pred             EEEEEecccc
Confidence            9999998754

>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=99.76  E-value=2e-18  Score=133.40  Aligned_cols=89  Identities=17%  Similarity=0.235  Sum_probs=81.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCce-eEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTI-TSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v-~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ....++|||+|||+.+++++|+++|+.||.| .+|+|+.+.+|+++|||||+|.+.++|.+|++. |+..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            3456789999999999999999999999999 899999999999999999999999999999987 99999999999999


Q ss_pred             hhhhHHHHHHH
Q 012257          397 AQRKEERRARL  407 (467)
Q Consensus       397 ~~~~~~~~~~~  407 (467)
                      +.+........
T Consensus        91 a~~~~~~~~~~  101 (114)
T 2cpy_A           91 VTLEDMREIEK  101 (114)
T ss_dssp             ECHHHHHHHHH
T ss_pred             CCHHHHHHHHh
Confidence            99887665543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=3.4e-18  Score=132.16  Aligned_cols=87  Identities=23%  Similarity=0.362  Sum_probs=81.0

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeE--------EEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVV--------SVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL  106 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~--------~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  106 (467)
                      ...++++|||+|||+++++++|+++|++||.|.        .|++..++.+++++|||||+|.+.++|++|++.|++..|
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            445689999999999999999999999999999        699999988999999999999999999999999999999


Q ss_pred             CCceeeeeecccCcc
Q 012257          107 NGKPIRIMYSYRDPT  121 (467)
Q Consensus       107 ~g~~~~v~~~~~~~~  121 (467)
                      .|+.|+|.++.....
T Consensus        91 ~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           91 QGSKLKVSLARKKPP  105 (113)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCCEEEEEECCCCCC
Confidence            999999999876544

>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=9.8e-19  Score=131.68  Aligned_cols=81  Identities=22%  Similarity=0.440  Sum_probs=74.3

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecC-CCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDL-STRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ...++|||+|||.++++++|+++|+.|| |.+|.+.+++ .+|+++|||||+|.+.++|.+|+ .+++..+.|+.|+|.+
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEe
Confidence            3579999999999999999999999999 9999999998 58999999999999999999999 7999999999999998


Q ss_pred             cccC
Q 012257          116 SYRD  119 (467)
Q Consensus       116 ~~~~  119 (467)
                      +...
T Consensus        95 a~~~   98 (100)
T 2j76_E           95 ADQA   98 (100)
T ss_dssp             CCCS
T ss_pred             ccCC
Confidence            8654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.4e-18  Score=131.40  Aligned_cols=84  Identities=24%  Similarity=0.492  Sum_probs=78.2

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ....+++|||+|||..+++++|+++|++||.|.+|++..+. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+
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            34466789999999999999999999999999999999986 58899999999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++++
T Consensus        99 ~a~~~  103 (106)
T 1p27_B           99 WCFVR  103 (106)
T ss_dssp             ESEES
T ss_pred             eecCC
Confidence            99764

>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=99.76  E-value=2.4e-18  Score=126.69  Aligned_cols=83  Identities=20%  Similarity=0.406  Sum_probs=77.4

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCc-cccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRR-SLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~-~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..+++|||+|||.++++++|+++|+.||.|.+|.+..+..++. ++|||||+|.+.++|++|++.|++..+.|+.|+|.+
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            4578999999999999999999999999999999999987766 899999999999999999999999999999999998


Q ss_pred             cccC
Q 012257          116 SYRD  119 (467)
Q Consensus       116 ~~~~  119 (467)
                      +...
T Consensus        82 a~~~   85 (88)
T 4a8x_A           82 VLAP   85 (88)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            7543

>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=99.76  E-value=2.4e-18  Score=126.90  Aligned_cols=81  Identities=21%  Similarity=0.430  Sum_probs=77.1

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      +.++|||+|||+++++++|+++|+.||.|.+|.+..++.+++++|||||+|.+.++|++|+ .+++..+.|+.|+|.++.
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            5789999999999999999999999999999999999989999999999999999999999 899999999999999886


Q ss_pred             cC
Q 012257          118 RD  119 (467)
Q Consensus       118 ~~  119 (467)
                      .+
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=99.76  E-value=1.7e-18  Score=128.94  Aligned_cols=85  Identities=18%  Similarity=0.229  Sum_probs=74.4

Q ss_pred             CCCCCCCccCeEEEcCCCC-CCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCc--ccC
Q 012257           31 VGDARQFVSTSLYVGDLDL-SVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFT--PLN  107 (467)
Q Consensus        31 ~~~~~~~~~~~l~v~nLp~-~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~--~~~  107 (467)
                      +......++++|||+|||+ +++|++|+++|++||.|.+|+|++++      |||||+|.+.++|.+|++.|++.  .+.
T Consensus         7 ~~~~~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k------g~aFVef~~~~~A~~Ai~~l~~~~~~~~   80 (102)
T 1x4d_A            7 GQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVF   80 (102)
T ss_dssp             CCCCCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEET
T ss_pred             CCCCCCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC------CEEEEEECCHHHHHHHHHHHcCCCceEC
Confidence            3444556799999999999 99999999999999999999998764      69999999999999999988754  599


Q ss_pred             CceeeeeecccCcc
Q 012257          108 GKPIRIMYSYRDPT  121 (467)
Q Consensus       108 g~~~~v~~~~~~~~  121 (467)
                      |++|+|.++.....
T Consensus        81 Gr~l~V~~a~~~~~   94 (102)
T 1x4d_A           81 GKPVRVHLSQKYKR   94 (102)
T ss_dssp             TEECEEEEECCCTT
T ss_pred             CcEEEEEECCCCCC
Confidence            99999999875543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.76  E-value=3.3e-18  Score=128.72  Aligned_cols=82  Identities=21%  Similarity=0.443  Sum_probs=76.7

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeE--------EEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITS--------CKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMV  387 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~--------v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  387 (467)
                      .....++|||+|||..+++++|+++|++||.|.+        +++..+. +|.++|||||+|.+.++|.+|++.|||..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            3456779999999999999999999999999999        9999985 789999999999999999999999999999


Q ss_pred             cccceEEehhh
Q 012257          388 VSKPLYVALAQ  398 (467)
Q Consensus       388 ~g~~l~v~~~~  398 (467)
                      .|+.|+|++|+
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999874

>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=99.76  E-value=2.3e-18  Score=131.35  Aligned_cols=84  Identities=36%  Similarity=0.609  Sum_probs=78.2

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|++..+. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567799999999999999999999999999999999885 68899999999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      +++++
T Consensus       102 ~a~~k  106 (108)
T 2jrs_A          102 HVTER  106 (108)
T ss_dssp             CSCSS
T ss_pred             EcccC
Confidence            99764

>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=99.76  E-value=3.8e-18  Score=130.55  Aligned_cols=84  Identities=30%  Similarity=0.490  Sum_probs=78.3

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      +....++++|||+|||+++++++|+++|+.||.|.+|++..++ +++++|||||+|.+.++|++|++.|++..+.|+.|+
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  101 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMN  101 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            3445668999999999999999999999999999999999998 999999999999999999999999999999999999


Q ss_pred             eeecc
Q 012257          113 IMYSY  117 (467)
Q Consensus       113 v~~~~  117 (467)
                      |.++.
T Consensus       102 V~~a~  106 (107)
T 3ulh_A          102 IQLVT  106 (107)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            98864

>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=2.5e-18  Score=131.41  Aligned_cols=84  Identities=24%  Similarity=0.414  Sum_probs=76.0

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .+.++|||+|||.++++++|+++|+.||.|.+|.+.+++.+|+++|||||+|.+.++|.+|++.+ +..+.|+.|+|.++
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVA  101 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEc
Confidence            45799999999999999999999999999999999999999999999999999999999999975 58899999999998


Q ss_pred             ccCcc
Q 012257          117 YRDPT  121 (467)
Q Consensus       117 ~~~~~  121 (467)
                      .....
T Consensus       102 ~~~~~  106 (109)
T 2rs2_A          102 FPRRA  106 (109)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            75543

>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=99.76  E-value=2.5e-18  Score=131.10  Aligned_cols=84  Identities=30%  Similarity=0.483  Sum_probs=78.9

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|++..+. ++.++|||||+|.+.++|.+|++.|||..++|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34567799999999999999999999999999999999987 78899999999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      ++++.
T Consensus        91 ~a~~~   95 (105)
T 1x5u_A           91 KASAH   95 (105)
T ss_dssp             ETTTT
T ss_pred             ECCCC
Confidence            99865

>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=99.76  E-value=3.7e-18  Score=130.63  Aligned_cols=82  Identities=35%  Similarity=0.513  Sum_probs=77.7

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|++..+.+|.++|||||+|.+.++|.+|++.|||..++|+.|+|+|
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34567799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hh
Q 012257          397 AQ  398 (467)
Q Consensus       397 ~~  398 (467)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=3e-18  Score=129.05  Aligned_cols=82  Identities=22%  Similarity=0.437  Sum_probs=76.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ....++|||+|||..+++++|+++|++||.|.+|+++.+. ++.++|||||+|.+.++|.+|++ ||+..++|+.|+|++
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            4567799999999999999999999999999999999986 68899999999999999999998 999999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      ++++
T Consensus        86 a~~~   89 (99)
T 2dgs_A           86 AEPR   89 (99)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9755

>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=99.76  E-value=3.2e-18  Score=135.17  Aligned_cols=92  Identities=24%  Similarity=0.381  Sum_probs=83.5

Q ss_pred             CCCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCc
Q 012257           30 GVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK  109 (467)
Q Consensus        30 ~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  109 (467)
                      .+.+....++++|||+|||+++++++|+++|+.||.|.+|.+..++.++.++|||||+|.+.++|++|++.|++..|.|+
T Consensus        13 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   92 (126)
T 3ex7_B           13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ   92 (126)
T ss_dssp             -CCBCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCe
Confidence            33455566789999999999999999999999999999999999998999999999999999999999999999999999


Q ss_pred             eeeeeecccCcc
Q 012257          110 PIRIMYSYRDPT  121 (467)
Q Consensus       110 ~~~v~~~~~~~~  121 (467)
                      .|+|.++.....
T Consensus        93 ~l~v~~a~~~~~  104 (126)
T 3ex7_B           93 PISVDWCFVRGP  104 (126)
T ss_dssp             BCEEEESEESSS
T ss_pred             EEEEEEecCCCC
Confidence            999999875543

>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=99.76  E-value=1e-17  Score=127.06  Aligned_cols=88  Identities=19%  Similarity=0.332  Sum_probs=79.5

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      .....+.++|||+|||+++++++|+++|+.||.|.+|.+.+++.+++++|||||+|.+.++|++|++  ++..+.|+.|+
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~   86 (103)
T 2cqg_A            9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCD   86 (103)
T ss_dssp             SCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEE
T ss_pred             CCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEE
Confidence            3444568999999999999999999999999999999999999999999999999999999999998  46789999999


Q ss_pred             eeecccCccc
Q 012257          113 IMYSYRDPTI  122 (467)
Q Consensus       113 v~~~~~~~~~  122 (467)
                      |.++......
T Consensus        87 v~~a~~~~~~   96 (103)
T 2cqg_A           87 CKLPNSKQSQ   96 (103)
T ss_dssp             EECCCTTCCC
T ss_pred             EEecCCCCcC
Confidence            9998765443

>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=3.5e-18  Score=132.25  Aligned_cols=83  Identities=27%  Similarity=0.404  Sum_probs=78.3

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ...+++|||+|||.++++++|+++|+.||.|.+|.+..++.+++++|||||+|.+.++|++|+ .|++..|.|+.|+|.+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~  100 (114)
T 2cq4_A           22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQA  100 (114)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEe
Confidence            346799999999999999999999999999999999999999999999999999999999999 8999999999999998


Q ss_pred             cccC
Q 012257          116 SYRD  119 (467)
Q Consensus       116 ~~~~  119 (467)
                      +...
T Consensus       101 a~~~  104 (114)
T 2cq4_A          101 SQAE  104 (114)
T ss_dssp             HHHH
T ss_pred             cCCC
Confidence            7644

>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=99.76  E-value=1.6e-18  Score=132.01  Aligned_cols=87  Identities=25%  Similarity=0.483  Sum_probs=80.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ..++|||+|||..+++++|+++|++||.|.++++..+. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+++.
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            34589999999999999999999999999999999885 78899999999999999999999999999999999999999


Q ss_pred             hhHHHHHH
Q 012257          399 RKEERRAR  406 (467)
Q Consensus       399 ~~~~~~~~  406 (467)
                      +.......
T Consensus        87 ~~~~~~~~   94 (104)
T 1p1t_A           87 SEKNKEEL   94 (104)
T ss_dssp             CTTHHHHH
T ss_pred             Cccchhhh
Confidence            87665543

>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=99.76  E-value=9.1e-18  Score=125.30  Aligned_cols=85  Identities=16%  Similarity=0.199  Sum_probs=74.3

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHh--CCcccCCc
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL--NFTPLNGK  109 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l--~~~~~~g~  109 (467)
                      +.....++++|||+|||++++|++|+++|++||.|.+|.+.++      +|||||+|.+.++|.+|++.+  ++..+.|+
T Consensus         8 ~~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr   81 (101)
T 2cq1_A            8 DKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQ   81 (101)
T ss_dssp             CCCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCc
Confidence            3455567899999999999999999999999999999999865      479999999999999999976  46679999


Q ss_pred             eeeeeecccCccc
Q 012257          110 PIRIMYSYRDPTI  122 (467)
Q Consensus       110 ~~~v~~~~~~~~~  122 (467)
                      .|+|.++......
T Consensus        82 ~l~V~~a~~~~~~   94 (101)
T 2cq1_A           82 PIYIQYSNHKELK   94 (101)
T ss_dssp             ECEEEECSCSSCC
T ss_pred             EEEEEEcCcccCc
Confidence            9999998765443

>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=99.76  E-value=4.4e-18  Score=129.15  Aligned_cols=83  Identities=28%  Similarity=0.500  Sum_probs=77.1

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|++..+..+ ++|||||+|.+.++|.+|++.|||..|+|+.|+|.+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999999998765 899999999999999999999999999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      ++++
T Consensus        90 a~~~   93 (103)
T 2cq3_A           90 ATAR   93 (103)
T ss_dssp             CCSS
T ss_pred             cccC
Confidence            9765

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.6e-18  Score=129.85  Aligned_cols=82  Identities=33%  Similarity=0.614  Sum_probs=77.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEE-EEeeC-CCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSC-KVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v-~i~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .+.++|||+|||..+++++|+++|++||.|.++ +++.+ .++.++|||||+|.+.++|.+|++.|||..++|+.|+|+|
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            356789999999999999999999999999999 99998 5888999999999999999999999999999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      ++++
T Consensus        83 a~~~   86 (96)
T 1x5t_A           83 AFKK   86 (96)
T ss_dssp             SCCC
T ss_pred             eccc
Confidence            9755

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=4e-18  Score=132.41  Aligned_cols=88  Identities=19%  Similarity=0.405  Sum_probs=80.5

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....+.++|||+|||+++++++|+++|+.||.|.+|.+.+++.+++++|||||+|.+.++|++|++. ++..|.|+.|+|
T Consensus        22 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V  100 (116)
T 1x4b_A           22 REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEP  100 (116)
T ss_dssp             CHHHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEE
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEE
Confidence            3344579999999999999999999999999999999999999999999999999999999999996 999999999999


Q ss_pred             eecccCccc
Q 012257          114 MYSYRDPTI  122 (467)
Q Consensus       114 ~~~~~~~~~  122 (467)
                      .++......
T Consensus       101 ~~a~~~~~~  109 (116)
T 1x4b_A          101 KRAVAREES  109 (116)
T ss_dssp             ECCSSCCCC
T ss_pred             EECCCCccC
Confidence            998766543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.76  E-value=3.5e-18  Score=132.54  Aligned_cols=84  Identities=30%  Similarity=0.568  Sum_probs=78.9

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      .....++|||+|||..+++++|+++|+.||.|.+|+++.+. ++.++|||||+|.+.++|.+|++.|||..|+|+.|+|.
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            44567899999999999999999999999999999999986 78999999999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++++
T Consensus        91 ~a~~~   95 (115)
T 2dgo_A           91 WATRK   95 (115)
T ss_dssp             ESSCC
T ss_pred             EccCC
Confidence            99765

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.76  E-value=5.2e-18  Score=136.86  Aligned_cols=87  Identities=28%  Similarity=0.498  Sum_probs=79.9

Q ss_pred             CCCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCc
Q 012257           30 GVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK  109 (467)
Q Consensus        30 ~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  109 (467)
                      ........+.++|||+|||.++++++|+++|++||.|.+|++.+++.+++++|||||+|.+.++|++|++.|++..+.|+
T Consensus        54 ~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  133 (140)
T 2ku7_A           54 GGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR  133 (140)
T ss_dssp             CSSCSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTE
T ss_pred             CCCCCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            33445556789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeeeec
Q 012257          110 PIRIMYS  116 (467)
Q Consensus       110 ~~~v~~~  116 (467)
                      .|+|.++
T Consensus       134 ~l~v~~A  140 (140)
T 2ku7_A          134 TIRVNLA  140 (140)
T ss_dssp             EEEEEC-
T ss_pred             EEEEEeC
Confidence            9999864

>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=3.7e-18  Score=128.51  Aligned_cols=84  Identities=11%  Similarity=0.228  Sum_probs=76.0

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ......++|||+|||++++|++|+++|+.||.+ +|+|+.++ +++++|||||+|.+.++|++|++ +++..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (102)
T 1wez_A           10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVEL   86 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEE
Confidence            445567999999999999999999999999965 99999998 89999999999999999999996 7999999999999


Q ss_pred             eecccCc
Q 012257          114 MYSYRDP  120 (467)
Q Consensus       114 ~~~~~~~  120 (467)
                      .++...+
T Consensus        87 ~~~~~~~   93 (102)
T 1wez_A           87 FLNSTAG   93 (102)
T ss_dssp             EEECCCC
T ss_pred             EECCCCC
Confidence            8876543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=1.2e-17  Score=129.37  Aligned_cols=85  Identities=25%  Similarity=0.391  Sum_probs=78.7

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....++++|||+|||+++++++|+++|+.||.|.+|++.+++ +++++|||||+|.+.++|++|++.|++..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   88 (114)
T 2do0_A           10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV   88 (114)
T ss_dssp             CCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEE
Confidence            344568999999999999999999999999999999999997 5899999999999999999999999999999999999


Q ss_pred             eecccC
Q 012257          114 MYSYRD  119 (467)
Q Consensus       114 ~~~~~~  119 (467)
                      .++...
T Consensus        89 ~~a~~~   94 (114)
T 2do0_A           89 KMDERA   94 (114)
T ss_dssp             EECSCC
T ss_pred             EEcccC
Confidence            997643

>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=99.75  E-value=7.1e-18  Score=126.77  Aligned_cols=85  Identities=16%  Similarity=0.142  Sum_probs=73.7

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCc--ccCCc
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFT--PLNGK  109 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~--~~~g~  109 (467)
                      +.....++++|||+|||++++|++|+++|++||.|.+|.+.++      +|||||+|.+.++|.+|++.+++.  .+.|+
T Consensus         8 ~~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr   81 (104)
T 1wex_A            8 SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             SCCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             CCCcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            3444567899999999999999999999999999999999864      479999999999999999988654  58999


Q ss_pred             eeeeeecccCccc
Q 012257          110 PIRIMYSYRDPTI  122 (467)
Q Consensus       110 ~~~v~~~~~~~~~  122 (467)
                      .|+|.++......
T Consensus        82 ~l~V~~a~~~~~~   94 (104)
T 1wex_A           82 QAFFNYSTSKRIT   94 (104)
T ss_dssp             BCEEEECSSSSCC
T ss_pred             EEEEEEccCcccc
Confidence            9999998765443

>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=99.75  E-value=7.9e-18  Score=127.64  Aligned_cols=83  Identities=18%  Similarity=0.247  Sum_probs=75.8

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEE-EEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVS-VRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~-v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ..+.++|||+|||+++++++|+++|+.||.|.+ |.|..+ .+++++|||||+|.+.++|++|++. ++..+.|+.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            355799999999999999999999999999987 888888 7899999999999999999999996 9999999999998


Q ss_pred             ecccCc
Q 012257          115 YSYRDP  120 (467)
Q Consensus       115 ~~~~~~  120 (467)
                      ++...+
T Consensus        90 ~~~~~~   95 (104)
T 1wg5_A           90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            876543

>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=99.75  E-value=1.4e-18  Score=129.90  Aligned_cols=80  Identities=18%  Similarity=0.242  Sum_probs=75.9

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      +.++|||+|||+++++++|+++|++||.|.++.++.++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999998764

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=3e-18  Score=131.20  Aligned_cols=84  Identities=26%  Similarity=0.485  Sum_probs=78.4

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC--CCCccceEEEEcCCHHHHHHHHHHh-CCcEecccceE
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP--NGISRGSGFVAFSTAEEASKALTEM-NGKMVVSKPLY  393 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~--~~~~~g~afV~f~~~~~A~~A~~~l-~g~~~~g~~l~  393 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|+++.+.  ++.++|||||+|.+.++|.+|++.| ||..|.|+.|+
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            44567899999999999999999999999999999999884  8889999999999999999999999 99999999999


Q ss_pred             Eehhhhh
Q 012257          394 VALAQRK  400 (467)
Q Consensus       394 v~~~~~~  400 (467)
                      |+|+++.
T Consensus        91 v~~a~~~   97 (107)
T 2cph_A           91 LEWADSE   97 (107)
T ss_dssp             EEECCCC
T ss_pred             EEeCCCC
Confidence            9999765

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=3.3e-18  Score=128.58  Aligned_cols=81  Identities=37%  Similarity=0.658  Sum_probs=75.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCC--C--CccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN--G--ISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~--~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      +.++|||+|||..+++++|+++|++||.|.+|++..+..  |  .++|||||+|.+.++|.+|++.|||..+.|+.|+|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            567899999999999999999999999999999998764  4  789999999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      ++++.
T Consensus        84 ~a~~~   88 (98)
T 2cpf_A           84 ISERA   88 (98)
T ss_dssp             CSSCS
T ss_pred             EccCC
Confidence            99765

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.75  E-value=2e-18  Score=130.54  Aligned_cols=92  Identities=22%  Similarity=0.398  Sum_probs=80.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecccC
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRD  119 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~  119 (467)
                      ++|||+|||+++++++|+++|++||.|.+|.+.++     ++|||||+|.+.++|++|++.|++..+.|+.|+|.++...
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            58999999999999999999999999999999887     5689999999999999999999999999999999998765


Q ss_pred             cccc--------cCCCccEEEcCCC
Q 012257          120 PTIR--------KSGAGNIFIKNLD  136 (467)
Q Consensus       120 ~~~~--------~~~~~~l~v~nlp  136 (467)
                      +...        .....+|||+||+
T Consensus        76 ~~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           76 PRRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             CCcccCCCCCccccCCCceecCCCC
Confidence            4221        1225679999986

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=3e-18  Score=130.34  Aligned_cols=83  Identities=34%  Similarity=0.537  Sum_probs=78.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhcc-CCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcE-ecccceEEe
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSE-FGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKM-VVSKPLYVA  395 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~-~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~-~~g~~l~v~  395 (467)
                      ....++|||+|||..+++++|+++|++ ||.|.+|+++.+.+|.++|||||+|.+.++|.+|++.|||.. ++|+.|+|+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            345678999999999999999999999 999999999999999999999999999999999999999999 999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      ++.++
T Consensus        86 ~a~~~   90 (104)
T 2dhg_A           86 VAIPK   90 (104)
T ss_dssp             BCCCC
T ss_pred             EccCC
Confidence            99755

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.2e-18  Score=130.62  Aligned_cols=83  Identities=31%  Similarity=0.443  Sum_probs=77.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ....++|||+|||..+++++|+++|++||.|.+|+++.+. ++.++|||||+|.+.++|.+|++.|||..|+|+.|+|.|
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            3466789999999999999999999999999999999885 688999999999999999999999999999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      +++.
T Consensus        89 a~~~   92 (102)
T 2cqb_A           89 AKPM   92 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9765

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=1.7e-18  Score=123.80  Aligned_cols=76  Identities=26%  Similarity=0.472  Sum_probs=73.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ++|||+|||+++++++|+++|++||.|.++.+.+++.+++++|||||+|.+.++|++|++.++ ..+.|+.++|.++
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            589999999999999999999999999999999999899999999999999999999999888 8999999999875

>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=99.75  E-value=3.3e-18  Score=127.75  Aligned_cols=80  Identities=23%  Similarity=0.321  Sum_probs=74.6

Q ss_pred             CCCceEEEecCCCCCCHHHHH----HhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          319 FEGLNLYVKNLDDSISDDKLK----ELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~----~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      ...++|||+|||..+++++|+    ++|++||.|.+|+++.+..+  +|||||+|.+.++|.+|++.|||..++|+.|+|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            356689999999999999999    99999999999999988766  889999999999999999999999999999999


Q ss_pred             ehhhhh
Q 012257          395 ALAQRK  400 (467)
Q Consensus       395 ~~~~~~  400 (467)
                      +++++.
T Consensus        85 ~~a~~~   90 (96)
T 2dgx_A           85 SLATGA   90 (96)
T ss_dssp             EECCCS
T ss_pred             EEcCCC
Confidence            998754

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=8.2e-18  Score=124.46  Aligned_cols=82  Identities=16%  Similarity=0.359  Sum_probs=76.8

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      .....++|||+|||+++++++|+++|+.| .|.+|.++++ .+|+++|||||+|.+.++|++|++ +++..+.|+.|+|.
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~   82 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVF   82 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEE
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEE
Confidence            34568999999999999999999999999 9999999999 789999999999999999999999 99999999999999


Q ss_pred             ecccC
Q 012257          115 YSYRD  119 (467)
Q Consensus       115 ~~~~~  119 (467)
                      ++...
T Consensus        83 ~a~~~   87 (91)
T 2dgw_A           83 REKSG   87 (91)
T ss_dssp             EESSC
T ss_pred             ECCcC
Confidence            98655

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=2.3e-18  Score=130.68  Aligned_cols=84  Identities=29%  Similarity=0.436  Sum_probs=78.0

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|++..+. ++.++|||||+|.+.++|.+|++.|||..++|+.|+|+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34467799999999999999999999999999999999886 58899999999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      +++..
T Consensus        89 ~a~~~   93 (103)
T 2dnm_A           89 VARYG   93 (103)
T ss_dssp             ECSSC
T ss_pred             ECCcC
Confidence            99754

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.9e-18  Score=131.20  Aligned_cols=84  Identities=26%  Similarity=0.464  Sum_probs=77.1

Q ss_pred             ccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       316 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ......++|||+|||..+++++|+++|++||.|.+|++..+.. .++|||||+|.+.++|.+|++.|||..++|+.|+|+
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3445678999999999999999999999999999999998864 489999999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      +++++
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            98754

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

Probab=99.75  E-value=3.9e-18  Score=126.57  Aligned_cols=82  Identities=27%  Similarity=0.425  Sum_probs=76.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|||+|||..+++++|+++|++||.|.++++..+ ++.++|||||+|.+.++|.+|++.|||..++|+.|+|+++
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            346779999999999999999999999999999999984 7889999999999999999999999999999999999998


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ++.
T Consensus        84 ~~~   86 (92)
T 2dgv_A           84 RNA   86 (92)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            754

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=4.7e-18  Score=127.99  Aligned_cols=83  Identities=24%  Similarity=0.423  Sum_probs=77.5

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCcee-EEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccc----
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTIT-SCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP----  391 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~-~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~----  391 (467)
                      ....++|||+|||..+++++|+++|++||.|. +|+++.+. ++.++|||||+|.+.++|.+|++.|||..+.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34677999999999999999999999999999 99999986 7889999999999999999999999999999999    


Q ss_pred             eEEehhhhh
Q 012257          392 LYVALAQRK  400 (467)
Q Consensus       392 l~v~~~~~~  400 (467)
                      |+|+|+++.
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999998754

>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=99.75  E-value=4.1e-18  Score=131.00  Aligned_cols=84  Identities=25%  Similarity=0.480  Sum_probs=78.4

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|+++.+. +|.++|||||+|.+.++|.+|+..|||..++|+.|+|+
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            34567789999999999999999999999999999999885 78899999999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++++
T Consensus       102 ~a~~~  106 (110)
T 1oo0_B          102 WCFVK  106 (110)
T ss_dssp             ESEES
T ss_pred             EcccC
Confidence            99765

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.75  E-value=1.9e-17  Score=130.18  Aligned_cols=85  Identities=27%  Similarity=0.450  Sum_probs=79.8

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ...++++|||+|||+++++++|+++|+.||.|.+|++.+++ +|+++|||||+|.+.++|++|++.+++..+.|+.|+|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            45668999999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             ecccCc
Q 012257          115 YSYRDP  120 (467)
Q Consensus       115 ~~~~~~  120 (467)
                      ++....
T Consensus       110 ~a~~~~  115 (124)
T 2kt5_A          110 LVASQI  115 (124)
T ss_dssp             EECCTT
T ss_pred             EeCCCC
Confidence            987543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.8e-18  Score=130.01  Aligned_cols=83  Identities=31%  Similarity=0.521  Sum_probs=77.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ..+.++|||+|||..+++++|+++|++||.|.+|++..+. ++.++|||||+|.+.++|.+|++.|||..|.|+.|+|+|
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3466799999999999999999999999999999999886 678899999999999999999999999999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      +++.
T Consensus        89 a~~~   92 (102)
T 1x5s_A           89 AGKS   92 (102)
T ss_dssp             EECC
T ss_pred             CCCC
Confidence            9765

>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=1e-17  Score=127.96  Aligned_cols=85  Identities=16%  Similarity=0.274  Sum_probs=74.8

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCC--cccCCc
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNF--TPLNGK  109 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~--~~~~g~  109 (467)
                      +.....++++|||+|||++++|++|+++|++||.|.+|+|+++      +|||||+|.+.++|.+|++.+++  ..+.|+
T Consensus        24 ~~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr   97 (119)
T 2ad9_A           24 SRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ   97 (119)
T ss_dssp             TTSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTB
T ss_pred             ccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCe
Confidence            3444567899999999999999999999999999999999876      47999999999999999998874  579999


Q ss_pred             eeeeeecccCccc
Q 012257          110 PIRIMYSYRDPTI  122 (467)
Q Consensus       110 ~~~v~~~~~~~~~  122 (467)
                      .|+|.++...+..
T Consensus        98 ~l~V~~a~~k~~~  110 (119)
T 2ad9_A           98 PIYIQFSNHKELK  110 (119)
T ss_dssp             CCEEEECSSSSCC
T ss_pred             EEEEEEccCCCCC
Confidence            9999998766544

>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=99.74  E-value=5.5e-18  Score=128.59  Aligned_cols=83  Identities=30%  Similarity=0.488  Sum_probs=76.7

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|++..+..+ ++|||||+|.+.++|.+|++.|||..+.|+.|+|+|
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            3456789999999999999999999999999999999998654 689999999999999999999999999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      +++.
T Consensus        90 a~~~   93 (103)
T 2cqi_A           90 ATTP   93 (103)
T ss_dssp             CCCT
T ss_pred             CCCC
Confidence            9864

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.74  E-value=2.2e-18  Score=122.49  Aligned_cols=75  Identities=21%  Similarity=0.467  Sum_probs=71.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        41 ~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      +|||+|||+++++++|+++|++||.|.+|.+.+++.+++++|||||+|.+.++|++|++ +++..+.|+.|+|.++
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            58999999999999999999999999999999999899999999999999999999998 9999999999999764

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=5e-18  Score=129.86  Aligned_cols=82  Identities=24%  Similarity=0.464  Sum_probs=75.7

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..+.++|||+|||.++++++|+++|++||.|.+|++.+++  +.++|||||+|.+.++|++|++.|++..+.|+.|+|.+
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4468999999999999999999999999999999999885  34889999999999999999999999999999999998


Q ss_pred             cccC
Q 012257          116 SYRD  119 (467)
Q Consensus       116 ~~~~  119 (467)
                      +...
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8653

>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=99.74  E-value=6.3e-18  Score=126.18  Aligned_cols=79  Identities=18%  Similarity=0.362  Sum_probs=71.6

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhC--CcEecccceEE
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN--GKMVVSKPLYV  394 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~--g~~~~g~~l~v  394 (467)
                      ...++++|||+|||+.+++++|+++|++||.|.+|+++++     +|||||+|.+.++|.+|++.|+  +..+.|+.|+|
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            3456789999999999999999999999999999998875     7899999999999999999874  67899999999


Q ss_pred             ehhhhh
Q 012257          395 ALAQRK  400 (467)
Q Consensus       395 ~~~~~~  400 (467)
                      +|++.+
T Consensus        86 ~~a~~~   91 (101)
T 2cq1_A           86 QYSNHK   91 (101)
T ss_dssp             EECSCS
T ss_pred             EEcCcc
Confidence            999754

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.74  E-value=3.4e-18  Score=133.32  Aligned_cols=82  Identities=35%  Similarity=0.544  Sum_probs=76.2

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|++..+. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+
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            34567899999999999999999999999999999999885 68899999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          396 LAQ  398 (467)
Q Consensus       396 ~~~  398 (467)
                      |++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            875

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.74  E-value=3.8e-18  Score=134.36  Aligned_cols=84  Identities=26%  Similarity=0.373  Sum_probs=78.4

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ...+.++|||+|||..+++++|+++|++||.|.+|++..+. ++.++|||||+|.+.++|.+|++.|||..|+|+.|+|+
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            34567789999999999999999999999999999999886 67899999999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++++
T Consensus       122 ~a~~~  126 (129)
T 2kxn_B          122 FSITK  126 (129)
T ss_dssp             CCSSS
T ss_pred             EecCC
Confidence            99765

>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=99.74  E-value=1.5e-18  Score=129.25  Aligned_cols=77  Identities=21%  Similarity=0.319  Sum_probs=70.6

Q ss_pred             CCCceEEEecCCC-CCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCc--EecccceEEe
Q 012257          319 FEGLNLYVKNLDD-SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGK--MVVSKPLYVA  395 (467)
Q Consensus       319 ~~~~~l~V~nlp~-~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~--~~~g~~l~v~  395 (467)
                      .++++|||+|||+ .+++++|+++|++||.|.+|+++++     +|||||+|.+.++|.+|++.||+.  .|.|++|+|+
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   87 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   87 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEE
Confidence            3677999999999 9999999999999999999999875     579999999999999999999865  5999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++..
T Consensus        88 ~a~~~   92 (102)
T 1x4d_A           88 LSQKY   92 (102)
T ss_dssp             EECCC
T ss_pred             ECCCC
Confidence            99854

>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=99.74  E-value=9e-18  Score=128.97  Aligned_cols=89  Identities=18%  Similarity=0.318  Sum_probs=80.4

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHH---HHHhcCCCeEEEEEEecCCCC---ccccEEEEEecChHHHHHHHHHhCCcc
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLY---DLFNQMGQVVSVRVCRDLSTR---RSLGYGYVNYNAAHEATRALDELNFTP  105 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~---~~f~~~G~v~~v~i~~~~~~~---~~~g~afV~f~~~~~A~~A~~~l~~~~  105 (467)
                      ...+....++|||+|||+++++++|+   ++|++||.|.+|.+.+++.++   +++|||||+|.+.++|++|++.|++..
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            34556678999999999999999999   999999999999999987754   456999999999999999999999999


Q ss_pred             cCCceeeeeecccCc
Q 012257          106 LNGKPIRIMYSYRDP  120 (467)
Q Consensus       106 ~~g~~~~v~~~~~~~  120 (467)
                      +.|+.|+|.++..++
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            999999999987665

>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=6.8e-18  Score=129.61  Aligned_cols=87  Identities=16%  Similarity=0.273  Sum_probs=79.6

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCC-eEEEEEE-ecCCCCccccEEEEEecChHHHHHHHHHhC--CcccCCce
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQ-VVSVRVC-RDLSTRRSLGYGYVNYNAAHEATRALDELN--FTPLNGKP  110 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~-v~~v~i~-~~~~~~~~~g~afV~f~~~~~A~~A~~~l~--~~~~~g~~  110 (467)
                      .+.+.++|||+|||+++++++|+++|+.||. |.+|.+. .++.+++++|||||+|.+.++|++|++.|+  +..+.|+.
T Consensus         4 ~s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~   83 (109)
T 2dis_A            4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQ   83 (109)
T ss_dssp             CCCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBC
T ss_pred             cccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCe
Confidence            3456899999999999999999999999998 9999999 888889999999999999999999999996  58999999


Q ss_pred             eeeeecccCcc
Q 012257          111 IRIMYSYRDPT  121 (467)
Q Consensus       111 ~~v~~~~~~~~  121 (467)
                      |+|.++.....
T Consensus        84 l~V~~a~~~~~   94 (109)
T 2dis_A           84 IAVDWAEPEID   94 (109)
T ss_dssp             CEEEESCSSCS
T ss_pred             EEEEEcCCCCC
Confidence            99999876544

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.74  E-value=2.8e-18  Score=130.89  Aligned_cols=87  Identities=13%  Similarity=0.164  Sum_probs=79.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCc---eeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGT---ITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~---v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      ....++|||+|||+.+++++|+++|+.||.   |.+|+++.+..|+++|||||+|.+.++|.+|+. +|+..++|+.|+|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            346678999999999999999999999988   899999999889999999999999999999999 9999999999999


Q ss_pred             ehhhhhHHHHH
Q 012257          395 ALAQRKEERRA  405 (467)
Q Consensus       395 ~~~~~~~~~~~  405 (467)
                      .++.+......
T Consensus        87 ~~a~~~~~~~~   97 (107)
T 2lmi_A           87 YEINNEDVDAL   97 (107)
T ss_dssp             EECCHHHHHHH
T ss_pred             EECCHHHHHHH
Confidence            99987765443

>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=4.2e-18  Score=131.52  Aligned_cols=83  Identities=13%  Similarity=0.189  Sum_probs=76.8

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCe-EEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQV-VSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v-~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ...+.++|||+|||+++++++|+++|+.||.| .+|+|+.++ +++++|||||+|.+.++|++|++. ++..|.|+.|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v   88 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            34567999999999999999999999999999 899999998 899999999999999999999986 999999999999


Q ss_pred             eecccC
Q 012257          114 MYSYRD  119 (467)
Q Consensus       114 ~~~~~~  119 (467)
                      .++...
T Consensus        89 ~~a~~~   94 (114)
T 2cpy_A           89 HVVTLE   94 (114)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            887543

>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=5.2e-18  Score=129.58  Aligned_cols=78  Identities=15%  Similarity=0.373  Sum_probs=71.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCC--cEecccceEEe
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNG--KMVVSKPLYVA  395 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g--~~~~g~~l~v~  395 (467)
                      ..++++|||+|||+.+++++|+++|++||.|.+|+++++     +|||||+|++.++|.+|++.|++  ..+.|+.|+|+
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            446779999999999999999999999999999999875     78999999999999999999884  68999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++.+
T Consensus       103 ~a~~k  107 (119)
T 2ad9_A          103 FSNHK  107 (119)
T ss_dssp             ECSSS
T ss_pred             EccCC
Confidence            99755

>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=99.74  E-value=7.6e-18  Score=124.19  Aligned_cols=79  Identities=19%  Similarity=0.430  Sum_probs=74.8

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      .++|||+|||..+++++|+++|++||.|.++++..+. ++.++|||||+|.+.++|.+|+ .|||..+.|+.|+|+++++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            4589999999999999999999999999999999986 7889999999999999999999 9999999999999999875


Q ss_pred             h
Q 012257          400 K  400 (467)
Q Consensus       400 ~  400 (467)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.74  E-value=5.4e-18  Score=133.79  Aligned_cols=84  Identities=18%  Similarity=0.258  Sum_probs=78.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCc---eeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGT---ITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~---v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ...++|||+|||+.+|+++|+++|+.||.   |.+|+|+.+..|+++|||||+|.+.++|.+|++ |||..|+|+.|+|.
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVF  120 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            45678999999999999999999999999   899999999889999999999999999999999 99999999999999


Q ss_pred             hhhhhHHH
Q 012257          396 LAQRKEER  403 (467)
Q Consensus       396 ~~~~~~~~  403 (467)
                      ++.+....
T Consensus       121 ~a~~~e~~  128 (136)
T 2hgl_A          121 KSHRTEMD  128 (136)
T ss_dssp             ECCHHHHH
T ss_pred             ECChHHHH
Confidence            99876543

>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=99.74  E-value=7.3e-18  Score=129.95  Aligned_cols=84  Identities=30%  Similarity=0.503  Sum_probs=78.1

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhC------CcEecc
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMN------GKMVVS  389 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~------g~~~~g  389 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|++..+. ++.++|||||+|.+.++|.+|++.||      |..++|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            34467789999999999999999999999999999999886 68899999999999999999999999      999999


Q ss_pred             cceEEehhhhh
Q 012257          390 KPLYVALAQRK  400 (467)
Q Consensus       390 ~~l~v~~~~~~  400 (467)
                      +.|+|.|+.++
T Consensus        91 ~~l~v~~a~~~  101 (111)
T 1x4h_A           91 RQLKVDLAVTR  101 (111)
T ss_dssp             CEEEEECCCCC
T ss_pred             EEEEEEECCCC
Confidence            99999999765

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=2.9e-18  Score=125.19  Aligned_cols=80  Identities=26%  Similarity=0.403  Sum_probs=74.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      .+.++|||+|||..+++++|+++|++||.|.++++..+. +|.++|||||+|.+.++|.+|++.|||..+.|+.|+++++
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            356789999999999999999999999999999999885 6889999999999999999999999999999999999876


Q ss_pred             h
Q 012257          398 Q  398 (467)
Q Consensus       398 ~  398 (467)
                      +
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.73  E-value=1.4e-17  Score=122.09  Aligned_cols=79  Identities=28%  Similarity=0.488  Sum_probs=73.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ....++|||+|||..+++++|+++|++||.|.+++++.+. +|.++|||||+|.+.++|.+|++ +++..++|+.|+|++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            4567799999999999999999999999999999999986 68999999999999999999996 588999999999987


Q ss_pred             h
Q 012257          397 A  397 (467)
Q Consensus       397 ~  397 (467)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=7.5e-18  Score=130.24  Aligned_cols=84  Identities=26%  Similarity=0.474  Sum_probs=78.0

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCcee--------EEEEeeC-CCCCccceEEEEcCCHHHHHHHHHHhCCcEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTIT--------SCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKMV  387 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~--------~v~i~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  387 (467)
                      .....++|||+|||..+++++|+++|++||.|.        .|++..+ .++.++|||||+|.+.++|.+|++.|||..|
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            345678999999999999999999999999999        6999998 4789999999999999999999999999999


Q ss_pred             cccceEEehhhhh
Q 012257          388 VSKPLYVALAQRK  400 (467)
Q Consensus       388 ~g~~l~v~~~~~~  400 (467)
                      .|+.|+|++++++
T Consensus        91 ~g~~l~V~~a~~~  103 (113)
T 2cpe_A           91 QGSKLKVSLARKK  103 (113)
T ss_dssp             TTEECEEECSSCC
T ss_pred             CCCEEEEEECCCC
Confidence            9999999999765

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.1e-17  Score=123.72  Aligned_cols=81  Identities=17%  Similarity=0.266  Sum_probs=76.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|||+|||..+++++|+++|+.| .|.+|+++.+.+|+++|||||+|.+.++|.+|++ |||..|+|+.|+|.++
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            3456789999999999999999999999 9999999999899999999999999999999999 9999999999999998


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      +++
T Consensus        85 ~~~   87 (91)
T 2dgw_A           85 KSG   87 (91)
T ss_dssp             SSC
T ss_pred             CcC
Confidence            754

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.73  E-value=4e-18  Score=135.55  Aligned_cols=90  Identities=24%  Similarity=0.372  Sum_probs=82.8

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      .+....+.++|||+|||+++++++|+++|+.||.|.+|++..++.+++++|||||+|.+.++|++|++.|++..+.|+.|
T Consensus        40 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l  119 (135)
T 2lea_A           40 PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL  119 (135)
T ss_dssp             SCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34455668999999999999999999999999999999999999899999999999999999999999999999999999


Q ss_pred             eeeecccCcc
Q 012257          112 RIMYSYRDPT  121 (467)
Q Consensus       112 ~v~~~~~~~~  121 (467)
                      +|.++.....
T Consensus       120 ~V~~a~~~~~  129 (135)
T 2lea_A          120 RVQMARYGRP  129 (135)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEECCCCCC
Confidence            9999876543

>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=1.2e-17  Score=138.21  Aligned_cols=93  Identities=20%  Similarity=0.333  Sum_probs=82.3

Q ss_pred             CCCCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC
Q 012257           29 GGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG  108 (467)
Q Consensus        29 ~~~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g  108 (467)
                      ..+.+....++++|||+|||+++++++|+++|+.||.|..|.|..++.+|.++|||||+|.+.++|.+|++.|++..|.|
T Consensus        62 ~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  141 (165)
T 1rk8_A           62 LEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG  141 (165)
T ss_dssp             ----CCCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            34455667778999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeeeeecccCcc
Q 012257          109 KPIRIMYSYRDPT  121 (467)
Q Consensus       109 ~~~~v~~~~~~~~  121 (467)
                      +.|.|.|+.....
T Consensus       142 ~~l~V~~a~~~~~  154 (165)
T 1rk8_A          142 QTIQVDWCFVKGP  154 (165)
T ss_dssp             EECEEEESEECC-
T ss_pred             EEEEEEEecCCCC
Confidence            9999999876543

>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=3e-17  Score=129.15  Aligned_cols=82  Identities=20%  Similarity=0.423  Sum_probs=77.6

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .+.++|||+|||.++++++|+++|+.||.|.+|.+.+++.+++++|||||+|.+.++|.+|+ .+++..|.|+.|+|.++
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  112 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK  112 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            35799999999999999999999999999999999999999999999999999999999999 69999999999999998


Q ss_pred             ccC
Q 012257          117 YRD  119 (467)
Q Consensus       117 ~~~  119 (467)
                      ...
T Consensus       113 ~~~  115 (124)
T 2jwn_A          113 RTN  115 (124)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.73  E-value=8.7e-18  Score=130.37  Aligned_cols=80  Identities=14%  Similarity=0.133  Sum_probs=74.9

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCC---eEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQ---VVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~---v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      ..+.++|||+|||+++++++|+++|+.||.   |.+|+|..++. |+++|||||+|.+.++|++|++ +++..|.|+.|+
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            345799999999999999999999999998   89999999986 9999999999999999999999 999999999999


Q ss_pred             eeecc
Q 012257          113 IMYSY  117 (467)
Q Consensus       113 v~~~~  117 (467)
                      |.++.
T Consensus        92 V~~a~   96 (118)
T 2db1_A           92 VFKSH   96 (118)
T ss_dssp             EEEEC
T ss_pred             EEECC
Confidence            98764

>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=99.73  E-value=8.5e-18  Score=130.09  Aligned_cols=82  Identities=20%  Similarity=0.459  Sum_probs=76.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ..++|||+|||..+++++|+++|+.||.|.+|+++.+. +|.++|||||+|.+.++|.+|+ .|||..|+|+.|+|++++
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            34689999999999999999999999999999999887 4889999999999999999999 999999999999999998


Q ss_pred             hhHH
Q 012257          399 RKEE  402 (467)
Q Consensus       399 ~~~~  402 (467)
                      +...
T Consensus       103 ~~~~  106 (114)
T 2cq4_A          103 AEKN  106 (114)
T ss_dssp             HHHH
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=99.73  E-value=8.4e-18  Score=127.77  Aligned_cols=82  Identities=22%  Similarity=0.428  Sum_probs=76.2

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCC--CCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN--GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      .....++|||+|||..+++++|+++|+.|| |.+|+++.+..  |.++|||||+|.+.++|.+|+ .|||..|.|+.|+|
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 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            345668999999999999999999999999 99999999874  889999999999999999999 99999999999999


Q ss_pred             ehhhhh
Q 012257          395 ALAQRK  400 (467)
Q Consensus       395 ~~~~~~  400 (467)
                      ++++++
T Consensus        89 ~~a~~~   94 (104)
T 1wi8_A           89 DVADQA   94 (104)
T ss_dssp             EECCCC
T ss_pred             EEccCC
Confidence            999765

>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=99.73  E-value=6.5e-18  Score=124.31  Aligned_cols=81  Identities=22%  Similarity=0.416  Sum_probs=74.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCC--CCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN--GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ..++|||+|||..+++++|+++|++||.|.++++..+..  +.++|+|||+|.+.++|.+|++.|||..++|+.|+|+++
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            456899999999999999999999999999999988873  337899999999999999999999999999999999998


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      .+.
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.73  E-value=1.5e-17  Score=124.05  Aligned_cols=80  Identities=18%  Similarity=0.233  Sum_probs=74.4

Q ss_pred             ccCeEEEcCCCCCCCHHHHH----HHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           38 VSTSLYVGDLDLSVNDSQLY----DLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~----~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      +.++|||+|||+++++++|+    ++|++||.|.+|++..++.+   +|||||+|.+.++|++|++.|++..+.|+.|+|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            46899999999999999999    99999999999999998765   789999999999999999999999999999999


Q ss_pred             eecccCc
Q 012257          114 MYSYRDP  120 (467)
Q Consensus       114 ~~~~~~~  120 (467)
                      .++....
T Consensus        85 ~~a~~~~   91 (96)
T 2dgx_A           85 SLATGAS   91 (96)
T ss_dssp             EECCCSS
T ss_pred             EEcCCCC
Confidence            9986543

>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=99.73  E-value=5.2e-18  Score=129.54  Aligned_cols=84  Identities=25%  Similarity=0.568  Sum_probs=77.8

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEe---cccce
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMV---VSKPL  392 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~---~g~~l  392 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|+++.+. ++.++|||||+|.+.++|.+|++.|||..+   .|+.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            34567799999999999999999999999999999999987 588999999999999999999999999998   89999


Q ss_pred             EEehhhhh
Q 012257          393 YVALAQRK  400 (467)
Q Consensus       393 ~v~~~~~~  400 (467)
                      +|+++++.
T Consensus        89 ~v~~a~~~   96 (106)
T 2dgp_A           89 QVKPADSE   96 (106)
T ss_dssp             EEEECCCC
T ss_pred             EEEECCcc
Confidence            99999765

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.73  E-value=1.3e-17  Score=126.47  Aligned_cols=82  Identities=22%  Similarity=0.399  Sum_probs=76.0

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      .....++|||+|||..+++++|+++|++|| |.+|+++.+. ++.++|||||+|.+.++|.+|+ .|||..|.|+.|+|.
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            345677999999999999999999999997 9999999987 6889999999999999999999 899999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      ++++.
T Consensus        89 ~a~~~   93 (103)
T 2dng_A           89 IAEGR   93 (103)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            99754

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.73  E-value=4.5e-18  Score=120.87  Aligned_cols=74  Identities=23%  Similarity=0.391  Sum_probs=70.5

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      +|||+|||..+++++|+++|++||.|.++++..+. +|.++|||||+|.+.++|.+|++ +||..++|+.|+|++|
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            48999999999999999999999999999999987 78899999999999999999998 9999999999999875

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.73  E-value=1.6e-17  Score=126.16  Aligned_cols=81  Identities=12%  Similarity=0.185  Sum_probs=74.4

Q ss_pred             CccCeEEEcCCCCCC------CHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCc-
Q 012257           37 FVSTSLYVGDLDLSV------NDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK-  109 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~------~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~-  109 (467)
                      ..+++|||+|||+++      ++++|+++|++||.|.+|.+.  +.+|+++|||||+|.+.++|.+|++.|++..+.|+ 
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            347899999999999      779999999999999999998  36789999999999999999999999999999999 


Q ss_pred             eeeeeecccC
Q 012257          110 PIRIMYSYRD  119 (467)
Q Consensus       110 ~~~v~~~~~~  119 (467)
                      .|+|.++...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999988644

>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=99.73  E-value=7.5e-18  Score=129.42  Aligned_cols=83  Identities=22%  Similarity=0.360  Sum_probs=75.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHH---HhhccCCceeEEEEeeCCC----CCccceEEEEcCCHHHHHHHHHHhCCcEeccc
Q 012257          318 KFEGLNLYVKNLDDSISDDKLK---ELFSEFGTITSCKVMRDPN----GISRGSGFVAFSTAEEASKALTEMNGKMVVSK  390 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~---~~F~~~G~v~~v~i~~~~~----~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  390 (467)
                      ....++|||+|||..+++++|+   ++|++||.|.+|++..+..    +.++|||||+|.+.++|.+|++.|||..|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3456789999999999999999   9999999999999988763    35679999999999999999999999999999


Q ss_pred             ceEEehhhhh
Q 012257          391 PLYVALAQRK  400 (467)
Q Consensus       391 ~l~v~~~~~~  400 (467)
                      .|+|+|++++
T Consensus        92 ~l~V~~a~~k  101 (111)
T 2cpi_A           92 TLKASLGTTK  101 (111)
T ss_dssp             EEEEESCCCC
T ss_pred             EEEEEecccc
Confidence            9999999865

>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=99.73  E-value=7.1e-18  Score=126.76  Aligned_cols=78  Identities=19%  Similarity=0.272  Sum_probs=70.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCc--EecccceEEe
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGK--MVVSKPLYVA  395 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~--~~~g~~l~v~  395 (467)
                      ..+.++|||+|||..+++++|+++|++||.|.+|+++++     +|||||+|.+.++|.+|++.|++.  .+.|+.|+|+
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            446779999999999999999999999999999998864     789999999999999999998765  4899999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++.+
T Consensus        87 ~a~~~   91 (104)
T 1wex_A           87 YSTSK   91 (104)
T ss_dssp             ECSSS
T ss_pred             EccCc
Confidence            99754

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1e-17  Score=129.71  Aligned_cols=87  Identities=16%  Similarity=0.252  Sum_probs=78.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCce----eEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTI----TSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v----~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      ....+|||+|||+.+++++|+++|++||.|    .+|+|+.+.+|+++|||||+|.+.++|.+|++. |+..|+|+.|.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            456789999999999999999999999875    689999999999999999999999999999986 999999999999


Q ss_pred             ehhhhhHHHHHH
Q 012257          395 ALAQRKEERRAR  406 (467)
Q Consensus       395 ~~~~~~~~~~~~  406 (467)
                      ..+.+.......
T Consensus       100 ~~a~~~e~~~~~  111 (123)
T 2dha_A          100 FRSTAAEVQQVL  111 (123)
T ss_dssp             EEECHHHHHHHH
T ss_pred             EECCHHHHHHHH
Confidence            999877665543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.73  E-value=6.6e-18  Score=121.81  Aligned_cols=73  Identities=14%  Similarity=0.268  Sum_probs=68.1

Q ss_pred             cCeEEEcCCCCCC------CHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCc-ee
Q 012257           39 STSLYVGDLDLSV------NDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK-PI  111 (467)
Q Consensus        39 ~~~l~v~nLp~~~------~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~-~~  111 (467)
                      +++|||+|||.++      ++++|+++|++||.|.+|.+.  +.+|+++|||||+|.+.++|++|++.|++..+.|+ .|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            4799999999999      679999999999999999987  35789999999999999999999999999999999 88


Q ss_pred             ee
Q 012257          112 RI  113 (467)
Q Consensus       112 ~v  113 (467)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            77

>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=99.73  E-value=5.6e-17  Score=125.51  Aligned_cols=83  Identities=24%  Similarity=0.450  Sum_probs=75.7

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc-------
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL-------  106 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~-------  106 (467)
                      ....+.++|||+|||+++++++|+++|+.||.|.+|++.+++ +++++|||||+|.+.++|++|++.|++..+       
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~   98 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   98 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCcccc
Confidence            344567999999999999999999999999999999999998 899999999999999999999999999998       


Q ss_pred             -CCceeeeeecc
Q 012257          107 -NGKPIRIMYSY  117 (467)
Q Consensus       107 -~g~~~~v~~~~  117 (467)
                       .++++.|.++.
T Consensus        99 ~~~~~l~v~~a~  110 (114)
T 1x5o_A           99 APTEPLLCKFSG  110 (114)
T ss_dssp             CCSSCBEEEECC
T ss_pred             CCCCceeEEccC
Confidence             56777887765

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.73  E-value=1.2e-17  Score=131.27  Aligned_cols=83  Identities=34%  Similarity=0.499  Sum_probs=78.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ...+++|||+|||..+++++|+++|+.||.|.+|++..+.+|.++|||||+|.+.++|.+|++.|||..++|+.|+|+++
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            34667999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      .+.
T Consensus       112 ~~~  114 (124)
T 2kt5_A          112 ASQ  114 (124)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            754

>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=99.73  E-value=2.7e-17  Score=135.00  Aligned_cols=86  Identities=26%  Similarity=0.421  Sum_probs=80.8

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ...++++|||+|||+++++++|+++|+.||.|.+|.|+.++.++.++|||||+|.+.++|++|++.|++..|.|+.|+|.
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            33568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccCc
Q 012257          115 YSYRDP  120 (467)
Q Consensus       115 ~~~~~~  120 (467)
                      |+....
T Consensus       115 ~a~~~~  120 (156)
T 1h2v_Z          115 WDAGFK  120 (156)
T ss_dssp             EESCCC
T ss_pred             ECCCCC
Confidence            987543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.1e-17  Score=126.69  Aligned_cols=81  Identities=19%  Similarity=0.399  Sum_probs=75.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ...+|||+|||+.+++++|+++|+.| .|.+|+|+.+.+|+++|||||+|.+.++|.+|+ .+|+..|+|+.|.|..+..
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            34589999999999999999999999 899999999999999999999999999999999 6999999999999998876


Q ss_pred             hHH
Q 012257          400 KEE  402 (467)
Q Consensus       400 ~~~  402 (467)
                      ...
T Consensus        93 ~~~   95 (109)
T 2dnn_A           93 RQW   95 (109)
T ss_dssp             HHH
T ss_pred             cch
Confidence            543

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

Probab=99.73  E-value=8.9e-18  Score=131.00  Aligned_cols=84  Identities=19%  Similarity=0.330  Sum_probs=74.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHH----HhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceE
Q 012257          318 KFEGLNLYVKNLDDSISDDKLK----ELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY  393 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~----~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  393 (467)
                      ..++++|||+|||+.+++++|+    ++|++||.|.+|.+..  ++.++|||||+|.+.++|.+|+..|||..+.|+.|+
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~--~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL--SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC--CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc--CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            3457799999999999999876    6999999999988754  578899999999999999999999999999999999


Q ss_pred             EehhhhhHHH
Q 012257          394 VALAQRKEER  403 (467)
Q Consensus       394 v~~~~~~~~~  403 (467)
                      |.|++.+...
T Consensus       104 V~~a~~~~~~  113 (127)
T 2a3j_A          104 ITFSETPQSQ  113 (127)
T ss_dssp             EEECCCCCHH
T ss_pred             EEEccCcchh
Confidence            9999866543

>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=99.73  E-value=3.6e-18  Score=128.58  Aligned_cols=81  Identities=21%  Similarity=0.427  Sum_probs=73.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC--CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP--NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ....++|||+|||..+++++|+++|+.|| |.+|++..+.  +|+++|||||+|.+.++|.+|+ .|||..++|+.|+|+
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            34667999999999999999999999999 9999999986  7899999999999999999999 899999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      +++++
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            98764

>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=99.73  E-value=1.8e-17  Score=128.33  Aligned_cols=83  Identities=29%  Similarity=0.619  Sum_probs=77.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEe--------cc
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV--------VS  389 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--------~g  389 (467)
                      ....++|||+|||..+++++|+++|+.||.|.+++++.+.++.++|||||+|.+.++|.+|++.|||..+        .+
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            3466799999999999999999999999999999999999999999999999999999999999999999        57


Q ss_pred             cceEEehhhhh
Q 012257          390 KPLYVALAQRK  400 (467)
Q Consensus       390 ~~l~v~~~~~~  400 (467)
                      ++|.|+|+++.
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            88999998753

>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=99.72  E-value=6.2e-18  Score=126.33  Aligned_cols=80  Identities=20%  Similarity=0.364  Sum_probs=73.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ..++|||+|||..+++++|+++|++||.|.+++++.+. ++.++|||||+|.+.++|.+|++.|||..+.|+.|+|+++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            45789999999999999999999999999988887765 78899999999999999999999999999999999999876


Q ss_pred             h
Q 012257          399 R  399 (467)
Q Consensus       399 ~  399 (467)
                      .
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            3

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.72  E-value=4.7e-18  Score=122.59  Aligned_cols=73  Identities=21%  Similarity=0.346  Sum_probs=68.1

Q ss_pred             ceEEEecCCCCC------CHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEeccc-ceEE
Q 012257          322 LNLYVKNLDDSI------SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSK-PLYV  394 (467)
Q Consensus       322 ~~l~V~nlp~~~------~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~-~l~v  394 (467)
                      ++|||+|||..+      ++++|+++|++||.|.++++. ..+|+++|||||+|.+.++|.+|++.|||..++|+ .|+|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            579999999999      679999999999999999988 46788999999999999999999999999999999 8887


Q ss_pred             e
Q 012257          395 A  395 (467)
Q Consensus       395 ~  395 (467)
                      +
T Consensus        81 ~   81 (81)
T 2krb_A           81 N   81 (81)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.72  E-value=1.8e-17  Score=129.24  Aligned_cols=81  Identities=17%  Similarity=0.317  Sum_probs=73.1

Q ss_pred             CccCeEEEcCCCCCCCHHHHH----HHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLY----DLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~----~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      .++++|||+|||+++++++|+    ++|++||.|.+|.+.+   +++++|||||+|.+.++|.+|++.|++..+.|+.|+
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            457899999999999999865    7999999999998853   678899999999999999999999999999999999


Q ss_pred             eeecccCc
Q 012257          113 IMYSYRDP  120 (467)
Q Consensus       113 v~~~~~~~  120 (467)
                      |.|+....
T Consensus       104 V~~a~~~~  111 (127)
T 2a3j_A          104 ITFSETPQ  111 (127)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCcc
Confidence            99987654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=5.1e-17  Score=119.80  Aligned_cols=79  Identities=23%  Similarity=0.408  Sum_probs=72.5

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.+.        +|||||+|.+.++|++|++.+++..+.|+.|+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            4568999999999999999999999999999999997        36999999999999999999999999999999999


Q ss_pred             cccCccc
Q 012257          116 SYRDPTI  122 (467)
Q Consensus       116 ~~~~~~~  122 (467)
                      +......
T Consensus        77 a~~~~~~   83 (90)
T 2dnq_A           77 SKNKSKA   83 (90)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            8765443

>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=99.72  E-value=6.3e-18  Score=127.04  Aligned_cols=82  Identities=22%  Similarity=0.378  Sum_probs=75.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ....++|||+|||..+++++|+++|++||.|.+++++.+. +|.++|||||+|.+.++|.+|++.|||..|+|+.|+|++
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            3456789999999999999999999999999888777664 788999999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          397 AQR  399 (467)
Q Consensus       397 ~~~  399 (467)
                      +..
T Consensus        92 a~~   94 (98)
T 2cqp_A           92 GSG   94 (98)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            864

>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=99.72  E-value=4.3e-17  Score=122.09  Aligned_cols=82  Identities=20%  Similarity=0.395  Sum_probs=73.8

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccC--Cce
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLN--GKP  110 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~--g~~  110 (467)
                      .....++++|||+|||+++++++|+++|++||.|.+|.+.++      +|||||+|.+.++|++|++.|++..+.  |+.
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~   84 (97)
T 1why_A           11 YGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRR   84 (97)
T ss_dssp             CCCCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCB
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcE
Confidence            334556899999999999999999999999999999999754      479999999999999999999999999  999


Q ss_pred             eeeeecccCc
Q 012257          111 IRIMYSYRDP  120 (467)
Q Consensus       111 ~~v~~~~~~~  120 (467)
                      |+|.++...+
T Consensus        85 l~V~~a~~~~   94 (97)
T 1why_A           85 LRVDFAKSGP   94 (97)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEECCCCC
Confidence            9999987653

>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=99.72  E-value=1.1e-17  Score=132.02  Aligned_cols=82  Identities=12%  Similarity=0.122  Sum_probs=76.0

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCC---eEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCce
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQ---VVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKP  110 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~---v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  110 (467)
                      ....+.++|||+|||+++++++|+++|+.||.   |.+|+|.+++. |+++|||||+|.+.++|++|++ +++..+.|+.
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~  116 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRY  116 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEE
Confidence            34456799999999999999999999999998   89999999986 9999999999999999999999 9999999999


Q ss_pred             eeeeecc
Q 012257          111 IRIMYSY  117 (467)
Q Consensus       111 ~~v~~~~  117 (467)
                      |+|.++.
T Consensus       117 i~V~~a~  123 (136)
T 2hgl_A          117 IEVFKSH  123 (136)
T ss_dssp             EEEEECC
T ss_pred             EEEEECC
Confidence            9998764

>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=3.4e-17  Score=123.68  Aligned_cols=83  Identities=20%  Similarity=0.384  Sum_probs=74.7

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ...++++|||+|||+++++++|+++|++||.|   +++.+ .+++++|||||+|.+.++|++|++.|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            45568999999999999999999999999977   56666 678899999999999999999999999999999999999


Q ss_pred             ecccCcc
Q 012257          115 YSYRDPT  121 (467)
Q Consensus       115 ~~~~~~~  121 (467)
                      ++.....
T Consensus        87 ~a~~~~~   93 (101)
T 2fc9_A           87 LQGPRGS   93 (101)
T ss_dssp             ECSSCCC
T ss_pred             EcCCCCC
Confidence            9876543

>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=99.72  E-value=1.4e-17  Score=131.43  Aligned_cols=85  Identities=24%  Similarity=0.485  Sum_probs=79.0

Q ss_pred             ccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       316 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      ......++|||+|||..+++++|+++|++||.|.+|+++.+. ++.++|||||+|.+.++|.+|++.|||..|+|+.|.|
T Consensus        17 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   96 (126)
T 3ex7_B           17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   96 (126)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            344567799999999999999999999999999999999886 8889999999999999999999999999999999999


Q ss_pred             ehhhhh
Q 012257          395 ALAQRK  400 (467)
Q Consensus       395 ~~~~~~  400 (467)
                      +|+.+.
T Consensus        97 ~~a~~~  102 (126)
T 3ex7_B           97 DWCFVR  102 (126)
T ss_dssp             EESEES
T ss_pred             EEecCC
Confidence            999755

>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=99.72  E-value=4e-17  Score=122.75  Aligned_cols=82  Identities=24%  Similarity=0.486  Sum_probs=74.3

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....++++|||+|||+++++++|+++|++||.|.+|++.++      +|||||+|.+.++|.+|++.|++..+.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v   83 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV   83 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEE
Confidence            34456899999999999999999999999999999999865      479999999999999999999999999999999


Q ss_pred             eecccCcc
Q 012257          114 MYSYRDPT  121 (467)
Q Consensus       114 ~~~~~~~~  121 (467)
                      .++.....
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpj_A           84 RFACHSAS   91 (99)
T ss_dssp             EESSCCSC
T ss_pred             EEcCCCCC
Confidence            99876544

>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=99.72  E-value=2.8e-18  Score=126.73  Aligned_cols=80  Identities=29%  Similarity=0.556  Sum_probs=74.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecccC
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRD  119 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~  119 (467)
                      ++|||+|||.++++++|+++|++||.|.+|.+.+++.+++++|||||+|.+.+ |.+|++.+++..+.|+.|+|.++...
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            68999999999999999999999999999999999999999999999999999 99999999999999999999998654


Q ss_pred             c
Q 012257          120 P  120 (467)
Q Consensus       120 ~  120 (467)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.7e-17  Score=128.76  Aligned_cols=84  Identities=27%  Similarity=0.404  Sum_probs=77.4

Q ss_pred             ccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       316 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      ......++|||+|||..+++++|+++|++||.|.+|+++.+. ++.++|||||+|.+.++|.+|++.+++ .|.|+.|+|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V   90 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   90 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEE
Confidence            344567899999999999999999999999999999999986 688999999999999999999999998 899999999


Q ss_pred             ehhhhh
Q 012257          395 ALAQRK  400 (467)
Q Consensus       395 ~~~~~~  400 (467)
                      +++...
T Consensus        91 ~~a~~~   96 (116)
T 2cqd_A           91 NLAYLG   96 (116)
T ss_dssp             EESTTT
T ss_pred             EEcccC
Confidence            999654

>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=99.72  E-value=2.5e-17  Score=126.28  Aligned_cols=82  Identities=20%  Similarity=0.287  Sum_probs=74.8

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|++..+  +.++|||||+|.+.++|.+|++.||+..|.|+.|+|+|
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 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3446679999999999999999999999999999999654  55789999999999999999999999999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      +++.
T Consensus        96 a~~~   99 (109)
T 1x4a_A           96 PRSG   99 (109)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            9754

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.9e-17  Score=125.44  Aligned_cols=79  Identities=18%  Similarity=0.244  Sum_probs=72.6

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..+.++|||+|||+++++++|+++|+.| .|.+|.|+.++. |+++|||||+|.+.++|++|+ .+++..+.|+.|+|..
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~   89 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSP   89 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEE
Confidence            3456899999999999999999999999 889999999975 999999999999999999999 5899999999999976


Q ss_pred             cc
Q 012257          116 SY  117 (467)
Q Consensus       116 ~~  117 (467)
                      +.
T Consensus        90 a~   91 (109)
T 2dnn_A           90 AT   91 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.72  E-value=7.8e-18  Score=127.89  Aligned_cols=81  Identities=20%  Similarity=0.272  Sum_probs=74.5

Q ss_pred             CCCceEEEecCCCCC------CHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEeccc-c
Q 012257          319 FEGLNLYVKNLDDSI------SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSK-P  391 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~------~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~-~  391 (467)
                      ...++|||+|||..+      ++++|+++|++||.|.+|++. ..+|.++|||||+|.+.++|.+|+..|||..++|+ .
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            346789999999999      789999999999999999998 56789999999999999999999999999999998 9


Q ss_pred             eEEehhhhh
Q 012257          392 LYVALAQRK  400 (467)
Q Consensus       392 l~v~~~~~~  400 (467)
                      |+|+++...
T Consensus        92 l~V~~a~~~  100 (105)
T 2nlw_A           92 FRVNLFTDF  100 (105)
T ss_dssp             EEEECSCCC
T ss_pred             EEEEEcchH
Confidence            999998643

>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=99.72  E-value=1.3e-17  Score=125.42  Aligned_cols=80  Identities=18%  Similarity=0.288  Sum_probs=73.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|||+|||+.+++++|+++|++||.+ +|+|+.+.+|+++|||||+|.+.++|.+|++ +|+..|+|+.|+|..+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            3456789999999999999999999999955 9999999999999999999999999999995 7999999999999887


Q ss_pred             hh
Q 012257          398 QR  399 (467)
Q Consensus       398 ~~  399 (467)
                      .+
T Consensus        90 ~~   91 (102)
T 1wez_A           90 ST   91 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=6.9e-18  Score=127.55  Aligned_cols=75  Identities=19%  Similarity=0.425  Sum_probs=69.8

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      .+++|||+|||.++++++|+++|++||.|.+|++.      +++|||||+|.+.++|.+|++.|++..+.|+.|+|.|+.
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            46899999999999999999999999999999997      345899999999999999999999999999999999875


Q ss_pred             c
Q 012257          118 R  118 (467)
Q Consensus       118 ~  118 (467)
                      .
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=6.8e-17  Score=123.46  Aligned_cols=79  Identities=24%  Similarity=0.261  Sum_probs=73.0

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC-----c
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG-----K  109 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g-----~  109 (467)
                      .....++|||+|||+++++++|+++|++||.|.+|.|..+       |||||+|.+.++|++|++.|++..|.|     +
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~   83 (108)
T 1x4c_A           11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   83 (108)
T ss_dssp             CCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcce
Confidence            3456899999999999999999999999999999999876       699999999999999999999999999     9


Q ss_pred             eeeeeecccCc
Q 012257          110 PIRIMYSYRDP  120 (467)
Q Consensus       110 ~~~v~~~~~~~  120 (467)
                      .|+|.++....
T Consensus        84 ~i~V~~a~~~~   94 (108)
T 1x4c_A           84 YIRVKVDGPRS   94 (108)
T ss_dssp             EEEEEESSCCS
T ss_pred             EEEEEeCCCCC
Confidence            99999987654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.72  E-value=1.4e-17  Score=134.00  Aligned_cols=84  Identities=33%  Similarity=0.510  Sum_probs=78.2

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      .....++|||+|||..+++++|+++|+.||.|++|+++.+. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+
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            34466799999999999999999999999999999999886 68889999999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      ++++.
T Consensus       118 ~a~~~  122 (139)
T 1u6f_A          118 LAASG  122 (139)
T ss_dssp             ESSCC
T ss_pred             ECCCC
Confidence            99865

>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=99.72  E-value=4.6e-17  Score=118.75  Aligned_cols=78  Identities=21%  Similarity=0.427  Sum_probs=71.2

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHh-CCcccCCcee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL-NFTPLNGKPI  111 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l-~~~~~~g~~~  111 (467)
                      +....+.++|||+|||.++++++|+++|++||.|.+|.+.++      +|||||+|.+.++|.+|++.| ++..+.|+.|
T Consensus         6 ~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l   79 (85)
T 2ytc_A            6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRL   79 (85)
T ss_dssp             CCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEEC
T ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEE
Confidence            334456899999999999999999999999999999999864      479999999999999999988 9999999999


Q ss_pred             eeeec
Q 012257          112 RIMYS  116 (467)
Q Consensus       112 ~v~~~  116 (467)
                      +|.|+
T Consensus        80 ~v~~a   84 (85)
T 2ytc_A           80 NVKWG   84 (85)
T ss_dssp             CEEEC
T ss_pred             EEEec
Confidence            99886

>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=99.71  E-value=1.8e-17  Score=130.15  Aligned_cols=82  Identities=13%  Similarity=0.209  Sum_probs=75.5

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..+.++|||+|||+++++++|+++|+.||.|.++.++.+..+|+++|||||+|.+.++|++|++ +++..|.|+.|+|.+
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            3456999999999999999999999999999987777777899999999999999999999999 999999999999988


Q ss_pred             ccc
Q 012257          116 SYR  118 (467)
Q Consensus       116 ~~~  118 (467)
                      +..
T Consensus       101 a~~  103 (124)
T 1wel_A          101 ITK  103 (124)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            753

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=9.3e-18  Score=127.82  Aligned_cols=83  Identities=25%  Similarity=0.421  Sum_probs=77.5

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      .....++|||+|||..+++++|+++|++||.|.+|+++.+. ++.++|||||+|.+.++|.+|++. ++..|+|+.|+|+
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            44567899999999999999999999999999999999985 788999999999999999999998 9999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      ++.++
T Consensus        91 ~a~~~   95 (105)
T 2dh8_A           91 PCTPR   95 (105)
T ss_dssp             CSCCS
T ss_pred             EccCC
Confidence            98765

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

Probab=99.71  E-value=1.9e-17  Score=125.12  Aligned_cols=76  Identities=20%  Similarity=0.322  Sum_probs=71.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ...++|||+|||..+++++|+++|++||.|.++++.+     ++|||||+|.+.++|.+|+..|||..++|+.|+|+|++
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 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-----EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            3567999999999999999999999999999999983     57899999999999999999999999999999999987


Q ss_pred             h
Q 012257          399 R  399 (467)
Q Consensus       399 ~  399 (467)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.71  E-value=8e-18  Score=127.03  Aligned_cols=78  Identities=22%  Similarity=0.293  Sum_probs=70.2

Q ss_pred             CCCCceEEEecCCCC-CCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCC--cEecccceEE
Q 012257          318 KFEGLNLYVKNLDDS-ISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNG--KMVVSKPLYV  394 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~-~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g--~~~~g~~l~v  394 (467)
                      ..++++|||+|||+. +++++|+++|++||.|.+|++.+     ++|||||+|.+.++|.+|++.|++  ..|.|+.|+|
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            346779999999998 99999999999999999999975     378999999999999999998865  5689999999


Q ss_pred             ehhhhh
Q 012257          395 ALAQRK  400 (467)
Q Consensus       395 ~~~~~~  400 (467)
                      +|++.+
T Consensus        97 ~~a~~~  102 (112)
T 1x4f_A           97 DLSEKY  102 (112)
T ss_dssp             EEECSC
T ss_pred             EECccc
Confidence            999754

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.71  E-value=4.3e-18  Score=135.07  Aligned_cols=83  Identities=20%  Similarity=0.376  Sum_probs=77.4

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeE--EEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCc----Eecc
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITS--CKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGK----MVVS  389 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~--v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~----~~~g  389 (467)
                      .....++|||+|||+.+++++|+++|++||.|..  |+|+++. +|+++|||||+|.+. +|.+|+..|||.    .++|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3456779999999999999999999999999977  9999998 899999999999999 999999999999    9999


Q ss_pred             cceEEehhhhh
Q 012257          390 KPLYVALAQRK  400 (467)
Q Consensus       390 ~~l~v~~~~~~  400 (467)
                      +.|+|+|+++.
T Consensus        98 r~l~V~~a~~~  108 (131)
T 2m2b_A           98 KTINVEFAKGS  108 (131)
T ss_dssp             CCCCCEECCCS
T ss_pred             EEEEEEECCCC
Confidence            99999999864

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=5.8e-17  Score=122.74  Aligned_cols=86  Identities=23%  Similarity=0.429  Sum_probs=77.6

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      .....++++|||+|||+++++++|+++|+.|   ..|.++.++.+++++|||||+|.+.++|++|++.|++..|.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2fc8_A            9 NARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT   85 (102)
T ss_dssp             SSSSCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            3445678999999999999999999999987   4788888988999999999999999999999999999999999999


Q ss_pred             eeecccCcc
Q 012257          113 IMYSYRDPT  121 (467)
Q Consensus       113 v~~~~~~~~  121 (467)
                      |.++.....
T Consensus        86 V~~a~~~~~   94 (102)
T 2fc8_A           86 LDWAKPKGE   94 (102)
T ss_dssp             EEECCCCCS
T ss_pred             EEEecCCCC
Confidence            999876544

>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=99.71  E-value=1.9e-17  Score=125.55  Aligned_cols=82  Identities=21%  Similarity=0.277  Sum_probs=75.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeE-EEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITS-CKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~-v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ....++|||+|||+.+++++|+++|++||.|.+ |+++.+.+|+++|||||+|.+.++|.+|++. |+..++|+.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            345679999999999999999999999999987 8999888999999999999999999999997 99999999999998


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      +...
T Consensus        91 ~~~~   94 (104)
T 1wg5_A           91 SSRA   94 (104)
T ss_dssp             ECTT
T ss_pred             CCHH
Confidence            8654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=2.3e-17  Score=124.64  Aligned_cols=81  Identities=28%  Similarity=0.427  Sum_probs=74.1

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .....++|||+|||..+++++|+++|++||.|   +++.+.++.++|||||+|.+.++|.+|++.|||..|.|+.|+|+|
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            34467899999999999999999999999987   566777888999999999999999999999999999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      ++++
T Consensus        88 a~~~   91 (101)
T 2fc9_A           88 QGPR   91 (101)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            9765

>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=99.71  E-value=2.6e-17  Score=120.10  Aligned_cols=77  Identities=27%  Similarity=0.444  Sum_probs=71.4

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHh-CCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM-NGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l-~g~~~~g~~l~v~  395 (467)
                      .....++|||+|||..+++++|+++|++||.|.++++.++     +|||||+|.+.++|.+|++.| +|..++|+.|+|+
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            3456678999999999999999999999999999999874     789999999999999999999 9999999999999


Q ss_pred             hhh
Q 012257          396 LAQ  398 (467)
Q Consensus       396 ~~~  398 (467)
                      |++
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            975

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=5.7e-17  Score=121.33  Aligned_cols=81  Identities=19%  Similarity=0.306  Sum_probs=71.8

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      .....+++|||+|||+++++++|+++|++||.|. +.++.+    +++|||||+|.+.++|++|++.|++..+.|+.|+|
T Consensus        14 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   88 (97)
T 2e5j_A           14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV   88 (97)
T ss_dssp             SSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            3445589999999999999999999999999986 666654    56789999999999999999999999999999999


Q ss_pred             eecccC
Q 012257          114 MYSYRD  119 (467)
Q Consensus       114 ~~~~~~  119 (467)
                      .++...
T Consensus        89 ~~a~~~   94 (97)
T 2e5j_A           89 ALARQQ   94 (97)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            988654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=9.9e-18  Score=119.83  Aligned_cols=75  Identities=32%  Similarity=0.565  Sum_probs=71.2

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ++|||+|||..+++++|+++|++||.|.++++..+. +|.++|+|||+|.+.++|.+|++.++ ..++|+.|+|++|
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            369999999999999999999999999999999986 68899999999999999999999999 9999999999886

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=3.6e-17  Score=120.60  Aligned_cols=76  Identities=18%  Similarity=0.451  Sum_probs=71.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ..+.++|||+|||..+++++|+++|++||.|.++++.       +|||||+|.+.++|.+|++.|||..++|+.|+|+|+
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            3467799999999999999999999999999999997       469999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      +++
T Consensus        78 ~~~   80 (90)
T 2dnq_A           78 KNK   80 (90)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            755

>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=99.71  E-value=4.6e-17  Score=126.21  Aligned_cols=81  Identities=22%  Similarity=0.393  Sum_probs=74.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ..+++|||+|||..+++++|+++|+.||.|.+|++..+  +.++|||||+|.+.++|.+|+..|||..++|+.|.|.|+.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            35679999999999999999999999999999999875  4568999999999999999999999999999999999998


Q ss_pred             hhH
Q 012257          399 RKE  401 (467)
Q Consensus       399 ~~~  401 (467)
                      +..
T Consensus        84 ~~~   86 (115)
T 3lqv_A           84 ANR   86 (115)
T ss_dssp             HHH
T ss_pred             CCh
Confidence            644

>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=99.71  E-value=4.5e-18  Score=125.64  Aligned_cols=79  Identities=30%  Similarity=0.518  Sum_probs=72.1

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      ++|||+|||..+++++|+++|++||.|.++++..+. +|.++|||||+|.+.+ |.+|+..|||..++|+.|+|+++.+.
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            479999999999999999999999999999999887 5889999999999999 99999999999999999999999865


Q ss_pred             H
Q 012257          401 E  401 (467)
Q Consensus       401 ~  401 (467)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.71  E-value=1.9e-17  Score=130.35  Aligned_cols=78  Identities=21%  Similarity=0.404  Sum_probs=73.9

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      .++|||+|||..+++++|+++|++||.|.+|++..+. +|.++|||||+|.+.++|.+|+ .|||..|+|+.|+|+++++
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            4589999999999999999999999999999999985 7889999999999999999999 8999999999999999874

>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=99.71  E-value=5.1e-17  Score=122.62  Aligned_cols=81  Identities=15%  Similarity=0.206  Sum_probs=71.4

Q ss_pred             CCCccCeEEEcCCCCC-CCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhC--CcccCCcee
Q 012257           35 RQFVSTSLYVGDLDLS-VNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN--FTPLNGKPI  111 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~-~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~--~~~~~g~~~  111 (467)
                      ...++++|||+|||++ ++|++|+++|++||.|.+|+|.+.      +|||||+|.+.++|.+|++.|+  +..+.|+.|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3567899999999998 999999999999999999999743      5899999999999999999885  456999999


Q ss_pred             eeeecccCcc
Q 012257          112 RIMYSYRDPT  121 (467)
Q Consensus       112 ~v~~~~~~~~  121 (467)
                      +|.++.....
T Consensus        95 ~V~~a~~~~~  104 (112)
T 1x4f_A           95 KVDLSEKYKK  104 (112)
T ss_dssp             EEEEECSCSS
T ss_pred             EEEECccccc
Confidence            9999875543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.71  E-value=2.8e-17  Score=125.17  Aligned_cols=79  Identities=29%  Similarity=0.575  Sum_probs=72.2

Q ss_pred             ccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       316 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ......++|||+|||..+++++|+++|++||.|.+|++.       +|||||+|.+.++|.+|++.|||..++|+.|+|+
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            344567899999999999999999999999999999998       5799999999999999999999999999999999


Q ss_pred             hhhhhH
Q 012257          396 LAQRKE  401 (467)
Q Consensus       396 ~~~~~~  401 (467)
                      |+++..
T Consensus        99 ~a~~~~  104 (108)
T 2jvo_A           99 YSKLPA  104 (108)
T ss_dssp             SCSCCC
T ss_pred             EecCCC
Confidence            998654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.71  E-value=2.5e-17  Score=125.87  Aligned_cols=82  Identities=30%  Similarity=0.520  Sum_probs=73.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ....++|||+|||..+++++|+++|+.||.|.+|++..+. +|.++|||||+|.+.++|.+|++.+ |..++|+.|+|.+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            3456789999999999999999999999999999999986 5889999999999999999999976 5999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      +.++
T Consensus       101 a~~~  104 (109)
T 2rs2_A          101 AFPR  104 (109)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8754

>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=8.8e-18  Score=119.38  Aligned_cols=75  Identities=15%  Similarity=0.388  Sum_probs=70.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        41 ~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      +|||+|||+++++++|+++|++||.|.+|.+.+++.+++++|||||+|.+.++|.+|++ +++..+.|+.++|.++
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            69999999999999999999999999999999999999999999999999999999998 5888999999998764

>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=99.70  E-value=2.4e-17  Score=129.42  Aligned_cols=86  Identities=20%  Similarity=0.347  Sum_probs=76.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeE-EEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITS-CKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~-v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ....++|||+|||+.+++++|+++|+.||.|.+ +.+..+.+|+++|||||+|.+.++|.+|++ |||..|+|+.|.|.+
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            345679999999999999999999999999988 455556689999999999999999999999 999999999999999


Q ss_pred             hhhhHHHH
Q 012257          397 AQRKEERR  404 (467)
Q Consensus       397 ~~~~~~~~  404 (467)
                      +..+....
T Consensus       101 a~~~~~~~  108 (124)
T 1wel_A          101 ITKKGMLE  108 (124)
T ss_dssp             ECHHHHHH
T ss_pred             CCHHHHHH
Confidence            98776433

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.70  E-value=1.7e-17  Score=125.87  Aligned_cols=78  Identities=23%  Similarity=0.219  Sum_probs=71.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCC-ceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFG-TITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G-~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ..++|||+|||+.+++++|+++|++|| .|..+++..+   .++|||||+|.+.++|.+|++.|||..++|+.|+|++++
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            456899999999999999999999999 8999998643   378999999999999999999999999999999999987


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ..
T Consensus       104 ~~  105 (111)
T 2jvr_A          104 NP  105 (111)
T ss_dssp             C-
T ss_pred             CC
Confidence            54

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=3.3e-17  Score=122.71  Aligned_cols=78  Identities=21%  Similarity=0.311  Sum_probs=72.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEec--ccceEEe
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVV--SKPLYVA  395 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~v~  395 (467)
                      ..+.++|||+|||..+++++|+++|++||.|.+|++..+     +|||||+|.+.++|.+|++.|||..+.  |+.|+|+
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            345678999999999999999999999999999999864     679999999999999999999999999  9999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++++
T Consensus        89 ~a~~~   93 (97)
T 1why_A           89 FAKSG   93 (97)
T ss_dssp             ECCCC
T ss_pred             ECCCC
Confidence            99764

>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=99.70  E-value=1.7e-17  Score=126.57  Aligned_cols=80  Identities=8%  Similarity=0.081  Sum_probs=74.7

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCC---eEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQ---VVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~---v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      .+.++|||+|||+++++++|+++|+.||.   |.+|.+..++. |+++|||||+|.+.++|++|++ +++..+.|+.|+|
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            45799999999999999999999999998   89999999987 9999999999999999999999 9999999999999


Q ss_pred             eeccc
Q 012257          114 MYSYR  118 (467)
Q Consensus       114 ~~~~~  118 (467)
                      .++..
T Consensus        87 ~~a~~   91 (107)
T 2lmi_A           87 YEINN   91 (107)
T ss_dssp             EECCH
T ss_pred             EECCH
Confidence            87653

>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=99.70  E-value=2.9e-17  Score=123.52  Aligned_cols=78  Identities=26%  Similarity=0.427  Sum_probs=72.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ..+.++|||+|||..+++++|+++|++||.|.+|++.++     +|||||+|.+.++|.+|++.|||..+.|+.|+|.|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            346679999999999999999999999999999999864     789999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ++.
T Consensus        87 ~~~   89 (99)
T 2cpj_A           87 CHS   89 (99)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            754

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.70  E-value=2.9e-17  Score=124.60  Aligned_cols=79  Identities=19%  Similarity=0.191  Sum_probs=70.9

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCC-CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMG-QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G-~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ..++|||+|||+++++++|+++|++|| .|..+.+..    ++++|||||+|.+.++|++|++.|++..+.|+.|+|.++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            468999999999999999999999999 899998853    247799999999999999999999999999999999988


Q ss_pred             ccCc
Q 012257          117 YRDP  120 (467)
Q Consensus       117 ~~~~  120 (467)
                      ...+
T Consensus       103 ~~~p  106 (111)
T 2jvr_A          103 DNPP  106 (111)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            6543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.1e-16  Score=118.63  Aligned_cols=81  Identities=23%  Similarity=0.414  Sum_probs=73.3

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      .....++++|||+|||+++++++|+++|++||.|.+|.+.+        +||||+|.+.++|++|++.|++..+.|+.|+
T Consensus         4 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   75 (92)
T 2dgt_A            4 GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMH   75 (92)
T ss_dssp             SCCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            34456789999999999999999999999999999999973        3999999999999999999999999999999


Q ss_pred             eeecccCcc
Q 012257          113 IMYSYRDPT  121 (467)
Q Consensus       113 v~~~~~~~~  121 (467)
                      |.++.....
T Consensus        76 V~~a~~~~~   84 (92)
T 2dgt_A           76 VQLSTSRLR   84 (92)
T ss_dssp             EEESSCCCS
T ss_pred             EEEccCCCC
Confidence            999876544

>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=4.5e-17  Score=126.25  Aligned_cols=81  Identities=14%  Similarity=0.243  Sum_probs=72.7

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeE--EEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVV--SVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~--~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      .....++|||+|||++++|++|+++|+.| .|.  +|+|+.|+. |+++|||||+|.+.++|++|++ +++..|.|+.|+
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~  114 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEE
Confidence            34567899999999999999999999999 566  999999986 9999999999999999999998 477899999999


Q ss_pred             eeeccc
Q 012257          113 IMYSYR  118 (467)
Q Consensus       113 v~~~~~  118 (467)
                      |..+..
T Consensus       115 V~~a~~  120 (126)
T 2hgm_A          115 VFKSSQ  120 (126)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            987643

>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=99.70  E-value=3.8e-17  Score=142.16  Aligned_cols=81  Identities=17%  Similarity=0.358  Sum_probs=76.4

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCC--CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMG--QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G--~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..++|||+|||+++++++|+++|+.||  .|.+|+|++|+.+++++|||||+|.+.++|++||+.|++..|.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            578999999999999999999999999  999999999999999999999999999999999999999999999999998


Q ss_pred             ccc
Q 012257          116 SYR  118 (467)
Q Consensus       116 ~~~  118 (467)
                      +..
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            753

>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=5.9e-17  Score=123.36  Aligned_cols=78  Identities=24%  Similarity=0.560  Sum_probs=71.6

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ...++++|||+|||+++++++|+++|++||.|.+|.+.        +|||||+|.+.++|++|++.|++..+.|+.|+|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34568999999999999999999999999999999997        4799999999999999999999999999999999


Q ss_pred             ecccCc
Q 012257          115 YSYRDP  120 (467)
Q Consensus       115 ~~~~~~  120 (467)
                      ++....
T Consensus        99 ~a~~~~  104 (108)
T 2jvo_A           99 YSKLPA  104 (108)
T ss_dssp             SCSCCC
T ss_pred             EecCCC
Confidence            987543

>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=1.4e-17  Score=124.92  Aligned_cols=83  Identities=33%  Similarity=0.537  Sum_probs=75.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHH----HhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceE
Q 012257          318 KFEGLNLYVKNLDDSISDDKLK----ELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY  393 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~----~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  393 (467)
                      ..++++|||+|||..+++++|+    ++|++||.|.+|++..  +|.++|||||+|.+.++|.+|++.|||..++|+.|+
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            3467799999999999999999    9999999999999874  467789999999999999999999999999999999


Q ss_pred             EehhhhhHH
Q 012257          394 VALAQRKEE  402 (467)
Q Consensus       394 v~~~~~~~~  402 (467)
                      |+|+++...
T Consensus        83 v~~a~~~~~   91 (97)
T 1nu4_A           83 IQYAKTDSD   91 (97)
T ss_dssp             EEECSSCCT
T ss_pred             EEEccCCCc
Confidence            999986543

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.70  E-value=7.1e-17  Score=132.46  Aligned_cols=82  Identities=23%  Similarity=0.299  Sum_probs=77.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ...++|||+|||..+++++|+++|++||.|.+|+|+.+. ++.++|||||+|.+.++|.+|++.|||..|.|+.|+|+|+
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            356799999999999999999999999999999999987 5889999999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ++.
T Consensus       117 ~~~  119 (156)
T 1h2v_Z          117 AGF  119 (156)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            864

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.70  E-value=8e-18  Score=127.20  Aligned_cols=82  Identities=18%  Similarity=0.291  Sum_probs=74.9

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .+.++|||+|||+++++++|+++|+.||.|.+ .++.+..+++++|||||+|.+.++|++|++ |++..+.|+.|+|.++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            45789999999999999999999999998888 667777788999999999999999999998 9999999999999998


Q ss_pred             ccCc
Q 012257          117 YRDP  120 (467)
Q Consensus       117 ~~~~  120 (467)
                      ....
T Consensus        93 ~~~~   96 (101)
T 1fj7_A           93 KGRD   96 (101)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7543

>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=99.70  E-value=6.8e-17  Score=120.56  Aligned_cols=77  Identities=21%  Similarity=0.400  Sum_probs=70.7

Q ss_pred             cCCCCceEEEecCCC-CCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDD-SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~-~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ...+.++|||+|||. .+++++|+++|++||.|.++++.       +|||||+|.+.++|.+|++.|||..++|+.|+|+
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            345678999999998 99999999999999999999983       6799999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++..
T Consensus        91 ~a~~~   95 (97)
T 2xnq_A           91 VSSSN   95 (97)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            98754

>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=99.70  E-value=1e-16  Score=119.64  Aligned_cols=76  Identities=17%  Similarity=0.470  Sum_probs=70.0

Q ss_pred             CCccCeEEEcCCCC-CCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           36 QFVSTSLYVGDLDL-SVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        36 ~~~~~~l~v~nLp~-~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ..++++|||+|||+ ++++++|+++|+.||.|.+|.+.        +|||||+|.+.++|.+|++.+++..+.|+.|+|.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34689999999998 99999999999999999999983        5799999999999999999999999999999999


Q ss_pred             ecccC
Q 012257          115 YSYRD  119 (467)
Q Consensus       115 ~~~~~  119 (467)
                      ++...
T Consensus        91 ~a~~~   95 (97)
T 2xnq_A           91 VSSSN   95 (97)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            87643

>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=1.2e-16  Score=121.08  Aligned_cols=81  Identities=22%  Similarity=0.426  Sum_probs=72.7

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....++++|||+|||+++++++|+++|+.||.|.+|.+.+        +||||+|.+.++|++|++.|++..+.|+.|+|
T Consensus         6 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   77 (103)
T 2dgu_A            6 SGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEI   77 (103)
T ss_dssp             CCCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEE
Confidence            3345689999999999999999999999999999999863        48999999999999999999999999999999


Q ss_pred             eecccCccc
Q 012257          114 MYSYRDPTI  122 (467)
Q Consensus       114 ~~~~~~~~~  122 (467)
                      .++......
T Consensus        78 ~~a~~~~~~   86 (103)
T 2dgu_A           78 VFAKPPDQK   86 (103)
T ss_dssp             EECCCCCCC
T ss_pred             EEcCCCccc
Confidence            998765443

>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=99.69  E-value=4.8e-17  Score=124.65  Aligned_cols=78  Identities=24%  Similarity=0.472  Sum_probs=73.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|||+|||..+++++|+++|++||.|.+|++..+     +|||||+|.+.++|.+|++.|||..++|+.|+|.|+
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            446779999999999999999999999999999999886     789999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ++.
T Consensus        97 ~~~   99 (109)
T 1x4g_A           97 KES   99 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.69  E-value=9.3e-17  Score=121.78  Aligned_cols=81  Identities=30%  Similarity=0.408  Sum_probs=75.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ....++|||+|||..+++++|+++|++||.|.+|+++.+. +|.++|||||+|.+.++|.+|++  ++..++|+.|.|.+
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            3456789999999999999999999999999999999986 68999999999999999999998  57899999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      +.++
T Consensus        90 a~~~   93 (103)
T 2cqg_A           90 PNSK   93 (103)
T ss_dssp             CCTT
T ss_pred             cCCC
Confidence            9865

>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=99.69  E-value=1.1e-16  Score=122.69  Aligned_cols=81  Identities=21%  Similarity=0.493  Sum_probs=74.5

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ....++|||+|||.++++++|+++|+.||.|.+|++.++      +|||||+|.+.++|.+|++.|++..+.|+.|+|.+
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            345799999999999999999999999999999999876      47999999999999999999999999999999999


Q ss_pred             cccCccc
Q 012257          116 SYRDPTI  122 (467)
Q Consensus       116 ~~~~~~~  122 (467)
                      +...+..
T Consensus        96 a~~~~~~  102 (109)
T 1x4g_A           96 GKESPDM  102 (109)
T ss_dssp             CCCCCSS
T ss_pred             cCCCCCC
Confidence            8776544

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=6.7e-17  Score=119.70  Aligned_cols=76  Identities=24%  Similarity=0.473  Sum_probs=71.1

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|||+|||..+++++|+++|++||.|.+|++.++       ||||+|.+.++|.+|++.|||..+.|+.|+|+++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~-------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS-------EEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC-------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            446779999999999999999999999999999999854       9999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      +++
T Consensus        80 ~~~   82 (92)
T 2dgt_A           80 TSR   82 (92)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            755

>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=99.69  E-value=3.1e-17  Score=123.02  Aligned_cols=82  Identities=26%  Similarity=0.516  Sum_probs=74.6

Q ss_pred             CCccCeEEEcCCCCCCCHHHHH----HHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLY----DLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~----~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      ..++++|||+|||.++++++|+    ++|++||.|.+|.+.+   ++.++|||||+|.+.++|.+|++.|++..+.|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            3568999999999999999999    9999999999999873   56788999999999999999999999999999999


Q ss_pred             eeeecccCc
Q 012257          112 RIMYSYRDP  120 (467)
Q Consensus       112 ~v~~~~~~~  120 (467)
                      +|.++....
T Consensus        82 ~v~~a~~~~   90 (97)
T 1nu4_A           82 RIQYAKTDS   90 (97)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEccCCC
Confidence            999987653

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=4.9e-17  Score=126.22  Aligned_cols=80  Identities=28%  Similarity=0.504  Sum_probs=75.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ..++|||+|||..+++++|+++|++||.|.+|+++.+. ++.++|||||+|.+.++|.+|++. ++..|+|+.|+|.++.
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            34689999999999999999999999999999999986 688999999999999999999998 9999999999999997


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ++
T Consensus       105 ~~  106 (116)
T 1x4b_A          105 AR  106 (116)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=4.2e-17  Score=125.00  Aligned_cols=79  Identities=14%  Similarity=0.201  Sum_probs=72.1

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ..++.++|||+|||+++++++|+++|++||.|.+|.+.+      ++|||||+|.+.++|++|++.|++..+.|+.|+|.
T Consensus         6 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   79 (111)
T 1whx_A            6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE   79 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            345689999999999999999999999999999998864      45799999999999999999999999999999999


Q ss_pred             ecccC
Q 012257          115 YSYRD  119 (467)
Q Consensus       115 ~~~~~  119 (467)
                      |+...
T Consensus        80 ~a~~~   84 (111)
T 1whx_A           80 WAPIG   84 (111)
T ss_dssp             EEETT
T ss_pred             ECCCC
Confidence            98653

>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=99.69  E-value=3.4e-17  Score=125.66  Aligned_cols=82  Identities=13%  Similarity=0.189  Sum_probs=74.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCc-eeEEEEe-eCC-CCCccceEEEEcCCHHHHHHHHHHhC--CcEecccceE
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGT-ITSCKVM-RDP-NGISRGSGFVAFSTAEEASKALTEMN--GKMVVSKPLY  393 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~-v~~v~i~-~~~-~~~~~g~afV~f~~~~~A~~A~~~l~--g~~~~g~~l~  393 (467)
                      .+.++|||+|||..+++++|+++|+.||. |.+++++ .+. +|.++|||||+|.+.++|.+|++.|+  +..++|+.|+
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            35678999999999999999999999998 9999998 454 57889999999999999999999996  5899999999


Q ss_pred             Eehhhhh
Q 012257          394 VALAQRK  400 (467)
Q Consensus       394 v~~~~~~  400 (467)
                      |.|+++.
T Consensus        86 V~~a~~~   92 (109)
T 2dis_A           86 VDWAEPE   92 (109)
T ss_dssp             EEESCSS
T ss_pred             EEEcCCC
Confidence            9999765

>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=99.69  E-value=3.3e-17  Score=127.07  Aligned_cols=86  Identities=21%  Similarity=0.252  Sum_probs=74.0

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..++++|||+|||+++++++|+++|+.||.|.++.+..+..+++++|||||+|.+.++|++|++.|++..+.|+.|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34679999999999999999999999999884433333333788999999999999999999999999999999999999


Q ss_pred             cccCcc
Q 012257          116 SYRDPT  121 (467)
Q Consensus       116 ~~~~~~  121 (467)
                      +.....
T Consensus       102 a~~~~~  107 (115)
T 2cpx_A          102 GKNKKQ  107 (115)
T ss_dssp             CCCCSC
T ss_pred             ccCCCC
Confidence            876544

>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=99.69  E-value=7.6e-17  Score=123.18  Aligned_cols=76  Identities=25%  Similarity=0.306  Sum_probs=71.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecc-----cceE
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVS-----KPLY  393 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-----~~l~  393 (467)
                      ...++|||+|||..+++++|+++|++||.|.+|+++.+      |||||+|.+.++|.+|++.|||..|.|     +.|+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~   86 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   86 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEE
Confidence            35678999999999999999999999999999999886      799999999999999999999999999     9999


Q ss_pred             Eehhhhh
Q 012257          394 VALAQRK  400 (467)
Q Consensus       394 v~~~~~~  400 (467)
                      |++++++
T Consensus        87 V~~a~~~   93 (108)
T 1x4c_A           87 VKVDGPR   93 (108)
T ss_dssp             EEESSCC
T ss_pred             EEeCCCC
Confidence            9999864

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.69  E-value=3.7e-17  Score=123.74  Aligned_cols=81  Identities=21%  Similarity=0.534  Sum_probs=75.5

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..++++|||+|||+++++++|+++|+.||.|.+|.+.+++ +|+++|||||+|.+.++|++|++  ++..+.|+.|.|.+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGP   82 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEE
Confidence            4467999999999999999999999999999999999998 99999999999999999999998  88899999999988


Q ss_pred             cccC
Q 012257          116 SYRD  119 (467)
Q Consensus       116 ~~~~  119 (467)
                      +...
T Consensus        83 a~~~   86 (102)
T 2xs2_A           83 AIRK   86 (102)
T ss_dssp             EEEC
T ss_pred             CCcC
Confidence            7644

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.69  E-value=6.6e-17  Score=130.33  Aligned_cols=81  Identities=32%  Similarity=0.459  Sum_probs=75.1

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      .....++|||+|||..+++++|+++|++||.|.+++++.+. ++.++|||||+|.+.++|.+|++.|||..+.|+.|+|+
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            34467799999999999999999999999999999999885 78899999999999999999999999999999999999


Q ss_pred             hh
Q 012257          396 LA  397 (467)
Q Consensus       396 ~~  397 (467)
                      ||
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            86

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=2.1e-16  Score=112.37  Aligned_cols=75  Identities=20%  Similarity=0.304  Sum_probs=66.7

Q ss_pred             ccCe-EEEcCCCCCCCHHH----HHHHHhcC-CCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           38 VSTS-LYVGDLDLSVNDSQ----LYDLFNQM-GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        38 ~~~~-l~v~nLp~~~~e~~----l~~~f~~~-G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      ++.+ |||+|||..+++++    |+++|++| |.|.+|       ++   |+|||.|.+.++|++|++.|++..+.||++
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i   76 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRI   76 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceE
Confidence            4555 99999999999988    56899999 599998       33   899999999999999999999999999999


Q ss_pred             eeeecccCccc
Q 012257          112 RIMYSYRDPTI  122 (467)
Q Consensus       112 ~v~~~~~~~~~  122 (467)
                      +|.++..+...
T Consensus        77 ~v~~A~~~sd~   87 (96)
T 2diu_A           77 IVSFTPKNREL   87 (96)
T ss_dssp             EEESSCCSCCC
T ss_pred             EEEecCCCcce
Confidence            99999876554

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=7.3e-17  Score=114.68  Aligned_cols=72  Identities=24%  Similarity=0.368  Sum_probs=64.5

Q ss_pred             CCce-EEEecCCCCCCHHH----HHHhhccC-CceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceE
Q 012257          320 EGLN-LYVKNLDDSISDDK----LKELFSEF-GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY  393 (467)
Q Consensus       320 ~~~~-l~V~nlp~~~~~~~----l~~~F~~~-G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  393 (467)
                      ++.+ |||+|||+.+++++    |+++|++| |+|.+|      ++   |+|||+|.+.++|.+|++.|+|..+.||+|+
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            4445 99999999999988    55899999 599998      22   8999999999999999999999999999999


Q ss_pred             Eehhhhh
Q 012257          394 VALAQRK  400 (467)
Q Consensus       394 v~~~~~~  400 (467)
                      |+||+.+
T Consensus        78 v~~A~~~   84 (96)
T 2diu_A           78 VSFTPKN   84 (96)
T ss_dssp             EESSCCS
T ss_pred             EEecCCC
Confidence            9999865

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.69  E-value=2.3e-16  Score=131.38  Aligned_cols=85  Identities=27%  Similarity=0.460  Sum_probs=79.3

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....++++|||+|||+++++++|+++|+.||.|.+|.|..++ ++.++|||||+|.+.++|++|++.+++..+.|+.|+|
T Consensus        83 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V  161 (177)
T 2f3j_A           83 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI  161 (177)
T ss_dssp             SSCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEE
Confidence            344567999999999999999999999999999999999998 8999999999999999999999999999999999999


Q ss_pred             eecccC
Q 012257          114 MYSYRD  119 (467)
Q Consensus       114 ~~~~~~  119 (467)
                      .++...
T Consensus       162 ~~a~~~  167 (177)
T 2f3j_A          162 QLVASQ  167 (177)
T ss_dssp             EEESSG
T ss_pred             EEecCC
Confidence            998654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=4.2e-16  Score=117.13  Aligned_cols=82  Identities=26%  Similarity=0.406  Sum_probs=73.0

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcC--CCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCc
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQM--GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGK  109 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~--G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  109 (467)
                      +.....++++|||+|||+++++++|+++|++|  |.|.+|++.        +|||||+|.+.++|++|++.|++..+.|+
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~   79 (99)
T 2cpd_A            8 DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGS   79 (99)
T ss_dssp             CCSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTE
T ss_pred             cccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            34445578999999999999999999999999  899998874        46999999999999999999999999999


Q ss_pred             eeeeeecccCcc
Q 012257          110 PIRIMYSYRDPT  121 (467)
Q Consensus       110 ~~~v~~~~~~~~  121 (467)
                      .|+|.++.....
T Consensus        80 ~l~v~~a~~~~~   91 (99)
T 2cpd_A           80 PIEVTLAKPVDK   91 (99)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEECCCCCC
Confidence            999999876543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.5e-16  Score=117.21  Aligned_cols=79  Identities=23%  Similarity=0.431  Sum_probs=72.1

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ...+.++|||+|||+++++++|+++|++||.|.+|++.+        +||||+|.+.++|++|++.|++..+.|+.|+|.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            345689999999999999999999999999999999973        389999999999999999999999999999999


Q ss_pred             ecccCcc
Q 012257          115 YSYRDPT  121 (467)
Q Consensus       115 ~~~~~~~  121 (467)
                      ++.....
T Consensus        77 ~a~~~~~   83 (90)
T 2dnp_A           77 LSTKGQK   83 (90)
T ss_dssp             ESCCCCC
T ss_pred             ECCCCCC
Confidence            9876543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.68  E-value=1e-16  Score=123.88  Aligned_cols=74  Identities=19%  Similarity=0.339  Sum_probs=68.5

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccce-EEEEcCCHHHHHHHHHHhCCcEecc--cceEEehhhh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGS-GFVAFSTAEEASKALTEMNGKMVVS--KPLYVALAQR  399 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~-afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v~~~~~  399 (467)
                      .|||+||++.+|+++|+++|++||.|.+|++..+    .+|| |||+|.+.++|.+|++.|||..|.|  +.|+|+|+++
T Consensus        30 ~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~  105 (130)
T 3zzy_A           30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  105 (130)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSC
T ss_pred             EEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCC
Confidence            5889999999999999999999999999999875    3567 9999999999999999999999988  8999999986


Q ss_pred             h
Q 012257          400 K  400 (467)
Q Consensus       400 ~  400 (467)
                      .
T Consensus       106 ~  106 (130)
T 3zzy_A          106 T  106 (130)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.68  E-value=4.7e-17  Score=124.69  Aligned_cols=75  Identities=24%  Similarity=0.305  Sum_probs=70.1

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ..++|||+|||..+++++|+++|++||.|.+|++..     ++|||||+|.+.++|.+|++.|||..+.|+.|.|.|++.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            356899999999999999999999999999999875     478999999999999999999999999999999999874

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=7.7e-17  Score=118.85  Aligned_cols=76  Identities=26%  Similarity=0.511  Sum_probs=70.8

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|||+|||..+++++|+++|++||.|.++++.++       ||||+|.+.++|.+|++.|||..++|+.|+|+++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~-------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS-------CEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC-------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            346678999999999999999999999999999999854       9999999999999999999999999999999998


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ++.
T Consensus        79 ~~~   81 (90)
T 2dnp_A           79 TKG   81 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

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

Probab=99.68  E-value=4.5e-17  Score=121.56  Aligned_cols=77  Identities=21%  Similarity=0.365  Sum_probs=70.2

Q ss_pred             CCCCceEEEecCCC-CCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDD-SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~-~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ..+.++|||+|||. .+++++|+++|++||.|.+|++.       +|||||+|.+.++|.+|++.|||..+.|+.|+|++
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            34677999999998 99999999999999999999984       57999999999999999999999999999999999


Q ss_pred             hhhhH
Q 012257          397 AQRKE  401 (467)
Q Consensus       397 ~~~~~  401 (467)
                      ++...
T Consensus        80 a~~~~   84 (96)
T 2kvi_A           80 SSSNA   84 (96)
T ss_dssp             EECCC
T ss_pred             cCcCC
Confidence            97553

>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=99.68  E-value=1.6e-17  Score=125.94  Aligned_cols=76  Identities=28%  Similarity=0.531  Sum_probs=70.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ...++|||+|||..+++++|+++|++||.|.+|++.+       +||||+|.+.++|.+|++.|||..|.|+.|+|+|++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   81 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK-------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAK   81 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS-------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcC
Confidence            3567899999999999999999999999999999874       499999999999999999999999999999999997


Q ss_pred             hhH
Q 012257          399 RKE  401 (467)
Q Consensus       399 ~~~  401 (467)
                      +..
T Consensus        82 ~~~   84 (103)
T 2dgu_A           82 PPD   84 (103)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            653

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=5.7e-17  Score=125.49  Aligned_cols=78  Identities=15%  Similarity=0.180  Sum_probs=71.5

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCe----EEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQV----VSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v----~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      .+.++|||+|||+++++++|+++|+.||.|    .+|.|+.+. +|+++|||||+|.+.++|++|++. ++..+.|+.|+
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            467899999999999999999999999975    699999984 899999999999999999999985 88999999998


Q ss_pred             eeec
Q 012257          113 IMYS  116 (467)
Q Consensus       113 v~~~  116 (467)
                      |..+
T Consensus        99 V~~a  102 (123)
T 2dha_A           99 LFRS  102 (123)
T ss_dssp             CEEE
T ss_pred             EEEC
Confidence            8655

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=7.4e-17  Score=120.71  Aligned_cols=79  Identities=23%  Similarity=0.359  Sum_probs=71.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|||+|||..+++++|+++|++||.|. ++++.+   .++|||||+|.+.++|.+|++.|||..++|+.|+|+++
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            34567999999999999999999999999996 666653   56899999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      +++
T Consensus        92 ~~~   94 (97)
T 2e5j_A           92 RQQ   94 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.68  E-value=2e-17  Score=130.88  Aligned_cols=84  Identities=14%  Similarity=0.252  Sum_probs=73.7

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ......++|||+|||++++|++|+++|+.|| |.+|+|++|+. ++++|||||+|.+.++|++|+ .+++..+.|+.|+|
T Consensus        41 ~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V  117 (139)
T 2hgn_A           41 VQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIEL  117 (139)
T ss_dssp             ----CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEE
Confidence            3445678999999999999999999999999 66999999975 999999999999999999999 68999999999999


Q ss_pred             eecccCc
Q 012257          114 MYSYRDP  120 (467)
Q Consensus       114 ~~~~~~~  120 (467)
                      ..+...+
T Consensus       118 ~~a~~~~  124 (139)
T 2hgn_A          118 FLNSTTG  124 (139)
T ss_dssp             EECCCSC
T ss_pred             EECCCCC
Confidence            8876543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.68  E-value=4e-17  Score=123.32  Aligned_cols=75  Identities=25%  Similarity=0.508  Sum_probs=71.3

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      ++|||+|||..+++++|+++|++||.|.+|++..+    ++|||||+|.+.++|.+|++.|||..++|+.|+|+++++.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            37999999999999999999999999999999987    6889999999999999999999999999999999999865

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

Probab=99.67  E-value=1.5e-16  Score=118.72  Aligned_cols=79  Identities=16%  Similarity=0.401  Sum_probs=70.6

Q ss_pred             CCCccCeEEEcCCCC-CCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           35 RQFVSTSLYVGDLDL-SVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~-~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ...++++|||+|||+ ++++++|+++|++||.|.+|.+.        +|||||+|.+.++|++|++.|++..+.|+.|+|
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            345689999999998 99999999999999999999984        479999999999999999999999999999999


Q ss_pred             eecccCcc
Q 012257          114 MYSYRDPT  121 (467)
Q Consensus       114 ~~~~~~~~  121 (467)
                      .++.....
T Consensus        78 ~~a~~~~~   85 (96)
T 2kvi_A           78 EVSSSNAR   85 (96)
T ss_dssp             EEEECCCC
T ss_pred             EEcCcCCC
Confidence            99876543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.50  E-value=3.4e-18  Score=132.74  Aligned_cols=87  Identities=21%  Similarity=0.379  Sum_probs=80.9

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEE--------EEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccC
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVS--------VRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLN  107 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~--------v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~  107 (467)
                      ..++++|||+|||+++++++|+++|++||.|.+        |.+..++.+++++|||||+|.+.++|++|++.|++..+.
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            356899999999999999999999999999999        999999889999999999999999999999999999999


Q ss_pred             CceeeeeecccCccc
Q 012257          108 GKPIRIMYSYRDPTI  122 (467)
Q Consensus       108 g~~~~v~~~~~~~~~  122 (467)
                      |+.|+|.++...+..
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999998766544

>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=99.67  E-value=3.1e-16  Score=120.30  Aligned_cols=76  Identities=24%  Similarity=0.447  Sum_probs=70.1

Q ss_pred             CCccCeEEEcCCCCC-CCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           36 QFVSTSLYVGDLDLS-VNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~-~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ...+++|||+|||++ +++++|+++|++||.|.+|.+        ++|||||+|.+.++|++|++.|++..+.|+.|+|.
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   95 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN   95 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            345689999999999 999999999999999999998        45899999999999999999999999999999999


Q ss_pred             ecccC
Q 012257          115 YSYRD  119 (467)
Q Consensus       115 ~~~~~  119 (467)
                      ++...
T Consensus        96 ~a~~~  100 (110)
T 1wf1_A           96 MAGEP  100 (110)
T ss_dssp             ESCCC
T ss_pred             ECCCC
Confidence            98744

>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=99.67  E-value=2.5e-17  Score=117.02  Aligned_cols=74  Identities=23%  Similarity=0.397  Sum_probs=69.4

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      +|||+|||..+++++|+++|++||.|.++++..+. +|.++|||||+|.+.++|.+|++. ++..++|+.|.|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            48999999999999999999999999999999886 588999999999999999999985 999999999999875

>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=99.67  E-value=1.3e-17  Score=158.88  Aligned_cols=82  Identities=18%  Similarity=0.385  Sum_probs=77.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      .+.++|||+|||..+|+++|.++|+.||.|..|.|+.+. +|.++|||||+|.+.++|.+||..|||..|+|+.|.|.|+
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            456799999999999999999999999999999999885 7889999999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ...
T Consensus       180 ~~~  182 (437)
T 3pgw_S          180 RGR  182 (437)
T ss_pred             CCC
Confidence            854

>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=1e-16  Score=128.63  Aligned_cols=77  Identities=19%  Similarity=0.325  Sum_probs=70.2

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecc--cceEEehhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVS--KPLYVALAQ  398 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v~~~~  398 (467)
                      ...|||+||++.+++++|+++|++||.|++|++..+.   ++|||||+|.+.++|.+|++.|||..|.|  +.|+|+|++
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~---~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS---SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            3468999999999999999999999999999997643   47899999999999999999999999965  999999998


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ++
T Consensus       123 ~~  124 (164)
T 1sjr_A          123 LT  124 (164)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>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=99.67  E-value=8.6e-17  Score=124.67  Aligned_cols=81  Identities=22%  Similarity=0.319  Sum_probs=73.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCcee--EEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTIT--SCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~--~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      ...++|||+|||+.+++++|+++|+.| .|.  +|+|+.+.+|+++|||||+|.+.++|.+|++. ++..|+|+.|+|..
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEE
Confidence            456789999999999999999999999 566  89999998899999999999999999999985 78999999999998


Q ss_pred             hhhhH
Q 012257          397 AQRKE  401 (467)
Q Consensus       397 ~~~~~  401 (467)
                      +..+.
T Consensus       118 a~~~e  122 (126)
T 2hgm_A          118 SSQEE  122 (126)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            87654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.67  E-value=1.1e-16  Score=119.78  Aligned_cols=82  Identities=16%  Similarity=0.390  Sum_probs=73.2

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ....++++|||+|||+++++++|+++|+.||.|..+     ..+++++|||||+|.+.++|.+|++.+++..+.|+.|+|
T Consensus        11 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   85 (96)
T 1fjc_A           11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            344578999999999999999999999999987766     347889999999999999999999999999999999999


Q ss_pred             eecccCc
Q 012257          114 MYSYRDP  120 (467)
Q Consensus       114 ~~~~~~~  120 (467)
                      .++....
T Consensus        86 ~~a~~~~   92 (96)
T 1fjc_A           86 YYTGEKG   92 (96)
T ss_dssp             EECSSSC
T ss_pred             EEcCCCC
Confidence            9986543

>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=99.67  E-value=6.5e-17  Score=121.99  Aligned_cols=77  Identities=22%  Similarity=0.427  Sum_probs=69.4

Q ss_pred             CCCCceEEE--ecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEe-----ccc
Q 012257          318 KFEGLNLYV--KNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV-----VSK  390 (467)
Q Consensus       318 ~~~~~~l~V--~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~-----~g~  390 (467)
                      ..++++|||  +||+..+++++|+++|++||.|.+|.+..+     +|||||+|.+.++|.+|++.|||+.+     .|+
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 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            345678999  679999999999999999999999988643     78999999999999999999999998     689


Q ss_pred             ceEEehhhh
Q 012257          391 PLYVALAQR  399 (467)
Q Consensus       391 ~l~v~~~~~  399 (467)
                      .|.|.|++.
T Consensus        97 ~l~v~~a~~  105 (114)
T 2cq2_A           97 TLYLNFVEK  105 (114)
T ss_dssp             ECEEEEESC
T ss_pred             EEEEEeccc
Confidence            999999864

>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=99.67  E-value=2.3e-16  Score=115.57  Aligned_cols=78  Identities=18%  Similarity=0.214  Sum_probs=71.6

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ++.+++|||+|||+++++++|+++|++| .|.++++.      +++|||||+|.+.++|++|++.+++..+.|+.|+|.+
T Consensus         2 s~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   74 (88)
T 1wg1_A            2 SSGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQL   74 (88)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEE
Confidence            4568999999999999999999999999 99999884      5779999999999999999999999999999999999


Q ss_pred             cccCc
Q 012257          116 SYRDP  120 (467)
Q Consensus       116 ~~~~~  120 (467)
                      +....
T Consensus        75 a~~~~   79 (88)
T 1wg1_A           75 QPTDA   79 (88)
T ss_dssp             CCCCC
T ss_pred             cCCCc
Confidence            86543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=2.7e-16  Score=118.99  Aligned_cols=81  Identities=27%  Similarity=0.433  Sum_probs=72.9

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      .....++|||+|||..+++++|+++|+.|+   .++++.+. ++.++|||||+|.+.++|.+|++.|||..|.|+.|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            345678899999999999999999999874   56777775 78899999999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++++
T Consensus        88 ~a~~~   92 (102)
T 2fc8_A           88 WAKPK   92 (102)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            99865

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.66  E-value=6e-17  Score=121.12  Aligned_cols=78  Identities=27%  Similarity=0.423  Sum_probs=71.4

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ...++|||+|||..+++++|+++|+.||.|..+    ..++.++|||||+|.+.++|.+|+..|||..++|+.|+|.+++
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   89 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcC
Confidence            356789999999999999999999999998766    4567889999999999999999999999999999999999987


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ++
T Consensus        90 ~~   91 (96)
T 1fjc_A           90 EK   91 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.66  E-value=1.6e-16  Score=132.25  Aligned_cols=83  Identities=34%  Similarity=0.499  Sum_probs=78.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|||+|||..+++++|+++|+.||.|.+|+|..+.++.++|||||+|.+.++|.+|++.|||..|+|+.|+|+|+
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34567999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ...
T Consensus       165 ~~~  167 (177)
T 2f3j_A          165 ASQ  167 (177)
T ss_dssp             SSG
T ss_pred             cCC
Confidence            754

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.66  E-value=1.8e-16  Score=119.40  Aligned_cols=79  Identities=15%  Similarity=0.218  Sum_probs=71.5

Q ss_pred             cCeEEEcCC----CCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecC----hHH----HHHHHH--HhCCc
Q 012257           39 STSLYVGDL----DLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNA----AHE----ATRALD--ELNFT  104 (467)
Q Consensus        39 ~~~l~v~nL----p~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~----~~~----A~~A~~--~l~~~  104 (467)
                      .++|||+||    |+.++|++|+++|+.||+|.++.++.|+.||+++|||||+|.+    +++    |.+|+.  .+++.
T Consensus         2 p~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~   81 (136)
T 2j8a_A            2 SCEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGC   81 (136)
T ss_dssp             CCEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCE
T ss_pred             CcEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCC
Confidence            378999999    9999999999999999999999999999999999999999996    434    888988  67999


Q ss_pred             ccCCceeeeeecc
Q 012257          105 PLNGKPIRIMYSY  117 (467)
Q Consensus       105 ~~~g~~~~v~~~~  117 (467)
                      .|.|+.|+|....
T Consensus        82 ~I~Gr~irV~ln~   94 (136)
T 2j8a_A           82 FIMGFKFEVILNK   94 (136)
T ss_dssp             EETTEEEEEEECC
T ss_pred             eecCcEEEEEECc
Confidence            9999999998654

>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=99.66  E-value=1.2e-16  Score=123.93  Aligned_cols=80  Identities=30%  Similarity=0.461  Sum_probs=72.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCce----eEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceE
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTI----TSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY  393 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v----~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  393 (467)
                      ..+.++|||+|||..+++++|+++|++||.|    ..+++.   ++.++|||||+|.+.++|.+|++.|||..++|+.|+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~---~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   98 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV   98 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE---CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC---CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            3466799999999999999999999999998    455554   678899999999999999999999999999999999


Q ss_pred             Eehhhhh
Q 012257          394 VALAQRK  400 (467)
Q Consensus       394 v~~~~~~  400 (467)
                      |+|+++.
T Consensus        99 v~~a~~~  105 (115)
T 2cpx_A           99 IEFGKNK  105 (115)
T ss_dssp             EEECCCC
T ss_pred             EEEccCC
Confidence            9999865

>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=99.66  E-value=1.9e-16  Score=117.62  Aligned_cols=78  Identities=27%  Similarity=0.421  Sum_probs=69.5

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCC-eEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCC-cccCCceeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQ-VVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNF-TPLNGKPIRIM  114 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~-v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~-~~~~g~~~~v~  114 (467)
                      .+.++|||+|||+++++++|+++|++||. |..+.+.       ++|||||+|.+.++|++|++.|++ ..+.|+.|+|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45799999999999999999999999998 6666652       458999999999999999999999 99999999999


Q ss_pred             ecccCcc
Q 012257          115 YSYRDPT  121 (467)
Q Consensus       115 ~~~~~~~  121 (467)
                      ++.....
T Consensus        79 ~a~~~~~   85 (93)
T 2cqh_A           79 YSVSKKL   85 (93)
T ss_dssp             ECCCCCC
T ss_pred             EccCccc
Confidence            9876543

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

Probab=99.66  E-value=1.1e-15  Score=114.39  Aligned_cols=79  Identities=19%  Similarity=0.336  Sum_probs=70.8

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ...+.++|||+||  ++++++|+++|++||.|.+|.+.      +++|||||+|.+.++|.+|++.|++..+.|+.|+|.
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~   82 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   82 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            3446799999996  89999999999999999999984      456899999999999999999999999999999999


Q ss_pred             ecccCcc
Q 012257          115 YSYRDPT  121 (467)
Q Consensus       115 ~~~~~~~  121 (467)
                      ++.....
T Consensus        83 ~a~~~~~   89 (97)
T 1x5p_A           83 IARKQPM   89 (97)
T ss_dssp             CCSSCCC
T ss_pred             ECCCCCC
Confidence            9876544

>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=3.5e-16  Score=116.93  Aligned_cols=79  Identities=25%  Similarity=0.260  Sum_probs=71.9

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEE-EEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSV-RVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v-~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..+++|||+|||+++++++|+++|+.||.|.++ .+..++.++    .|||+|.+.++|++|++.|++..+.|+.|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            457899999999999999999999999999999 588776654    399999999999999999999999999999999


Q ss_pred             cccC
Q 012257          116 SYRD  119 (467)
Q Consensus       116 ~~~~  119 (467)
                      +...
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            8755

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=7.4e-16  Score=114.49  Aligned_cols=78  Identities=21%  Similarity=0.266  Sum_probs=69.7

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ...+++|||+|||+++++++|+++|+.||.|.+|  ..++.+++   ||||+|.+.++|++|++ +++..+.|+.|+|.+
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            3457899999999999999999999999999987  55655655   99999999999999999 999999999999998


Q ss_pred             cccC
Q 012257          116 SYRD  119 (467)
Q Consensus       116 ~~~~  119 (467)
                      +...
T Consensus        79 a~~~   82 (94)
T 2e5g_A           79 REQK   82 (94)
T ss_dssp             SCCS
T ss_pred             CCcC
Confidence            7644

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.66  E-value=6.3e-17  Score=122.49  Aligned_cols=80  Identities=24%  Similarity=0.489  Sum_probs=75.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ..++|||+|||..+++++|+++|+.||.|.+|++..+.+|.++|||||+|.+.++|.+|++  ++..++|+.|.|.++.+
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            4568999999999999999999999999999999999999999999999999999999998  99999999999999876


Q ss_pred             hH
Q 012257          400 KE  401 (467)
Q Consensus       400 ~~  401 (467)
                      +.
T Consensus        86 ~~   87 (102)
T 2xs2_A           86 KQ   87 (102)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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=99.66  E-value=1.2e-16  Score=118.56  Aligned_cols=76  Identities=22%  Similarity=0.363  Sum_probs=68.5

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCc-eeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCC-cEecccceEEeh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGT-ITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNG-KMVVSKPLYVAL  396 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~-v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g-~~~~g~~l~v~~  396 (467)
                      ...++|||+|||..+++++|+++|++||. |..+.+.      ++|||||+|.+.++|.+|++.||| ..++|+.|+|+|
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~   79 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDY   79 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEE
Confidence            45678999999999999999999999999 6666653      478999999999999999999999 999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      ++++
T Consensus        80 a~~~   83 (93)
T 2cqh_A           80 SVSK   83 (93)
T ss_dssp             CCCC
T ss_pred             ccCc
Confidence            9754

>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=99.66  E-value=3e-17  Score=129.88  Aligned_cols=80  Identities=19%  Similarity=0.274  Sum_probs=73.8

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ...++|||+|||+.+++++|+++|++|| |.+|+|+.+.+|+++|||||+|.+.++|.+|+ .+|+..|+|+.|.|..+.
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECC
Confidence            3556899999999999999999999999 67999999999999999999999999999999 789999999999999876


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ..
T Consensus       122 ~~  123 (139)
T 2hgn_A          122 TT  123 (139)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.66  E-value=1.8e-16  Score=119.40  Aligned_cols=80  Identities=19%  Similarity=0.347  Sum_probs=71.4

Q ss_pred             ceEEEecC----CCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCC----HHH----HHHHHH--HhCCcE
Q 012257          322 LNLYVKNL----DDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFST----AEE----ASKALT--EMNGKM  386 (467)
Q Consensus       322 ~~l~V~nl----p~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~----~~~----A~~A~~--~l~g~~  386 (467)
                      ..|||+||    |+.+++++|+++|+.||+|.++.++.|+ +|.++|||||+|.+    .++    |.+|+.  .|+|..
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            47999999    9999999999999999999999999998 78999999999996    322    899988  789999


Q ss_pred             ecccceEEehhhhhH
Q 012257          387 VVSKPLYVALAQRKE  401 (467)
Q Consensus       387 ~~g~~l~v~~~~~~~  401 (467)
                      |+|+.|+|.+.+...
T Consensus        83 I~Gr~irV~ln~~g~   97 (136)
T 2j8a_A           83 IMGFKFEVILNKHSI   97 (136)
T ss_dssp             ETTEEEEEEECCTTH
T ss_pred             ecCcEEEEEECcccH
Confidence            999999999976443

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.47  E-value=7.9e-18  Score=130.66  Aligned_cols=84  Identities=21%  Similarity=0.468  Sum_probs=77.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeE--------EEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecc
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITS--------CKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVS  389 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~--------v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  389 (467)
                      .+.++|||+|||..+++++|+++|++||.|.+        |++..+. ++.++|||||+|.+.++|.+|++.|||..+.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            35568999999999999999999999999998        8898885 68899999999999999999999999999999


Q ss_pred             cceEEehhhhhHH
Q 012257          390 KPLYVALAQRKEE  402 (467)
Q Consensus       390 ~~l~v~~~~~~~~  402 (467)
                      +.|+|++++++..
T Consensus        85 ~~l~V~~a~~~~~   97 (116)
T 2lcw_A           85 NPIKVSFATRRAD   97 (116)
Confidence            9999999987654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.65  E-value=4e-16  Score=120.25  Aligned_cols=73  Identities=22%  Similarity=0.276  Sum_probs=66.8

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccce-EEEEcCCHHHHHHHHHHhCCcEecc--cceEEehhhh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGS-GFVAFSTAEEASKALTEMNGKMVVS--KPLYVALAQR  399 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~-afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v~~~~~  399 (467)
                      .|||+||++.+++++|+++|++||.|.+|++...     .|| |||+|.+.++|.+|++.|||..|.|  +.|+|+|+++
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~  101 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP  101 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecC
Confidence            4689999999999999999999999999999763     276 9999999999999999999999987  6899999986


Q ss_pred             h
Q 012257          400 K  400 (467)
Q Consensus       400 ~  400 (467)
                      .
T Consensus       102 ~  102 (124)
T 2e5i_A          102 T  102 (124)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.65  E-value=2.6e-16  Score=115.30  Aligned_cols=74  Identities=22%  Similarity=0.356  Sum_probs=68.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ..++|||+|||..+++++|+++|++| .|.++++.     +++|||||+|.+.++|.+|++.|||..++|+.|+|+++..
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            45689999999999999999999999 99999984     5789999999999999999999999999999999999854

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=5.3e-16  Score=116.56  Aligned_cols=76  Identities=33%  Similarity=0.489  Sum_probs=70.2

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccC--CceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEF--GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~--G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ....++|||+|||..+++++|+++|++|  |.|.++++.       +|||||+|.+.++|.+|+..|||..++|+.|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT   84 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            3466799999999999999999999999  999999875       4599999999999999999999999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |+++.
T Consensus        85 ~a~~~   89 (99)
T 2cpd_A           85 LAKPV   89 (99)
T ss_dssp             CCCCC
T ss_pred             ECCCC
Confidence            99764

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.65  E-value=2.5e-17  Score=124.47  Aligned_cols=80  Identities=28%  Similarity=0.390  Sum_probs=71.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeC-CCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ...++|||+|||..+++++|+++|+.||.|.. +++.+ .+|.++|||||+|.+.++|.+|++ |||..+.|+.|+|.++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            35679999999999999999999999999887 44444 468889999999999999999998 9999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      +++
T Consensus        93 ~~~   95 (101)
T 1fj7_A           93 KGR   95 (101)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            764

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.65  E-value=8.4e-16  Score=115.63  Aligned_cols=83  Identities=17%  Similarity=0.267  Sum_probs=73.3

Q ss_pred             CCCceEEEecCCC-----CCCHHHHHHhhccCCceeEEEEeeCC--CCCccceEEEEcCCHHHHHHHHHHhCCcEecccc
Q 012257          319 FEGLNLYVKNLDD-----SISDDKLKELFSEFGTITSCKVMRDP--NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP  391 (467)
Q Consensus       319 ~~~~~l~V~nlp~-----~~~~~~l~~~F~~~G~v~~v~i~~~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  391 (467)
                      .++++|+|.|+..     .-++++|++.|++||.|.+|+|..++  ++.++|+|||+|.+.++|.+|++.|||+.++|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4667999999963     23789999999999999999999876  3678999999999999999999999999999999


Q ss_pred             eEEehhhhhH
Q 012257          392 LYVALAQRKE  401 (467)
Q Consensus       392 l~v~~~~~~~  401 (467)
                      |.|.|+....
T Consensus        86 i~v~~a~~~~   95 (105)
T 2pe8_A           86 VKACFYNLDK   95 (105)
T ss_dssp             CEEEECCHHH
T ss_pred             EEEEEcCHHH
Confidence            9999998643

>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=99.65  E-value=2.6e-16  Score=120.75  Aligned_cols=75  Identities=23%  Similarity=0.532  Sum_probs=69.7

Q ss_pred             CCCceEEEecCCCC-CCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDS-ISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~-~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ...++|||+|||.. +++++|+++|++||.|.+|++       ++|||||+|.+.++|.+|++.|||..++|+.|+|+|+
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            34579999999999 999999999999999999998       4679999999999999999999999999999999998


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      +..
T Consensus        98 ~~~  100 (110)
T 1wf1_A           98 GEP  100 (110)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            743

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

Probab=99.65  E-value=5.3e-16  Score=116.04  Aligned_cols=76  Identities=32%  Similarity=0.476  Sum_probs=69.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|||+||  .+++++|+++|++||.|.+|++.     .++|||||+|.+.++|.+|++.|||..++|+.|+|.|+
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            346679999996  89999999999999999999985     35789999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      +++
T Consensus        85 ~~~   87 (97)
T 1x5p_A           85 RKQ   87 (97)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            754

>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=99.64  E-value=1.1e-15  Score=122.77  Aligned_cols=78  Identities=18%  Similarity=0.175  Sum_probs=70.5

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC--ceeeeeec
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG--KPIRIMYS  116 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g--~~~~v~~~  116 (467)
                      ..+|||+||++.+++++|+++|++||.|++|++..+.    ++|||||+|.+.++|++|++.|++..|.|  +.|+|.|+
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            4678999999999999999999999999999997543    46899999999999999999999999966  99999998


Q ss_pred             ccCc
Q 012257          117 YRDP  120 (467)
Q Consensus       117 ~~~~  120 (467)
                      ....
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            7653

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=4.6e-16  Score=120.04  Aligned_cols=78  Identities=18%  Similarity=0.296  Sum_probs=67.9

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCC---CccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLST---RRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      ...+++|||+|||+++++++|+++|++||.|. +.++.++.+   |+++|||||+|.+.++|++|++.++  .+.|+.+.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEE
Confidence            35689999999999999999999999999999 888888777   7999999999999999999999884  36777776


Q ss_pred             eeec
Q 012257          113 IMYS  116 (467)
Q Consensus       113 v~~~  116 (467)
                      +..+
T Consensus        82 ~~~~   85 (114)
T 2dnl_A           82 CVSS   85 (114)
T ss_dssp             EECC
T ss_pred             eccC
Confidence            6543

>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=5.4e-16  Score=113.44  Aligned_cols=76  Identities=17%  Similarity=0.400  Sum_probs=63.1

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEe--cccceEEeh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV--VSKPLYVAL  396 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~  396 (467)
                      .+..+|||+|||+.+++++|+++|++||.|.+|+++.+    ++|||||+|.+.++|.+    ++|..+  .|+.|.|++
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~   80 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISN   80 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEE
Confidence            45678999999999999999999999999999999885    68999999999999883    566665  489999999


Q ss_pred             hhhhHH
Q 012257          397 AQRKEE  402 (467)
Q Consensus       397 ~~~~~~  402 (467)
                      +.++..
T Consensus        81 a~~k~~   86 (89)
T 3d2w_A           81 AEPKHN   86 (89)
T ss_dssp             CC----
T ss_pred             cCCCCc
Confidence            987653

>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=1.4e-16  Score=151.73  Aligned_cols=152  Identities=15%  Similarity=0.298  Sum_probs=107.3

Q ss_pred             HHHHHHhcCCCeEEEEEEe----cC-CCCccccEE--EEEecChHHHHHHHHHhCCcccCC---------------ceee
Q 012257           55 QLYDLFNQMGQVVSVRVCR----DL-STRRSLGYG--YVNYNAAHEATRALDELNFTPLNG---------------KPIR  112 (467)
Q Consensus        55 ~l~~~f~~~G~v~~v~i~~----~~-~~~~~~g~a--fV~f~~~~~A~~A~~~l~~~~~~g---------------~~~~  112 (467)
                      .|..+|..+|+|..|..+.    ++ .+....|++  |+.|.+..++..++..++.....+               ..+.
T Consensus         8 ~L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~~~~~   87 (437)
T 3pgw_S            8 NLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELK   87 (437)
T ss_pred             cHHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            3788999999998874332    22 122222333  778877655543332211111110               1111


Q ss_pred             eeecccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCC
Q 012257          113 IMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGM  191 (467)
Q Consensus       113 v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~  191 (467)
                      +......+.......++|||+|||..+|+++|.++|+.||.|..|.|+.+ .+|.++|||||+|.+.++|..||+.|+|.
T Consensus        88 ~~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~  167 (437)
T 3pgw_S           88 MWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGK  167 (437)
T ss_pred             hcCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCC
Confidence            11111222223344579999999999999999999999999999999988 68899999999999999999999999999


Q ss_pred             ccCCeeeEecccccc
Q 012257          192 LLNDKQVFVGPFLRK  206 (467)
Q Consensus       192 ~~~g~~~~v~~~~~~  206 (467)
                      .|.|+.|.|.++...
T Consensus       168 ~i~gr~i~V~~a~~~  182 (437)
T 3pgw_S          168 KIDGRRVLVDVERGR  182 (437)
T ss_pred             EECCEEEEEEEeCCC
Confidence            999999999887654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.64  E-value=2e-15  Score=116.64  Aligned_cols=77  Identities=18%  Similarity=0.215  Sum_probs=69.2

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccE-EEEEecChHHHHHHHHHhCCcccCC--ceeeeee
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGY-GYVNYNAAHEATRALDELNFTPLNG--KPIRIMY  115 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~-afV~f~~~~~A~~A~~~l~~~~~~g--~~~~v~~  115 (467)
                      --+|||+||++.+++++|+++|++||.|.+|++..+.     +|+ |||+|.+.++|++|++.|++..|.|  +.|+|.+
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~  102 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  102 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEe
Confidence            3567799999999999999999999999999998753     366 9999999999999999999999988  8899999


Q ss_pred             cccCc
Q 012257          116 SYRDP  120 (467)
Q Consensus       116 ~~~~~  120 (467)
                      +....
T Consensus       103 ak~~~  107 (130)
T 3zzy_A          103 SKLTS  107 (130)
T ss_dssp             CSCSS
T ss_pred             cCCCc
Confidence            87653

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=6.3e-16  Score=116.63  Aligned_cols=77  Identities=22%  Similarity=0.355  Sum_probs=67.6

Q ss_pred             CCccCeEEE--cCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc-----CC
Q 012257           36 QFVSTSLYV--GDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL-----NG  108 (467)
Q Consensus        36 ~~~~~~l~v--~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~-----~g  108 (467)
                      ..++++|||  +||+++++|++|+++|++||.|.+|.+..+      +|||||+|.+.++|++|++.||+..+     .|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            345789999  779999999999999999999999988643      57999999999999999999999887     67


Q ss_pred             ceeeeeeccc
Q 012257          109 KPIRIMYSYR  118 (467)
Q Consensus       109 ~~~~v~~~~~  118 (467)
                      +.|.|.++..
T Consensus        96 ~~l~v~~a~~  105 (114)
T 2cq2_A           96 ITLYLNFVEK  105 (114)
T ss_dssp             EECEEEEESC
T ss_pred             cEEEEEeccc
Confidence            8888877653

>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=99.63  E-value=2.5e-16  Score=127.11  Aligned_cols=83  Identities=28%  Similarity=0.475  Sum_probs=72.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEE------EEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccc
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSC------KVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP  391 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v------~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  391 (467)
                      ..+.++|||+|||..+++++|+++|+.||.|..+      .+....+|.++|||||+|.+.++|.+|+..|||..+.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            4567899999999999999999999999998764      1222246888999999999999999999999999999999


Q ss_pred             eEEehhhhh
Q 012257          392 LYVALAQRK  400 (467)
Q Consensus       392 l~v~~~~~~  400 (467)
                      |.|.|+++.
T Consensus       122 l~V~~a~~~  130 (143)
T 3egn_A          122 MVVQFARSA  130 (143)
T ss_dssp             CEEEECCCS
T ss_pred             EEEEECCCC
Confidence            999999754

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.63  E-value=1.7e-15  Score=113.99  Aligned_cols=85  Identities=8%  Similarity=0.087  Sum_probs=74.7

Q ss_pred             CCCCccCeEEEcCCCC-----CCCHHHHHHHHhcCCCeEEEEEEecCCC-CccccEEEEEecChHHHHHHHHHhCCcccC
Q 012257           34 ARQFVSTSLYVGDLDL-----SVNDSQLYDLFNQMGQVVSVRVCRDLST-RRSLGYGYVNYNAAHEATRALDELNFTPLN  107 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~-----~~~e~~l~~~f~~~G~v~~v~i~~~~~~-~~~~g~afV~f~~~~~A~~A~~~l~~~~~~  107 (467)
                      ....++++|+|+||..     +.++++|++.|++||.|.+|+|.+++.+ ++++|+|||+|.+.++|.+|++.||+..+.
T Consensus         3 i~~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~   82 (105)
T 2pe8_A            3 MGKCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFG   82 (105)
T ss_dssp             GGGSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            3456789999999973     3468999999999999999999998654 688999999999999999999999999999


Q ss_pred             Cceeeeeeccc
Q 012257          108 GKPIRIMYSYR  118 (467)
Q Consensus       108 g~~~~v~~~~~  118 (467)
                      |+.|+|.++..
T Consensus        83 Gr~i~v~~a~~   93 (105)
T 2pe8_A           83 GRVVKACFYNL   93 (105)
T ss_dssp             TEECEEEECCH
T ss_pred             CcEEEEEEcCH
Confidence            99999988753

>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=99.62  E-value=7.2e-16  Score=118.98  Aligned_cols=70  Identities=24%  Similarity=0.269  Sum_probs=62.7

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      .+..++|||+|||+++++++|+++|++||.|.+|.|..+       |||||+|.+.++|++|++.|++..|.|+.++
T Consensus        13 ~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~   82 (115)
T 3beg_B           13 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   82 (115)
T ss_dssp             ----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEee
Confidence            346799999999999999999999999999999999766       7999999999999999999999999999833

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.62  E-value=1.2e-14  Score=111.97  Aligned_cols=75  Identities=19%  Similarity=0.267  Sum_probs=66.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccE-EEEEecChHHHHHHHHHhCCcccCC--ceeeeeec
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGY-GYVNYNAAHEATRALDELNFTPLNG--KPIRIMYS  116 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~-afV~f~~~~~A~~A~~~l~~~~~~g--~~~~v~~~  116 (467)
                      ..|||+||++.+++++|+++|++||.|.+|+|...      .|+ |||+|.+.++|.+|++.|++..|.|  +.|+|.++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            44679999999999999999999999999999752      175 9999999999999999999999987  58999988


Q ss_pred             ccCc
Q 012257          117 YRDP  120 (467)
Q Consensus       117 ~~~~  120 (467)
                      ....
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            6553

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=1.3e-15  Score=113.22  Aligned_cols=76  Identities=20%  Similarity=0.327  Sum_probs=66.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ..++|||+|||..+++++|+++|++||.|.+| +....+|.   ||||+|.+.++|.+|++ |||..++|+.|+|+++.+
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v-~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~   81 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV-VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQ   81 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE-EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE-EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCc
Confidence            45689999999999999999999999999987 33333444   99999999999999999 999999999999998754


Q ss_pred             h
Q 012257          400 K  400 (467)
Q Consensus       400 ~  400 (467)
                      +
T Consensus        82 ~   82 (94)
T 2e5g_A           82 K   82 (94)
T ss_dssp             S
T ss_pred             C
Confidence            3

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=6e-16  Score=115.66  Aligned_cols=79  Identities=24%  Similarity=0.368  Sum_probs=70.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEE-EeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCK-VMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~-i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ...++|||+|||..+++++|+++|++||.|.+++ ++.+..   .+.|||+|.+.++|.+|++.|||..++|+.|+|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            3567899999999999999999999999999995 777643   234999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      .++
T Consensus        90 ~~~   92 (96)
T 2e44_A           90 PDE   92 (96)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            865

>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=99.62  E-value=2.1e-16  Score=127.55  Aligned_cols=84  Identities=23%  Similarity=0.297  Sum_probs=72.4

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEE-----EecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCce
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRV-----CRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKP  110 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i-----~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~  110 (467)
                      ..++++|||+|||+++++++|+++|+.||.|.++.+     ++...+++++|||||+|.+.++|.+|++.|++..+.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            456799999999999999999999999998876410     111246789999999999999999999999999999999


Q ss_pred             eeeeecccC
Q 012257          111 IRIMYSYRD  119 (467)
Q Consensus       111 ~~v~~~~~~  119 (467)
                      |+|.++...
T Consensus       122 l~V~~a~~~  130 (143)
T 3egn_A          122 MVVQFARSA  130 (143)
T ss_dssp             CEEEECCCS
T ss_pred             EEEEECCCC
Confidence            999998654

>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=99.62  E-value=7.2e-16  Score=118.96  Aligned_cols=74  Identities=26%  Similarity=0.333  Sum_probs=65.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccc-----eEE
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP-----LYV  394 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-----l~v  394 (467)
                      ..++|||+|||..+++++|+++|++||.|.+|+++.+      |||||+|.+.++|.+|++.|||..|+|+.     |+|
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v   88 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   88 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEe
Confidence            4568999999999999999999999999999999876      79999999999999999999999999999     555


Q ss_pred             ehhhh
Q 012257          395 ALAQR  399 (467)
Q Consensus       395 ~~~~~  399 (467)
                      ..+.+
T Consensus        89 ~~~~~   93 (115)
T 3beg_B           89 KVDGP   93 (115)
T ss_dssp             EECC-
T ss_pred             ccCCC
Confidence            55443

>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=99.61  E-value=1.2e-15  Score=111.73  Aligned_cols=73  Identities=22%  Similarity=0.534  Sum_probs=67.4

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcC----C-------CeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCc
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQM----G-------QVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFT  104 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~----G-------~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~  104 (467)
                      ++++++|||+|||+++++++|+++|++|    |       .|.++++.++      +|||||+|.+.++|.+|+ .+++.
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~   75 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGI   75 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCC
Confidence            4578999999999999999999999999    8       9999998765      479999999999999999 89999


Q ss_pred             ccCCceeeeee
Q 012257          105 PLNGKPIRIMY  115 (467)
Q Consensus       105 ~~~g~~~~v~~  115 (467)
                      .+.|+.|+|..
T Consensus        76 ~~~g~~l~V~r   86 (87)
T 2hzc_A           76 IFQGQSLKIRR   86 (87)
T ss_dssp             EETTEECEEEC
T ss_pred             EECCeEEEEeC
Confidence            99999999863

>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=99.61  E-value=1.1e-15  Score=111.85  Aligned_cols=78  Identities=17%  Similarity=0.281  Sum_probs=62.0

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ...+.++|||+|||++++|++|+++|++||.|.+|++.++     ++|||||+|.+.++|+++..  ....+.|+.+.|.
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~--~~~~~~g~~v~v~   79 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG--EDLIIKGISVHIS   79 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTT--CEEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcC--CCcccCCEEEEEE
Confidence            3456899999999999999999999999999999999874     67999999999999984322  1234579999998


Q ss_pred             ecccC
Q 012257          115 YSYRD  119 (467)
Q Consensus       115 ~~~~~  119 (467)
                      ++...
T Consensus        80 ~a~~k   84 (89)
T 3d2w_A           80 NAEPK   84 (89)
T ss_dssp             ECC--
T ss_pred             EcCCC
Confidence            87643

>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=99.59  E-value=1.1e-15  Score=112.16  Aligned_cols=79  Identities=18%  Similarity=0.286  Sum_probs=67.2

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      +.++++|||+|||+++++++|+++|++||.|.+|++.++     ++|||||+|.+.++|++|...  ...+.|+.|+|.+
T Consensus         2 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~   74 (88)
T 1wf0_A            2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISN   74 (88)
T ss_dssp             CSCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEe
Confidence            346899999999999999999999999999999999865     568999999999999876442  3456999999998


Q ss_pred             cccCcc
Q 012257          116 SYRDPT  121 (467)
Q Consensus       116 ~~~~~~  121 (467)
                      +.....
T Consensus        75 a~~~~~   80 (88)
T 1wf0_A           75 AEPKHN   80 (88)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            876544

>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=99.59  E-value=3.5e-15  Score=109.24  Aligned_cols=71  Identities=20%  Similarity=0.479  Sum_probs=66.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccC----C-------ceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEec
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEF----G-------TITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVV  388 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~----G-------~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~  388 (467)
                      ..++|||+|||..+++++|+++|++|    |       .|.++++.++     +|||||+|.+.++|.+|+ .|||..++
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~~~~   78 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGIIFQ   78 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCCEEC
Confidence            45689999999999999999999999    8       9999998865     789999999999999999 99999999


Q ss_pred             ccceEEeh
Q 012257          389 SKPLYVAL  396 (467)
Q Consensus       389 g~~l~v~~  396 (467)
                      |+.|+|+.
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            99999973

>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=99.59  E-value=4.4e-15  Score=125.57  Aligned_cols=81  Identities=20%  Similarity=0.288  Sum_probs=73.7

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      .++|||+|||..+++++|+++|++||.|.+|+++++.+|.++|||||+|.+.++|.+|+..++ ..++|+.|.|.+++..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDDY  187 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHHH
Confidence            458999999999999999999999999999999999999999999999999999999998654 5999999999998765


Q ss_pred             HH
Q 012257          401 EE  402 (467)
Q Consensus       401 ~~  402 (467)
                      ..
T Consensus       188 ~~  189 (193)
T 2voo_A          188 FA  189 (193)
T ss_dssp             --
T ss_pred             HH
Confidence            43

>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=99.57  E-value=6.4e-15  Score=110.88  Aligned_cols=83  Identities=17%  Similarity=0.330  Sum_probs=72.1

Q ss_pred             CCCceEEEecC--CCCCC--------HHHHHHhhccCCceeEEEEeeCCCC---CccceEEEEcCCHHHHHHHHHHhCCc
Q 012257          319 FEGLNLYVKNL--DDSIS--------DDKLKELFSEFGTITSCKVMRDPNG---ISRGSGFVAFSTAEEASKALTEMNGK  385 (467)
Q Consensus       319 ~~~~~l~V~nl--p~~~~--------~~~l~~~F~~~G~v~~v~i~~~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~  385 (467)
                      .+++.|.+.|+  +..+.        +++|++.|++||.|.+|+|+++..+   .++|+|||+|.+.++|.+|+..|||+
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            35678999998  33333        3699999999999999999988743   67899999999999999999999999


Q ss_pred             EecccceEEehhhhhH
Q 012257          386 MVVSKPLYVALAQRKE  401 (467)
Q Consensus       386 ~~~g~~l~v~~~~~~~  401 (467)
                      .++|+.|+|+|+....
T Consensus        83 ~f~GR~i~v~~~~~~~   98 (105)
T 3v4m_A           83 KFANRVVVTKYCDPDS   98 (105)
T ss_dssp             EETTEECEEEEECHHH
T ss_pred             EeCCCEEEEEEeCHHH
Confidence            9999999999987654

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

Probab=99.57  E-value=3.8e-15  Score=128.25  Aligned_cols=79  Identities=24%  Similarity=0.423  Sum_probs=70.4

Q ss_pred             CCCceEEEecCCCCC---------CHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEe--
Q 012257          319 FEGLNLYVKNLDDSI---------SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV--  387 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~---------~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--  387 (467)
                      ...++|||+||+..+         ++++|+++|++||.|++|+|+.     ++|||||+|.+.++|..|++.|+|..|  
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            356799999999988         7999999999999999999986     488999999999999999999999999  


Q ss_pred             ----------cccceEEehhhhhHH
Q 012257          388 ----------VSKPLYVALAQRKEE  402 (467)
Q Consensus       388 ----------~g~~l~v~~~~~~~~  402 (467)
                                .|+.|.|+||+....
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                      899999999986644

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=4.6e-15  Score=114.40  Aligned_cols=76  Identities=14%  Similarity=0.234  Sum_probs=65.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCC----CCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN----GISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~----~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ..++|||+|||..+++++|+++|++||.|. ++++.+..    |+++|||||+|.+.++|.+|++.|+  .++|+.+.+.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~   83 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCV   83 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEec
Confidence            567899999999999999999999999999 88777653    6899999999999999999999984  3677777766


Q ss_pred             hhh
Q 012257          396 LAQ  398 (467)
Q Consensus       396 ~~~  398 (467)
                      .+.
T Consensus        84 ~~~   86 (114)
T 2dnl_A           84 SSP   86 (114)
T ss_dssp             CCS
T ss_pred             cCC
Confidence            543

>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=99.56  E-value=8.5e-15  Score=123.80  Aligned_cols=80  Identities=14%  Similarity=0.293  Sum_probs=72.8

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ...++|||+|||+++++++|+++|+.||.|.+|.+.++. +++++|||||+|.+.++|.+|++.++ ..+.|+.|+|.+.
T Consensus       107 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~  184 (193)
T 2voo_A          107 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFK  184 (193)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEET
T ss_pred             cccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEh
Confidence            346999999999999999999999999999999999986 58999999999999999999998654 5899999999886


Q ss_pred             cc
Q 012257          117 YR  118 (467)
Q Consensus       117 ~~  118 (467)
                      ..
T Consensus       185 ~~  186 (193)
T 2voo_A          185 DD  186 (193)
T ss_dssp             TT
T ss_pred             HH
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=99.56  E-value=2.3e-15  Score=110.32  Aligned_cols=75  Identities=19%  Similarity=0.365  Sum_probs=63.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ..++|||+|||..+++++|+++|++||.|.+|+++.+    ++|||||+|.+.++|.+|+.  ....+.|+.|+|+++++
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecCC
Confidence            4578999999999999999999999999999999875    67899999999999975422  12344899999999876


Q ss_pred             h
Q 012257          400 K  400 (467)
Q Consensus       400 ~  400 (467)
                      +
T Consensus        78 ~   78 (88)
T 1wf0_A           78 K   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.54  E-value=2.3e-15  Score=113.21  Aligned_cols=72  Identities=22%  Similarity=0.451  Sum_probs=62.6

Q ss_pred             EecCCCCCCHHHHHHhh------------ccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceE
Q 012257          326 VKNLDDSISDDKLKELF------------SEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY  393 (467)
Q Consensus       326 V~nlp~~~~~~~l~~~F------------~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  393 (467)
                      +.||+..+++++|++.|            ++||.|.+|+|.++..++++|||||+|.+.++|.+|+..|||+.++|+.|+
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            34555556666666555            999999999999988889999999999999999999999999999999999


Q ss_pred             Eehh
Q 012257          394 VALA  397 (467)
Q Consensus       394 v~~~  397 (467)
                      |+|+
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>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=99.52  E-value=8.6e-14  Score=106.76  Aligned_cols=86  Identities=14%  Similarity=0.135  Sum_probs=72.1

Q ss_pred             CCCCCccCeEEEcCCCCCCC-----------HHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHh
Q 012257           33 DARQFVSTSLYVGDLDLSVN-----------DSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL  101 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~-----------e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l  101 (467)
                      ..+..++++|+|+||....+           +++|+++|++||.|.+|.| .++   .++|||||+|.+.++|.+|++.|
T Consensus         9 ~~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~l   84 (112)
T 2dit_A            9 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTL   84 (112)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHS
T ss_pred             CCCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHc
Confidence            34556799999999954332           5799999999999999966 444   27899999999999999999999


Q ss_pred             CCcccCCceeeeeecccCccc
Q 012257          102 NFTPLNGKPIRIMYSYRDPTI  122 (467)
Q Consensus       102 ~~~~~~g~~~~v~~~~~~~~~  122 (467)
                      ++..+.|+.|+|.++......
T Consensus        85 ng~~~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           85 DGRWFGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             TTCEETTEECEEEECCSCCCS
T ss_pred             CCCEECCcEEEEEEeCCCCCc
Confidence            999999999999998765443

>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=99.52  E-value=4.4e-14  Score=108.38  Aligned_cols=80  Identities=19%  Similarity=0.255  Sum_probs=68.7

Q ss_pred             CCCCceEEEecCCCCCC-----------HHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcE
Q 012257          318 KFEGLNLYVKNLDDSIS-----------DDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKM  386 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~-----------~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  386 (467)
                      ..++++|+|.||.....           +++|+++|++||.|.+|.| .+.  .++|||||+|.+.++|.+|+..|||..
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            34677999999944332           5899999999999999966 443  378999999999999999999999999


Q ss_pred             ecccceEEehhhhh
Q 012257          387 VVSKPLYVALAQRK  400 (467)
Q Consensus       387 ~~g~~l~v~~~~~~  400 (467)
                      ++|+.|+|.|+.+.
T Consensus        89 ~~gr~l~v~~a~~~  102 (112)
T 2dit_A           89 FGGRQITAQAWDGT  102 (112)
T ss_dssp             ETTEECEEEECCSC
T ss_pred             ECCcEEEEEEeCCC
Confidence            99999999998754

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

Probab=99.52  E-value=2.2e-14  Score=123.56  Aligned_cols=80  Identities=21%  Similarity=0.425  Sum_probs=71.0

Q ss_pred             CCCccCeEEEcCCCCCC---------CHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcc
Q 012257           35 RQFVSTSLYVGDLDLSV---------NDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTP  105 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~---------~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~  105 (467)
                      ....+++|||+||+.++         +|++|+++|++||.|.+|+|+.+      +|||||+|.+.++|++|++.|++..
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~  203 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQT  203 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCC
T ss_pred             cccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCE
Confidence            35678999999999998         79999999999999999999854      5899999999999999999999999


Q ss_pred             c------------CCceeeeeecccCc
Q 012257          106 L------------NGKPIRIMYSYRDP  120 (467)
Q Consensus       106 ~------------~g~~~~v~~~~~~~  120 (467)
                      +            .|+.|.|.|+...+
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             EeccccccccccCCCCEEEEEEccCCC
Confidence            9            89999999997654

>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=99.51  E-value=3.8e-14  Score=108.60  Aligned_cols=81  Identities=20%  Similarity=0.351  Sum_probs=71.2

Q ss_pred             CCceEEEecCC--CCC---CHHHHHHhhccCCceeEEEEeeCCC-----CCccceEEEEcCCHHHHHHHHHHhCCcEecc
Q 012257          320 EGLNLYVKNLD--DSI---SDDKLKELFSEFGTITSCKVMRDPN-----GISRGSGFVAFSTAEEASKALTEMNGKMVVS  389 (467)
Q Consensus       320 ~~~~l~V~nlp--~~~---~~~~l~~~F~~~G~v~~v~i~~~~~-----~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  389 (467)
                      ++++|++.|+-  .++   .+++|++.|++||.|.+|+|+++..     +.++|++||+|.+.++|.+|++.|||+.++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            67789999993  222   3689999999999999999998753     4678999999999999999999999999999


Q ss_pred             cceEEehhhhh
Q 012257          390 KPLYVALAQRK  400 (467)
Q Consensus       390 ~~l~v~~~~~~  400 (467)
                      +.|+|+|+...
T Consensus        99 R~i~v~~~~~~  109 (118)
T 3ue2_A           99 RKVVAEVYDQE  109 (118)
T ss_dssp             EECEEEEECHH
T ss_pred             cEEEEEEcChH
Confidence            99999998754

>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=99.50  E-value=5.2e-14  Score=105.88  Aligned_cols=81  Identities=14%  Similarity=0.203  Sum_probs=71.1

Q ss_pred             CccCeEEEcCC--CCCCC--------HHHHHHHHhcCCCeEEEEEEecCCC--CccccEEEEEecChHHHHHHHHHhCCc
Q 012257           37 FVSTSLYVGDL--DLSVN--------DSQLYDLFNQMGQVVSVRVCRDLST--RRSLGYGYVNYNAAHEATRALDELNFT  104 (467)
Q Consensus        37 ~~~~~l~v~nL--p~~~~--------e~~l~~~f~~~G~v~~v~i~~~~~~--~~~~g~afV~f~~~~~A~~A~~~l~~~  104 (467)
                      .+++.|.|.|+  |.++.        +++|++.|++||.|.+|+|.++..+  ++++|+|||+|.+.++|.+|++.||+.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            46899999998  44443        3689999999999999999988754  367899999999999999999999999


Q ss_pred             ccCCceeeeeecc
Q 012257          105 PLNGKPIRIMYSY  117 (467)
Q Consensus       105 ~~~g~~~~v~~~~  117 (467)
                      .+.||.|++.+..
T Consensus        83 ~f~GR~i~v~~~~   95 (105)
T 3v4m_A           83 KFANRVVVTKYCD   95 (105)
T ss_dssp             EETTEECEEEEEC
T ss_pred             EeCCCEEEEEEeC
Confidence            9999999998864

>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=1.3e-13  Score=105.58  Aligned_cols=80  Identities=15%  Similarity=0.162  Sum_probs=70.9

Q ss_pred             ccCeEEEcCCCC--C---CCHHHHHHHHhcCCCeEEEEEEecCC----CCccccEEEEEecChHHHHHHHHHhCCcccCC
Q 012257           38 VSTSLYVGDLDL--S---VNDSQLYDLFNQMGQVVSVRVCRDLS----TRRSLGYGYVNYNAAHEATRALDELNFTPLNG  108 (467)
Q Consensus        38 ~~~~l~v~nLp~--~---~~e~~l~~~f~~~G~v~~v~i~~~~~----~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g  108 (467)
                      ++++|+|.|+-.  +   --+++|++.|++||.|.+|+|.++..    +++++|+|||+|.+.++|.+|++.||+..|.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            689999999842  2   23589999999999999999999865    45788999999999999999999999999999


Q ss_pred             ceeeeeecc
Q 012257          109 KPIRIMYSY  117 (467)
Q Consensus       109 ~~~~v~~~~  117 (467)
                      +.|++.+..
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999998864

>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=99.45  E-value=2.9e-14  Score=107.17  Aligned_cols=72  Identities=28%  Similarity=0.503  Sum_probs=63.7

Q ss_pred             EcCCCCCCCHHHHHHHH------------hcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           44 VGDLDLSVNDSQLYDLF------------NQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        44 v~nLp~~~~e~~l~~~f------------~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      +.|||+++++++|+++|            ++||.|.+|+|.++. +++++|||||+|.+.++|.+|++.||+..+.|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56677777888777666            999999999999886 47899999999999999999999999999999999


Q ss_pred             eeeec
Q 012257          112 RIMYS  116 (467)
Q Consensus       112 ~v~~~  116 (467)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99876

>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=99.44  E-value=5.4e-13  Score=101.38  Aligned_cols=81  Identities=15%  Similarity=0.208  Sum_probs=68.8

Q ss_pred             CCCceEEEecCCC--CC--------CHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEec
Q 012257          319 FEGLNLYVKNLDD--SI--------SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVV  388 (467)
Q Consensus       319 ~~~~~l~V~nlp~--~~--------~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~  388 (467)
                      .++++|.+.|+=.  ..        .+++|++.|++||.|.+|+|.++.   ++|+|||+|.+.++|.+|++.|||+.++
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            4677899999832  21        136889999999999999997653   4899999999999999999999999999


Q ss_pred             ccceEEehhhhhHH
Q 012257          389 SKPLYVALAQRKEE  402 (467)
Q Consensus       389 g~~l~v~~~~~~~~  402 (467)
                      |+.|+|+|+....-
T Consensus        82 GR~i~v~~~~~~~y   95 (114)
T 3s6e_A           82 GKMITAAYVPLPTY   95 (114)
T ss_dssp             TEECEEEEECHHHH
T ss_pred             CEEEEEEEEcHHHH
Confidence            99999999976544

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.42  E-value=7.7e-13  Score=97.94  Aligned_cols=64  Identities=23%  Similarity=0.401  Sum_probs=57.0

Q ss_pred             CCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          331 DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       331 ~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      ..+++++|+++|++||.|.+|+++    ++++|||||+|.+.++|.+|++.+++  +.|+.|+|+|+++.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~   90 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQ   90 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCC
Confidence            568999999999999999999998    35789999999999999999998554  67999999998754

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.42  E-value=2.9e-12  Score=94.79  Aligned_cols=76  Identities=17%  Similarity=0.249  Sum_probs=64.7

Q ss_pred             cCeEEEcCCC-------CCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           39 STSLYVGDLD-------LSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        39 ~~~l~v~nLp-------~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      ..+|.|.-..       .++++++|+++|++||.|.+|.|.     ++++|||||+|.+.++|.+|++.++  .+.|+.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV--GLVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeE
Confidence            6678887765       458999999999999999999997     3577999999999999999999744  4789999


Q ss_pred             eeeecccCcc
Q 012257          112 RIMYSYRDPT  121 (467)
Q Consensus       112 ~v~~~~~~~~  121 (467)
                      +|.|+...+.
T Consensus        83 ~V~~a~~~~~   92 (100)
T 2d9o_A           83 KISWLEGQPQ   92 (100)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEEccCCCC
Confidence            9999876543

>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=1e-12  Score=119.51  Aligned_cols=77  Identities=25%  Similarity=0.452  Sum_probs=66.8

Q ss_pred             cCCCCceEEEec--CCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEec---cc-
Q 012257          317 DKFEGLNLYVKN--LDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVV---SK-  390 (467)
Q Consensus       317 ~~~~~~~l~V~n--lp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~---g~-  390 (467)
                      ...++.+|||+|  |+..++|++|+++|++||.|++|++..     +||||||+|.+.++|.+|++.|||..+.   |+ 
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            345777999999  578999999999999999999988754     4789999999999999999999999884   44 


Q ss_pred             -ceEEehhh
Q 012257          391 -PLYVALAQ  398 (467)
Q Consensus       391 -~l~v~~~~  398 (467)
                       .|.|.|+.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             68888873

>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=99.32  E-value=2.6e-12  Score=116.89  Aligned_cols=75  Identities=23%  Similarity=0.375  Sum_probs=64.0

Q ss_pred             CCccCeEEEcC--CCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc---CCc-
Q 012257           36 QFVSTSLYVGD--LDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL---NGK-  109 (467)
Q Consensus        36 ~~~~~~l~v~n--Lp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~---~g~-  109 (467)
                      +.++++|||+|  |+..++|++|+++|++||.|.+|.+..      ++|||||+|.+.++|++|++.||+..+   .|+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            56789999999  578999999999999999999998754      458999999999999999999999876   344 


Q ss_pred             -eeeeeec
Q 012257          110 -PIRIMYS  116 (467)
Q Consensus       110 -~~~v~~~  116 (467)
                       .+.+.+.
T Consensus        89 ~~ly~~~~   96 (345)
T 3tht_A           89 ITLYLNFV   96 (345)
T ss_dssp             EECEEEEC
T ss_pred             eEEEEEEe
Confidence             4555554

>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=6.7e-12  Score=95.34  Aligned_cols=77  Identities=18%  Similarity=0.237  Sum_probs=66.1

Q ss_pred             CccCeEEEcCCCCCCC----------HHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc
Q 012257           37 FVSTSLYVGDLDLSVN----------DSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL  106 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~----------e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  106 (467)
                      .++++|.|.|+=..-.          +++|++.|++||.|.+|.|.++.    ++|+|||+|.+.++|.+|++.||+..+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            4688999999854322          24789999999999999997653    479999999999999999999999999


Q ss_pred             CCceeeeeecc
Q 012257          107 NGKPIRIMYSY  117 (467)
Q Consensus       107 ~g~~~~v~~~~  117 (467)
                      .|+.|++.++.
T Consensus        81 ~GR~i~v~~~~   91 (114)
T 3s6e_A           81 AGKMITAAYVP   91 (114)
T ss_dssp             TTEECEEEEEC
T ss_pred             CCEEEEEEEEc
Confidence            99999998864

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.29  E-value=5.5e-12  Score=88.89  Aligned_cols=73  Identities=25%  Similarity=0.426  Sum_probs=63.5

Q ss_pred             CCCceEEEecCC----CCCCH----HHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEeccc
Q 012257          319 FEGLNLYVKNLD----DSISD----DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSK  390 (467)
Q Consensus       319 ~~~~~l~V~nlp----~~~~~----~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  390 (467)
                      ++..+|+|.-.+    ..+.+    .+|.+.|++||.|..+++..+       .+||+|.+.++|.+|++ |||..++||
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d-------~~fVtF~d~~sAlaAi~-mnG~~v~Gr   76 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED-------KMWVTFLEGSSALNVLS-LNGKELLNR   76 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS-------SEEEEESSHHHHHHGGG-GTTCEETTE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC-------CEEEEECChHHHHHHHh-cCCeEeCCe
Confidence            455688888776    34444    688999999999999999997       59999999999999998 999999999


Q ss_pred             ceEEehhhh
Q 012257          391 PLYVALAQR  399 (467)
Q Consensus       391 ~l~v~~~~~  399 (467)
                      .|+|+++++
T Consensus        77 ~LkV~lkt~   85 (91)
T 2dnr_A           77 TITIALKSP   85 (91)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEeCCC
Confidence            999999875

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.19  E-value=9.9e-11  Score=88.66  Aligned_cols=82  Identities=22%  Similarity=0.264  Sum_probs=71.0

Q ss_pred             cCCCCceEEEecCCCC-CCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCC-HHHHHHHHHHhC--CcEecccce
Q 012257          317 DKFEGLNLYVKNLDDS-ISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFST-AEEASKALTEMN--GKMVVSKPL  392 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~-~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~-~~~A~~A~~~l~--g~~~~g~~l  392 (467)
                      .-..++.|+|+||+.. +++++|+++|+.||.|.+|.+.++..     .|||+|.+ ..+|..|+..|+  +..|.|..+
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~-----tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK-----EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS-----EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC-----EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            4457789999999999 99999999999999999999988744     79999999 899999999995  778899999


Q ss_pred             EEehhhhhHHH
Q 012257          393 YVALAQRKEER  403 (467)
Q Consensus       393 ~v~~~~~~~~~  403 (467)
                      +++......+.
T Consensus        89 ~~evL~GeeE~   99 (121)
T 1owx_A           89 TWEVLEGEVEK   99 (121)
T ss_dssp             EEEECCHHHHH
T ss_pred             EEEECCCHHHH
Confidence            99876544433

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.12  E-value=5.5e-11  Score=84.12  Aligned_cols=74  Identities=15%  Similarity=0.208  Sum_probs=64.0

Q ss_pred             cCCCCceEEEecCCCC-----CCH----HHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEe
Q 012257          317 DKFEGLNLYVKNLDDS-----ISD----DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV  387 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~-----~~~----~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  387 (467)
                      ..++..+|+|.-++..     +.+    .+|.+.|++||.|..+++..+       .+||+|.+.++|.+||+ |||..+
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d-------~~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GGGSEE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC-------cEEEEEcChHHHHHHHh-cCCeee
Confidence            3456678999988742     333    578899999999999999998       59999999999999998 999999


Q ss_pred             cccceEEehhh
Q 012257          388 VSKPLYVALAQ  398 (467)
Q Consensus       388 ~g~~l~v~~~~  398 (467)
                      +||.|+|++..
T Consensus        83 ~Gr~L~V~~k~   93 (95)
T 1ufw_A           83 KGRAVKISGPS   93 (95)
T ss_dssp             TTEEEEEECCC
T ss_pred             CCeEEEEeccC
Confidence            99999999865

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.10  E-value=4.6e-10  Score=85.01  Aligned_cols=75  Identities=17%  Similarity=0.148  Sum_probs=65.8

Q ss_pred             CCCccCeEEEcCCCCC-CCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecC-hHHHHHHHHHhC--CcccCCce
Q 012257           35 RQFVSTSLYVGDLDLS-VNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNA-AHEATRALDELN--FTPLNGKP  110 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~-~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~-~~~A~~A~~~l~--~~~~~g~~  110 (467)
                      .-...+.|+|+||+.+ +++++|+++|+.||.|..|.+.++..      .|||.|.+ .++|..|++.++  +..|.|..
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~   87 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKE   87 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcE
Confidence            3456799999999999 99999999999999999999988875      59999999 799999999984  67788887


Q ss_pred             eeeee
Q 012257          111 IRIMY  115 (467)
Q Consensus       111 ~~v~~  115 (467)
                      +++..
T Consensus        88 ~~~ev   92 (121)
T 1owx_A           88 VTWEV   92 (121)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            77753

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.02  E-value=9.7e-10  Score=77.47  Aligned_cols=73  Identities=22%  Similarity=0.296  Sum_probs=61.5

Q ss_pred             CccCeEEEcCCCC----C-CCH---HHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC
Q 012257           37 FVSTSLYVGDLDL----S-VND---SQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG  108 (467)
Q Consensus        37 ~~~~~l~v~nLp~----~-~~e---~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g  108 (467)
                      ++..+|+|.-.+.    + .++   .+|.+.|+.||.|..+++..++        +||+|.+.++|.+|++ |++..+.|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCC
Confidence            3567888887762    2 232   5789999999999999998875        8999999999999998 99999999


Q ss_pred             ceeeeeeccc
Q 012257          109 KPIRIMYSYR  118 (467)
Q Consensus       109 ~~~~v~~~~~  118 (467)
                      +.|+|....+
T Consensus        76 r~LkV~lkt~   85 (91)
T 2dnr_A           76 RTITIALKSP   85 (91)
T ss_dssp             EEEEEEECCC
T ss_pred             eEEEEEeCCC
Confidence            9999987653

>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=98.97  E-value=8e-10  Score=96.04  Aligned_cols=69  Identities=19%  Similarity=0.329  Sum_probs=62.0

Q ss_pred             CCHHHHHHhhccCCceeEEEEeeCC-----CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhhH
Q 012257          333 ISDDKLKELFSEFGTITSCKVMRDP-----NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKE  401 (467)
Q Consensus       333 ~~~~~l~~~F~~~G~v~~v~i~~~~-----~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  401 (467)
                      -.+++|++.|++||.|.+++|.++.     ++.++|++||+|.+.++|.+|+..|||+.++||.|.+.|.....
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~~~  214 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQER  214 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCHHH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCHHH
Confidence            3568999999999999999998664     34889999999999999999999999999999999999987543

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.85  E-value=2.5e-09  Score=75.64  Aligned_cols=71  Identities=18%  Similarity=0.316  Sum_probs=61.0

Q ss_pred             CccCeEEEcCCCCC------CCH---HHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccC
Q 012257           37 FVSTSLYVGDLDLS------VND---SQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLN  107 (467)
Q Consensus        37 ~~~~~l~v~nLp~~------~~e---~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~  107 (467)
                      ++..+|+|.-++..      -++   .+|.+.|+.||.|..+++..|+        +||+|.+.++|.+|++ |++..+.
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~   83 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeC
Confidence            45689999988743      232   4689999999999999998875        8999999999999998 9999999


Q ss_pred             Cceeeeeec
Q 012257          108 GKPIRIMYS  116 (467)
Q Consensus       108 g~~~~v~~~  116 (467)
                      |+.|+|..-
T Consensus        84 Gr~L~V~~k   92 (95)
T 1ufw_A           84 GRAVKISGP   92 (95)
T ss_dssp             TEEEEEECC
T ss_pred             CeEEEEecc
Confidence            999999753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.80  E-value=4.6e-08  Score=70.39  Aligned_cols=77  Identities=18%  Similarity=0.196  Sum_probs=69.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccC-----CceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEF-----GTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~-----G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      ..++|-+-|||..+++..|+.+.+++     |.++.+.+..+..     =|+|+|.|..+|.+|.-+|+|..|.|++|++
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~-----GAivef~d~~~AgKasLaL~G~ef~gr~Lr~   94 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN-----GAIIIFRDSKFAAKMLMILNGSQFQGKVIRS   94 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT-----EEEEECSCHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC-----ceEEEEccchhhHHHHhhcCCeeecCeEEEe
Confidence            46789999999999999999999999     9999999999843     6999999999999999999999999999999


Q ss_pred             ehhhhhH
Q 012257          395 ALAQRKE  401 (467)
Q Consensus       395 ~~~~~~~  401 (467)
                      .-.....
T Consensus        95 gTv~eL~  101 (117)
T 2l9w_A           95 GTINDMK  101 (117)
T ss_dssp             ECHHHHH
T ss_pred             cCHHHHH
Confidence            8655443

>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=98.78  E-value=1.4e-08  Score=88.24  Aligned_cols=79  Identities=15%  Similarity=0.167  Sum_probs=65.1

Q ss_pred             cCeEEEcCCCC-----CCCHHHHHHHHhcCCCeEEEEEEecCCC----CccccEEEEEecChHHHHHHHHHhCCcccCCc
Q 012257           39 STSLYVGDLDL-----SVNDSQLYDLFNQMGQVVSVRVCRDLST----RRSLGYGYVNYNAAHEATRALDELNFTPLNGK  109 (467)
Q Consensus        39 ~~~l~v~nLp~-----~~~e~~l~~~f~~~G~v~~v~i~~~~~~----~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~  109 (467)
                      ++.+.+.|+-.     +-.+++|++.|++||.|.++.|.++..+    ++++|++||+|.+.++|.+|++.|++..+.||
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            34455555432     2345789999999999999999965544    48999999999999999999999999999999


Q ss_pred             eeeeeecc
Q 012257          110 PIRIMYSY  117 (467)
Q Consensus       110 ~~~v~~~~  117 (467)
                      .|.+.+..
T Consensus       204 ~i~~~~~~  211 (222)
T 3dxb_A          204 KVVAEVYD  211 (222)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEEcC
Confidence            99998764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.59  E-value=8.5e-07  Score=63.54  Aligned_cols=88  Identities=18%  Similarity=0.229  Sum_probs=73.2

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcC-----CCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQM-----GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~-----G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      ...+|.|.|||++++++.|.-+|+.-     |+|.+|....        +.|+|+|.+.+.|++.++. ....+.+..+.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEE
Confidence            46899999999999999999999872     5999998865        2699999999999999984 45678999999


Q ss_pred             eeecccCcccccCCCccEEEcCCCCcCC
Q 012257          113 IMYSYRDPTIRKSGAGNIFIKNLDKSID  140 (467)
Q Consensus       113 v~~~~~~~~~~~~~~~~l~v~nlp~~~t  140 (467)
                      |.....      ....++++.+|++.++
T Consensus        78 V~P~~~------~~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           78 LRPAPP------RAPARLLLQGLPPGTS   99 (104)
T ss_dssp             EEECCC------CCCCCCCCCSCCCCCC
T ss_pred             EEcCCC------CCcceEeeecCCCCCC
Confidence            976543      3456899999998875

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.32  E-value=2.4e-06  Score=61.61  Aligned_cols=71  Identities=18%  Similarity=0.210  Sum_probs=65.9

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcC-----CCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQM-----GQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~-----G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      ..++|-+-|||-.+++..|+.+++.+     |.+..|.+..|..      -|+|+|.+..+|-+|.-.|+|..|.|+.|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~------GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN------GAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT------EEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC------ceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            47899999999999999999999999     9999999988864      599999999999999988999999999999


Q ss_pred             ee
Q 012257          113 IM  114 (467)
Q Consensus       113 v~  114 (467)
                      +.
T Consensus        94 ~g   95 (117)
T 2l9w_A           94 SG   95 (117)
T ss_dssp             EE
T ss_pred             ec
Confidence            84

>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=97.96  E-value=1.7e-05  Score=57.22  Aligned_cols=73  Identities=19%  Similarity=0.255  Sum_probs=62.6

Q ss_pred             CceEEEecCCCCC-CH----HHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          321 GLNLYVKNLDDSI-SD----DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       321 ~~~l~V~nlp~~~-~~----~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ..+|+|.||+..+ ..    +.++++|..|+.+.....++.-.     -..|.|.+.++|.+|...||+..++|+.|+|=
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR-----Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~Y   79 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK-----RVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT-----EEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce-----EEEEEeCChHHHHHHHHHhccceecCceeEEE
Confidence            3479999998755 22    57789999999998888777532     67899999999999999999999999999999


Q ss_pred             hhh
Q 012257          396 LAQ  398 (467)
Q Consensus       396 ~~~  398 (467)
                      |++
T Consensus        80 Fgq   82 (104)
T 1wey_A           80 FAQ   82 (104)
T ss_dssp             CCC
T ss_pred             ecC
Confidence            987

>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=97.86  E-value=4.3e-05  Score=55.15  Aligned_cols=73  Identities=16%  Similarity=0.248  Sum_probs=62.3

Q ss_pred             cCeEEEcCCCCCC-C--H--HHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           39 STSLYVGDLDLSV-N--D--SQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        39 ~~~l~v~nLp~~~-~--e--~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      .++|+|.||+.++ .  +  +.++++|+.|+++.....++.=+      =..|.|.+.++|.+|...|++..+.|+.+++
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR------Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT------EEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce------EEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            5789999998854 2  2  46799999999888888776543      3789999999999999999999999999999


Q ss_pred             eecc
Q 012257          114 MYSY  117 (467)
Q Consensus       114 ~~~~  117 (467)
                      .+..
T Consensus        79 YFgq   82 (104)
T 1wey_A           79 YFAQ   82 (104)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            9876

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.81  E-value=0.00013  Score=52.36  Aligned_cols=68  Identities=19%  Similarity=0.343  Sum_probs=57.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhcc-----CCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSE-----FGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~-----~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      ...+|.|.|||+.+.++.|.-+|+.     -|.|.++.....       -|+|+|.+.+.|+++++. ..+.|.+..|.|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~~-------~AvItF~d~~va~rVL~k-~~H~L~~~~LsV   78 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGC-------GGVLTFREPADAERVLAQ-ADHELHGAQLSL   78 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEETT-------EEEEEESSHHHHHHHHTC-SCCBSSSSBCEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcCC-------cEEEEEcChHHHHHHhcC-CcceecCeEEEE
Confidence            4568999999999999999999976     268999887652       899999999999999873 367888888888


Q ss_pred             e
Q 012257          395 A  395 (467)
Q Consensus       395 ~  395 (467)
                      .
T Consensus        79 ~   79 (104)
T 2dhx_A           79 R   79 (104)
T ss_dssp             E
T ss_pred             E
Confidence            5

>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=97.75  E-value=0.00015  Score=51.50  Aligned_cols=67  Identities=10%  Similarity=0.139  Sum_probs=54.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCc--cccEEEEEecChHHHHHHHHHhCCccc
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRR--SLGYGYVNYNAAHEATRALDELNFTPL  106 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~--~~g~afV~f~~~~~A~~A~~~l~~~~~  106 (467)
                      ++|.|++||+.++|+++.+.+..+..+........+.+..  ..+-|||.|.+.+++....+.+++..|
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F   70 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEE
Confidence            6899999999999999999999988766555555443322  225699999999999999999988766

>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=97.70  E-value=0.00014  Score=51.34  Aligned_cols=56  Identities=25%  Similarity=0.356  Sum_probs=47.3

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhC
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN  383 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  383 (467)
                      ...||+-+.|..+...||.++|+.||.| .|+++.|      ..|||.|.+.+.|..|++.+.
T Consensus        15 r~HVf~l~FP~ewKt~DI~~lFs~fggv-~I~WidD------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           15 RDHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDD------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEET------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCeEEEEeCChhhhhHHHHHHhhccCCE-EEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            3345555999999999999999999976 6788776      289999999999999998764

>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=97.67  E-value=0.00032  Score=49.81  Aligned_cols=68  Identities=9%  Similarity=0.228  Sum_probs=58.0

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCC---CCccceEEEEcCCHHHHHHHHHHhCCcEecc
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN---GISRGSGFVAFSTAEEASKALTEMNGKMVVS  389 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  389 (467)
                      .+|.|++||+.+||+++.+.++....+..........   .....-|+|.|.+.+++....+.++|+.|.+
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            3699999999999999999999999888777766652   1234689999999999999999999999854

>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=97.35  E-value=0.00026  Score=50.27  Aligned_cols=54  Identities=26%  Similarity=0.399  Sum_probs=46.7

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhC
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN  383 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  383 (467)
                      .||+-+.|..+...||.++|+.||.| .|+++.|      ..|||.|.+.+.|..|+..+.
T Consensus         7 HV~~l~FP~ewKt~Di~~lFs~fggv-~I~WidD------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDD------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEECCTTCCHHHHHHHTTTSEEE-EEEEEET------TEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEEeCChhhhhHHHHHHHhccCCE-EEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            34444999999999999999999966 7888886      289999999999999999765

>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=97.31  E-value=0.0009  Score=49.79  Aligned_cols=71  Identities=15%  Similarity=0.127  Sum_probs=56.4

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC-ceeeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG-KPIRIMY  115 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g-~~~~v~~  115 (467)
                      ...+-|.|-+.|+. .-+.|.++|++||.|++....    .  ......|.|.+..+|++||. .|+..+.| -.|-|.+
T Consensus        22 ~~~~wVtVFGFp~~-~~~~VL~~F~~~G~Iv~~~~~----~--~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           22 LDDTWVTVFGFPQA-SASYILLQFAQYGNILKHVMS----N--TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKP   93 (119)
T ss_dssp             GGGGEEEEECCCGG-GHHHHHHHHHTTSCEEEEEEC----S--SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEE
T ss_pred             CCCCEEEEECCCHH-HHHHHHHHHHhhCcEEEeccC----C--CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEE
Confidence            34788999999986 477899999999999988762    1  12489999999999999998 68888875 3355544

>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=97.22  E-value=0.0013  Score=49.02  Aligned_cols=71  Identities=14%  Similarity=0.174  Sum_probs=56.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecc-cceEEehh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVS-KPLYVALA  397 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-~~l~v~~~  397 (467)
                      ....|.|.+.|... -..|.+.|++||.|.+.....     ...+-.|.|++..+|++|+. .||..++| -.|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~-----~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC-----CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            45579999999885 677889999999999887622     23499999999999999997 59999975 45666654

>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=97.18  E-value=0.0018  Score=45.80  Aligned_cols=56  Identities=16%  Similarity=0.281  Sum_probs=43.9

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHh
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL  101 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l  101 (467)
                      ....||+-+.|+.....||.++|+.||.| .|+=+-|.       .|||.|.+++.|..|++.+
T Consensus        14 ~r~HVf~l~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             CCCeEEEEeCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            33344444999999999999999999954 44444442       6999999999999999865

>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=97.05  E-value=0.0012  Score=46.88  Aligned_cols=53  Identities=23%  Similarity=0.388  Sum_probs=42.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhC
Q 012257           41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN  102 (467)
Q Consensus        41 ~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  102 (467)
                      .++| +.|+.....||.++|+.||. ..|.=+-|  |     .|||.|.+++.|..|++.+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidD--T-----sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD--T-----SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEET--T-----EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcC--C-----eEEEEecCHHHHHHHHHhcc
Confidence            3455 99999999999999999983 34444444  2     69999999999999999764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.88  E-value=0.00042  Score=65.31  Aligned_cols=56  Identities=7%  Similarity=0.191  Sum_probs=44.2

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHH
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE  100 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~  100 (467)
                      .|+|+|. .|..+++.+|.++|++||+|.++.+.+++.     -||.|+|.+.+++..+++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g-----~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG-----LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS-----EEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC-----eEEEEEeCCHHHHHHHHhc
Confidence            5789998 799999999999999999999999987654     4999999999999988764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.62  E-value=0.0022  Score=45.76  Aligned_cols=69  Identities=10%  Similarity=0.057  Sum_probs=48.5

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCC-Cc-cccEEEEEecChHHHHHHHHHhCCccc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLST-RR-SLGYGYVNYNAAHEATRALDELNFTPL  106 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~-~~-~~g~afV~f~~~~~A~~A~~~l~~~~~  106 (467)
                      .+-+|.|+.||+.+||+++.+.+..+=.+........+.+ +. ...-|||.|.+.++.....+..++..|
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F   78 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIF   78 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            4678999999999999999888876533221111111111 11 114699999999999999999888766

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.60  E-value=0.0041  Score=44.32  Aligned_cols=68  Identities=7%  Similarity=0.176  Sum_probs=52.0

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCC---CCccceEEEEcCCHHHHHHHHHHhCCcEecc
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN---GISRGSGFVAFSTAEEASKALTEMNGKMVVS  389 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  389 (467)
                      -+|.|+.||+.+||+++.+.++..-.+..........   ...-.-|+|.|.+.++...-.+..+|..|.+
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            4699999999999999999888765554333332221   1123579999999999999999999999854

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.23  E-value=0.006  Score=46.01  Aligned_cols=79  Identities=23%  Similarity=0.312  Sum_probs=57.4

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeE-EEEeeCC-------------CC-CccceEEEEcCCHHHHHHHHHHhCCcE
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITS-CKVMRDP-------------NG-ISRGSGFVAFSTAEEASKALTEMNGKM  386 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~-v~i~~~~-------------~~-~~~g~afV~f~~~~~A~~A~~~l~g~~  386 (467)
                      ..|.|.+.|.... ..+.+.|++||.|.+ +...++.             .. ....+.-|+|++..+|.+|+. .||..
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            3588889976644 567799999999876 2221100             00 124688999999999999997 59999


Q ss_pred             ecccceEEehhhhhHH
Q 012257          387 VVSKPLYVALAQRKEE  402 (467)
Q Consensus       387 ~~g~~l~v~~~~~~~~  402 (467)
                      |+|.-|-|...++...
T Consensus        86 i~G~mIGV~Py~~~~v  101 (132)
T 3p3d_A           86 FNGVLLGVIPYTKDAV  101 (132)
T ss_dssp             ETTEECEEEECCHHHH
T ss_pred             eCcEEEEEEECCHHHH
Confidence            9999888887764443

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.84  E-value=0.0049  Score=58.16  Aligned_cols=54  Identities=20%  Similarity=0.306  Sum_probs=40.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHH
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT  380 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~  380 (467)
                      ++|+|. .+..+++.+|.++|++||.|.++....+. |   .||.|+|.+.+++..++.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-g---~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-G---LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-S---EEEEEECC---CCHHHHS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-C---eEEEEEeCCHHHHHHHHh
Confidence            479998 68899999999999999999999887652 2   599999999999887764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.70  E-value=0.01  Score=44.71  Aligned_cols=76  Identities=17%  Similarity=0.221  Sum_probs=52.9

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEE-EEEEec------------CCCC-ccccEEEEEecChHHHHHHHHHhCCc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVS-VRVCRD------------LSTR-RSLGYGYVNYNAAHEATRALDELNFT  104 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~-v~i~~~------------~~~~-~~~g~afV~f~~~~~A~~A~~~l~~~  104 (467)
                      .+.|.|-+-|+ .....|.++|++||.|.+ +...+.            +-.. ...+...|+|++..+|.+|+. .|+.
T Consensus         7 e~~VtVFGFp~-~~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPE-TMANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCG-GGHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCH-HHHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            45677778866 556788999999998776 211110            0000 123578999999999999998 6999


Q ss_pred             ccCCceeeeeec
Q 012257          105 PLNGKPIRIMYS  116 (467)
Q Consensus       105 ~~~g~~~~v~~~  116 (467)
                      .|.|.-|-|.+.
T Consensus        85 ii~G~mIGV~Py   96 (132)
T 3p3d_A           85 VFNGVLLGVIPY   96 (132)
T ss_dssp             EETTEECEEEEC
T ss_pred             EeCcEEEEEEEC
Confidence            999976666544

>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=89.54  E-value=0.9  Score=43.83  Aligned_cols=54  Identities=26%  Similarity=0.400  Sum_probs=45.1

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhC
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN  383 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  383 (467)
                      .+++-..|..+...+|.+.|+.||.| +|+++.+      ..|||.|.+.+.|..++..++
T Consensus       441 ~vl~v~f~~~~~~~~i~~~fs~fg~v-~V~widd------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          441 HVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDD------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GEEEEECCTTCCHHHHHHHGGGGCCC-EEEECSS------SEEEEECSCHHHHHHHHHHHT
T ss_pred             cEEEEeCCCCCCHHHHHHHHHhcCCE-EEEEEcC------CeEEEEECCHHHHHHHHHHHH
Confidence            34444599999999999999999966 7776665      389999999999999999885

>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=88.92  E-value=1.2  Score=43.08  Aligned_cols=62  Identities=18%  Similarity=0.244  Sum_probs=46.9

Q ss_pred             CCCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhC
Q 012257           31 VGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN  102 (467)
Q Consensus        31 ~~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  102 (467)
                      .++...++ ..++|+ +|......+|.+.|+.||.| +|.-+-+       ..|||.|.+.++|..+++.+.
T Consensus       433 ~d~~~~R~-~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          433 PDLQPKRD-HVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             CCCCCCGG-GEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CCCCCCcC-cEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHHHHH
Confidence            34433443 467776 88888999999999999954 5544333       269999999999999999875

>3iot_A Maltose-binding protein, huntingtin fusion protei; HTT-EX1, HD, sugar transport, transport, apoptos disease mutation, nucleus; 3.50A {Escherichia coli k-12} PDB: 3io6_A 3io4_A 3ior_A 3iou_A 3iov_A 3iow_A

Probab=82.62  E-value=0.31  Score=46.55  Aligned_cols=10  Identities=0%  Similarity=-0.220  Sum_probs=5.4

Q ss_pred             CHHHHHHHHh
Q 012257          140 DNKALHDTFS  149 (467)
Q Consensus       140 t~~~l~~~f~  149 (467)
                      |-++|.+...
T Consensus       128 Twdel~~~a~  137 (449)
T 3iot_A          128 TWEEIPALDK  137 (449)
T ss_dssp             BGGGHHHHHH
T ss_pred             CHHHHHHHHH
Confidence            5556655544

---

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	467
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	8e-26
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-25
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-24
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-20
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-18
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-18
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-20
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	7e-19
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-17
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-14
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-18
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	8e-18
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	7e-16
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-14
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	7e-18
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-17
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-15
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-14
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-17
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-16
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	8e-15
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-17
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	7e-17
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-16
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	7e-15
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-13
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-16
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	4e-14
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-11
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	9e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-16
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-15
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-14
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-13
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-16
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-13
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-16
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-16
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	8e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-16
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-16
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-13
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-16
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-14
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	7e-13
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	4e-16
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-15
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	4e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-15
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-11
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-15
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	4e-15
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-13
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-11
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-15
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-15
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-15
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-11
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-15
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	9e-14
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	4e-15
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	9e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-15
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-10
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:) 5e-15
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-14
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:) 3e-11
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:) 3e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	8e-15
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-13
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-11
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	8e-15
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-12
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-14
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-14
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-13
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-13
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-14
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-09
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	7e-08
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	5e-04
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-14
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-13
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-14
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-14
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-14
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	5e-13
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-10
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-14
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-13
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	8e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-14
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	7e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	5e-14
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	6e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	8e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-10
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-14
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-13
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	7e-14
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-09
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	6e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-13
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-11
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-13
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-12
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-09
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-13
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	4e-13
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	8e-12
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	8e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-13
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-12
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	7e-11
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-13
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	9e-12
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	7e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	5e-13
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-12
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	6e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	5e-13
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	8e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-13
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-10
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	5e-13
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	8e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	5e-09
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-13
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-11
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	9e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	6e-11
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	6e-11
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	6e-08
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-12
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-09
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-12
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	5e-12
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	5e-11
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	8e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-12
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-11
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	6e-11
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-10
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	4e-12
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-12
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-08
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	5e-12
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-10
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	6e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-11
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-10
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	6e-12
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	7e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-05
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	7e-12
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	8e-11
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-10
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	4e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-12
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	5e-11
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-10
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-12
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-11
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-11
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	5e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-11
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-10
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	8e-07
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	3e-11
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	6e-10
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	7e-08
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	4e-11
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	8e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	6e-08
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	7e-06
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-11
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-10
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-10
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	5e-11
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-09
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	5e-11
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	4e-09
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-10
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	4e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-10
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	8e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	4e-08
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	4e-10
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-09
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	8e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	4e-10
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-09
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-10
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-09
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	9e-10
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-09
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-09
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-09
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	4e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-09
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	1e-08
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	2e-06
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	3e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	5e-05
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	7e-06
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-05
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-04
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	7e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	8e-08
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	3e-05
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	8e-08
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	9e-06
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-08
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	9e-08
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	3e-06
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	3e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	6e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	2e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	8e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	1e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.004
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-07
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-07
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	8e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-04
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-07
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-06
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	5e-06
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	3e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	6e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	4e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	7e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.002
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	8e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	4e-04
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	5e-04

>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 =  101 bits (252), Expect = 8e-26
 Identities = 45/174 (25%), Positives = 70/174 (40%), Gaps = 4/174 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           +FI  L     +++L   F  +G +  C V  D    +SRG+GFV +   E   +A++  
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 189 NGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITST 248
              +            R+  +   A  T    ++V  + E T E  L+  F ++G I   
Sbjct: 69  PHKVDGRVVEPKRAVSREDSQRPGAHLT-VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 127

Query: 249 AVMRDAD-GKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
            +M D   GK + F FV FDD D   + V        +     V KA  K E  
Sbjct: 128 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQEMA 180

>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 =  100 bits (248), Expect = 3e-25
 Identities = 39/199 (19%), Positives = 77/199 (38%), Gaps = 20/199 (10%)

Query: 209 RESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFD 267
           +E    +     +++  LS  TT++ L+  F ++G +T   VMRD +  +S+ FGFV + 
Sbjct: 1   KEPEQLRK----LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 56

Query: 268 DPDDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVK 327
             ++   ++ A   K             ++  +        +              ++V 
Sbjct: 57  TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK-------------KIFVG 103

Query: 328 NLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEMNGKM 386
            + +   +  L++ F ++G I   ++M D   G  RG  FV F   +   K +       
Sbjct: 104 GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHT 162

Query: 387 VVSKPLYVALAQRKEERRA 405
           V      V  A  K+E  +
Sbjct: 163 VNGHNCEVRKALSKQEMAS 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 = 97.8 bits (242), Expect = 2e-24
 Identities = 46/176 (26%), Positives = 71/176 (40%), Gaps = 5/176 (2%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L++G L     D  L   F Q G +    V RD +T+RS G+G+V Y    E   A++  
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 102 NFTPLNGKPIRIMYSYRDPTIRKSGA---GNIFIKNLDKSIDNKALHDTFSTFGNILSCK 158
                           R+ + R         IF+  + +  +   L D F  +G I   +
Sbjct: 69  PHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE 128

Query: 159 VATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQERESTA 213
           + TD   G+ RG+ FV FD+ +S    +       +N     V   L KQE  S +
Sbjct: 129 IMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSKQEMASAS 183

>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 = 83.9 bits (207), Expect = 1e-20
 Identities = 63/90 (70%), Positives = 77/90 (85%), Gaps = 1/90 (1%)

Query: 120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEE 179
           P++RKSG GNIFIKNLDKSIDNKAL+DTFS FGNILSCKV  D  G S+GYGFV F+ +E
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQE 59

Query: 180 SAKSAIDKLNGMLLNDKQVFVGPFLRKQER 209
           +A+ AI+K+NGMLLND++VFVG F  ++ER
Sbjct: 60  AAERAIEKMNGMLLNDRKVFVGRFKSRKER 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 = 77.4 bits (190), Expect = 3e-18
 Identities = 30/89 (33%), Positives = 53/89 (59%), Gaps = 1/89 (1%)

Query: 212 TADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDD 271
           +  K+   N+++KNL ++     L   F  FG I S  V+ D +G SK +GFV+F+  + 
Sbjct: 2   SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEA 60

Query: 272 AARSVEALNGKKFDDKEWYVGKAQKKYER 300
           A R++E +NG   +D++ +VG+ + + ER
Sbjct: 61  AERAIEKMNGMLLNDRKVFVGRFKSRKER 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 = 76.6 bits (188), Expect = 5e-18
 Identities = 36/81 (44%), Positives = 54/81 (66%), Gaps = 1/81 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           N+++KNLD SI +  L + FS FG I SCKV+ D NG S+G GFV F T E A +A+ +M
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 68

Query: 383 NGKMVVSKPLYVALAQRKEER 403
           NG ++  + ++V   + ++ER
Sbjct: 69  NGMLLNDRKVFVGRFKSRKER 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 = 59.7 bits (144), Expect = 5e-12
 Identities = 23/83 (27%), Positives = 46/83 (55%), Gaps = 2/83 (2%)

Query: 34  ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
            R+    ++++ +LD S+++  LYD F+  G ++S +V  D     S GYG+V++     
Sbjct: 3   LRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEA 60

Query: 94  ATRALDELNFTPLNGKPIRIMYS 116
           A RA++++N   LN + + +   
Sbjct: 61  AERAIEKMNGMLLNDRKVFVGRF 83

>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 = 81.5 bits (201), Expect = 8e-20
 Identities = 44/79 (55%), Positives = 58/79 (73%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           SLYVGDL   V ++ LY+ F+  G ++S+RVCRD+ TRRSLGY YVN+    +A RALD 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 101 LNFTPLNGKPIRIMYSYRD 119
           +NF  + GKP+RIM+S RD
Sbjct: 62  MNFDVIKGKPVRIMWSQRD 80

>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 = 78.8 bits (194), Expect = 7e-19
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           +LYV +L   +++  L E FS  G I S +V RD     S G  +V F    +A +AL  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 382 MNGKMVVSKPLYVALAQR 399
           MN  ++  KP+ +  +QR
Sbjct: 62  MNFDVIKGKPVRIMWSQR 79

>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 = 74.6 bits (183), Expect = 2e-17
 Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
           ++YV +L    TE  L + F   G I S  V RD    +S  + +VNF  P DA R+++ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 279 LNGKKFDDKEWYVGKAQK 296
           +N      K   +  +Q+
Sbjct: 62  MNFDVIKGKPVRIMWSQR 79

>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 = 65.7 bits (160), Expect = 3e-14
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           ++++ +L   +    L++ FS  G ILS +V  D    +S GY +V F     A+ A+D 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 188 LNGMLLNDKQVFVGP 202
           +N  ++  K V +  
Sbjct: 62  MNFDVIKGKPVRIMW 76

>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 = 78.8 bits (194), Expect = 1e-18
 Identities = 17/92 (18%), Positives = 40/92 (43%), Gaps = 3/92 (3%)

Query: 213 ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD--GKSKCFGFVNFDDPD 270
             K   + + V+N+     + +++++F  FG + +  + +     G  + FGFV+F    
Sbjct: 3   PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 271 DAARSVEAL-NGKKFDDKEWYVGKAQKKYERE 301
           DA ++  AL +      +   +  A  +   +
Sbjct: 63  DAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 76.1 bits (187), Expect = 8e-18
 Identities = 22/94 (23%), Positives = 44/94 (46%), Gaps = 3/94 (3%)

Query: 314 ETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN--GISRGSGFVAFST 371
           +   K     + V+N+    +  +++ELFS FG + + ++ +     G  RG GFV F T
Sbjct: 1   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 60

Query: 372 AEEASKALTEM-NGKMVVSKPLYVALAQRKEERR 404
            ++A KA   + +   +  + L +  A  +   +
Sbjct: 61  KQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 70.7 bits (173), Expect = 7e-16
 Identities = 18/92 (19%), Positives = 52/92 (56%), Gaps = 2/92 (2%)

Query: 34  ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLS-TRRSLGYGYVNYNAAH 92
            ++  ++ + V ++    N  ++ +LF+  G++ +VR+ + ++ T    G+G+V++    
Sbjct: 3   PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 93  EATRALDEL-NFTPLNGKPIRIMYSYRDPTIR 123
           +A +A + L + T L G+ + + ++  + T++
Sbjct: 63  DAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 66.9 bits (163), Expect = 2e-14
 Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 3/81 (3%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD--SLGQSRGYGFVQFDNEES 180
           +K     I ++N+    + + + + FSTFG + + ++       G  RG+GFV F  ++ 
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 63

Query: 181 AKSAIDKL-NGMLLNDKQVFV 200
           AK A + L +   L  +++ +
Sbjct: 64  AKKAFNALCHSTHLYGRRLVL 84

>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 = 77.0 bits (189), Expect = 7e-18
 Identities = 21/101 (20%), Positives = 44/101 (43%), Gaps = 2/101 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             +Y++NL    T +++  IFG++G I           +++   +V ++D  DA  + + 
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQI--RVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKF 319
           L+G    ++   V         +     K E+ LK   +K+
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKY 106

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.7 bits (183), Expect = 4e-17
 Identities = 18/93 (19%), Positives = 44/93 (47%), Gaps = 3/93 (3%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LY++NL   I+ +++ ++F ++G I            +RG+ +V +    +A  A   ++
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQI--RVGNTPETRGTAYVVYEDIFDAKNACDHLS 67

Query: 384 GKMVVSKPLYVALAQ-RKEERRARLQAQFSQMR 415
           G  V ++ L V      +  ++   + +  Q++
Sbjct: 68  GFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLK 100

>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 = 69.7 bits (170), Expect = 2e-15
 Identities = 25/118 (21%), Positives = 54/118 (45%), Gaps = 16/118 (13%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           ++I+NL   I  + ++D F  +G I   +    +  ++RG  +V +++   AK+A D L+
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQIR--VGNTPETRGTAYVVYEDIFDAKNACDHLS 67

Query: 190 GMLLNDKQVFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITS 247
           G  + ++ + V  +   +  +    K +              E+ LK +  ++GI T 
Sbjct: 68  GFNVCNRYLVVLYYNANRAFQKMDTKKK--------------EEQLKLLKEKYGINTD 111

>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 = 66.2 bits (161), Expect = 5e-14
 Identities = 22/88 (25%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 38  VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
           V+  LY+ +L   +   ++YD+F + G +  +RV     TR   G  YV Y    +A  A
Sbjct: 6   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNA 62

Query: 98  LDELNFTPLNGKPIRIMYSYRDPTIRKS 125
            D L+   +  + + ++Y   +   +K 
Sbjct: 63  CDHLSGFNVCNRYLVVLYYNANRAFQKM 90

>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 = 75.4 bits (185), Expect = 1e-17
 Identities = 28/75 (37%), Positives = 42/75 (56%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L V NLD  +SD  ++ELF+EFGT+    V  D +G S G+  V F    +A KA+ + N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 384 GKMVVSKPLYVALAQ 398
           G  +  +P+ + L  
Sbjct: 63  GVPLDGRPMNIQLVT 77

>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 = 71.5 bits (175), Expect = 2e-16
 Identities = 20/71 (28%), Positives = 37/71 (52%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           + V NL    ++ D++++F EFG +   AV  D  G+S     V+F+   DA ++++  N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 281 GKKFDDKEWYV 291
           G   D +   +
Sbjct: 63  GVPLDGRPMNI 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 = 67.3 bits (164), Expect = 8e-15
 Identities = 19/73 (26%), Positives = 37/73 (50%)

Query: 128 GNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
           G + + NLD  + +  + + F+ FG +    V  D  G+S G   V F+ +  A  A+ +
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 188 LNGMLLNDKQVFV 200
            NG+ L+ + + +
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 = 61.1 bits (148), Expect = 1e-12
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L V +LD  V+D+ + +LF + G +    V  D  + RSLG   V++    +A +A+ + 
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQY 61

Query: 102 NFTPLNGKPIRIMYS 116
           N  PL+G+P+ I   
Sbjct: 62  NGVPLDGRPMNIQLV 76

>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 = 74.3 bits (182), Expect = 3e-17
 Identities = 29/82 (35%), Positives = 47/82 (57%), Gaps = 4/82 (4%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN----GISRGSGFVAFSTAEEASKAL 379
           L++KNL+ S +++ LK +FS+ G I SC + +  N     +S G GFV +   E+A KAL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 380 TEMNGKMVVSKPLYVALAQRKE 401
            ++ G  V    L V +++R  
Sbjct: 61  KQLQGHTVDGHKLEVRISERAT 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 = 73.1 bits (179), Expect = 7e-17
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 4/80 (5%)

Query: 222 YVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD----GKSKCFGFVNFDDPDDAARSVE 277
           ++KNL+ +TTE+ LK +F + G I S  + +  +      S  FGFV +  P+ A ++++
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 278 ALNGKKFDDKEWYVGKAQKK 297
            L G   D  +  V  +++ 
Sbjct: 62  QLQGHTVDGHKLEVRISERA 81

>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 = 61.2 bits (148), Expect = 1e-12
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATD----SLGQSRGYGFVQFDNEESAKSAI 185
           +FIKNL+ S   + L   FS  G I SC ++       +  S G+GFV++   E A+ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 186 DKLNGMLLNDKQVFV 200
            +L G  ++  ++ V
Sbjct: 61  KQLQGHTVDGHKLEV 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 = 60.8 bits (147), Expect = 2e-12
 Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVS---VRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           L++ +L+ S  +  L  +F+++G + S    +         S+G+G+V Y    +A +AL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 99  DELNFTPLNGKPIRIMYSYRDP 120
            +L    ++G  + +  S R  
Sbjct: 61  KQLQGHTVDGHKLEVRISERAT 82

>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 = 72.8 bits (178), Expect = 1e-16
 Identities = 23/92 (25%), Positives = 42/92 (45%), Gaps = 5/92 (5%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDP 269
           +T  +     +YV  L+E   +  L   F  FG IT   +  D + +  + F FV F+  
Sbjct: 2   ATTKRV----LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 57

Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKKYERE 301
           +DAA +++ +N  +   +   V  A+    +E
Sbjct: 58  EDAAAAIDNMNESELFGRTIRVNLAKPMRIKE 89

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.8 bits (165), Expect = 7e-15
 Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 1/81 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           LYV  L + + D  L   F  FG IT  ++  D      RG  FV F  AE+A+ A+  M
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 383 NGKMVVSKPLYVALAQRKEER 403
           N   +  + + V LA+    +
Sbjct: 68  NESELFGRTIRVNLAKPMRIK 88

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.1 bits (153), Expect = 3e-13
 Identities = 23/78 (29%), Positives = 40/78 (51%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              LYVG L   V+D  L+  F   G +  +++  D  T +  G+ +V +  A +A  A+
Sbjct: 5   KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64

Query: 99  DELNFTPLNGKPIRIMYS 116
           D +N + L G+ IR+  +
Sbjct: 65  DNMNESELFGRTIRVNLA 82

>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 = 60.8 bits (147), Expect = 2e-12
 Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDKL 188
           +++  L + +D+K LH  F  FG+I   ++  D   +  RG+ FV+F+  E A +AID +
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 189 NGMLLNDKQVFVGPFLRKQERE 210
           N   L  + + V      + +E
Sbjct: 68  NESELFGRTIRVNLAKPMRIKE 89

>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 = 73.2 bits (179), Expect = 1e-16
 Identities = 25/87 (28%), Positives = 48/87 (55%), Gaps = 1/87 (1%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPD 270
           ++  K+    ++V N+     + DL+++FG+FG I    ++ + +  SK FGFV F++  
Sbjct: 4   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFGFVTFENSA 62

Query: 271 DAARSVEALNGKKFDDKEWYVGKAQKK 297
           DA R+ E L+G   + ++  V  A  +
Sbjct: 63  DADRAREKLHGTVVEGRKIEVNNATAR 89

>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 = 65.9 bits (160), Expect = 4e-14
 Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            L+V N+     D  L+++F +FG I   +++ +    S+G GFV F  + +A +A  ++
Sbjct: 13  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKL 71

Query: 383 NGKMVVSKPLYVALAQRK 400
           +G +V  + + V  A  +
Sbjct: 72  HGTVVEGRKIEVNNATAR 89

>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 = 58.2 bits (140), Expect = 2e-11
 Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 4/89 (4%)

Query: 124 KSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKS 183
           KS    + + N+     +  L   F  FG IL  ++  +    S+G+GFV F+N   A  
Sbjct: 8   KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-RGSKGFGFVTFENSADADR 66

Query: 184 AIDKLNGMLLNDKQVFVGPFLRKQEREST 212
           A +KL+G ++  +++ V        R  T
Sbjct: 67  AREKLHGTVVEGRKIEVN---NATARVMT 92

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 9e-11
 Identities = 20/78 (25%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              L+V ++     D  L  +F Q G+++ V +  +   R S G+G+V +  + +A RA 
Sbjct: 11  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAR 68

Query: 99  DELNFTPLNGKPIRIMYS 116
           ++L+ T + G+ I +  +
Sbjct: 69  EKLHGTVVEGRKIEVNNA 86

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.6 bits (178), Expect = 2e-16
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 8/83 (9%)

Query: 323 NLYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
            +++ NL+   +    ++ +FS++G I  C V +       G  FV +     A  A+  
Sbjct: 17  RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK-------GFAFVQYVNERNARAAVAG 69

Query: 382 MNGKMVVSKPLYVALAQRKEERR 404
            +G+M+  + L + LA   +  R
Sbjct: 70  EDGRMIAGQVLDINLAAEPKVNR 92

>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 = 68.4 bits (167), Expect = 5e-15
 Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 8/84 (9%)

Query: 219 NNVYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
           + V++ NL+     + D++ IF ++G I   +V +        F FV + +  +A  +V 
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG-------FAFVQYVNERNARAAVA 68

Query: 278 ALNGKKFDDKEWYVGKAQKKYERE 301
             +G+    +   +  A +     
Sbjct: 69  GEDGRMIAGQVLDINLAAEPKVNR 92

>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 = 66.0 bits (161), Expect = 3e-14
 Identities = 23/107 (21%), Positives = 52/107 (48%), Gaps = 11/107 (10%)

Query: 24  GIANNGGVGDARQFVSTSLYVGDLD-LSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLG 82
           G + + G  D R  +++ +++G+L+ L V  S +  +F++ G++V   V +        G
Sbjct: 1   GSSGSSGKTDPRS-MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------G 51

Query: 83  YGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRKSGAGN 129
           + +V Y     A  A+   +   + G+ + I  +  +P + +SG  +
Sbjct: 52  FAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA-AEPKVNRSGPSS 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 = 62.6 bits (152), Expect = 5e-13
 Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 8/84 (9%)

Query: 129 NIFIKNLD-KSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
            +FI NL+   +    +   FS +G I+ C V        +G+ FVQ+ NE +A++A+  
Sbjct: 17  RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAG 69

Query: 188 LNGMLLNDKQVFVGPFLRKQERES 211
            +G ++  + + +      +   S
Sbjct: 70  EDGRMIAGQVLDINLAAEPKVNRS 93

>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 = 72.1 bits (176), Expect = 2e-16
 Identities = 23/82 (28%), Positives = 45/82 (54%), Gaps = 2/82 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMR--DPNGISRGSGFVAFSTAEEASKALTE 381
           +++ NLD  I +  L + FS FG I     +      G S+G  F+ F++ + +  A+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 382 MNGKMVVSKPLYVALAQRKEER 403
           MNG+ + ++P+ V+ A +K+ +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 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 = 69.0 bits (168), Expect = 2e-15
 Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVM--RDADGKSKCFGFVNFDDPDDAARSVEA 278
           +++ NL     E  L   F  FG+I  T  +      G SK + F+NF   D +  ++EA
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 279 LNGKKFDDKEWYVGKAQKKYER 300
           +NG+   ++   V  A KK  +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 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 = 63.2 bits (153), Expect = 2e-13
 Identities = 21/81 (25%), Positives = 47/81 (58%), Gaps = 1/81 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSV-RVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           +++G+LD  +++  LYD F+  G ++   ++ RD  T  S GY ++N+ +   +  A++ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 101 LNFTPLNGKPIRIMYSYRDPT 121
           +N   L  +PI + Y+++  +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.3 bits (148), Expect = 1e-12
 Identities = 31/82 (37%), Positives = 46/82 (56%), Gaps = 2/82 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL--GQSRGYGFVQFDNEESAKSAIDK 187
           IFI NLD  ID K L+DTFS FG IL           G S+GY F+ F + +++ +AI+ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 188 LNGMLLNDKQVFVGPFLRKQER 209
           +NG  L ++ + V    +K  +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 71.9 bits (176), Expect = 2e-16
 Identities = 31/84 (36%), Positives = 50/84 (59%), Gaps = 3/84 (3%)

Query: 317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEA 375
           +  +  NLYV NL  +I+DD+L  +F ++G+I    ++RD   G  RG  FV ++  EEA
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 376 SKALTEMNGKMV--VSKPLYVALA 397
            +A++ +N  +    S+PL V LA
Sbjct: 62  QEAISALNNVIPEGGSQPLSVRLA 85

>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 = 70.8 bits (173), Expect = 5e-16
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDA 272
           +  +  N+YV NL  T T+D L  IFG++G I+    +     G+ +   FV ++  ++A
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 273 ARSVEALNGKKFD 285
             ++ ALN    +
Sbjct: 62  QEAISALNNVIPE 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 = 64.2 bits (156), Expect = 1e-13
 Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
            T+LYV +L  ++ D QL  +F + G +V   + RD  T R  G  +V YN   EA  A+
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 99  DELNFTPLNG--KPIRIMY 115
             LN     G  +P+ +  
Sbjct: 66  SALNNVIPEGGSQPLSVRL 84

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 61.5 bits (149), Expect = 8e-13
 Identities = 21/67 (31%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+++ NL ++I +  L   F  +G+I+   +  D L G+ RG  FV+++  E A+ AI  
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 188 LNGMLLN 194
           LN ++  
Sbjct: 68  LNNVIPE 74

>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 = 71.6 bits (175), Expect = 2e-16
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+ +L  +F   G I +  +MRD   G S  + FV+F    D+ R+++ 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 279 LNGKKFDDKEWYVGKAQ 295
           LNG    +K   V  A+
Sbjct: 64  LNGITVRNKRLKVSYAR 80

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 71.6 bits (175), Expect = 3e-16
 Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 1/77 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           NL V  L   ++D +L  LF   G I +C++MRD   G S G  FV F++  ++ +A+  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 382 MNGKMVVSKPLYVALAQ 398
           +NG  V +K L V+ A+
Sbjct: 64  LNGITVRNKRLKVSYAR 80

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 66.9 bits (163), Expect = 1e-14
 Identities = 24/78 (30%), Positives = 44/78 (56%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           +T+L V  L   + D +LY LF  +G + + R+ RD  T  S GY +V++ +  ++ RA+
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 99  DELNFTPLNGKPIRIMYS 116
             LN   +  K +++ Y+
Sbjct: 62  KVLNGITVRNKRLKVSYA 79

>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 = 62.7 bits (152), Expect = 3e-13
 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCK-VATDSLGQSRGYGFVQFDNEESAKSAIDK 187
           N+ +  L + + ++ L+  F   G I +C+ +     G S GY FV F +E  ++ AI  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 188 LNGMLLNDKQVFV 200
           LNG+ + +K++ V
Sbjct: 64  LNGITVRNKRLKV 76

>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 = 72.0 bits (176), Expect = 3e-16
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 2/97 (2%)

Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGF 263
           R+     + ++     V+   L+      DL+  F   G +    ++ D +  +SK   +
Sbjct: 5   REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 64

Query: 264 VNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           V F +      ++  L G++       V  +Q +  R
Sbjct: 65  VEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAEKNR 100

>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 = 67.0 bits (163), Expect = 2e-14
 Identities = 19/96 (19%), Positives = 43/96 (44%), Gaps = 2/96 (2%)

Query: 309 EQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFV 367
           E     + ++ +   ++   L   I    L++ FS  G +   +++ D N   S+G  +V
Sbjct: 6   EPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV 65

Query: 368 AFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEER 403
            F   +    A+  + G+ ++  P+ V  +Q ++ R
Sbjct: 66  EFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNR 100

>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 = 62.4 bits (151), Expect = 7e-13
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           + +++   L   +    L D F+ +G+V  VR+  D ++RRS G  YV +        A+
Sbjct: 18  ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 77

Query: 99  DELNFTPLNGKPIRIMYS 116
             L    L G PI +  S
Sbjct: 78  -GLTGQRLLGVPIIVQAS 94

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 2e-10
 Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 4/101 (3%)

Query: 110 PIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLG-QSR 168
           P+R       P  R +    +F   L   I  + L D FS  G +   ++ +D    +S+
Sbjct: 3   PVREPVDNLSPEERDAR--TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 60

Query: 169 GYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVGPFLRKQER 209
           G  +V+F   +S       L G  L    + V     ++ R
Sbjct: 61  GIAYVEFCEIQSVP-LAIGLTGQRLLGVPIIVQASQAEKNR 100

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.7 bits (175), Expect = 4e-16
 Identities = 28/86 (32%), Positives = 43/86 (50%), Gaps = 1/86 (1%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKA 378
           EG NL++ +L     D  L ++F  FG + S KV  D    +S+  GFV++     A  A
Sbjct: 17  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 379 LTEMNGKMVVSKPLYVALAQRKEERR 404
           +  MNG  +  K L V L + K + +
Sbjct: 77  IQSMNGFQIGMKRLKVQLKRSKNDSK 102

>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 = 69.0 bits (168), Expect = 3e-15
 Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 1/83 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
            N+++ +L +   + DL ++F  FG + S  V  D     SKCFGFV++D+P  A  +++
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 278 ALNGKKFDDKEWYVGKAQKKYER 300
           ++NG +   K   V   + K + 
Sbjct: 79  SMNGFQIGMKRLKVQLKRSKNDS 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 = 58.2 bits (140), Expect = 2e-11
 Identities = 20/78 (25%), Positives = 35/78 (44%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             +L++  L     D  L  +F   G VVS +V  D  T  S  +G+V+Y+    A  A+
Sbjct: 18  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 77

Query: 99  DELNFTPLNGKPIRIMYS 116
             +N   +  K +++   
Sbjct: 78  QSMNGFQIGMKRLKVQLK 95

>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 = 57.4 bits (138), Expect = 4e-11
 Identities = 28/82 (34%), Positives = 45/82 (54%), Gaps = 1/82 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
           N+FI +L +   ++ L   F  FGN++S KV  D     S+ +GFV +DN  SA++AI  
Sbjct: 20  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 79

Query: 188 LNGMLLNDKQVFVGPFLRKQER 209
           +NG  +  K++ V     K + 
Sbjct: 80  MNGFQIGMKRLKVQLKRSKNDS 101

>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 = 69.7 bits (170), Expect = 1e-15
 Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 1/86 (1%)

Query: 213 ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITST-AVMRDADGKSKCFGFVNFDDPDD 271
           +++ +   VYV  L E  +E  L ++F + G + +T        G+ + +GFV F   +D
Sbjct: 4   SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 63

Query: 272 AARSVEALNGKKFDDKEWYVGKAQKK 297
           A  +++ ++  K   K   V KA   
Sbjct: 64  ADYAIKIMDMIKLYGKPIRVNKASAH 89

>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 = 68.1 bits (166), Expect = 6e-15
 Identities = 25/88 (28%), Positives = 46/88 (52%), Gaps = 1/88 (1%)

Query: 316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEE 374
           +++ +   +YV  LD+ +S+  L ELF + G + +  + +D   G  +G GFV F + E+
Sbjct: 4   SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 63

Query: 375 ASKALTEMNGKMVVSKPLYVALAQRKEE 402
           A  A+  M+   +  KP+ V  A    +
Sbjct: 64  ADYAIKIMDMIKLYGKPIRVNKASAHNK 91

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.7 bits (152), Expect = 4e-13
 Identities = 27/78 (34%), Positives = 46/78 (58%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             ++YVG LD  V++  L++LF Q G VV+  + +D  T +  GYG+V + +  +A  A+
Sbjct: 9   DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 68

Query: 99  DELNFTPLNGKPIRIMYS 116
             ++   L GKPIR+  +
Sbjct: 69  KIMDMIKLYGKPIRVNKA 86

>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 = 56.6 bits (136), Expect = 6e-11
 Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNE 178
           P   ++    +++  LD+ +    L + F   G +++  +  D   GQ +GYGFV+F +E
Sbjct: 2   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 179 ESAKSAIDKLNGMLLNDKQVFV 200
           E A  AI  ++ + L  K + V
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRV 83

>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 = 69.6 bits (170), Expect = 2e-15
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 6/82 (7%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           + ++Y G +   + D  +   F+  GQ++ +RV  +        Y +V ++    A  A+
Sbjct: 18  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHAI 71

Query: 99  DELNFTPLNGKPIRIMYSYRDP 120
             +N T + G  ++  +    P
Sbjct: 72  VSVNGTTIEGHVVKCYWGKESP 93

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.8 bits (168), Expect = 4e-15
 Identities = 21/94 (22%), Positives = 41/94 (43%), Gaps = 7/94 (7%)

Query: 307 KFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGF 366
           +FE  + +++ K     +Y   +   ++D  +++ FS FG I   +V  +         F
Sbjct: 6   RFEDVVNQSSPK--NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-----YSF 58

Query: 367 VAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK 400
           V FST E A+ A+  +NG  +    +     +  
Sbjct: 59  VRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 92

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 3e-13
 Identities = 17/89 (19%), Positives = 35/89 (39%), Gaps = 8/89 (8%)

Query: 209 RESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDD 268
            +S+        VY   ++   T+  +++ F  FG I    V  +     K + FV F  
Sbjct: 12  NQSSPKNCT---VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFST 63

Query: 269 PDDAARSVEALNGKKFDDKEWYVGKAQKK 297
            + AA ++ ++NG   +         ++ 
Sbjct: 64  HESAAHAIVSVNGTTIEGHVVKCYWGKES 92

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 2e-11
 Identities = 25/97 (25%), Positives = 43/97 (44%), Gaps = 12/97 (12%)

Query: 107 NGKPIRIMYSYRDPTIRKSGAGN--IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL 164
           N K +R      +  + +S   N  ++   +   + ++ +  TFS FG I+  +V  +  
Sbjct: 1   NTKQLRF-----EDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-- 53

Query: 165 GQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFVG 201
              +GY FV+F   ESA  AI  +NG  +    V   
Sbjct: 54  ---KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY 87

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.2 bits (169), Expect = 2e-15
 Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 1/81 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEAL 279
           +YV NLS  TTE+ + ++F + G I    +  D     +  F FV +    DA  ++  +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 280 NGKKFDDKEWYVGKAQKKYER 300
           NG + DD+           E 
Sbjct: 70  NGTRLDDRIIRTDWDAGFKEG 90

>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 = 69.2 bits (169), Expect = 2e-15
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGS-GFVAFSTAEEASKALTEM 382
           LYV NL    +++++ ELFS+ G I    +  D    +     FV + +  +A  A+  +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 383 NGKMVVSKPLYVALAQRKEERR 404
           NG  +  + +        +E R
Sbjct: 70  NGTRLDDRIIRTDWDAGFKEGR 91

>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 = 68.8 bits (168), Expect = 3e-15
 Identities = 22/78 (28%), Positives = 43/78 (55%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S +LYVG+L     + Q+Y+LF++ G +  + +  D   + + G+ +V Y +  +A  A+
Sbjct: 7   SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 66

Query: 99  DELNFTPLNGKPIRIMYS 116
             +N T L+ + IR  + 
Sbjct: 67  RYINGTRLDDRIIRTDWD 84

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.8 bits (142), Expect = 1e-11
 Identities = 16/72 (22%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLG-QSRGYGFVQFDNEESAKSAIDKL 188
           +++ NL      + +++ FS  G+I    +  D +   + G+ FV++ +   A++A+  +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 189 NGMLLNDKQVFV 200
           NG  L+D+ +  
Sbjct: 70  NGTRLDDRIIRT 81

>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 = 68.9 bits (168), Expect = 3e-15
 Identities = 28/88 (31%), Positives = 41/88 (46%), Gaps = 6/88 (6%)

Query: 324 LYVKNLDDSISDDKLK----ELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +Y+ NL++ I  D+LK     +FS FG I    V R      RG  FV F     A+ AL
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 63

Query: 380 TEMNGKMVVSKPLYVALAQRKEERRARL 407
             M G     KP+ +  A+   +  A++
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTDSDIIAKM 91

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.7 bits (157), Expect = 9e-14
 Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 6/90 (6%)

Query: 219 NNVYVKNLSETTTEDDLKK----IFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAAR 274
           + +Y+ NL+E   +D+LKK    IF  FG I    V R      +   FV F +   A  
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATN 61

Query: 275 SVEALNGKKFDDKEWYVGKAQKKYEREMEL 304
           ++ ++ G  F DK   +  A+   +   ++
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 91

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 2e-10
 Identities = 25/86 (29%), Positives = 37/86 (43%), Gaps = 6/86 (6%)

Query: 130 IFIKNLDKSIDNKAL----HDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAI 185
           I+I NL++ I    L    H  FS FG IL   V+     + RG  FV F    SA +A+
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 63

Query: 186 DKLNGMLLNDKQVFVGPFLRKQERES 211
             + G    DK + +       +  +
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTDSDIIA 89

>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 = 54.3 bits (130), Expect = 4e-10
 Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 7/85 (8%)

Query: 39  STSLYVGDLDLSVNDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEA 94
           + ++Y+ +L+  +   +L    + +F++ GQ++ + V R L  R   G  +V +     A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVSSA 59

Query: 95  TRALDELNFTPLNGKPIRIMYSYRD 119
           T AL  +   P   KP+RI Y+  D
Sbjct: 60  TNALRSMQGFPFYDKPMRIQYAKTD 84

>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 = 69.0 bits (168), Expect = 4e-15
 Identities = 15/100 (15%), Positives = 31/100 (31%), Gaps = 10/100 (10%)

Query: 323 NLYVKNLDDSI-----SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASK 377
            L     +D +     +  K + LF  +   T+ +  +           + FS    A+ 
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAAD 61

Query: 378 ALTEMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPP 417
           A   ++    + K + +  AQ      + L         P
Sbjct: 62  ARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSGP 101

>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 = 55.6 bits (133), Expect = 2e-10
 Identities = 12/87 (13%), Positives = 28/87 (32%), Gaps = 11/87 (12%)

Query: 39  STSLYVGDLDLSVNDS-----QLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
           S+ L     +  V        +   LF    +  + +  +            +N++    
Sbjct: 5   SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLS 58

Query: 94  ATRALDELNFTPLNGKPIRIMYSYRDP 120
           A  A   L+ T   GK +++ ++    
Sbjct: 59  AADARLRLHKTEFLGKEMKLYFAQTLH 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 = 52.9 bits (126), Expect = 2e-09
 Identities = 13/92 (14%), Positives = 27/92 (29%), Gaps = 10/92 (10%)

Query: 125 SGAGNIFIKNLDKSI-----DNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEE 179
           SG+  +     +  +             F T+    + +       +S     + F N  
Sbjct: 3   SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-----KSFKRVRINFSNPL 57

Query: 180 SAKSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
           SA  A  +L+      K++ +          S
Sbjct: 58  SAADARLRLHKTEFLGKEMKLYFAQTLHIGSS 89

>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 = 50.9 bits (121), Expect = 9e-09
 Identities = 17/92 (18%), Positives = 32/92 (34%), Gaps = 10/92 (10%)

Query: 219 NNVYVKNL-----SETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAA 273
           + +          SE+ T    + +F  +   T+    +           +NF +P  AA
Sbjct: 6   SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAA 60

Query: 274 RSVEALNGKKFDDKEWYVGKAQKKYEREMELK 305
            +   L+  +F  KE  +  AQ  +     L 
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTLHIGSSHLA 92

>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 = 68.1 bits (166), Expect = 5e-15
 Identities = 25/88 (28%), Positives = 43/88 (48%), Gaps = 1/88 (1%)

Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAA 273
           D  +   +YV NLS   TE  + ++F + G   S  ++ +    +  + FV F +  DAA
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-HTSNDPYCFVEFYEHRDAA 62

Query: 274 RSVEALNGKKFDDKEWYVGKAQKKYERE 301
            ++ A+NG+K   KE  V  A     ++
Sbjct: 63  AALAAMNGRKILGKEVKVNWATTPSSQK 90

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.0 bits (163), Expect = 1e-14
 Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LYV NL   +++  + +LFS+ G   SCK++ +         FV F    +A+ AL  MN
Sbjct: 11  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAAMN 69

Query: 384 GKMVVSKPLYVALAQRKEERR 404
           G+ ++ K + V  A     ++
Sbjct: 70  GRKILGKEVKVNWATTPSSQK 90

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 1e-11
 Identities = 21/86 (24%), Positives = 43/86 (50%), Gaps = 3/86 (3%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             +LYVG+L   V +  +  LF+Q+G   S ++  +     +  Y +V +    +A  AL
Sbjct: 8   PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE--HTSNDPYCFVEFYEHRDAAAAL 65

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRK 124
             +N   + GK +++ ++   P+ +K
Sbjct: 66  AAMNGRKILGKEVKVNWA-TTPSSQK 90

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 1e-10
 Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +++ NL + +    +   FS  G   SCK+ T+    +  Y FV+F     A +A+  +N
Sbjct: 11  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH-TSNDPYCFVEFYEHRDAAAALAAMN 69

Query: 190 GMLLNDKQVFVGPFLRKQERE 210
           G  +  K+V V        ++
Sbjct: 70  GRKILGKEVKVNWATTPSSQK 90

>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 = 68.5 bits (167), Expect = 5e-15
 Identities = 14/94 (14%), Positives = 39/94 (41%), Gaps = 2/94 (2%)

Query: 198 VFVGPFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK 257
           ++  P    Q  +    ++  ++V ++   +   E+   ++  ++G +    V  +    
Sbjct: 9   IYRNPQNSSQSADGL--RSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDH 66

Query: 258 SKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYV 291
                +V F   +DA ++V  LN + F+ +  + 
Sbjct: 67  LVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 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 = 67.0 bits (163), Expect = 2e-14
 Identities = 14/74 (18%), Positives = 35/74 (47%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           ++ ++   D   ++   E+  ++G +    V  +      G+ +V F   E+A KA+ ++
Sbjct: 29  DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 383 NGKMVVSKPLYVAL 396
           N +    +P++  L
Sbjct: 89  NNRWFNGQPIHAEL 102

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 3e-11
 Identities = 18/91 (19%), Positives = 38/91 (41%), Gaps = 1/91 (1%)

Query: 26  ANNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGY 85
            N+    D  +   + + + +      +    ++  + G+V  + VC +      +G  Y
Sbjct: 14  QNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVY 72

Query: 86  VNYNAAHEATRALDELNFTPLNGKPIRIMYS 116
           V +    +A +A+ +LN    NG+PI    S
Sbjct: 73  VKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 3e-11
 Identities = 16/91 (17%), Positives = 32/91 (35%), Gaps = 7/91 (7%)

Query: 117 YRDPTIRKSGAG-------NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRG 169
           YR+P      A        ++ ++        +   +    +G +    V  +      G
Sbjct: 10  YRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVG 69

Query: 170 YGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
             +V+F  EE A+ A+  LN    N + +  
Sbjct: 70  NVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100

>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 = 67.4 bits (164), Expect = 8e-15
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARSVE 277
             + V  LS  TTE DL+++F ++G I   +++ D    +S+ F FV F++ DDA  + E
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 278 ALNGKKFDDKEWYV 291
             NG + D +   V
Sbjct: 70  RANGMELDGRRIRV 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 = 63.6 bits (154), Expect = 1e-13
 Identities = 21/75 (28%), Positives = 38/75 (50%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           +  L V  L L   +  L ++F++ G +  V +  D  +RRS G+ +V +    +A  A 
Sbjct: 9   NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68

Query: 99  DELNFTPLNGKPIRI 113
           +  N   L+G+ IR+
Sbjct: 69  ERANGMELDGRRIRV 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 = 61.3 bits (148), Expect = 1e-12
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG-ISRGSGFVAFSTAEEASKALTE 381
            L V  L    ++  L+E+FS++G I    ++ D     SRG  FV F   ++A +A   
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 382 MNGKMVVSKPLYV 394
            NG  +  + + V
Sbjct: 71  ANGMELDGRRIRV 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 = 57.0 bits (137), Expect = 4e-11
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDK 187
            + +  L      + L + FS +G I    +  D   + SRG+ FV F+N + AK A ++
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 188 LNGMLLNDKQVFV 200
            NGM L+ +++ V
Sbjct: 71  ANGMELDGRRIRV 83

>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 = 67.4 bits (164), Expect = 8e-15
 Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N+ V  L +  T+++ + +FG  G I +   V     G+S  +GFVN+ DP DA +++  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 279 LNGKKFDDKEWYVGKAQ 295
           LNG +   K   V  A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.2 bits (153), Expect = 2e-13
 Identities = 27/77 (35%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
           NL V  L  +++ ++ + LF   G I SCK++RD   G S G GFV +   ++A KA+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 382 MNGKMVVSKPLYVALAQ 398
           +NG  + +K + V+ A+
Sbjct: 64  LNGLRLQTKTIKVSYAR 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.3 bits (148), Expect = 1e-12
 Identities = 27/77 (35%), Positives = 45/77 (58%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T+L V  L  ++   +   LF  +G++ S ++ RD  T +SLGYG+VNY    +A +A++
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 100 ELNFTPLNGKPIRIMYS 116
            LN   L  K I++ Y+
Sbjct: 63  TLNGLRLQTKTIKVSYA 79

>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 = 56.7 bits (136), Expect = 5e-11
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFG-NILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK 187
           N+ +  L +++  +     F + G       V     GQS GYGFV + + + A+ AI+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 188 LNGMLLNDKQVFV 200
           LNG+ L  K + V
Sbjct: 64  LNGLRLQTKTIKV 76

>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 = 67.4 bits (164), Expect = 1e-14
 Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 1/85 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALTE 381
            L+V+NL  + S++ L++LFS +G ++      D      +G  FV F   E A KA  E
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 382 MNGKMVVSKPLYVALAQRKEERRAR 406
           ++G++   + L+V  +  K+E    
Sbjct: 70  VDGQVFQGRMLHVLPSTIKKEASQS 94

>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 = 65.9 bits (160), Expect = 4e-14
 Identities = 24/84 (28%), Positives = 45/84 (53%), Gaps = 1/84 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITS-TAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
             ++V+NLS T++E+DL+K+F  +G ++     +     K K F FV F  P+ A ++  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 278 ALNGKKFDDKEWYVGKAQKKYERE 301
            ++G+ F  +  +V  +  K E  
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEAS 92

>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 = 64.7 bits (157), Expect = 1e-13
 Identities = 19/88 (21%), Positives = 40/88 (45%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S  L+V +L  + ++  L  LF+  G +  +    D  T++  G+ +V +     A +A 
Sbjct: 8   SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAY 67

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSG 126
            E++     G+ + ++ S       +SG
Sbjct: 68  AEVDGQVFQGRMLHVLPSTIKKEASQSG 95

>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 = 62.4 bits (151), Expect = 6e-13
 Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 1/90 (1%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKS 183
           SG+G +F++NL  +   + L   FS +G +       D    + +G+ FV F   E A  
Sbjct: 6   SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 184 AIDKLNGMLLNDKQVFVGPFLRKQERESTA 213
           A  +++G +   + + V P   K+E   + 
Sbjct: 66  AYAEVDGQVFQGRMLHVLPSTIKKEASQSG 95

>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 = 67.9 bits (165), Expect = 1e-14
 Identities = 20/109 (18%), Positives = 39/109 (35%), Gaps = 6/109 (5%)

Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDP-DDA 272
           +K      +  +L + T  +DL  +F   G I     +R         G + F +   +A
Sbjct: 7   EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEA 61

Query: 273 ARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKETADKFEG 321
               +  N      +   V     + E E E   K  +  +E+ +K++ 
Sbjct: 62  LGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWKS 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 = 53.7 bits (128), Expect = 1e-09
 Identities = 19/95 (20%), Positives = 32/95 (33%), Gaps = 6/95 (6%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFST-AEEASKALT 380
           L  +  +LDD    + L  LFS  G I     +R         G + F   A+EA     
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-----KEGIILFKEKAKEALGKAK 66

Query: 381 EMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMR 415
           + N   +  +   V     + E       +  + +
Sbjct: 67  DANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQ 101

>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 = 48.6 bits (115), Expect = 7e-08
 Identities = 19/89 (21%), Positives = 28/89 (31%), Gaps = 6/89 (6%)

Query: 123 RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNE-ESA 181
            K G    F  +LD     + LH  FS  G I           +    G + F  + + A
Sbjct: 7   EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFV-----RGAKEGIILFKEKAKEA 61

Query: 182 KSAIDKLNGMLLNDKQVFVGPFLRKQERE 210
                  N   L  +   V   + + E E
Sbjct: 62  LGKAKDANNGNLQLRNKEVTWEVLEGEVE 90

>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 = 37.5 bits (86), Expect = 5e-04
 Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 7/86 (8%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNY-NAAHEATRAL 98
              + GDLD       L+ LF+  G++  +   R          G + +   A EA    
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKA 65

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRK 124
            + N   L  +   + +   +  + K
Sbjct: 66  KDANNGNLQLRNKEVTWEVLEGEVEK 91

>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 = 66.6 bits (162), Expect = 1e-14
 Identities = 26/78 (33%), Positives = 47/78 (60%), Gaps = 3/78 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG-ISRGSGFVAFSTAEEASKALTE 381
           NLYV  L  +++  +L++LFS++G I + +++ D    +SRG GF+ F    EA +A+  
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 382 MNGKMV--VSKPLYVALA 397
           +NG+     ++P+ V  A
Sbjct: 68  LNGQKPSGATEPITVKFA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 2e-13
 Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAARS 275
           R  N+YV  L +T T+ +L+++F ++G I ++ ++ D     S+  GF+ FD   +A  +
Sbjct: 5   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 276 VEALNGKKFDDKE 288
           ++ LNG+K     
Sbjct: 65  IKGLNGQKPSGAT 77

>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 = 58.9 bits (142), Expect = 7e-12
 Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 2/79 (2%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
            +LYV  L  ++   +L  LF+Q G++++ R+  D  T  S G G++ ++   EA  A+ 
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 100 ELNFTPLNG--KPIRIMYS 116
            LN    +G  +PI + ++
Sbjct: 67  GLNGQKPSGATEPITVKFA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 2e-11
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           N+++  L K++  K L   FS +G I++ ++  D   G SRG GF++FD    A+ AI  
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 188 LNGMLLNDK 196
           LNG   +  
Sbjct: 68  LNGQKPSGA 76

>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 = 67.0 bits (163), Expect = 2e-14
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 2/82 (2%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
            L++  L    +++ L+  + ++G +T C VMRDP    SRG GFV FS+  E   A+  
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 80

Query: 382 MNGKMVVSKPLYVALAQRKEER 403
                +  + +    A  +EE 
Sbjct: 81  ARPHSIDGRVVEPKRAVAREES 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 = 66.2 bits (161), Expect = 3e-14
 Identities = 20/96 (20%), Positives = 40/96 (41%), Gaps = 2/96 (2%)

Query: 206 KQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIIT-STAVMRDADGKSKCFGFV 264
                   +K +F  +++  LS  TTE+ L+  + ++G +T    +   A  +S+ FGFV
Sbjct: 8   VPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFV 67

Query: 265 NFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
            F    +   ++        D +     +A  + E 
Sbjct: 68  TFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREES 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 = 58.5 bits (141), Expect = 2e-11
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 2/82 (2%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
            +FI  L      ++L + +  +G +  C V  D    +SRG+GFV F +     +A+  
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 80

Query: 188 LNGMLLNDKQVFVGPFLRKQER 209
                ++ + V     + ++E 
Sbjct: 81  ARPHSIDGRVVEPKRAVAREES 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 = 56.2 bits (135), Expect = 1e-10
 Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              L++G L     +  L + + Q G++    V RD +++RS G+G+V +++  E   A+
Sbjct: 20  FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 79

Query: 99  DELNFTPLNGKPIRI 113
                  ++G+ +  
Sbjct: 80  -AARPHSIDGRVVEP 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 = 66.2 bits (161), Expect = 2e-14
 Identities = 28/80 (35%), Positives = 45/80 (56%), Gaps = 1/80 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVE 277
             + V NLSE T E DL+++F  FG I+   + +D   G+SK F F++F   +DAAR++ 
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 278 ALNGKKFDDKEWYVGKAQKK 297
            ++G  +D     V  A+  
Sbjct: 69  GVSGFGYDHLILNVEWAKPS 88

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.8 bits (152), Expect = 5e-13
 Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 1/80 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
            + V NL +   +  L+ELF  FG+I+   + +D   G S+G  F++F   E+A++A+  
Sbjct: 10  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 69

Query: 382 MNGKMVVSKPLYVALAQRKE 401
           ++G       L V  A+   
Sbjct: 70  VSGFGYDHLILNVEWAKPST 89

>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 = 60.8 bits (147), Expect = 2e-12
 Identities = 14/84 (16%), Positives = 43/84 (51%)

Query: 33  DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAH 92
           + R   + ++ V +L     ++ L +LF   G +  + + +D +T +S G+ +++++   
Sbjct: 2   NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 61

Query: 93  EATRALDELNFTPLNGKPIRIMYS 116
           +A RA+  ++    +   + + ++
Sbjct: 62  DAARAIAGVSGFGYDHLILNVEWA 85

>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 = 55.4 bits (133), Expect = 1e-10
 Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 120 PTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNE 178
           P  R      I + NL +      L + F  FG+I    +A D   GQS+G+ F+ F   
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 179 ESAKSAIDKLNGMLLNDKQVFV 200
           E A  AI  ++G   +   + V
Sbjct: 61  EDAARAIAGVSGFGYDHLILNV 82

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.8 bits (160), Expect = 3e-14
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 3/82 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTE 381
           +L V  L    ++  LKE FS FG +   +V +D   G S+G GFV F+  E   K +++
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 382 MNGKMVVSKPLYVALAQRKEER 403
            +  M+  +     L   K+ +
Sbjct: 70  RH--MIDGRWCDCKLPNSKQSQ 89

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.1 bits (153), Expect = 3e-13
 Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 3/86 (3%)

Query: 217 RFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARS 275
           + +++ V  L   TTE DLK+ F  FG +    V +D   G SK FGFV F + +   + 
Sbjct: 7   KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 66

Query: 276 VEALNGKKFDDKEWYVGKAQKKYERE 301
           +   +    D +         K  ++
Sbjct: 67  MSQRH--MIDGRWCDCKLPNSKQSQD 90

>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 = 61.5 bits (149), Expect = 1e-12
 Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           ++ L V  L     +  L + F+  G+V+ V+V +DL T  S G+G+V +       + +
Sbjct: 8   TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 67

Query: 99  DELNFTPLNGKPIRIMYS 116
            + +   ++G+       
Sbjct: 68  SQRHM--IDGRWCDCKLP 83

>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 = 58.8 bits (142), Expect = 8e-12
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
           ++ +  L      + L + FSTFG +L  +V  D   G S+G+GFV+F   E+    + +
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 188 LNGMLLNDKQVFVGPFLRKQERE 210
            +   ++ +         KQ ++
Sbjct: 70  RHM--IDGRWCDCKLPNSKQSQD 90

>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 = 65.0 bits (158), Expect = 4e-14
 Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           +++  L    + + L+E F +FG +  C VMRDP    SRG GFV F       K L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 383 NGKMVVSKPLYVALA 397
           +   + SK +   +A
Sbjct: 62  SRHELDSKTIDPKVA 76

>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 = 60.8 bits (147), Expect = 1e-12
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           +++  LS  TT++ L++ FG+FG +     +      +S+ FGFV F D     + +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61

Query: 280 NGKKFDDKEWYVGKA 294
           +  + D K      A
Sbjct: 62  SRHELDSKTIDPKVA 76

>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 = 60.0 bits (145), Expect = 2e-12
 Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           +++G L        L + F Q G+V    V RD  T+RS G+G+V +       + L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 102 NFTPLNGKPIRIMYSY 117
           +   L+ K I    ++
Sbjct: 62  SRHELDSKTIDPKVAF 77

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.8 bits (142), Expect = 7e-12
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           +FI  L      + L + F  FG +  C V  D L  +SRG+GFV F ++      +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 189 NGMLLNDKQVFV 200
           +   L+ K +  
Sbjct: 62  SRHELDSKTIDP 73

>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 = 65.0 bits (158), Expect = 5e-14
 Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 7/88 (7%)

Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDP 269
           E T    +   +YV+NL  +T+E+ ++K F          V      K + + FV+F + 
Sbjct: 2   EDTMSSVK--ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNR 54

Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKK 297
           +DA  +++ALNGK  D     V  A+  
Sbjct: 55  EDAVEAMKALNGKVLDGSPIEVTLAKPV 82

>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 = 59.3 bits (143), Expect = 6e-12
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 5/80 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LYV+NL  S S++ +++ F+        +V        R   FV FS  E+A +A+  +N
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKALN 65

Query: 384 GKMVVSKPLYVALAQRKEER 403
           GK++   P+ V LA+  ++ 
Sbjct: 66  GKVLDGSPIEVTLAKPVDKD 85

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 8e-11
 Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 6/87 (6%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           S    ++++NL  S   + +   F+        +V      + R Y FV F N E A  A
Sbjct: 6   SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEA 60

Query: 185 IDKLNGMLLNDKQVFVGPFLRKQERES 211
           +  LNG +L+   + V    +  +++S
Sbjct: 61  MKALNGKVLDGSPIEVT-LAKPVDKDS 86

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.0 bits (132), Expect = 2e-10
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 6/75 (8%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LYV +L LS ++  +   FN +      RV      ++   Y +V+++   +A  A+  L
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKAL 64

Query: 102 NFTPLNGKPIRIMYS 116
           N   L+G PI +  +
Sbjct: 65  NGKVLDGSPIEVTLA 79

>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 = 65.0 bits (158), Expect = 6e-14
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEF-GIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           +++  L     +D +K++   F  +     V   A G SK + F  + D +   +++  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 280 NGKKFDDKEWYVGKAQKK 297
           NG +  DK+  V +A   
Sbjct: 64  NGMQLGDKKLLVQRASVG 81

>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 = 63.9 bits (155), Expect = 2e-13
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           L++  L + ++DD++KEL + FG + +  +++D   G+S+G  F  +       +A+  +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 383 NGKMVVSKPLYVALAQRKEE 402
           NG  +  K L V  A    +
Sbjct: 64  NGMQLGDKKLLVQRASVGAK 83

>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 = 60.4 bits (146), Expect = 2e-12
 Identities = 19/79 (24%), Positives = 36/79 (45%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L++G L   +ND Q+ +L    G + +  + +D +T  S GY +  Y   +   +A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 102 NFTPLNGKPIRIMYSYRDP 120
           N   L  K + +  +    
Sbjct: 64  NGMQLGDKKLLVQRASVGA 82

>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 = 58.1 bits (140), Expect = 2e-11
 Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAI 185
           A  +FI  L   +++  + +  ++FG + +  +  DS  G S+GY F ++ +      AI
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 186 DKLNGMLLNDKQVFV 200
             LNGM L DK++ V
Sbjct: 61  AGLNGMQLGDKKLLV 75

>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 = 65.1 bits (158), Expect = 7e-14
 Identities = 9/92 (9%), Positives = 33/92 (35%), Gaps = 5/92 (5%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAV---MRDADGKSKCFGFVNFDDPDDAARSVE 277
           +++  + +    +++ +   +        +         K++ F FV ++    AA +  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 278 ALNGKKF--DDKEWYVGKAQKKYEREMELKGK 307
            L   +      +  V  A+ + + + ++   
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.6 bits (154), Expect = 3e-13
 Identities = 10/92 (10%), Positives = 31/92 (33%), Gaps = 5/92 (5%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKV---MRDPNGISRGSGFVAFSTAEEASKALT 380
           L++  +      +++ E  ++        +          +RG  FV + +   A+ A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 381 EMNGKMVV--SKPLYVALAQRKEERRARLQAQ 410
           ++    +      + V  A+ + +    +   
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 14/86 (16%), Positives = 35/86 (40%), Gaps = 5/86 (5%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVA---TDSLGQSRGYGFVQFDNEESAKSAID 186
           +FI  + K    + + +  +     +   +         ++RG+ FV++++  +A  A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 187 KLNG--MLLNDKQVFVGPFLRKQERE 210
           KL    + L   Q+ V     + + +
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEIDVD 89

>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 = 51.2 bits (122), Expect = 6e-09
 Identities = 12/81 (14%), Positives = 31/81 (38%), Gaps = 4/81 (4%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVS--VRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
             L++G +       ++ +   ++ + V   +         ++ G+ +V Y +   A  A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 98  LDELNFTP--LNGKPIRIMYS 116
             +L      L G  I + ++
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWA 82

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 64.2 bits (156), Expect = 1e-13
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARS 275
           T+ + ++V NL    TE++++K+F ++G      + +D     K FGF+  +    A  +
Sbjct: 6   TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIA 60

Query: 276 VEALNGKKFDDKEWYVGKAQKK 297
              L+      K+  V  A   
Sbjct: 61  KVELDNMPLRGKQLRVRFACHS 82

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.1 bits (148), Expect = 1e-12
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 6/84 (7%)

Query: 318 KFEGLN-LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEAS 376
            F   + L+V NL   I+++++++LF ++G      + +D        GF+   T   A 
Sbjct: 4   TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAE 58

Query: 377 KALTEMNGKMVVSKPLYVALAQRK 400
            A  E++   +  K L V  A   
Sbjct: 59  IAKVELDNMPLRGKQLRVRFACHS 82

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.5 bits (136), Expect = 5e-11
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 6/84 (7%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
            + L+VG+L   + + ++  LF + G+   V + +D        +G++       A  A 
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAK 61

Query: 99  DELNFTPLNGKPIRIMYSYRDPTI 122
            EL+  PL GK +R+ ++    ++
Sbjct: 62  VELDNMPLRGKQLRVRFACHSASL 85

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.6 bits (131), Expect = 3e-10
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           +    +F+ NL   I  + +   F  +G      +      + +G+GF++ +    A+ A
Sbjct: 6   TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-----HKDKGFGFIRLETRTLAEIA 60

Query: 185 IDKLNGMLLNDKQVFV 200
             +L+ M L  KQ+ V
Sbjct: 61  KVELDNMPLRGKQLRV 76

>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 = 63.9 bits (155), Expect = 1e-13
 Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 6/83 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N +Y+ NLS   T DDL+++FG+  +  +  V+         + FV++ D + A R++E 
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIET 56

Query: 279 LNGK-KFDDKEWYVGKAQKKYER 300
           L+GK +   K   V  +  K  R
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKLR 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 = 60.9 bits (147), Expect = 1e-12
 Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           LY+ NL  +++ D L++LF +     + +V+        G  FV +     A +A+  ++
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLS 58

Query: 384 GKMVV-SKPLYVALAQRKEER 403
           GK+ +  K + V  +  K+ R
Sbjct: 59  GKVELHGKIMEVDYSVSKKLR 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 = 55.1 bits (132), Expect = 2e-10
 Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 6/81 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           ++I NL  ++    L   F      L+ +V         GY FV + ++  A  AI+ L+
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETLS 58

Query: 190 GML-LNDKQVFVGPFLRKQER 209
           G + L+ K + V   + K+ R
Sbjct: 59  GKVELHGKIMEVDYSVSKKLR 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 = 50.5 bits (120), Expect = 6e-09
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LY+G+L  +V    L  LF      ++ +V          GY +V+Y   + A RA++ L
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETL 57

Query: 102 N-FTPLNGKPIRIMYS 116
           +    L+GK + + YS
Sbjct: 58  SGKVELHGKIMEVDYS 73

>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 = 63.9 bits (155), Expect = 2e-13
 Identities = 27/91 (29%), Positives = 43/91 (47%), Gaps = 5/91 (5%)

Query: 208 ERESTADKTRFNN-VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNF 266
           E   T+ K R    +  KNLS   TED+LK++F +   I     +   DGKSK   ++ F
Sbjct: 5   EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEF 60

Query: 267 DDPDDAARSVEALNGKKFDDKEWYVGKAQKK 297
               DA +++E   G + D +   +    +K
Sbjct: 61  KSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 91

>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 = 63.1 bits (153), Expect = 4e-13
 Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            L  KNL  +I++D+LKE+F +   I         +G S+G  ++ F +  +A K L E 
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEK 73

Query: 383 NGKMVVSKPLYVALAQRKEERR 404
            G  +  + + +     K   R
Sbjct: 74  QGAEIDGRSVSLYYTGEKGGTR 95

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 59.3 bits (143), Expect = 8e-12
 Identities = 12/78 (15%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           + +L   +L  ++ + +L ++F    ++            +S G  Y+ + +  +A + L
Sbjct: 16  ARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKNL 70

Query: 99  DELNFTPLNGKPIRIMYS 116
           +E     ++G+ + + Y+
Sbjct: 71  EEKQGAEIDGRSVSLYYT 88

>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 = 53.5 bits (128), Expect = 8e-10
 Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 6/84 (7%)

Query: 119 DPTIRK--SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFD 176
           DP   K    A  +  KNL  +I    L + F     I          G+S+G  +++F 
Sbjct: 6   DPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQD----GKSKGIAYIEFK 61

Query: 177 NEESAKSAIDKLNGMLLNDKQVFV 200
           +E  A+  +++  G  ++ + V +
Sbjct: 62  SEADAEKNLEEKQGAEIDGRSVSL 85

>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 = 62.8 bits (152), Expect = 3e-13
 Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 1/83 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCK-VMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           L+V  L    ++  L+++FS++G I+    V       SRG GFV F   ++A  A+  M
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 383 NGKMVVSKPLYVALAQRKEERRA 405
           NGK V  + + V  A +  + R+
Sbjct: 68  NGKSVDGRQIRVDQAGKSSDNRS 90

>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 = 60.1 bits (145), Expect = 3e-12
 Identities = 28/81 (34%), Positives = 50/81 (61%), Gaps = 1/81 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEAL 279
           ++V  LS  T E  L+++F ++G I+   V++D + + S+ FGFV F++ DDA  ++ A+
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 280 NGKKFDDKEWYVGKAQKKYER 300
           NGK  D ++  V +A K  + 
Sbjct: 68  NGKSVDGRQIRVDQAGKSSDN 88

>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 = 56.3 bits (135), Expect = 7e-11
 Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKS 183
           S  G +F+  L    + ++L   FS +G I    V  D   Q SRG+GFV F+N + AK 
Sbjct: 3   SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 62

Query: 184 AIDKLNGMLLNDKQVFVGPFLRKQERES 211
           A+  +NG  ++ +Q+ V    +  +  S
Sbjct: 63  AMMAMNGKSVDGRQIRVDQAGKSSDNRS 90

>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 = 54.0 bits (129), Expect = 5e-10
 Identities = 25/82 (30%), Positives = 45/82 (54%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L+VG L    N+  L  +F++ GQ+  V V +D  T+RS G+G+V +    +A  A+  +
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 102 NFTPLNGKPIRIMYSYRDPTIR 123
           N   ++G+ IR+  + +    R
Sbjct: 68  NGKSVDGRQIRVDQAGKSSDNR 89

>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 = 63.1 bits (153), Expect = 5e-13
 Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 5/87 (5%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTE 381
           L + V+NL   ++ D L ++FS+FGT+            ++    + ++    A  A   
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLS 64

Query: 382 MNGKMVV--SKPLYVALAQRKEERRAR 406
           ++G+ +      L +  ++        
Sbjct: 65  LDGQNIYNACCTLRIDFSKLTSLNVKY 91

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.6 bits (144), Expect = 9e-12
 Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 6/92 (6%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
            + V+NL    T D L +IF +FG +            ++    + + DP  A  +  +L
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSL 65

Query: 280 NGKKFDDKEWYVGKAQKKYEREMELKGKFEQS 311
           +G+   +    +   +  + +   L  K+   
Sbjct: 66  DGQNIYNACCTL---RIDFSKLTSLNVKYNND 94

>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 = 53.9 bits (129), Expect = 7e-10
 Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 3/69 (4%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           S    I ++NL   +    LH  FS FG +L     T     ++    +Q+ +  SA+ A
Sbjct: 5   SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHA 61

Query: 185 IDKLNGMLL 193
              L+G  +
Sbjct: 62  KLSLDGQNI 70

>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 = 51.6 bits (123), Expect = 5e-09
 Identities = 14/79 (17%), Positives = 29/79 (36%), Gaps = 6/79 (7%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
             + V +L   V    L+ +F++ G V+ +        + +     + Y     A  A  
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT----KNNQFQALLQYADPVSAQHAKL 63

Query: 100 ELNFTPL--NGKPIRIMYS 116
            L+   +      +RI +S
Sbjct: 64  SLDGQNIYNACCTLRIDFS 82

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.9 bits (152), Expect = 5e-13
 Identities = 22/91 (24%), Positives = 41/91 (45%), Gaps = 7/91 (7%)

Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFV 264
           ++QE++ T       N+Y+ NL  +  E +L+ +   FG + ST ++RD+ G S+  GF 
Sbjct: 12  KQQEQDPT-------NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFA 64

Query: 265 NFDDPDDAARSVEALNGKKFDDKEWYVGKAQ 295
             +  +     +   NGK            +
Sbjct: 65  RMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 95

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.0 bits (147), Expect = 2e-12
 Identities = 27/95 (28%), Positives = 47/95 (49%)

Query: 304 LKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRG 363
           LK    Q+      + +  NLY+ NL  S+ + +L+ +   FG + S +++RD +G SRG
Sbjct: 1   LKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG 60

Query: 364 SGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ 398
            GF    + E+    +   NGK + + P   A  +
Sbjct: 61  VGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 95

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.9 bits (126), Expect = 1e-09
 Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 7/85 (8%)

Query: 118 RDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDN 177
           +DPT       N++I NL  S+D + L +    FG ++S ++  DS G SRG GF + ++
Sbjct: 16  QDPT-------NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMES 68

Query: 178 EESAKSAIDKLNGMLLNDKQVFVGP 202
            E  ++ I   NG  +        P
Sbjct: 69  TEKCEAVIGHFNGKFIKTPPGVSAP 93

>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 = 48.6 bits (115), Expect = 6e-08
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
            T+LY+ +L LS+++ +L ++       V        S+  S G G+    +  +    +
Sbjct: 18  PTNLYISNLPLSMDEQELENMLKPF-GQVISTRILRDSSGTSRGVGFARMESTEKCEAVI 76

Query: 99  DELNFTPLNGKPIRIMYS 116
              N   +   P     +
Sbjct: 77  GHFNGKFIKTPPGVSAPT 94

>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 = 62.4 bits (151), Expect = 5e-13
 Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 2/82 (2%)

Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDA 272
           +  +   +++  LS  TT++ L+  F ++G +T   VMRD +  +S+ FGFV +   ++ 
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61

Query: 273 ARSVEALNGKKFDDKEWYVGKA 294
             ++ A    K D +     +A
Sbjct: 62  DAAMNA-RPHKVDGRVVEPKRA 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.1 bits (140), Expect = 1e-11
 Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           L++  L    +D+ L+  F ++GT+T C VMRDPN   SRG GFV ++T EE   A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 67

Query: 383 NGKMVVSKPLYVALA 397
               V  + +    A
Sbjct: 68  RPHKVDGRVVEPKRA 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 7e-10
 Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           +FI  L     +++L   F  +G +  C V  D    +SRG+GFV +   E   +A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 67

Query: 189 NGMLLNDKQVFV 200
               ++ + V  
Sbjct: 68  RPHKVDGRVVEP 79

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 8e-10
 Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           L++G L     D  L   F Q G +    V RD +T+RS G+G+V Y    E   A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 67

Query: 102 NFTPLNGKPIRI 113
               ++G+ +  
Sbjct: 68  RPHKVDGRVVEP 79

>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 = 61.9 bits (150), Expect = 5e-13
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEAL 279
           +++  LS  TT+ DLK  F +FG +    +  D     S+ FGFV F + +   + ++  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-Q 60

Query: 280 NGKKFDDKEWYVGKA 294
              K + K     +A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>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 = 57.7 bits (139), Expect = 2e-11
 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALTEM 382
           +++  L    +   LK+ FS+FG +  C +  DP    SRG GFV F  +E   K + + 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 383 NGKMVVSKPLYVALA 397
               +  K +    A
Sbjct: 61  KEHKLNGKVIDPKRA 75

>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 = 56.9 bits (137), Expect = 3e-11
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           +++G L        L D F++ G+VV   +  D  T RS G+G+V +  +    + + + 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 102 NFTPLNGKPIRI 113
               LNGK I  
Sbjct: 61  KEHKLNGKVIDP 72

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 7e-10
 Identities = 24/72 (33%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDKL 188
           +FI  L      K L D FS FG ++ C +  D +   SRG+GFV F   ES    +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 189 NGMLLNDKQVFV 200
               LN K +  
Sbjct: 61  KEHKLNGKVIDP 72

>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 = 62.4 bits (151), Expect = 5e-13
 Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 1/80 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
             ++V ++ E   ED++++ F ++G I      +    G SK +  V ++    A  + E
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 278 ALNGKKFDDKEWYVGKAQKK 297
           ALNG +   +   V     K
Sbjct: 68  ALNGAEIMGQTIQVDWCFVK 87

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 61.7 bits (149), Expect = 1e-12
 Identities = 20/82 (24%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG-ISRGSGFVAFSTAEEASKA 378
           EG  L+V ++ +   +D+++E F ++G I +  +  D     S+G   V + T ++A  A
Sbjct: 6   EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 379 LTEMNGKMVVSKPLYVALAQRK 400
              +NG  ++ + + V     K
Sbjct: 66  KEALNGAEIMGQTIQVDWCFVK 87

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 59.0 bits (142), Expect = 8e-12
 Identities = 17/79 (21%), Positives = 36/79 (45%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              L+V  +     + ++ + F   G++ ++ +  D  T  S GY  V Y    +A  A 
Sbjct: 7   GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 66

Query: 99  DELNFTPLNGKPIRIMYSY 117
           + LN   + G+ I++ + +
Sbjct: 67  EALNGAEIMGQTIQVDWCF 85

>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 = 50.9 bits (121), Expect = 5e-09
 Identities = 15/73 (20%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDK 187
            +F+ ++ +      + + F  +G I +  +  D     S+GY  V+++  + A +A + 
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 188 LNGMLLNDKQVFV 200
           LNG  +  + + V
Sbjct: 69  LNGAEIMGQTIQV 81

>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 = 62.5 bits (151), Expect = 6e-13
 Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 9/96 (9%)

Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD---------ADGKSKCFGFV 264
           + +  + +YV+ L+++ T DDL   F + G++                   GK K    V
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 265 NFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           +++DP  A  +VE  +GK F   +  V  A+KK   
Sbjct: 64  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 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 = 61.3 bits (148), Expect = 2e-12
 Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 9/96 (9%)

Query: 317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP---------NGISRGSGFV 367
           +  +   +YV+ L+DS++ D L + F + G +   K    P          G  +G   V
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 368 AFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEER 403
           ++     A  A+   +GK      L V+LA++K   
Sbjct: 64  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 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 = 58.6 bits (141), Expect = 2e-11
 Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 8/90 (8%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQV--------VSVRVCRDLSTRRSLGYGYVNYNA 90
           ++++YV  L+ SV    L D F Q G V          + +  D  T +  G   V+Y  
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 91  AHEATRALDELNFTPLNGKPIRIMYSYRDP 120
              A  A++  +     G  +++  + + P
Sbjct: 68  PPTAKAAVEWFDGKDFQGSKLKVSLARKKP 97

>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 = 53.6 bits (128), Expect = 9e-10
 Identities = 18/92 (19%), Positives = 38/92 (41%), Gaps = 9/92 (9%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL---------GQSRGYGFVQFDNEE 179
            I+++ L+ S+    L D F   G +   K     +         G+ +G   V +++  
Sbjct: 10  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 69

Query: 180 SAKSAIDKLNGMLLNDKQVFVGPFLRKQERES 211
           +AK+A++  +G      ++ V    +K    S
Sbjct: 70  TAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 101

>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 = 61.4 bits (148), Expect = 1e-12
 Identities = 13/76 (17%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           +++ N   + T+ +++ +  +   +  S  +       S+ F +++    +DA   VE L
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 280 NGKKFDDKEWYVGKAQ 295
           NG K +        + 
Sbjct: 64  NGLKIEGYTLVTKVSN 79

>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 = 56.3 bits (135), Expect = 6e-11
 Identities = 11/76 (14%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALTEM 382
           L++ N   S +   +++L  +   +     +       SR   ++  ++ E+A   + ++
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 383 NGKMVVSKPLYVALAQ 398
           NG  +    L   ++ 
Sbjct: 64  NGLKIEGYTLVTKVSN 79

>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 = 56.3 bits (135), Expect = 6e-11
 Identities = 13/77 (16%), Positives = 29/77 (37%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
            +L++ +   S     + DL   +  V        L    S  + Y++  +  +A   ++
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 100 ELNFTPLNGKPIRIMYS 116
           +LN   + G  +    S
Sbjct: 62  KLNGLKIEGYTLVTKVS 78

>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 = 47.9 bits (113), Expect = 6e-08
 Identities = 12/72 (16%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNIL-SCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +++ N   S   + + D       +  S ++ +     SR + ++   ++E A+  ++KL
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 189 NGMLLNDKQVFV 200
           NG+ +    +  
Sbjct: 64  NGLKIEGYTLVT 75

>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 = 61.7 bits (149), Expect = 1e-12
 Identities = 18/101 (17%), Positives = 40/101 (39%), Gaps = 10/101 (9%)

Query: 203 FLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFG 262
            LR +  E+ +  T+   V    L    + + L  +  + G++ +  +  +     K + 
Sbjct: 5   LLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYS 59

Query: 263 FVNFDDPDDAARSVEALNGKKFDDKE-----WYVGKAQKKY 298
           F  +   +++ R+   LNGK+  D        Y+   +K  
Sbjct: 60  FARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQ 100

>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 = 51.6 bits (123), Expect = 4e-09
 Identities = 17/95 (17%), Positives = 39/95 (41%), Gaps = 10/95 (10%)

Query: 309 EQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVA 368
            + ++  +   + L +    L + +S ++L  +  + G + +  +  +         F  
Sbjct: 8   HEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP-----YSFAR 62

Query: 369 FSTAEEASKALTEMNGKMVV-----SKPLYVALAQ 398
           + T EE+ +A   +NGK VV        LY+   +
Sbjct: 63  YRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE 97

>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 = 47.0 bits (111), Expect = 2e-07
 Identities = 12/68 (17%), Positives = 23/68 (33%), Gaps = 5/68 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +    L   +    L       G + +  +       ++ Y F ++   E +K A   LN
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLM-----PPNKPYSFARYRTTEESKRAYVTLN 77

Query: 190 GMLLNDKQ 197
           G  + D  
Sbjct: 78  GKEVVDDL 85

>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 = 40.5 bits (94), Expect = 4e-05
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 9/82 (10%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S  +  G L   V+ +QL  +  + G V ++ +  +        Y +  Y    E+ RA 
Sbjct: 20  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAY 73

Query: 99  DELN---FTPLNGKPIRIMYSY 117
             LN        G+ I +  ++
Sbjct: 74  VTLNGKEVVDDLGQKITLYLNF 95

>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 = 61.2 bits (148), Expect = 1e-12
 Identities = 17/76 (22%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALTE 381
            + V+N+  ++S D++ + F  +  I     ++    G+  G   VAF + +EA+ A+ +
Sbjct: 11  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 382 MNGKMVVSKPLYVALA 397
           +N + + S+ + + L 
Sbjct: 71  LNDRPIGSRKVKLVLG 86

>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 = 59.3 bits (143), Expect = 5e-12
 Identities = 15/82 (18%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDP 269
           +++ K     + V+N+  T + D++   F  + +I  +  ++    G       V F+  
Sbjct: 2   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 61

Query: 270 DDAARSVEALNGKKFDDKEWYV 291
           D+A  +V  LN +    ++  +
Sbjct: 62  DEATAAVIDLNDRPIGSRKVKL 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 = 56.6 bits (136), Expect = 5e-11
 Identities = 14/75 (18%), Positives = 32/75 (42%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
            T + V ++  +V+  ++ D F     +      +        G   V + +  EAT A+
Sbjct: 9   PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 68

Query: 99  DELNFTPLNGKPIRI 113
            +LN  P+  + +++
Sbjct: 69  IDLNDRPIGSRKVKL 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 = 55.4 bits (133), Expect = 1e-10
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 124 KSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSC-KVATDSLGQSRGYGFVQFDNEESAK 182
           K G   I ++N+  ++    + D F  +  I     +  +  G   G   V F++ + A 
Sbjct: 6   KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 65

Query: 183 SAIDKLNGMLLNDKQVFV 200
           +A+  LN   +  ++V +
Sbjct: 66  AAVIDLNDRPIGSRKVKL 83

>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 = 61.2 bits (148), Expect = 1e-12
 Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 2/77 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           +YV NL   I    ++++F ++G I    +            FV F    +A  A+   +
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG--GPPFAFVEFEDPRDAEDAVYGRD 74

Query: 384 GKMVVSKPLYVALAQRK 400
           G       L V   +  
Sbjct: 75  GYDYDGYRLRVEFPRSG 91

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.8 bits (147), Expect = 2e-12
 Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           +YV NL       D++ +F ++G I    +          F FV F+DP DA  +V   +
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG--GPPFAFVEFEDPRDAEDAVYGRD 74

Query: 281 GKKFDDKEWYVGKAQKK 297
           G  +D     V   +  
Sbjct: 75  GYDYDGYRLRVEFPRSG 91

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 6e-12
 Identities = 14/88 (15%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              +YVG+L   +    + D+F + G +  + +           + +V +    +A  A+
Sbjct: 14  DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP---PFAFVEFEDPRDAEDAV 70

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSG 126
              +    +G  +R+ +       R +G
Sbjct: 71  YGRDGYDYDGYRLRVEFPRSG---RGTG 95

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 8e-10
 Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           I++ NL   I  K + D F  +G I    +          + FV+F++   A+ A+   +
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--GGPPFAFVEFEDPRDAEDAVYGRD 74

Query: 190 GMLLNDKQVFV 200
           G   +  ++ V
Sbjct: 75  GYDYDGYRLRV 85

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 62.2 bits (150), Expect = 2e-12
 Identities = 34/139 (24%), Positives = 59/139 (42%), Gaps = 7/139 (5%)

Query: 1   MAQV-QVQPQAPVAVAAQPSPATNGIANNGGVGDARQ--FVSTSLYVGDLDLSVNDSQLY 57
           M+Q+  V    P    AQ          +           V  +L V  +  +V++ QL 
Sbjct: 1   MSQIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLR 60

Query: 58  DLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY 117
            LF + G + SV++  D  TR+S GYG+V + +   A +A+  LN   +  K +++  + 
Sbjct: 61  QLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA 120

Query: 118 ----RDPTIRKSGAGNIFI 132
               R       G GN ++
Sbjct: 121 SGHQRPGIAGAVGDGNGYL 139

>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 = 59.5 bits (143), Expect = 2e-11
 Identities = 22/97 (22%), Positives = 40/97 (41%), Gaps = 1/97 (1%)

Query: 205 RKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCF-GF 263
                +   +     N+ V  +  T  E  L+++F  +G I S  ++ D + +     GF
Sbjct: 29  HIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGF 88

Query: 264 VNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKKYER 300
           V F     A +++  LNG    +K   V  A   ++R
Sbjct: 89  VKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR 125

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 58.0 bits (139), Expect = 6e-11
 Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 1/85 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVA-FSTAEEASKALTE 381
           NL V  +  ++ + +L++LF  +G I S K++ D             F +   A +A+  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 382 MNGKMVVSKPLYVALAQRKEERRAR 406
           +NG  +++K L VALA    +R   
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGI 128

>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 = 57.2 bits (137), Expect = 1e-10
 Identities = 26/96 (27%), Positives = 43/96 (44%), Gaps = 1/96 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGY-GFVQFDNEESAKSAIDK 187
           N+ +  +  ++D   L   F  +G I S K+  D   +     GFV+F +  SA+ AI  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 188 LNGMLLNDKQVFVGPFLRKQERESTADKTRFNNVYV 223
           LNG  + +K++ V       +R   A      N Y+
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139

>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 = 59.6 bits (144), Expect = 4e-12
 Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFG-IITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
           ++V  LS  T E+ +++ FG FG + +    M +   K + F F+ F + +   + +E  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 280 NGKKFDDKEWYVGKA 294
                   +  +  A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 57.7 bits (139), Expect = 1e-11
 Identities = 12/72 (16%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VG L     + ++ + F   G+V S+ +  D  T +  G+ ++ +       + + E 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60

Query: 102 NFTPLNGKPIRI 113
            +  +      I
Sbjct: 61  KYHNVGLSKCEI 72

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.9 bits (137), Expect = 3e-11
 Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 2/75 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           ++V  L     ++K++E F  FG + S ++  D      RG  F+ F   E   K + E 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60

Query: 383 NGKMVVSKPLYVALA 397
               V      + +A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 55.0 bits (132), Expect = 2e-10
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           IF+  L      + + + F  FG + S ++  D+   + RG+ F+ F  EE  K  ++K 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 189 NGMLLNDKQVFV 200
               +   +  +
Sbjct: 61  KYHNVGLSKCEI 72

>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 = 59.4 bits (143), Expect = 4e-12
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           ++V  LS  TT +D+K  F +FG +    +M D    + + FGFV F+  D   +  E +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 280 NGKKFDDKEWYVGKA 294
           +  + ++K     KA
Sbjct: 61  HFHEINNKMVECKKA 75

>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 = 56.7 bits (136), Expect = 4e-11
 Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VG L ++     +   F Q G+V    +  D +T R  G+G+V + +     +   E+
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 102 NFTPLNGKPIRI 113
           +F  +N K +  
Sbjct: 61  HFHEINNKMVEC 72

>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 = 56.3 bits (135), Expect = 5e-11
 Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN-GISRGSGFVAFSTAEEASKALTEM 382
           ++V  L  + + + +K  F +FG +    +M D      RG GFV F + +   K   E+
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 383 NGKMVVSKPLYVALA 397
           +   + +K +    A
Sbjct: 61  HFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.7 bits (118), Expect = 1e-08
 Identities = 16/72 (22%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVAT-DSLGQSRGYGFVQFDNEESAKSAIDKL 188
           IF+  L  +   + +   F  FG +    +    +  + RG+GFV F++E+  +    ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 189 NGMLLNDKQVFV 200
           +   +N+K V  
Sbjct: 61  HFHEINNKMVEC 72

>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 = 59.6 bits (143), Expect = 5e-12
 Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 1/85 (1%)

Query: 213 ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDA 272
           ++ T   N+++ NL+   +  +LK    E       AV+    G ++ FG+V+F+  +D 
Sbjct: 8   SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDL 67

Query: 273 ARSVEALNGKKFDDKEWYVGKAQKK 297
            +++E L G K    E  + K + +
Sbjct: 68  EKALE-LTGLKVFGNEIKLEKPKGR 91

>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 = 55.3 bits (132), Expect = 2e-10
 Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 1/90 (1%)

Query: 311 SLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFS 370
            + E ++     NL++ NL+ + S  +LK   SE        V+    G +R  G+V F 
Sbjct: 3   HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFE 62

Query: 371 TAEEASKALTEMNGKMVVSKPLYVALAQRK 400
           +AE+  KAL  + G  V    + +   + +
Sbjct: 63  SAEDLEKALE-LTGLKVFGNEIKLEKPKGR 91

>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 = 48.8 bits (115), Expect = 3e-08
 Identities = 15/78 (19%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             +L++G+L+ + + ++L    +++     + V     T  +  +GYV++ +A +  +AL
Sbjct: 13  PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKAL 71

Query: 99  DELNFTPLNGKPIRIMYS 116
           + L    + G  I++   
Sbjct: 72  E-LTGLKVFGNEIKLEKP 88

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 6e-12
 Identities = 13/82 (15%), Positives = 35/82 (42%), Gaps = 6/82 (7%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            ++V      +++D+L+E FS++G +    + +     +    FV F+  + A       
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFA----FVTFADDQIAQSLC--G 60

Query: 383 NGKMVVSKPLYVALAQRKEERR 404
              ++    ++++ A+ K    
Sbjct: 61  EDLIIKGISVHISNAEPKHNSN 82

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 5e-11
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           + V+V   +   TED+L++ F ++G      +        + F FV F D   A      
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYG----DVMDVFIPKPFRAFAFVTFADDQIAQSLCG- 60

Query: 279 LNGKKFDDKEWYVGKAQKKYER 300
                      ++  A+ K+  
Sbjct: 61  -EDLIIKGISVHISNAEPKHNS 81

>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 = 55.8 bits (134), Expect = 1e-10
 Identities = 16/87 (18%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           SG+  +F+      +    L + FS +G+++   +        R + FV F +++ A+S 
Sbjct: 3   SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSL 58

Query: 185 IDKLNGMLLNDKQVFVGPFLRKQERES 211
                 +++    V +     K    S
Sbjct: 59  CG--EDLIIKGISVHISNAEPKHNSNS 83

>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 = 47.3 bits (112), Expect = 1e-07
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 7/78 (8%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S+ ++VG     + + +L + F+Q G V+ V +      +    + +V +     A    
Sbjct: 5   SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLC 59

Query: 99  DELNFTPLNGKPIRIMYS 116
                  + G  + I  +
Sbjct: 60  G--EDLIIKGISVHISNA 75

>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 = 59.5 bits (144), Expect = 6e-12
 Identities = 20/110 (18%), Positives = 39/110 (35%), Gaps = 14/110 (12%)

Query: 292 GKAQKKYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSC 351
           G ++ ++ER + +K  F     E              + + I +D L+   S+FG I   
Sbjct: 1   GPSRMRHERVVIIKNMFHPMDFEDDP----------LVLNEIRED-LRVECSKFGQIRKL 49

Query: 352 KVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKE 401
            +         G   V+F   EEA   +  ++G+    + +         
Sbjct: 50  LLFDRHP---DGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT 96

>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 = 51.1 bits (122), Expect = 7e-09
 Identities = 16/88 (18%), Positives = 31/88 (35%), Gaps = 14/88 (15%)

Query: 221 VYVKNL-----------SETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDP 269
           V +KN+                 +DL+    +FG I    +             V+F DP
Sbjct: 11  VIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDP 67

Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKK 297
           ++A   ++ L+G+ F  ++         
Sbjct: 68  EEADYCIQTLDGRWFGGRQITAQAWDGT 95

>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 = 47.2 bits (112), Expect = 2e-07
 Identities = 14/57 (24%), Positives = 19/57 (33%), Gaps = 3/57 (5%)

Query: 144 LHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
           L    S FG I    +         G   V F + E A   I  L+G     +Q+  
Sbjct: 36  LRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.7 bits (95), Expect = 3e-05
 Identities = 11/59 (18%), Positives = 19/59 (32%), Gaps = 1/59 (1%)

Query: 58  DLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS 116
           DL  +  +   +R       R   G   V++    EA   +  L+     G+ I     
Sbjct: 35  DLRVECSKFGQIRKLLLF-DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

>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 = 58.9 bits (142), Expect = 7e-12
 Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 7/81 (8%)

Query: 320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL 379
           +G  LYV   D  ++   L+  FS FG I    +            FV +   E A +A+
Sbjct: 4   KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-----NCAFVTYEKMESADQAV 56

Query: 380 TEMNGKMVVSKPLYVALAQRK 400
            E+NG  V S  L V +A+++
Sbjct: 57  AELNGTQVESVQLKVNIARKQ 77

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 8e-11
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             +LYV   D  +  + L   F+  G ++ + +             +V Y     A +A+
Sbjct: 5   GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAV 56

Query: 99  DELNFTPLNGKPIRIMYSYRDP 120
            ELN T +    +++  + + P
Sbjct: 57  AELNGTQVESVQLKVNIARKQP 78

>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 = 55.4 bits (133), Expect = 1e-10
 Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N +YV       T   L+  F  FG I   ++        +   FV ++  + A ++V  
Sbjct: 6   NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAE 58

Query: 279 LNGKKFDDKEWYVGKAQKK 297
           LNG + +  +  V  A+K+
Sbjct: 59  LNGTQVESVQLKVNIARKQ 77

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 4e-07
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 7/72 (9%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            +++   D  +    L   FS FGNI+   +        R   FV ++  ESA  A+ +L
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLSM-----DPPRNCAFVTYEKMESADQAVAEL 59

Query: 189 NGMLLNDKQVFV 200
           NG  +   Q+ V
Sbjct: 60  NGTQVESVQLKV 71

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (143), Expect = 7e-12
 Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTE 381
            LY+KNL   +++  L  LF+ F       +      G  RG  F+ F   E A +AL  
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 382 MNGKMVVSKPLYVALAQRKEER 403
           +NG  +  K L +   + K++R
Sbjct: 80  VNGYKLYGKILVIEFGKNKKQR 101

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.1 bits (137), Expect = 5e-11
 Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 1/83 (1%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVE 277
             +Y+KNLS   TE DL  +F  F       +      G+ +   F+ F + + A +++ 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 278 ALNGKKFDDKEWYVGKAQKKYER 300
            +NG K   K   +   + K +R
Sbjct: 79  LVNGYKLYGKILVIEFGKNKKQR 101

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.6 bits (133), Expect = 2e-10
 Identities = 18/78 (23%), Positives = 33/78 (42%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           +  LY+ +L   V +  L  LF +  +     +   + T R  G  ++ +     A +AL
Sbjct: 18  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 77

Query: 99  DELNFTPLNGKPIRIMYS 116
             +N   L GK + I + 
Sbjct: 78  HLVNGYKLYGKILVIEFG 95

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.5 bits (112), Expect = 1e-07
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDK 187
            +++KNL   +  + L   F+ F       +    + G+ RG  F+ F N+E A  A+  
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 188 LNGMLLNDKQVFVGPFLRKQER 209
           +NG  L  K + +     K++R
Sbjct: 80  VNGYKLYGKILVIEFGKNKKQR 101

>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 = 59.4 bits (143), Expect = 8e-12
 Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 1/83 (1%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKC-FGFVNFDDPDDAARSVEA 278
           +V+V N+    TE+ LK IF E G + S  ++ D +      +GF  + D + A  ++  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 279 LNGKKFDDKEWYVGKAQKKYERE 301
           LNG++F  +   V  A  +  +E
Sbjct: 70  LNGREFSGRALRVDNAASEKNKE 92

>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 = 57.5 bits (138), Expect = 4e-11
 Identities = 22/97 (22%), Positives = 46/97 (47%), Gaps = 3/97 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALTE 381
           +++V N+    ++++LK++FSE G + S +++ D      +G GF  +   E A  A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 382 MNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPV 418
           +NG+    + L V  A  ++ +            P +
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEEL--KSLGTGAPVI 104

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.9 bits (134), Expect = 1e-10
 Identities = 25/93 (26%), Positives = 49/93 (52%), Gaps = 2/93 (2%)

Query: 119 DPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDN 177
           DP + +S   ++F+ N+      + L D FS  G ++S ++  D      +GYGF ++ +
Sbjct: 1   DPAVDRS-LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 178 EESAKSAIDKLNGMLLNDKQVFVGPFLRKQERE 210
           +E+A SA+  LNG   + + + V     ++ +E
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKE 92

>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 = 52.8 bits (126), Expect = 2e-09
 Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 3/91 (3%)

Query: 41  SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDE 100
           S++VG++     + QL D+F+++G VVS R+  D  T +  GYG+  Y     A  A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 101 LNFTPLNGKPIRIMYSYRDPT---IRKSGAG 128
           LN    +G+ +R+  +  +     ++  G G
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 57.8 bits (139), Expect = 2e-11
 Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 4/82 (4%)

Query: 219 NNVYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADG--KSKCFGFVNFDDPDDAARS 275
             + ++NLS E   E+ L++ F  FG I    +         + C  F+ F++ D A R+
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 276 VEALNGKKFDDKEWYVGKAQKK 297
           ++ +N     ++E  V  A KK
Sbjct: 65  LQ-MNRSLLGNREISVSLADKK 85

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 54.0 bits (129), Expect = 5e-10
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 320 EGLNLYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVA--FSTAEEAS 376
           EG  + ++NL  + + ++ L+E F  FG+I    +       S  +      F   + A 
Sbjct: 3   EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 377 KALTEMNGKMVVSKPLYVALAQRK 400
           +AL +MN  ++ ++ + V+LA +K
Sbjct: 63  RAL-QMNRSLLGNREISVSLADKK 85

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.0 bits (111), Expect = 1e-07
 Identities = 11/84 (13%), Positives = 30/84 (35%), Gaps = 3/84 (3%)

Query: 39  STSLYVGDLDLSV-NDSQLYDLFNQ-MGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATR 96
              + + +L   + +++ L + F                    +    ++ +     A R
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 97  ALDELNFTPLNGKPIRIMYSYRDP 120
           AL ++N + L  + I +  + + P
Sbjct: 64  AL-QMNRSLLGNREISVSLADKKP 86

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.7 bits (97), Expect = 1e-05
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 129 NIFIKNLDKS-IDNKALHDTFSTFGNILSCKVAT--DSLGQSRGYGFVQFDNEESAKSAI 185
            I I+NL    +D   L ++F  FG+I    +         +    F+ F+N++SA+ A+
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 186 DKLNGMLLNDKQVFV 200
            ++N  LL ++++ V
Sbjct: 66  -QMNRSLLGNREISV 79

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.9 bits (139), Expect = 2e-11
 Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 7/95 (7%)

Query: 316 ADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEE 374
           +D  EG  ++++NL     ++ L E+  +FG +   +V+  P+   S+G  F  F T E 
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 375 ASKALTEMN------GKMVVSKPLYVALAQRKEER 403
           A K L   +      G  +  + L V LA  ++E 
Sbjct: 63  AQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.6 bits (133), Expect = 1e-10
 Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 7/95 (7%)

Query: 213 ADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDD 271
           +D T    V+++NLS  + E+ L ++  +FG +    V+       SK   F  F   + 
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 272 AARSVEALN------GKKFDDKEWYVGKAQKKYER 300
           A + + A +      G K D ++  V  A  + E 
Sbjct: 63  AQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.4 bits (122), Expect = 5e-09
 Identities = 14/84 (16%), Positives = 33/84 (39%), Gaps = 6/84 (7%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             ++++ +L     +  L ++  Q G +  VRV     T  S G  +  +     A + L
Sbjct: 8   GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 67

Query: 99  DELNF------TPLNGKPIRIMYS 116
              +         L+G+ +++  +
Sbjct: 68  AAASLEAEGGGLKLDGRQLKVDLA 91

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.2 bits (106), Expect = 8e-07
 Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 7/88 (7%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEESAKSAIDK 187
            +FI+NL    + +AL +    FG++   +V      + S+G  F QF  +E+A+  +  
Sbjct: 10  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 69

Query: 188 LN------GMLLNDKQVFVGPFLRKQER 209
            +      G+ L+ +Q+ V   + + E 
Sbjct: 70  ASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.9 bits (139), Expect = 3e-11
 Identities = 21/95 (22%), Positives = 43/95 (45%), Gaps = 3/95 (3%)

Query: 210 ESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGII-TSTAVMRDADGKSKCFGFVNFDD 268
           E   +  +    ++ N+  + T+ D+ +      +   +  V+ D +G+      V F +
Sbjct: 1   EGDVNSAKVC-AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKN 59

Query: 269 PDDAARSVEALNGKKFDDKEWYVGKAQKKYEREME 303
            DDA +S   L+ KK + +E +V     +  RE+E
Sbjct: 60  EDDARKSER-LHRKKLNGREAFVHVVTLEDMREIE 93

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.1 bits (129), Expect = 6e-10
 Identities = 15/101 (14%), Positives = 35/101 (34%), Gaps = 8/101 (7%)

Query: 322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAFSTAEEASKALT 380
           +  ++ N+  SI+   + +         +   +    NG   G   V F   ++A K+  
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE- 67

Query: 381 EMNGKMVVSKPLYVALAQRKEERRARLQAQFSQMRPPVGPR 421
            ++ K +  +  +V +   ++ R            P  G  
Sbjct: 68  RLHRKKLNGREAFVHVVTLEDMREIEKN------PPAQGKS 102

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.3 bits (114), Expect = 7e-08
 Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 2/83 (2%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDK 187
              I N+  SI    +           +       + GQ  G   VQF NE+ A+ +  +
Sbjct: 10  CAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-R 68

Query: 188 LNGMLLNDKQVFVGPFLRKQERE 210
           L+   LN ++ FV     +  RE
Sbjct: 69  LHRKKLNGREAFVHVVTLEDMRE 91

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.7 bits (136), Expect = 4e-11
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 2/85 (2%)

Query: 214 DKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAA 273
           +  +  +VY+K      T DD+K+   + G + +  + R      K   FV FD  + A 
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 61

Query: 274 RSVEALNGKKFDDKEWYVGKAQKKY 298
           + VE   G+K+ + +  +   +  Y
Sbjct: 62  KFVE-TPGQKYKETDLLI-LFKDDY 84

>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 = 50.5 bits (120), Expect = 8e-09
 Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           ++Y+K      + D +KE   + G + + ++ R  +   +GS FV F + E A K + E 
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ET 66

Query: 383 NGKMVVSKPLYVALA 397
            G+      L +   
Sbjct: 67  PGQKYKETDLLILFK 81

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 6e-08
 Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
           +++IK          + +     G +L+ ++        +G  FV FD+ ESAK  + + 
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ET 66

Query: 189 NGMLLNDKQVFV 200
            G    +  + +
Sbjct: 67  PGQKYKETDLLI 78

>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 = 42.0 bits (98), Expect = 7e-06
 Identities = 11/78 (14%), Positives = 31/78 (39%), Gaps = 2/78 (2%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           + S+Y+           + +     GQV+++++ R    +   G  +V +++   A + +
Sbjct: 6   NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFV 64

Query: 99  DELNFTPLNGKPIRIMYS 116
            E          + I++ 
Sbjct: 65  -ETPGQKYKETDLLILFK 81

>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 = 57.1 bits (137), Expect = 4e-11
 Identities = 12/77 (15%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRV-----CRDLSTRRSLGYGYVNYNAAHEATR 96
           LYVG++   + +  + D FN   ++  +          +   +   + ++ + +  E T+
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 97  ALDELNFTPLNGKPIRI 113
           A+   +     G+ ++I
Sbjct: 64  AMA-FDGIIFQGQSLKI 79

>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 = 54.4 bits (130), Expect = 3e-10
 Identities = 12/77 (15%), Positives = 31/77 (40%), Gaps = 7/77 (9%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN------GISRGSGFVAFSTAEEASK 377
           LYV N+   I+++ + + F+    +                   +   F+ F + +E ++
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 378 ALTEMNGKMVVSKPLYV 394
           A+   +G +   + L +
Sbjct: 64  AMA-FDGIIFQGQSLKI 79

>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 = 54.4 bits (130), Expect = 3e-10
 Identities = 12/81 (14%), Positives = 34/81 (41%), Gaps = 7/81 (8%)

Query: 127 AGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL------GQSRGYGFVQFDNEES 180
           A  +++ N+   I  +A+ D F+    +     A  +        Q + + F++F + + 
Sbjct: 1   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 60

Query: 181 AKSAIDKLNGMLLNDKQVFVG 201
              A+   +G++   + + + 
Sbjct: 61  TTQAMA-FDGIIFQGQSLKIR 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 = 54.0 bits (129), Expect = 5e-10
 Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 7/80 (8%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMR------DADGKSKCFGFVNFDDPDDAAR 274
           +YV N+    TE+ +   F     +                 + K F F+ F   D+  +
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 275 SVEALNGKKFDDKEWYVGKA 294
           ++   +G  F  +   + + 
Sbjct: 64  AMA-FDGIIFQGQSLKIRRP 82

>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 = 57.4 bits (138), Expect = 5e-11
 Identities = 24/89 (26%), Positives = 36/89 (40%), Gaps = 1/89 (1%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T ++VG L     D+ L   F   G +    V  D  T +S GYG+V       A RA  
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 100 ELNFTPLNGKPIRIMYSYRDPTIRKSGAG 128
           + N   ++G+   +  +Y     R    G
Sbjct: 71  DPNPI-IDGRKANVNLAYLGAKPRSLQTG 98

>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 = 56.3 bits (135), Expect = 1e-10
 Identities = 26/83 (31%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 216 TRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADG-KSKCFGFVNFDDPDDAAR 274
           T F  ++V  L   TT+  L+K F  FG I    V+ D    KS+ +GFV   D   A R
Sbjct: 8   TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 67

Query: 275 SVEALNGKKFDDKEWYVGKAQKK 297
           + +  N    D ++  V  A   
Sbjct: 68  ACKDPNP-IIDGRKANVNLAYLG 89

>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 = 54.7 bits (131), Expect = 4e-10
 Identities = 26/91 (28%), Positives = 41/91 (45%), Gaps = 3/91 (3%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALTE 381
            ++V  L    +D  L++ F  FG I    V+ D     SRG GFV  +    A +A  +
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 382 MNGKMVVSKPLYVALAQRKEERRARLQAQFS 412
            N  ++  +   V LA    + R+ LQ  F+
Sbjct: 72  PNP-IIDGRKANVNLAYLGAKPRS-LQTGFA 100

>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 = 52.8 bits (126), Expect = 2e-09
 Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 7/86 (8%)

Query: 116 SYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQ 174
           S +D T  K     IF+  L     + +L   F  FG+I    V TD   G+SRGYGFV 
Sbjct: 4   SQKDTTFTK-----IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 58

Query: 175 FDNEESAKSAIDKLNGMLLNDKQVFV 200
             +  +A+ A    N + ++ ++  V
Sbjct: 59  MADRAAAERACKDPNPI-IDGRKANV 83

>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 = 57.0 bits (137), Expect = 5e-11
 Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 2/82 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
            ++ NL    TE+ +K+ F    I         ++  + K FG+  F+D D       +L
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLS-ALSL 76

Query: 280 NGKKFDDKEWYVGKAQKKYERE 301
           N +   +K   V  A +  +++
Sbjct: 77  NEESLGNKRIRVDVADQAQDKD 98

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 2e-10
 Identities = 14/82 (17%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKV-MRDPNGISRGSGFVAFSTAEEASKALTEM 382
            ++ NL   ++++ +KE F                    +G G+  F   +    AL  +
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SL 76

Query: 383 NGKMVVSKPLYVALAQRKEERR 404
           N + + +K + V +A + +++ 
Sbjct: 77  NEESLGNKRIRVDVADQAQDKD 98

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (123), Expect = 4e-09
 Identities = 16/90 (17%), Positives = 31/90 (34%), Gaps = 1/90 (1%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
             + ++G+L   V +  + + F  +            +  R  G+GY  +        AL
Sbjct: 15  PYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGAG 128
             LN   L  K IR+  + +        + 
Sbjct: 75  -SLNEESLGNKRIRVDVADQAQDKDSGPSS 103

>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 = 47.8 bits (113), Expect = 1e-07
 Identities = 18/83 (21%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
            F+ NL   +  +++ + F              S   + +G+G+ +F++ +S  SA+  L
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SL 76

Query: 189 NGMLLNDKQVFVGPFLRKQERES 211
           N   L +K++ V    + Q+++S
Sbjct: 77  NEESLGNKRIRVDVADQAQDKDS 99

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 1e-10
 Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 2/75 (2%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGK-SKCFGFVNFDDPDDAARSVEAL 279
           ++V  + E T E  L+  F ++G I    +M D      + F FV FDD D   + +   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK-IVIQ 63

Query: 280 NGKKFDDKEWYVGKA 294
                +     V KA
Sbjct: 64  KYHTVNGHNCEVRKA 78

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 2e-08
 Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 2/75 (2%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFSTAEEASKALTEM 382
           ++V  + +   +  L++ F ++G I   ++M D      RG  FV F   +   K +   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQ 63

Query: 383 NGKMVVSKPLYVALA 397
               V      V  A
Sbjct: 64  KYHTVNGHNCEVRKA 78

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.6 bits (115), Expect = 3e-08
 Identities = 13/72 (18%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           ++VG +     +  L D F Q G++  + +  D  + +  G+ +V +   H++   +   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKIVIQ 63

Query: 102 NFTPLNGKPIRI 113
            +  +NG    +
Sbjct: 64  KYHTVNGHNCEV 75

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 4e-08
 Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 7/81 (8%)

Query: 121 TIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ-SRGYGFVQFDNEE 179
           T++K     IF+  + +  +   L D F  +G I   ++ TD      RG+ FV FD+ +
Sbjct: 1   TVKK-----IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 55

Query: 180 SAKSAIDKLNGMLLNDKQVFV 200
           S    +       +N     V
Sbjct: 56  SVDKIV-IQKYHTVNGHNCEV 75

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.5 bits (133), Expect = 2e-10
 Identities = 20/97 (20%), Positives = 46/97 (47%), Gaps = 8/97 (8%)

Query: 27  NNGGVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYV 86
           ++G +G  +   +T L+VG L  + + + L   F++ G + ++   +  S      + Y+
Sbjct: 5   SSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYI 58

Query: 87  NYNAAHEATRALDELNFTPLNG--KPIRIMYSYRDPT 121
            Y +   A  A  ++   PL G  + +R+ ++   P+
Sbjct: 59  QYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS 95

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.8 bits (121), Expect = 8e-09
 Identities = 12/70 (17%), Positives = 26/70 (37%), Gaps = 5/70 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             ++V  L   T+   L + F  FG I +   ++        F ++ ++  D A  +   
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAK 72

Query: 279 LNGKKFDDKE 288
           + G      +
Sbjct: 73  MRGFPLGGPD 82

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.9 bits (116), Expect = 4e-08
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 7/80 (8%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            L+V  L  + S   L   F  FG+I +   ++  +       ++ + + + A  A  +M
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS-----FAYIQYESLDAAQAACAKM 73

Query: 383 NGKMV--VSKPLYVALAQRK 400
            G  +    + L V  A+  
Sbjct: 74  RGFPLGGPDRRLRVDFAKSG 93

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.0 bits (98), Expect = 1e-05
 Identities = 19/88 (21%), Positives = 40/88 (45%), Gaps = 11/88 (12%)

Query: 107 NGKPIRIMYSYRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQ 166
           +G   +I Y   +PT R      +++  L  +    AL   F  FG+I +         +
Sbjct: 3   SGSSGKIGYGKANPTTR------LWVGGLGPNTSLAALAREFDRFGSIRTIDH-----VK 51

Query: 167 SRGYGFVQFDNEESAKSAIDKLNGMLLN 194
              + ++Q+++ ++A++A  K+ G  L 
Sbjct: 52  GDSFAYIQYESLDAAQAACAKMRGFPLG 79

>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 = 53.6 bits (128), Expect = 4e-10
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDAD-GKSKCFGFVNFDDPDDAARSVEAL 279
           +Y++ L   TT+ DL K+   +G I ST  + D    K K +GFV+FD P  A ++V AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 280 NGKKFDDK 287
                  +
Sbjct: 61  KASGVQAQ 68

>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 = 52.1 bits (124), Expect = 1e-09
 Identities = 18/71 (25%), Positives = 35/71 (49%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           LY+  L     D  L  L    G++VS +   D +T +  GYG+V++++   A +A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 102 NFTPLNGKPIR 112
             + +  +  +
Sbjct: 61  KASGVQAQMAK 71

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 3e-08
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEM 382
           LY++ L    +D  L +L   +G I S K + D      +G GFV F +   A KA+T +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 383 NGKMVVSKPL 392
               V ++  
Sbjct: 61  KASGVQAQMA 70

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (104), Expect = 8e-07
 Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSL-GQSRGYGFVQFDNEESAKSAIDKL 188
           ++I+ L     ++ L      +G I+S K   D    + +GYGFV FD+  +A+ A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 189 NGMLLNDKQV 198
               +  +  
Sbjct: 61  KASGVQAQMA 70

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.4 bits (130), Expect = 4e-10
 Identities = 19/82 (23%), Positives = 29/82 (35%), Gaps = 6/82 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             V V  L  + +  DLK    E G +    V +D        G V +   +D   ++  
Sbjct: 16  FRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD------GMGMVEYLRKEDMEYALRK 69

Query: 279 LNGKKFDDKEWYVGKAQKKYER 300
           L+  KF   E      +   ER
Sbjct: 70  LDDTKFRSHEGETSYIRVYPER 91

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.2 bits (127), Expect = 1e-09
 Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           + V  L  S S   LK+   E G +    V +D  G       V +   E+   AL +++
Sbjct: 18  VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMG------MVEYLRKEDMEYALRKLD 71

Query: 384 GKMVVSKPLYVALAQRKEERRA 405
                S     +  +   ER +
Sbjct: 72  DTKFRSHEGETSYIRVYPERSS 93

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.8 bits (105), Expect = 1e-06
 Identities = 22/88 (25%), Positives = 29/88 (32%), Gaps = 8/88 (9%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              + V  L  S +   L D   + G V    V +D       G G V Y    +   AL
Sbjct: 15  DFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-------GMGMVEYLRKEDMEYAL 67

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSG 126
            +L+ T          Y  R    R SG
Sbjct: 68  RKLDDTKFRSHEGETSYI-RVYPERSSG 94

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.0 bits (103), Expect = 2e-06
 Identities = 17/82 (20%), Positives = 29/82 (35%), Gaps = 6/82 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + +  L  S   + L D     G++    V      Q  G G V++  +E  + A+ KL+
Sbjct: 18  VLVSGLPPSGSWQDLKDHMREAGDVCYADV------QKDGMGMVEYLRKEDMEYALRKLD 71

Query: 190 GMLLNDKQVFVGPFLRKQERES 211
                  +          ER S
Sbjct: 72  DTKFRSHEGETSYIRVYPERSS 93

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.4 bits (130), Expect = 5e-10
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 7/83 (8%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           ++V+ L +S+ +  L E   +FGTI    +M            V F   + A + +T   
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-----QALVEFENIDSAKECVTFAA 72

Query: 384 GK--MVVSKPLYVALAQRKEERR 404
                +  +  +   +  K   R
Sbjct: 73  DVPVYIAGQQAFFNYSTSKRITR 95

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.7 bits (123), Expect = 4e-09
 Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 7/81 (8%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             V+V+ L E+  E DL +   +FG I    +M       K    V F++ D A   V  
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTF 70

Query: 279 LNGKKF--DDKEWYVGKAQKK 297
                     ++ +   +  K
Sbjct: 71  AADVPVYIAGQQAFFNYSTSK 91

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.3 bits (96), Expect = 2e-05
 Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 7/73 (9%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL- 188
           + ++ L +S+    L +    FG I    +        +    V+F+N +SAK  +    
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMM-----MPFKRQALVEFENIDSAKECVTFAA 72

Query: 189 -NGMLLNDKQVFV 200
              + +  +Q F 
Sbjct: 73  DVPVYIAGQQAFF 85

>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 = 53.2 bits (127), Expect = 9e-10
 Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 6/78 (7%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            + VKNL    +  ++ +L  ++               ++ + FV     E+A  A+   
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLKYCYVDR------NKRTAFVTLLNGEQAQNAIQMF 60

Query: 383 NGKMVVSKPLYVALAQRK 400
           +      K L V L    
Sbjct: 61  HQYSFRGKDLIVQLQPTD 78

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 2e-09
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 125 SGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           SG+  I +KNL +  + + +HD    +              +++   FV   N E A++A
Sbjct: 3   SGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVD------RNKRTAFVTLLNGEQAQNA 56

Query: 185 IDKLNGMLLNDKQVFV 200
           I   +      K + V
Sbjct: 57  IQMFHQYSFRGKDLIV 72

>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 = 52.1 bits (124), Expect = 2e-09
 Identities = 11/79 (13%), Positives = 29/79 (36%), Gaps = 6/79 (7%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           + + VKNL + +   ++  +  ++ +             +K   FV   + + A  +++ 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDR------NKRTAFVTLLNGEQAQNAIQM 59

Query: 279 LNGKKFDDKEWYVGKAQKK 297
            +   F  K+  V      
Sbjct: 60  FHQYSFRGKDLIVQLQPTD 78

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 1e-08
 Identities = 13/86 (15%), Positives = 28/86 (32%), Gaps = 7/86 (8%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S+ + V +L    N  +++DL             +     R+    +V      +A  A+
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAI 57

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRK 124
              +     GK + +     D  +  
Sbjct: 58  QMFHQYSFRGKDLIVQLQPTDALLCS 83

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.7 bits (123), Expect = 3e-09
 Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 7/76 (9%)

Query: 219 NNVYVKNLSETTTEDDLKKIF---GEFGIITSTAVMRDADGK----SKCFGFVNFDDPDD 271
           N V+V  LS+   + ++ K     G+FG I    +                +V +   +D
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 272 AARSVEALNGKKFDDK 287
           A R+++ +N    D +
Sbjct: 69  ALRAIQCVNNVVVDGR 84

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.8 bits (118), Expect = 2e-08
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 323 NLYVKNLDDSISDD---KLKELFSEFGTITSCKVMRDPNG----ISRGSGFVAFSTAEEA 375
            ++V  L   ++D    K  E F +FG I    +    +         S +V +  +E+A
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 376 SKALTEMNGKMVVSKPLYVA 395
            +A+  +N  +V  + L  +
Sbjct: 70  LRAIQCVNNVVVDGRTLKAS 89

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.7 bits (115), Expect = 4e-08
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 42  LYVGDLDLSVNDSQLYDLFN---QMGQVVSVRVCRDLSTRRS---LGYGYVNYNAAHEAT 95
           ++V  L   + D ++        + G++  V +    S   S       YV Y  + +A 
Sbjct: 11  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 70

Query: 96  RALDELNFTPLNGKPIRI 113
           RA+  +N   ++G+ ++ 
Sbjct: 71  RAIQCVNNVVVDGRTLKA 88

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.3 bits (96), Expect = 1e-05
 Identities = 13/85 (15%), Positives = 32/85 (37%), Gaps = 7/85 (8%)

Query: 121 TIRKSGAGNIFIKNLDKSIDN---KALHDTFSTFGNILSCKVATDSLG----QSRGYGFV 173
           ++R      +F+  L + + +       + F  FG I    +   +            +V
Sbjct: 2   SVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYV 61

Query: 174 QFDNEESAKSAIDKLNGMLLNDKQV 198
            +   E A  AI  +N ++++ + +
Sbjct: 62  TYIRSEDALRAIQCVNNVVVDGRTL 86

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.9 bits (124), Expect = 4e-09
 Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 4/80 (5%)

Query: 225 NLSETTTEDDLKKIFGEFGIITSTAVMRDADGKS---KCFGFVNFDDPDDAARSVEALNG 281
           +       +D++    ++G++ S  + R  DG         FV F    D  ++++ L G
Sbjct: 21  DEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 80

Query: 282 KKFDDKEWYVGKA-QKKYER 300
           +KF ++           Y R
Sbjct: 81  RKFANRVVVTKYCDPDSYHR 100

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 1e-07
 Identities = 13/80 (16%), Positives = 34/80 (42%), Gaps = 3/80 (3%)

Query: 328 NLDDSISDDKLKELFSEFGTITSCKVMRDPNG---ISRGSGFVAFSTAEEASKALTEMNG 384
           + +     + +++  S++G + S ++ R  +G      G  FV F++  +  KA+  + G
Sbjct: 21  DEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 80

Query: 385 KMVVSKPLYVALAQRKEERR 404
           +   ++ +           R
Sbjct: 81  RKFANRVVVTKYCDPDSYHR 100

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 12/84 (14%), Positives = 28/84 (33%), Gaps = 2/84 (2%)

Query: 35  RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRR--SLGYGYVNYNAAH 92
              V     + D +       + D  ++ G V S+ + R +        G  +V + +  
Sbjct: 10  MNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVF 69

Query: 93  EATRALDELNFTPLNGKPIRIMYS 116
           +  +A+  L       + +   Y 
Sbjct: 70  DCQKAMQGLTGRKFANRVVVTKYC 93

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 12/60 (20%), Positives = 23/60 (38%), Gaps = 3/60 (5%)

Query: 144 LHDTFSTFGNILSCKVATD---SLGQSRGYGFVQFDNEESAKSAIDKLNGMLLNDKQVFV 200
           + D  S +G + S ++            G  FV+F +    + A+  L G    ++ V  
Sbjct: 31  VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 90

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.9 bits (118), Expect = 1e-08
 Identities = 23/93 (24%), Positives = 32/93 (34%), Gaps = 6/93 (6%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
           N V V  L  + +  DLK    E G +    V RD        G V F   +D   +V  
Sbjct: 1   NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRK 54

Query: 279 LNGKKFDDKEWYVGKAQKKYEREMELKGKFEQS 311
           L+  KF   E      + K +          +S
Sbjct: 55  LDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRS 87

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.3 bits (101), Expect = 2e-06
 Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 6/81 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           + V  L  S S   LK+   E G +    V RD  G       V F   E+ + A+ +++
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTG------VVEFVRKEDMTYAVRKLD 56

Query: 384 GKMVVSKPLYVALAQRKEERR 404
                S     A  + K +  
Sbjct: 57  NTKFRSHEGETAYIRVKVDGP 77

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.3 bits (93), Expect = 3e-05
 Identities = 19/86 (22%), Positives = 29/86 (33%), Gaps = 7/86 (8%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           + V  L  S +   L D   + G V    V RD       G G V +    + T A+ +L
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKL 55

Query: 102 NFTPLNGKPIRIMYSYRDPTIRKSGA 127
           + T          Y        +S +
Sbjct: 56  DNTKFRSHEGETAYIRVKVDGPRSPS 81

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.5 bits (91), Expect = 5e-05
 Identities = 16/88 (18%), Positives = 28/88 (31%), Gaps = 6/88 (6%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + +  L  S   + L D     G++    V         G G V+F  +E    A+ KL+
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADV------YRDGTGVVEFVRKEDMTYAVRKLD 56

Query: 190 GMLLNDKQVFVGPFLRKQERESTADKTR 217
                  +        K +   +    R
Sbjct: 57  NTKFRSHEGETAYIRVKVDGPRSPSYGR 84

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.5 bits (117), Expect = 1e-08
 Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 2/75 (2%)

Query: 220 NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEAL 279
            V VKNL ++  ++ + K F   G I    V      K+  F  + F   D A  ++   
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS-LKKNFRFARIEFARYDGALAAITK- 59

Query: 280 NGKKFDDKEWYVGKA 294
             K     E  V   
Sbjct: 60  THKVVGQNEIIVSHL 74

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.8 bits (97), Expect = 7e-06
 Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 3/74 (4%)

Query: 40  TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD 99
           T++ V +L  S N +++Y  F   G ++ V V   L       +  + +     A  A+ 
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR--FARIEFARYDGALAAI- 57

Query: 100 ELNFTPLNGKPIRI 113
                 +    I +
Sbjct: 58  TKTHKVVGQNEIIV 71

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.0 bits (95), Expect = 1e-05
 Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 2/72 (2%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            + VKNL  S + +K+ + F   G I    V        R    + F+  + A  A+T  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR-FARIEFARYDGALAAIT-K 59

Query: 383 NGKMVVSKPLYV 394
             K+V    + V
Sbjct: 60  THKVVGQNEIIV 71

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 37.5 bits (86), Expect = 2e-04
 Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            + +KNL KS +   ++  F   G I+   VA       R +  ++F   + A +AI   
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR-FARIEFARYDGALAAI-TK 59

Query: 189 NGMLLNDKQVFV 200
              ++   ++ V
Sbjct: 60  THKVVGQNEIIV 71

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.8 bits (118), Expect = 2e-08
 Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 5/84 (5%)

Query: 324 LYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
           L V NL+ + ++   L  LF  +G +   K++ +          V  +   +A  A++ +
Sbjct: 5   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN----ALVQMADGNQAQLAMSHL 60

Query: 383 NGKMVVSKPLYVALAQRKEERRAR 406
           NG  +  KP+ + L++ +  +  R
Sbjct: 61  NGHKLHGKPIRITLSKHQNVQLPR 84

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 7e-08
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 219 NNVYVKNLS-ETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVE 277
           + + V NL+ E  T   L  +FG +G +    ++ +     K    V   D + A  ++ 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMS 58

Query: 278 ALNGKKFDDKEWYVGKAQKK 297
            LNG K   K   +  ++ +
Sbjct: 59  HLNGHKLHGKPIRITLSKHQ 78

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 8e-08
 Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 6/79 (7%)

Query: 39  STSLYVGDLD-LSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRA 97
           ++ L V +L+   V    L+ LF   G V  V++  +           V     ++A  A
Sbjct: 2   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLA 56

Query: 98  LDELNFTPLNGKPIRIMYS 116
           +  LN   L+GKPIRI  S
Sbjct: 57  MSHLNGHKLHGKPIRITLS 75

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 3e-05
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 126 GAGNIFIKNLD-KSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSA 184
           G   + + NL+ + +  ++L   F  +G++   K+        +    VQ  +   A+ A
Sbjct: 1   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF----NKKENALVQMADGNQAQLA 56

Query: 185 IDKLNGMLLNDKQVFV 200
           +  LNG  L+ K + +
Sbjct: 57  MSHLNGHKLHGKPIRI 72

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.8 bits (113), Expect = 8e-08
 Identities = 17/84 (20%), Positives = 37/84 (44%), Gaps = 8/84 (9%)

Query: 324 LYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKAL--T 380
           +++ +         +L +L   FG I++  ++   N       F+  +T E+A  A+   
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN-----EAFIEMATTEDAQAAVDYY 65

Query: 381 EMNGKMVVSKPLYVALAQRKEERR 404
                +V  KP+ V L+Q+ +  +
Sbjct: 66  TTTPALVFGKPVRVHLSQKYKRIK 89

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.0 bits (98), Expect = 9e-06
 Identities = 15/92 (16%), Positives = 32/92 (34%), Gaps = 9/92 (9%)

Query: 35  RQFVSTSLYVGDLDLS-VNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHE 93
           R      +++ D         QL  L    G + +  +   ++        ++      +
Sbjct: 4   RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN------EAFIEMATTED 57

Query: 94  ATRALD--ELNFTPLNGKPIRIMYSYRDPTIR 123
           A  A+D        + GKP+R+  S +   I+
Sbjct: 58  AQAAVDYYTTTPALVFGKPVRVHLSQKYKRIK 89

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.2 bits (96), Expect = 2e-05
 Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 8/80 (10%)

Query: 221 VYVKNL-SETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA- 278
           V++ +          L ++   FG+I++  ++           F+     +DA  +V+  
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYY 65

Query: 279 -LNGKKFDDKEWYVGKAQKK 297
                    K   V  +QK 
Sbjct: 66  TTTPALVFGKPVRVHLSQKY 85

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 9e-08
 Identities = 14/91 (15%), Positives = 34/91 (37%), Gaps = 2/91 (2%)

Query: 314 ETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAE 373
            +     G  ++++ L    +++ +   FS    +    +   P+G   G   V F+T E
Sbjct: 8   SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGPDGRVTGEADVEFATHE 66

Query: 374 EASKALTEMNGKMVVSKPLYVALAQRKEERR 404
           +A  A+   +   +  + + + L        
Sbjct: 67  DAVAAM-AKDKANMQHRYVELFLNSTAGTSG 96

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 2e-07
 Identities = 14/87 (16%), Positives = 30/87 (34%), Gaps = 2/87 (2%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPD 270
           S+   T  + V+++ L    TE+D+   F     +    +    DG+      V F   +
Sbjct: 8   SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGPDGRVTGEADVEFATHE 66

Query: 271 DAARSVEALNGKKFDDKEWYVGKAQKK 297
           DA  ++   +      +   +      
Sbjct: 67  DAVAAMA-KDKANMQHRYVELFLNSTA 92

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 5e-05
 Identities = 7/89 (7%), Positives = 27/89 (30%), Gaps = 3/89 (3%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              +++  L     ++ +Y+ F+ +  +                   V +    +A  A+
Sbjct: 15  GHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTG--EADVEFATHEDAVAAM 72

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRKSGA 127
              +   +  + + +  +    T     +
Sbjct: 73  -AKDKANMQHRYVELFLNSTAGTSGSGPS 100

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (90), Expect = 1e-04
 Identities = 12/82 (14%), Positives = 27/82 (32%), Gaps = 2/82 (2%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + ++ L        +++ FS    +          G+  G   V+F   E A +A+   +
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNPMRVHIE-IGPDGRVTGEADVEFATHEDAVAAM-AKD 75

Query: 190 GMLLNDKQVFVGPFLRKQERES 211
              +  + V +          S
Sbjct: 76  KANMQHRYVELFLNSTAGTSGS 97

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.3 bits (114), Expect = 9e-08
 Identities = 23/112 (20%), Positives = 46/112 (41%), Gaps = 4/112 (3%)

Query: 202 PFLRKQERESTADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKC 260
           P  +K+ R  +  +  F  VY+K L        +   F +  I+  +  +    +GK+  
Sbjct: 3   PSGQKRSRSRSPHEAGFC-VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATG 61

Query: 261 FGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQKK-YEREMELKGKFEQS 311
            GFV F +  D   ++   + +   ++   V    KK    ++++  K  QS
Sbjct: 62  EGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQS 112

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.1 bits (103), Expect = 3e-06
 Identities = 14/94 (14%), Positives = 33/94 (35%), Gaps = 2/94 (2%)

Query: 313 KETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGI-SRGSGFVAFST 371
           +  +    G  +Y+K L     +  + + F +   +     +       + G GFV F  
Sbjct: 10  RSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN 69

Query: 372 AEEASKALTEMNGKMVVSKPLYVALAQRKEERRA 405
             +   AL   + + + ++ + V    +K     
Sbjct: 70  EADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEK 102

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.3 bits (88), Expect = 3e-04
 Identities = 12/86 (13%), Positives = 30/86 (34%), Gaps = 1/86 (1%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
              +Y+  L     +  + D F ++  V            ++ G G+V +    +   AL
Sbjct: 18  GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL 77

Query: 99  DELNFTPLNGKPIRIMYSYRDPTIRK 124
              +   +  + I++    +   + K
Sbjct: 78  -CRHKQYMGNRFIQVHPITKKGMLEK 102

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 1e-07
 Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 4/77 (5%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            L++ N+  S+S++ LK LFS  G +         +        +   + EEA +AL ++
Sbjct: 12  TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA---LIQMGSVEEAVQALIDL 68

Query: 383 NGKMVV-SKPLYVALAQ 398
           +   +  +  L V+ ++
Sbjct: 69  HNHDLGENHHLRVSFSK 85

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 1e-06
 Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 5/79 (6%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S +L++ ++  SV++  L  LF+  G V    V      ++      +   +  EA +AL
Sbjct: 10  SATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQAL 65

Query: 99  DELNFTPL-NGKPIRIMYS 116
            +L+   L     +R+ +S
Sbjct: 66  IDLHNHDLGENHHLRVSFS 84

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 6e-06
 Identities = 10/68 (14%), Positives = 28/68 (41%), Gaps = 3/68 (4%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             +++ N+  + +E+DLK +F   G +           K +    +     ++A +++  
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVV---KGFKFFQKDRKMALIQMGSVEEAVQALID 67

Query: 279 LNGKKFDD 286
           L+     +
Sbjct: 68  LHNHDLGE 75

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 3e-04
 Identities = 13/67 (19%), Positives = 27/67 (40%), Gaps = 3/67 (4%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            + + N+  S+  + L   FS+ G ++          + R    +Q  + E A  A+  L
Sbjct: 12  TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDL 68

Query: 189 NGMLLND 195
           +   L +
Sbjct: 69  HNHDLGE 75

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.8 bits (110), Expect = 2e-07
 Identities = 18/92 (19%), Positives = 43/92 (46%), Gaps = 10/92 (10%)

Query: 317 DKFEGL---NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAE 373
           DK +G     L+++ L   +++ ++  L   FG +T+  +++  N       F+  +T E
Sbjct: 1   DKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN-----QAFLELATEE 55

Query: 374 EASKALTEMNGK--MVVSKPLYVALAQRKEER 403
            A   +   +     + ++P+Y+  +  KE +
Sbjct: 56  AAITMVNYYSAVTPHLRNQPIYIQYSNHKELK 87

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.1 bits (90), Expect = 8e-05
 Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 8/82 (9%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           S  L++  L   V ++++  L    G+V ++ + +  +        ++       A   +
Sbjct: 8   SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN------QAFLELATEEAAITMV 61

Query: 99  DE--LNFTPLNGKPIRIMYSYR 118
           +        L  +PI I YS  
Sbjct: 62  NYYSAVTPHLRNQPIYIQYSNH 83

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (89), Expect = 1e-04
 Identities = 12/81 (14%), Positives = 31/81 (38%), Gaps = 7/81 (8%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             ++++ L    TE ++  +   FG +T+  +++      K   F+     + A   V  
Sbjct: 9   RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNY 63

Query: 279 LNGKK--FDDKEWYVGKAQKK 297
            +       ++  Y+  +  K
Sbjct: 64  YSAVTPHLRNQPIYIQYSNHK 84

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.4 bits (78), Expect = 0.004
 Identities = 9/74 (12%), Positives = 29/74 (39%), Gaps = 7/74 (9%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDK- 187
            + I+ L   +    +      FG + +  +      + +   F++   EE+A + ++  
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKVTNILM-----LKGKNQAFLELATEEAAITMVNYY 64

Query: 188 -LNGMLLNDKQVFV 200
                 L ++ +++
Sbjct: 65  SAVTPHLRNQPIYI 78

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.2 bits (111), Expect = 2e-07
 Identities = 19/83 (22%), Positives = 29/83 (34%), Gaps = 5/83 (6%)

Query: 323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM 382
            +  KNL       +++E FS FG++    +          +  V F    EA KA   +
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG-----ITAIVEFLEPLEARKAFRHL 66

Query: 383 NGKMVVSKPLYVALAQRKEERRA 405
                   PLY+  A       A
Sbjct: 67  AYSKFHHVPLYLEWAPIGVFGAA 89

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.5 bits (109), Expect = 4e-07
 Identities = 19/105 (18%), Positives = 33/105 (31%), Gaps = 6/105 (5%)

Query: 211 STADKTRFN-NVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDP 269
           S+    R    +  KNL   T   ++++ F  FG +    +             V F +P
Sbjct: 2   SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-----GITAIVEFLEP 56

Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKGKFEQSLKE 314
            +A ++   L   KF     Y+  A          K   +     
Sbjct: 57  LEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPA 101

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.6 bits (99), Expect = 8e-06
 Identities = 12/95 (12%), Positives = 32/95 (33%), Gaps = 6/95 (6%)

Query: 30  GVGDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYN 89
           G   +     T +   +L      +++ + F++ G +  V +              V + 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------ITAIVEFL 54

Query: 90  AAHEATRALDELNFTPLNGKPIRIMYSYRDPTIRK 124
              EA +A   L ++  +  P+ + ++        
Sbjct: 55  EPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAA 89

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.0 bits (87), Expect = 3e-04
 Identities = 15/89 (16%), Positives = 28/89 (31%), Gaps = 5/89 (5%)

Query: 129 NIFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKL 188
            I  KNL        + +TFS FG++    +      +      V+F     A+ A   L
Sbjct: 12  VILAKNLPAGTLAAEIQETFSRFGSLGRVLL-----PEGGITAIVEFLEPLEARKAFRHL 66

Query: 189 NGMLLNDKQVFVGPFLRKQERESTADKTR 217
                +   +++          +   K  
Sbjct: 67  AYSKFHHVPLYLEWAPIGVFGAAPQKKDS 95

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {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: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 2e-07
 Identities = 20/96 (20%), Positives = 41/96 (42%), Gaps = 2/96 (2%)

Query: 311 SLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRD-PNGISRGSGFVAF 369
           S   + D      + ++ L    S +++ + FS    + +   +     G S G  FV F
Sbjct: 5   SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF 64

Query: 370 STAEEASKALTEMNGKMVVSKPLYVALAQRKEERRA 405
           ++ E A KAL   + + +  + + +  + R E R +
Sbjct: 65  ASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVRTS 99

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {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: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.0 bits (108), Expect = 4e-07
 Identities = 14/97 (14%), Positives = 41/97 (42%), Gaps = 5/97 (5%)

Query: 211 STADKTRFNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDP 269
           ++ D      V ++ L    +++++ + F    I+ +   +     G+S    FV F   
Sbjct: 8   NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQ 67

Query: 270 DDAARSVEALNGKKFDDKEWYVGKAQKKYEREMELKG 306
           + A ++++  + ++   +   + K+ +    E+   G
Sbjct: 68  EIAEKALK-KHKERIGHRYIEIFKSSRA---EVRTSG 100

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 43.7 bits (102), Expect = 2e-06
 Identities = 18/79 (22%), Positives = 27/79 (34%), Gaps = 5/79 (6%)

Query: 219 NNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEA 278
             +++ NL E T E  L  +F +F                    FV F     +  + EA
Sbjct: 9   QILFLTNLPEETNEMMLSMLFNQFPGF----KEVRLVPNRHDIAFVEFTTELQSNAAKEA 64

Query: 279 LNGKKFDD-KEWYVGKAQK 296
           L G K        +  A+K
Sbjct: 65  LQGFKITPTHAMKITFAKK 83

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 42.5 bits (99), Expect = 5e-06
 Identities = 15/77 (19%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           L++ NL +  ++  L  LF++F      +++ + + I+    FV F+T  +++ A   + 
Sbjct: 11  LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIA----FVEFTTELQSNAAKEALQ 66

Query: 384 GKMVV-SKPLYVALAQR 399
           G  +  +  + +  A++
Sbjct: 67  GFKITPTHAMKITFAKK 83

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 37.5 bits (86), Expect = 3e-04
 Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 6/81 (7%)

Query: 39  STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRAL 98
           +  L++ +L    N+  L  LFNQ      VR+  +          +V +    ++  A 
Sbjct: 8   NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFTTELQSNAAK 62

Query: 99  DELNFTPL-NGKPIRIMYSYR 118
           + L    +     ++I ++ +
Sbjct: 63  EALQGFKITPTHAMKITFAKK 83

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 36.4 bits (83), Expect = 6e-04
 Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 4/66 (6%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           +F+ NL +  +   L   F+ F      ++            FV+F  E  + +A + L 
Sbjct: 11  LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVP----NRHDIAFVEFTTELQSNAAKEALQ 66

Query: 190 GMLLND 195
           G  +  
Sbjct: 67  GFKITP 72

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.6 bits (99), Expect = 4e-06
 Identities = 9/77 (11%), Positives = 26/77 (33%), Gaps = 6/77 (7%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           + ++ L    T  ++  +  ++ +            K K   FV   + + A  ++   +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYEL------KYCFVDKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 281 GKKFDDKEWYVGKAQKK 297
             +  ++E  V      
Sbjct: 55  QSRLRERELSVQLQPTD 71

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.8 bits (97), Expect = 7e-06
 Identities = 12/77 (15%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN 383
           + ++ L   +++ ++ +L S+       ++        +G+ FV     E+A  A+   +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSD------YELKYCFVDKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 384 GKMVVSKPLYVALAQRK 400
              +  + L V L    
Sbjct: 55  QSRLRERELSVQLQPTD 71

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.9 bits (79), Expect = 0.002
 Identities = 10/81 (12%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 42  LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL 101
           + +  L   V + +++DL +           +     +  G  +V      +A  A++  
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY-------ELKYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 102 NFTPLNGKPIRIMYSYRDPTI 122
           + + L  + + +     D  +
Sbjct: 54  HQSRLRERELSVQLQPTDALL 74

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.1 bits (96), Expect = 2e-05
 Identities = 11/78 (14%), Positives = 26/78 (33%), Gaps = 8/78 (10%)

Query: 221 VYVKNLSETTTEDDLKKIFGEFGIITSTAVMRDADGKSKCFGFVNFDDPDDAARSVEALN 280
           V V    + +    L + F ++G I    +          +  + +     A +++   +
Sbjct: 7   VTVFGFPQASASYILLQ-FAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKALS-KD 59

Query: 281 GKKFDDKE-WYVGKAQKK 297
           G+ F +     V     K
Sbjct: 60  GRIFGESIMIGVKPCIDK 77

>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 = 38.8 bits (90), Expect = 8e-05
 Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 8/78 (10%)

Query: 325 YVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNG 384
            V     + +   L + F+++G I    +             + + +  +A KAL   +G
Sbjct: 8   TVFGFPQASASYILLQ-FAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKAL-SKDG 60

Query: 385 KMVVSKP-LYVALAQRKE 401
           ++      + V     K 
Sbjct: 61  RIFGESIMIGVKPCIDKN 78

>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 = 36.8 bits (85), Expect = 4e-04
 Identities = 13/81 (16%), Positives = 33/81 (40%), Gaps = 6/81 (7%)

Query: 130 IFIKNLDKSIDNKALHDTFSTFGNILSCKVATDSLGQSRGYGFVQFDNEESAKSAIDKLN 189
           + +    ++  +  L   F+ +GNIL   ++         +  +++ ++  A+ A+ K  
Sbjct: 7   VTVFGFPQASASYIL-LQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKALSKDG 60

Query: 190 GMLLNDKQVFVGPFLRKQERE 210
            +      + V P + K   E
Sbjct: 61  RIFGESIMIGVKPCIDKNVME 81

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.3 bits (85), Expect = 5e-04
 Identities = 16/99 (16%), Positives = 37/99 (37%), Gaps = 6/99 (6%)

Query: 305 KGKFEQSLKETADKFEGLNLYVKNLDD-SISDDKLKELFSEFGTITSCKVMRDPNGISRG 363
           +GK +Q   +  +   G  +++ NL     SD  + +L   +G I +  +MR  +     
Sbjct: 4   EGKPDQKFDQKQE--LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFI- 60

Query: 364 SGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKEE 402
              +       A              + + V L+++ ++
Sbjct: 61  --EMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKK 97

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	467
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.97
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.96
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.86
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.85
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.85
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.85
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.85
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.84
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.84
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.84
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.84
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.84
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.84
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.84
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.83
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.83
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.83
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.83
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.83
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.83
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.82
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.82
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.82
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.82
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.82
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.81
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.81
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.81
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.81
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.81
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.81
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.81
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.81
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.8
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.8
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.8
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.8
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.8
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.79
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.79
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.79
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.79
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.79
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.79
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.79
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.79
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.79
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.79
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.78
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.78
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.78
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.78
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.78
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.78
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.78
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.78
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.77
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.77
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.77
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.77
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.77
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.77
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.77
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.76
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.76
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	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
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.76
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.76
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.75
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.75
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.75
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.75
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.75
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.75
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.75
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.75
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.75
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.75
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.74
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.74
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.74
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.74
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.74
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.74
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.74
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.74
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.74
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.73
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.73
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.73
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.73
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.73
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.73
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.73
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.73
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.72
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.72
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.72
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.72
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.72
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.72
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.72
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.71
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.71
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.71
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.71
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.71
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.71
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.71
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.7
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.7
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.7
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.7
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.7
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.69
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.69
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.69
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.69
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.69
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.68
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.68
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.68
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.67
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.67
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.67
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.65
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.65
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.64
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.64
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.62
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	99.62
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.55
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.55
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.52
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	99.52
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.51
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.49
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.46
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.45
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.43
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.43
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.41
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.38
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.36
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.14
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.9
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.78
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.76
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.61
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.61
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.71
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.04

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=4.3e-30  Score=216.30  Aligned_cols=169  Identities=26%  Similarity=0.451  Sum_probs=149.2

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ..|+|||+|||+++++++|+++|++||.|.++.+.++..++.++|||||+|.+.++|.+|+. +.+..+.++.+.+.+..
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhh
Confidence            45899999999999999999999999999999999999999999999999999999999998 45666778887776654


Q ss_pred             cCccc----ccCCCccEEEcCCCCcCCHHHHHHHHhhcCCeEEEEEeeC-CCCCceeEEEEEeCCHHHHHHHHHHhcCCc
Q 012257          118 RDPTI----RKSGAGNIFIKNLDKSIDNKALHDTFSTFGNILSCKVATD-SLGQSRGYGFVQFDNEESAKSAIDKLNGML  192 (467)
Q Consensus       118 ~~~~~----~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~v~~~~~~~~-~~g~~~~~afV~f~~~~~A~~a~~~l~~~~  192 (467)
                      .....    .....++|||+|||..+++++|+++|+.||.|..+.+..+ .+|.++|+|||+|.+.++|.+|++ +++..
T Consensus        84 ~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~  162 (183)
T d1u1qa_          84 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHT  162 (183)
T ss_dssp             CTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEE
T ss_pred             hcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCe
Confidence            43322    2344578999999999999999999999999999999998 678999999999999999999997 68889


Q ss_pred             cCCeeeEecccccccc
Q 012257          193 LNDKQVFVGPFLRKQE  208 (467)
Q Consensus       193 ~~g~~~~v~~~~~~~~  208 (467)
                      +.|+.|.|.++.++.+
T Consensus       163 ~~G~~i~V~~A~~k~e  178 (183)
T d1u1qa_         163 VNGHNCEVRKALSKQE  178 (183)
T ss_dssp             ETTEEEEEEECCCHHH
T ss_pred             ECCEEEEEEecCCccc
Confidence            9999999988766543

>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=99.96  E-value=4.4e-28  Score=203.85  Aligned_cols=173  Identities=23%  Similarity=0.420  Sum_probs=146.9

Q ss_pred             ccceeecCCCccCCHHHHHHhhcccCCeeEEEEEEC-CCCCceeEEEEEeCCHHHHHHHHHHhCCCccCCceEEEccccc
Q 012257          218 FNNVYVKNLSETTTEDDLKKIFGEFGIITSTAVMRD-ADGKSKCFGFVNFDDPDDAARSVEALNGKKFDDKEWYVGKAQK  296 (467)
Q Consensus       218 ~~~l~v~nlp~~~~~~~l~~~f~~~g~v~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~l~~~~~~~  296 (467)
                      .++|||+|||..+++++|+++|++||.|.++.++.+ ..+.++|+|||+|.+.++|..|+. ..+..+.++.+.+.+...
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            378999999999999999999999999999999987 568899999999999999999998 556666677666655433


Q ss_pred             chHHHHHhhhhhhhhhhccccCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHH
Q 012257          297 KYEREMELKGKFEQSLKETADKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEA  375 (467)
Q Consensus       297 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A  375 (467)
                      ...            ..........++|||+|||..+++++|+++|+.||.|..+.+..+. +|.++|+|||+|.+.++|
T Consensus        85 ~~~------------~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A  152 (183)
T d1u1qa_          85 RED------------SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV  152 (183)
T ss_dssp             TTG------------GGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHH
T ss_pred             ccc------------ccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHH
Confidence            211            1111223455689999999999999999999999999999999976 588999999999999999


Q ss_pred             HHHHHHhCCcEecccceEEehhhhhHHHH
Q 012257          376 SKALTEMNGKMVVSKPLYVALAQRKEERR  404 (467)
Q Consensus       376 ~~A~~~l~g~~~~g~~l~v~~~~~~~~~~  404 (467)
                      .+|++ +++..++|+.|+|++|.++++..
T Consensus       153 ~~Al~-~~~~~~~G~~i~V~~A~~k~e~~  180 (183)
T d1u1qa_         153 DKIVI-QKYHTVNGHNCEVRKALSKQEMA  180 (183)
T ss_dssp             HHHHT-SSCEEETTEEEEEEECCCHHHHH
T ss_pred             HHHHH-hCCCeECCEEEEEEecCCccccc
Confidence            99997 79999999999999998876543

>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=99.86  E-value=1.1e-21  Score=141.41  Aligned_cols=85  Identities=21%  Similarity=0.372  Sum_probs=79.7

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      .++.+.++|||+|||+++++++|+++|+.||.|.+|++.+|+.+|+++|||||+|.+.++|++|++.||+..+.|+.|+|
T Consensus         2 ~~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V   81 (88)
T d1rk8a_           2 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV   81 (88)
T ss_dssp             CCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccc
Q 012257          114 MYSYR  118 (467)
Q Consensus       114 ~~~~~  118 (467)
                      .|+..
T Consensus        82 ~~a~~   86 (88)
T d1rk8a_          82 DWCFV   86 (88)
T ss_dssp             EESEE
T ss_pred             EEecC
Confidence            99864

>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=99.85  E-value=6.4e-21  Score=150.90  Aligned_cols=83  Identities=29%  Similarity=0.457  Sum_probs=78.7

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ...++|||+|||+++++++|+++|++||.|.+|.|.+++.+|+++|||||+|.+.++|.+|++.|++..|.|+.|+|.++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccC
Q 012257          117 YRD  119 (467)
Q Consensus       117 ~~~  119 (467)
                      ...
T Consensus       120 ~~~  122 (139)
T d1u6fa1         120 ASG  122 (139)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            644

>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=1.9e-21  Score=138.76  Aligned_cols=80  Identities=30%  Similarity=0.563  Sum_probs=77.0

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      .++|||+|||+++++++|+++|++||.|.++++.+++.+|+++|||||+|.+.++|++|++.|++..+.|+.|+|.|+.+
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            57899999999999999999999999999999999999999999999999999999999999999999999999999853

>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=99.85  E-value=3.6e-21  Score=140.24  Aligned_cols=83  Identities=27%  Similarity=0.454  Sum_probs=79.2

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ..+++|||+|||+++++++|+++|+.||+|.+|.+.+++.+++++|||||+|.+.++|.+|++.|++..+.|+.|+|.|+
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            46899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccC
Q 012257          117 YRD  119 (467)
Q Consensus       117 ~~~  119 (467)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>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=99.85  E-value=2.6e-21  Score=136.89  Aligned_cols=79  Identities=54%  Similarity=0.997  Sum_probs=75.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      .+|||+|||++++|++|+++|++||+|.+|+|.+++.+|+++|||||+|.+.++|.+|++.|++..+.|+.|+|.|+..
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~~   79 (80)
T d1cvja1           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            3699999999999999999999999999999999999999999999999999999999999999999999999999853

>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=99.84  E-value=1.8e-21  Score=138.92  Aligned_cols=79  Identities=35%  Similarity=0.601  Sum_probs=75.0

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      .++|||+|||..+++++|+++|++||.|.++++.++. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+||++
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            3579999999999999999999999999999999875 788999999999999999999999999999999999999975

>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=99.84  E-value=3.3e-21  Score=138.94  Aligned_cols=82  Identities=26%  Similarity=0.493  Sum_probs=76.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ..+++|||+|||..+++++|+++|++||.|.+|++..+. +|.++|||||+|.+.++|.+|+..|||..+.|+.|+|+||
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            456789999999999999999999999999999999986 7899999999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            764

>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=6.9e-21  Score=140.85  Aligned_cols=86  Identities=20%  Similarity=0.334  Sum_probs=80.5

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      +..+++|||+|||+++++++|+++|++||.|.+|++.+|+.+++++|||||+|.+.++|++|++.|++..|.|+.|+|.+
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            34578899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCcc
Q 012257          116 SYRDPT  121 (467)
Q Consensus       116 ~~~~~~  121 (467)
                      +.....
T Consensus        85 a~~~~~   90 (99)
T d1whwa_          85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             CCCCCc
Confidence            876543

>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=99.84  E-value=4.8e-21  Score=139.53  Aligned_cols=83  Identities=33%  Similarity=0.576  Sum_probs=78.8

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ..++|||+|||.++++++|+++|++||.|.+|++.+++.+|+++|||||+|.+.++|++|++.|++..+.|+.|+|.++.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            35899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCc
Q 012257          118 RDP  120 (467)
Q Consensus       118 ~~~  120 (467)
                      ...
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            543

>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=99.84  E-value=5.4e-21  Score=136.46  Aligned_cols=77  Identities=27%  Similarity=0.455  Sum_probs=74.1

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      .++++|||+|||++++|++|+++|++||.|.+|++.+++.+++++|||||+|.+.++|++|++.|++..|.|+.|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999986

>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=7e-21  Score=135.84  Aligned_cols=80  Identities=34%  Similarity=0.571  Sum_probs=76.6

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      .++|||+|||++++|++|+++|++||.|.+|++.++..+++++|||||+|.+.++|++|++.|++..+.|+.|+|.|+.+
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999753

>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=5.5e-21  Score=136.38  Aligned_cols=78  Identities=35%  Similarity=0.632  Sum_probs=74.4

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ++|||+|||..+++++|+++|++||.|.+|+++++. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+||+|
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            479999999999999999999999999999999875 688999999999999999999999999999999999999976

>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=99.84  E-value=5.6e-21  Score=138.47  Aligned_cols=81  Identities=28%  Similarity=0.479  Sum_probs=76.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      +..+|||+|||..+++++|+++|++||.|.+|++..+. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+||+
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            55689999999999999999999999999999999986 68899999999999999999999999999999999999998


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ++
T Consensus        87 p~   88 (90)
T d2cq0a1          87 PS   88 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.84  E-value=6.8e-21  Score=138.04  Aligned_cols=83  Identities=16%  Similarity=0.349  Sum_probs=78.8

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .++++|||+|||.++++++|+++|++||+|.+|++.+++.+|.++|||||+|.+.++|.+|++.|++..+.|+.|+|.|+
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccC
Q 012257          117 YRD  119 (467)
Q Consensus       117 ~~~  119 (467)
                      .+.
T Consensus        86 kp~   88 (90)
T d2cq0a1          86 KPS   88 (90)
T ss_dssp             SCC
T ss_pred             eCC
Confidence            643

>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=99.84  E-value=8.8e-21  Score=138.41  Aligned_cols=87  Identities=21%  Similarity=0.502  Sum_probs=79.4

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecC-CCCccccEEEEEecChHHHHHHHHHh-CCcccCCceee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDL-STRRSLGYGYVNYNAAHEATRALDEL-NFTPLNGKPIR  112 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l-~~~~~~g~~~~  112 (467)
                      +...+++|||+|||+++++++|+++|+.||.|.+|+++++. .+|+++|||||+|.+.++|.+|++.| ++..+.|+.|+
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            34567899999999999999999999999999999998875 47899999999999999999999998 88999999999


Q ss_pred             eeecccCcc
Q 012257          113 IMYSYRDPT  121 (467)
Q Consensus       113 v~~~~~~~~  121 (467)
                      |.|+..+..
T Consensus        84 V~~A~~~~~   92 (94)
T d2cpha1          84 LEWADSEVT   92 (94)
T ss_dssp             EEECCCCCC
T ss_pred             EEEcCCCCC
Confidence            999976643

>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=4.6e-21  Score=135.55  Aligned_cols=77  Identities=35%  Similarity=0.518  Sum_probs=73.7

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      +|||+|||+.+++++|+++|++||.|.+|+|+++. +|+++|||||+|.+.++|.+|++.|||..+.|+.|+|+|++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            69999999999999999999999999999999987 688999999999999999999999999999999999999863

>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=99.84  E-value=4.2e-21  Score=134.93  Aligned_cols=76  Identities=37%  Similarity=0.569  Sum_probs=74.0

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      .|||+|||..+++++|+++|++||.|.++++..+.+|+++|||||+|.+.++|.+|++.|||..++|+.|+|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            5999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.83  E-value=3.7e-21  Score=139.14  Aligned_cols=82  Identities=28%  Similarity=0.497  Sum_probs=78.3

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ..++|||+|||+++++++|+++|++||+|.+|++.+|+.+|+++|||||+|.+.++|++|++.+++..+.|+.|+|.++.
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            46899999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             cC
Q 012257          118 RD  119 (467)
Q Consensus       118 ~~  119 (467)
                      +.
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.83  E-value=1.2e-20  Score=139.98  Aligned_cols=83  Identities=24%  Similarity=0.384  Sum_probs=79.0

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ++++|||+|||+++++++|+++|+.||.|.++.+..++.+|+++|||||+|.+.++|++|++.|++..|.|+.|+|.|+.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCc
Q 012257          118 RDP  120 (467)
Q Consensus       118 ~~~  120 (467)
                      .+.
T Consensus        97 ~k~   99 (102)
T d2cpza1          97 SKN   99 (102)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            654

>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=3.9e-21  Score=143.73  Aligned_cols=87  Identities=29%  Similarity=0.514  Sum_probs=81.0

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      |...++.++|||+|||+++++++|+++|++||.|.+|++.+++.+|+++|||||+|.+.++|.+|++.|++..+.|+.|+
T Consensus         2 P~~~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~   81 (104)
T d1p1ta_           2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALR   81 (104)
T ss_dssp             CCSHHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBE
T ss_pred             CCCCCCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            44556678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecccC
Q 012257          113 IMYSYRD  119 (467)
Q Consensus       113 v~~~~~~  119 (467)
                      |.++...
T Consensus        82 V~~a~~~   88 (104)
T d1p1ta_          82 VDNAASE   88 (104)
T ss_dssp             EEETTCT
T ss_pred             EEECCCC
Confidence            9987543

>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=99.83  E-value=7.5e-21  Score=138.49  Aligned_cols=83  Identities=30%  Similarity=0.471  Sum_probs=77.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ...++|||+|||..+++++|+++|++||.|.+++++.+. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+||
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            345689999999999999999999999999999999876 7899999999999999999999999999999999999999


Q ss_pred             hhhH
Q 012257          398 QRKE  401 (467)
Q Consensus       398 ~~~~  401 (467)
                      +++.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8653

>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=9.2e-21  Score=135.46  Aligned_cols=80  Identities=24%  Similarity=0.397  Sum_probs=76.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecccC
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRD  119 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~  119 (467)
                      .+|||+|||++++|++|+++|++||+|.+|++.+|+.+|+++|||||+|.+.++|.+|++.+++..+.|+.|+|.++...
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            47999999999999999999999999999999999999999999999999999999999999999999999999998644

>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=99.83  E-value=5.3e-21  Score=138.32  Aligned_cols=81  Identities=32%  Similarity=0.464  Sum_probs=76.5

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ..++|||+|||..+++++|+++|++||.|.+|+++.+. +|.++|||||+|.+.++|.+|+..|||..++|+.|+|+|++
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            45689999999999999999999999999999999887 58999999999999999999999999999999999999998


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ++
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.9e-20  Score=133.95  Aligned_cols=80  Identities=29%  Similarity=0.522  Sum_probs=74.1

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC--ceeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG--KPIRIM  114 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g--~~~~v~  114 (467)
                      ...++|||+|||+++++++|+++|++||+|.++++++|+.+|+++|||||+|.+.++|.+|++.||+..+.|  ++|+|.
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            346789999999999999999999999999999999999999999999999999999999999999999988  447777


Q ss_pred             ec
Q 012257          115 YS  116 (467)
Q Consensus       115 ~~  116 (467)
                      |+
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            64

>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=2.8e-20  Score=133.23  Aligned_cols=80  Identities=33%  Similarity=0.538  Sum_probs=75.0

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC--ceeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG--KPIRIM  114 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g--~~~~v~  114 (467)
                      ...++|||+|||++++|++|+++|++||.|.++++++++.+|+++|||||+|.+.++|.+|++.+++..+.|  ++|+|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            346789999999999999999999999999999999999999999999999999999999999999998876  889998


Q ss_pred             ec
Q 012257          115 YS  116 (467)
Q Consensus       115 ~~  116 (467)
                      |+
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            74

>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=99.82  E-value=2e-20  Score=134.77  Aligned_cols=82  Identities=21%  Similarity=0.371  Sum_probs=75.4

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ..+++|||+|||++++|++|+++|+.||.|.+|+|.+|+.+|+++|||||+|.+.++|++|++.  ...+.|+.|+|.++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            4578999999999999999999999999999999999999999999999999999999999984  34789999999988


Q ss_pred             ccCc
Q 012257          117 YRDP  120 (467)
Q Consensus       117 ~~~~  120 (467)
                      ....
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6543

>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=99.82  E-value=1.9e-20  Score=133.90  Aligned_cols=78  Identities=35%  Similarity=0.697  Sum_probs=72.6

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecc--cceEEeh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVS--KPLYVAL  396 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v~~  396 (467)
                      ..++|||+|||..+++++|+++|++||.|.+++++.+. +|.++|||||+|.+.++|.+|++.|||..+.|  ++|+|+|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            45679999999999999999999999999999999986 68899999999999999999999999999987  5599988


Q ss_pred             h
Q 012257          397 A  397 (467)
Q Consensus       397 ~  397 (467)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=7.2e-21  Score=132.82  Aligned_cols=76  Identities=26%  Similarity=0.455  Sum_probs=72.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      |+|||+|||++++|++|+++|++||.|.++++.+|+.+|+++|||||+|.+.++|++|++ +++..+.|+.|+|..+
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            689999999999999999999999999999999999999999999999999999999997 7999999999999765

>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=99.82  E-value=1.7e-20  Score=139.11  Aligned_cols=84  Identities=33%  Similarity=0.524  Sum_probs=78.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .+++++|||+|||..+++++|+++|+.||.|.+++++.+. +|.++|||||+|.+.++|.+|++.|||..|+|+.|+|+|
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~   94 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL   94 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3466789999999999999999999999999999999876 789999999999999999999999999999999999999


Q ss_pred             hhhhH
Q 012257          397 AQRKE  401 (467)
Q Consensus       397 ~~~~~  401 (467)
                      ++++.
T Consensus        95 a~~k~   99 (102)
T d2cpza1          95 KRSKN   99 (102)
T ss_dssp             CCCSC
T ss_pred             eCCCC
Confidence            98764

>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=99.82  E-value=2.2e-20  Score=135.99  Aligned_cols=81  Identities=23%  Similarity=0.317  Sum_probs=76.2

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      .+++|||+|||.++++++|+++|++||.|.+|+++.+. +|.++|||||+|.+.++|.+|++.|||..++|+.|+|+|+.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            56689999999999999999999999999999999986 68899999999999999999999999999999999999986


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ..
T Consensus        86 ~~   87 (93)
T d1h2vz_          86 GF   87 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.82  E-value=2.8e-20  Score=133.27  Aligned_cols=79  Identities=38%  Similarity=0.694  Sum_probs=73.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecc--cceEEe
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVS--KPLYVA  395 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v~  395 (467)
                      ...++|||+|||..+++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|++.|||..+.|  ++|+|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            355679999999999999999999999999999999986 78999999999999999999999999999976  889999


Q ss_pred             hh
Q 012257          396 LA  397 (467)
Q Consensus       396 ~~  397 (467)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=3.5e-20  Score=131.98  Aligned_cols=79  Identities=27%  Similarity=0.487  Sum_probs=74.4

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      +.++|||+|||+++++++|+++|+.||.|.++.+.+|+.+|+++|||||+|.+.++|++|++ +++..|.|+.|+|..+.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            46899999999999999999999999999999999999999999999999999999999997 68889999999997653

>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=99.82  E-value=2.4e-20  Score=135.39  Aligned_cols=84  Identities=29%  Similarity=0.528  Sum_probs=79.2

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .+.++|||+|||+++++++|+++|++||.|..+.+.++..++.++|||||+|.+.++|++|++.|++..|.|+.|+|.++
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            35788999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccCc
Q 012257          117 YRDP  120 (467)
Q Consensus       117 ~~~~  120 (467)
                      ..+.
T Consensus        83 ~~~~   86 (90)
T d1x5sa1          83 GKSS   86 (90)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            6554

>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=99.81  E-value=5.2e-20  Score=136.77  Aligned_cols=81  Identities=27%  Similarity=0.452  Sum_probs=75.9

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ..++|||+|||++++|++|+++|+.||.|.+|++.+++.+|+++|||||+|.+.++|++|++.+++ .+.|+.|+|.++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            457899999999999999999999999999999999999999999999999999999999998776 6999999999886


Q ss_pred             cC
Q 012257          118 RD  119 (467)
Q Consensus       118 ~~  119 (467)
                      ..
T Consensus        88 ~~   89 (103)
T d2cqda1          88 LG   89 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.81  E-value=2.3e-20  Score=136.16  Aligned_cols=82  Identities=26%  Similarity=0.482  Sum_probs=75.9

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC--CCCccceEEEEcCCHHHHHHHHHHh-CCcEecccceEEe
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP--NGISRGSGFVAFSTAEEASKALTEM-NGKMVVSKPLYVA  395 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~--~~~~~g~afV~f~~~~~A~~A~~~l-~g~~~~g~~l~v~  395 (467)
                      ....+|||+|||..+++++|+++|++||.|.+|+++++.  +|.++|||||+|.+.++|.+|++.| ||..++|++|+|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            355689999999999999999999999999999998874  6889999999999999999999998 8999999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      ||+..
T Consensus        86 ~A~~~   90 (94)
T d2cpha1          86 WADSE   90 (94)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99754

>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=4.8e-20  Score=134.28  Aligned_cols=82  Identities=28%  Similarity=0.504  Sum_probs=76.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|||+|||..+++++|+++|++||.|.+|++..+..+ ++|||||+|.+.++|.+|++.|||..++|+.|+|+||
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            345668999999999999999999999999999999988755 6899999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      +++
T Consensus        87 ~~r   89 (93)
T d2cq3a1          87 TAR   89 (93)
T ss_dssp             CSS
T ss_pred             CcC
Confidence            865

>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=1.9e-20  Score=133.04  Aligned_cols=78  Identities=14%  Similarity=0.296  Sum_probs=68.6

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ++|||+|||.++|+++|+++|++||.|..+.++.+. .|.++|||||+|.+.++|.+|++.|||..+.|++|+|+|++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            589999999999999999999999999888776554 788999999999999999999999999999999999999976

>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=99.81  E-value=3.3e-20  Score=136.76  Aligned_cols=80  Identities=28%  Similarity=0.407  Sum_probs=76.0

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ++.++|||+|||++++|++|+++|+.||.|.+|.+++++.+|+++|||||+|.+.++|.+|++ |++..|.|+.|+|.++
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEEC
Confidence            456899999999999999999999999999999999999999999999999999999999996 9999999999999876


Q ss_pred             c
Q 012257          117 Y  117 (467)
Q Consensus       117 ~  117 (467)
                      .
T Consensus        95 ~   95 (101)
T d2cq4a1          95 Q   95 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=3.5e-20  Score=138.44  Aligned_cols=84  Identities=26%  Similarity=0.508  Sum_probs=77.5

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      .++|||+|||..+++++|+++|++||.|.+|+++.+. +|+++|||||+|.+.++|.+|++.|||..|.|+.|+|+++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            3479999999999999999999999999999999876 689999999999999999999999999999999999999986


Q ss_pred             hHHHH
Q 012257          400 KEERR  404 (467)
Q Consensus       400 ~~~~~  404 (467)
                      ...+.
T Consensus        88 ~~~~~   92 (104)
T d1p1ta_          88 EKNKE   92 (104)
T ss_dssp             TTHHH
T ss_pred             CCCcc
Confidence            65433

>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=99.81  E-value=1.7e-20  Score=134.03  Aligned_cols=78  Identities=27%  Similarity=0.554  Sum_probs=74.5

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      +|||+|||..+++++|+++|++||.|.++++.++. +|.++|||||+|.+.++|.+|++.|||..++|+.|.|+|++..
T Consensus         3 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_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            59999999999999999999999999999999986 6899999999999999999999999999999999999999753

>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=99.81  E-value=4.3e-20  Score=129.67  Aligned_cols=76  Identities=32%  Similarity=0.561  Sum_probs=72.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        41 ~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      +|||+|||+++++++|+++|++||.|.++++..++ +++++|||||+|.+.++|++|++.+|+..+.|+.|+|.++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999986 78999999999999999999999999999999999998764

>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=99.81  E-value=6.7e-20  Score=130.70  Aligned_cols=75  Identities=28%  Similarity=0.413  Sum_probs=71.3

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      ++++|||+|||..+|+++|+++|++||.|.+|++..+. +|+++|||||+|.+.++|.+|++.|||..++|+.|+|
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            45689999999999999999999999999999999886 5889999999999999999999999999999999987

>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=1.1e-19  Score=131.61  Aligned_cols=81  Identities=23%  Similarity=0.428  Sum_probs=75.0

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .+.++|||+|||.+++|++|+++|+.||+|.+|++.+++.++  +|||||+|.+.++|.+|++.+++..+.|+.|+|.|+
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            457899999999999999999999999999999999987654  689999999999999999999999999999999998


Q ss_pred             ccC
Q 012257          117 YRD  119 (467)
Q Consensus       117 ~~~  119 (467)
                      ...
T Consensus        84 ~~~   86 (90)
T d2cqia1          84 TTP   86 (90)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            654

>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=3e-20  Score=131.93  Aligned_cols=79  Identities=16%  Similarity=0.248  Sum_probs=69.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      ++|||+|||+++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++|++.|++..+.|+.|+|.++.+
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            7999999999999999999999999999999988888999999999999999999999999999999999999998753

>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=99.80  E-value=6.1e-20  Score=127.69  Aligned_cols=74  Identities=28%  Similarity=0.499  Sum_probs=70.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        41 ~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      +|||+|||++++|++|+++|++||+|.++.+.+++.+++++|||||+|.+.++|++|++ +++..+.|+.|+|..
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeE
Confidence            59999999999999999999999999999999999999999999999999999999997 788899999999854

>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=99.80  E-value=6.7e-20  Score=132.71  Aligned_cols=82  Identities=29%  Similarity=0.474  Sum_probs=75.3

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ..+.++|||+|||..+++++|+++|+.||.|.+|+++.+..+ .+|||||+|.+.++|.+|++.|||..+.|+.|+|.||
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            345678999999999999999999999999999999988654 4789999999999999999999999999999999999


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ++.
T Consensus        84 ~~~   86 (90)
T d2cqia1          84 TTP   86 (90)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            754

>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=99.80  E-value=5.1e-20  Score=135.78  Aligned_cols=81  Identities=20%  Similarity=0.452  Sum_probs=75.3

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      .++|||+|||..+++++|+++|+.||.|.+|+++++. +|+++|||||+|.+.++|.+|++ |||..|+|+.|+|+++++
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            3579999999999999999999999999999999986 68999999999999999999995 999999999999999876


Q ss_pred             hHH
Q 012257          400 KEE  402 (467)
Q Consensus       400 ~~~  402 (467)
                      .+.
T Consensus        97 ~~n   99 (101)
T d2cq4a1          97 EKN   99 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            653

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=6.3e-20  Score=135.58  Aligned_cols=81  Identities=30%  Similarity=0.450  Sum_probs=76.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ..++|||+|||+.+++++|+++|++||.|.+|+++.+. +++++|||||+|.+.++|.+|++.|||..|+|+.|+|.+++
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45579999999999999999999999999999999876 78999999999999999999999999999999999999998


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ++
T Consensus        87 ~~   88 (99)
T d1whwa_          87 IK   88 (99)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.80  E-value=2.9e-20  Score=129.69  Aligned_cols=75  Identities=32%  Similarity=0.557  Sum_probs=70.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ++|||+|||..+++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|++ ++++.++|+.|.|+.|
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            469999999999999999999999999999999987 58999999999999999999997 7999999999999875

>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=99.80  E-value=1.4e-20  Score=135.99  Aligned_cols=79  Identities=43%  Similarity=0.757  Sum_probs=73.9

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhhH
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRKE  401 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~~  401 (467)
                      .+|||+|||..+++++|+++|++||.|.++++..+..+ ++|||||+|.+.++|.+|++.|||..++|+.|+|++++++.
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~-~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTB-CCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            47999999999999999999999999999999988644 78999999999999999999999999999999999998764

>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=99.80  E-value=3.6e-19  Score=129.55  Aligned_cols=83  Identities=23%  Similarity=0.438  Sum_probs=75.8

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ....++|||+|||+++++++|+++|+.||+|.+|++..++.+  ++|||||+|.+.++|.+|++.+++..+.|+.|+|.+
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~--~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC--CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            345778999999999999999999999999999999988643  689999999999999999999999999999999999


Q ss_pred             cccCc
Q 012257          116 SYRDP  120 (467)
Q Consensus       116 ~~~~~  120 (467)
                      +..+.
T Consensus        86 A~~r~   90 (93)
T d2cq3a1          86 ATARV   90 (93)
T ss_dssp             CCSSC
T ss_pred             cCcCC
Confidence            87653

>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=99.80  E-value=1.3e-19  Score=129.95  Aligned_cols=77  Identities=25%  Similarity=0.560  Sum_probs=72.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCC---ccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTR---RSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        42 l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~---~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      |||+|||+++++++|+++|++||.|.++++.+++.++   +++|||||+|.+.++|++|++.+++..+.|+.|+|.++..
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            7999999999999999999999999999999987665   5789999999999999999999999999999999999754

>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=99.79  E-value=8.5e-20  Score=134.94  Aligned_cols=81  Identities=21%  Similarity=0.456  Sum_probs=76.1

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      +.++|||+|||+++++++|+++|++||.|.++.|.+|+.++.++|||||+|.+.++|.+|++ +++..|.|+.|.|.++.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            45899999999999999999999999999999999999999999999999999999999997 78889999999998876


Q ss_pred             cC
Q 012257          118 RD  119 (467)
Q Consensus       118 ~~  119 (467)
                      +.
T Consensus        98 ~k   99 (103)
T d1x4ba1          98 AR   99 (103)
T ss_dssp             SC
T ss_pred             cc
Confidence            54

>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=99.79  E-value=1.1e-19  Score=130.33  Aligned_cols=76  Identities=38%  Similarity=0.679  Sum_probs=70.8

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCC----CccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNG----ISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       324 l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~----~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      |||+|||.++++++|+++|++||.|.+++++++..+    .++|||||+|.+.++|.+|++.|||..++|+.|+|+|++.
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            799999999999999999999999999999987632    4689999999999999999999999999999999999864

>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=6e-20  Score=127.10  Aligned_cols=74  Identities=15%  Similarity=0.388  Sum_probs=69.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        41 ~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      +|||+|||+++++++|+++|++||.|.+|++.+++.+++++|||||+|.+.++|++|++ .++..+.|+.++|..
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~   74 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKV   74 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEEC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEE
Confidence            69999999999999999999999999999999999999999999999999999999997 466789999998864

>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=99.79  E-value=8e-20  Score=132.62  Aligned_cols=81  Identities=32%  Similarity=0.547  Sum_probs=75.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      +..+|||+|||..+++++|+++|++||.|.++.++.+. +|.++|||||+|.+.++|.+|+..|||..++|+.|+|+++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45579999999999999999999999999999988765 68899999999999999999999999999999999999987


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ++
T Consensus        84 ~~   85 (90)
T d1x5sa1          84 KS   85 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.79  E-value=8.3e-20  Score=130.29  Aligned_cols=78  Identities=27%  Similarity=0.663  Sum_probs=73.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeEEE-EEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecccC
Q 012257           42 LYVGDLDLSVNDSQLYDLFNQMGQVVSV-RVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRD  119 (467)
Q Consensus        42 l~v~nLp~~~~e~~l~~~f~~~G~v~~v-~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~  119 (467)
                      |||+|||++++|++|+++|++||.|.++ ++.+++.+|+++|||||+|.+.++|.+|++.+++..+.|+.|+|.++...
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            7999999999999999999999998664 78889999999999999999999999999999999999999999998654

>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=99.79  E-value=3e-19  Score=126.10  Aligned_cols=77  Identities=16%  Similarity=0.441  Sum_probs=73.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .++|||+|||+++++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|.+|++ +++..|.|+.|+|..+
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            5899999999999999999999999999999999999999999999999999999999996 8999999999999754

>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=3.1e-19  Score=132.07  Aligned_cols=84  Identities=17%  Similarity=0.336  Sum_probs=77.2

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhC------CcccCCc
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN------FTPLNGK  109 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~------~~~~~g~  109 (467)
                      ..+.++|||+|||++++|++|+++|++||.|.++.+..++.+++++|||||+|.+.++|.+|++.++      +..+.|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3457899999999999999999999999999999999999999999999999999999999999886      5678999


Q ss_pred             eeeeeecccC
Q 012257          110 PIRIMYSYRD  119 (467)
Q Consensus       110 ~~~v~~~~~~  119 (467)
                      .|+|.++..+
T Consensus        85 ~l~v~~a~~k   94 (98)
T d1x4ha1          85 QLKVDLAVTR   94 (98)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEEECCCC
Confidence            9999988654

>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=99.79  E-value=2.2e-19  Score=129.27  Aligned_cols=79  Identities=30%  Similarity=0.440  Sum_probs=72.9

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ...+|||+|||+++|+++|+++|++||.|.+|+|+.+. +|.++|||||+|.+.++|.+|++.  ++.|+|+.|.|+++.
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            45679999999999999999999999999999999986 699999999999999999999984  558999999999997


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ++
T Consensus        85 ~k   86 (90)
T d2cqga1          85 SK   86 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            65

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=3e-19  Score=127.02  Aligned_cols=77  Identities=34%  Similarity=0.533  Sum_probs=72.1

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      .++|||+|||..+++++|+++|+.||.|.+++++.+. +|.++|||||+|.+.++|.+|++ ++++.|+|+.|+|+.|.
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            4589999999999999999999999999999999987 59999999999999999999997 69999999999998764

>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=99.79  E-value=1.9e-19  Score=133.70  Aligned_cols=81  Identities=28%  Similarity=0.416  Sum_probs=74.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ...++|||+|||..+++++|+++|++||.|.+|+++.+. +|+++|||||+|.+.++|.+|++.+|+ .|+|+.|+|+++
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            345679999999999999999999999999999999987 689999999999999999999998876 799999999998


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ...
T Consensus        87 ~~~   89 (103)
T d2cqda1          87 YLG   89 (103)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            754

>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=99.79  E-value=1.3e-19  Score=134.15  Aligned_cols=80  Identities=30%  Similarity=0.600  Sum_probs=75.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      +.++|||+|||..+++++|+++|++||.|..+++..+.++.++|||||+|.+.++|.+|++.|||..|.|+++.|.+++|
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            45689999999999999999999999999999999998999999999999999999999999999999999999987764

>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=99.79  E-value=2.6e-19  Score=133.29  Aligned_cols=89  Identities=22%  Similarity=0.350  Sum_probs=79.9

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCe--------EEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCc
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQV--------VSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFT  104 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v--------~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~  104 (467)
                      +......++|||+|||.++++++|+++|+.||.|        ..+.+.+++.+|+++|||||+|.+.++|.+|++.|++.
T Consensus         2 p~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~   81 (101)
T d2cpea1           2 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   81 (101)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCC
Confidence            4455678999999999999999999999999987        46777788888999999999999999999999999999


Q ss_pred             ccCCceeeeeecccCcc
Q 012257          105 PLNGKPIRIMYSYRDPT  121 (467)
Q Consensus       105 ~~~g~~~~v~~~~~~~~  121 (467)
                      .|.|+.|+|.++..++.
T Consensus        82 ~~~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          82 DFQGSKLKVSLARKKPP   98 (101)
T ss_dssp             EETTEECEEECSSCCCC
T ss_pred             EECCEEEEEEEcCCCCC
Confidence            99999999999876543

>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=99.78  E-value=1e-19  Score=129.82  Aligned_cols=77  Identities=36%  Similarity=0.711  Sum_probs=71.4

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCceeEE-EEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          324 LYVKNLDDSISDDKLKELFSEFGTITSC-KVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       324 l~V~nlp~~~~~~~l~~~F~~~G~v~~v-~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      |||+|||.++++++|+++|++||.|.++ +++++. +|+++|||||+|.+.++|.+|++.|||..++|++|+|+|+.++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k   79 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK   79 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCC
Confidence            7999999999999999999999999764 677765 6889999999999999999999999999999999999998765

>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=99.78  E-value=1.3e-19  Score=129.78  Aligned_cols=82  Identities=13%  Similarity=0.271  Sum_probs=71.5

Q ss_pred             CccCeEEEcCCCCCCC-HHHHHHHHhcCCCeEEEEEEe-cCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           37 FVSTSLYVGDLDLSVN-DSQLYDLFNQMGQVVSVRVCR-DLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~-e~~l~~~f~~~G~v~~v~i~~-~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      .+.++|||+|||++++ |++|+++|++||.|.+|+|.. ++.+++++|||||+|.+.++|.+|++ +++..+.|+.|+|.
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~   80 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVS   80 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            3579999999999875 567999999999999999876 45678999999999999999999996 99999999999999


Q ss_pred             ecccC
Q 012257          115 YSYRD  119 (467)
Q Consensus       115 ~~~~~  119 (467)
                      ++..+
T Consensus        81 ~a~~k   85 (86)
T d2ghpa3          81 LADKK   85 (86)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            98754

>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=99.78  E-value=8.1e-20  Score=130.90  Aligned_cols=80  Identities=26%  Similarity=0.525  Sum_probs=70.4

Q ss_pred             CCceEEEecCCCCCC-HHHHHHhhccCCceeEEEEeeCC--CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          320 EGLNLYVKNLDDSIS-DDKLKELFSEFGTITSCKVMRDP--NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~-~~~l~~~F~~~G~v~~v~i~~~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .+++|||+|||..++ +++|+++|++||.|++|++..+.  +++++|||||+|.+.++|.+|++ |||..++|+.|+|++
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            456899999999886 55699999999999999997653  78899999999999999999995 999999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      ++++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9754

>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=99.78  E-value=2.8e-19  Score=127.23  Aligned_cols=78  Identities=18%  Similarity=0.372  Sum_probs=71.5

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEec-ccceEEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVV-SKPLYVA  395 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~v~  395 (467)
                      +.+++++|||+|||..+++++|+++|++||.|.+|++.++    .+|||||+|.+.++|.+|++.|||..+. |+.|+|+
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            4567789999999999999999999999999999999875    3679999999999999999999999985 6899999


Q ss_pred             hhh
Q 012257          396 LAQ  398 (467)
Q Consensus       396 ~~~  398 (467)
                      ||+
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            986

>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=99.78  E-value=2.1e-19  Score=124.95  Aligned_cols=74  Identities=30%  Similarity=0.542  Sum_probs=69.4

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      .|||+|||+++++++|+++|++||.|.++++..+. +|+++|||||+|.+.++|.+|++ +++..|+|+.|.|+.|
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            38999999999999999999999999999999987 68899999999999999999997 7999999999999754

>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=5e-19  Score=126.21  Aligned_cols=79  Identities=22%  Similarity=0.356  Sum_probs=74.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ..++|||+|||..+|+++|+++|+.||.|.+|++..+.+|.++|||||+|.+.++|.+|++ ++|..+.|+.|.|.|+..
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~d   83 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   83 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcCC
Confidence            3458999999999999999999999999999999999999999999999999999999996 799999999999998753

>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=99.78  E-value=2.4e-19  Score=131.04  Aligned_cols=77  Identities=25%  Similarity=0.478  Sum_probs=72.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      +..++|||+|||..+++++|+++|++||.|.+|++.++     +|||||+|.+.++|.+|+..|||..|+|+.|+|+|++
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34568999999999999999999999999999999876     7899999999999999999999999999999999997


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      +.
T Consensus        91 ~~   92 (96)
T d1x4ga1          91 ES   92 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.78  E-value=4.7e-19  Score=134.87  Aligned_cols=104  Identities=21%  Similarity=0.401  Sum_probs=86.1

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ..+++|||+|||.++++++|+++|+.||.|.+|++..+   +.++|||||+|.+.++|.+|++.|++..|.|+.|+|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34789999999999999999999999999999999754   457899999999999999999999999999999999987


Q ss_pred             ccCcccccCCCccEEEcCCCCcCCHHHHHHHHhhcCC
Q 012257          117 YRDPTIRKSGAGNIFIKNLDKSIDNKALHDTFSTFGN  153 (467)
Q Consensus       117 ~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~g~  153 (467)
                      .......          .......++++..+.+.+|.
T Consensus        82 ~~~~~~~----------~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          82 NANRAFQ----------KMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             CHHHHTT----------TSCHHHHHHHHHHHHHHHCC
T ss_pred             CCCchhh----------hhHHHHHHHHHHHHHHHhCC
Confidence            6433221          12223456777788887773

>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=99.78  E-value=2e-19  Score=142.15  Aligned_cols=81  Identities=35%  Similarity=0.539  Sum_probs=76.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ..++|||+|||.++++++|+++|++||.|.+|+++++. +|+++|||||+|.+.++|.+|++.|||..|+|+.|+|+|++
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            34689999999999999999999999999999999886 68899999999999999999999999999999999999987


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ..
T Consensus       121 ~~  122 (139)
T d1u6fa1         121 SG  122 (139)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=5.3e-19  Score=126.07  Aligned_cols=78  Identities=14%  Similarity=0.278  Sum_probs=73.0

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ..++|||+|||.++++++|+++|+.||+|.+|.+.++. +|+++|||||+|.+.++|++|++ +++..+.|+.|.|.|..
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            46899999999999999999999999999999998875 78999999999999999999997 79999999999998864

>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=99.77  E-value=7.4e-19  Score=130.04  Aligned_cols=81  Identities=23%  Similarity=0.395  Sum_probs=75.0

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..+.++|||+|||+++++++|+++|+.||.|.++.+..+. +++++|||||+|.+.++|++|++.||+..|.|+++.+.+
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~   93 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP   93 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCC
Confidence            3456899999999999999999999999999999999885 789999999999999999999999999999999999976


Q ss_pred             cc
Q 012257          116 SY  117 (467)
Q Consensus       116 ~~  117 (467)
                      +.
T Consensus        94 ~~   95 (101)
T d1x5oa1          94 TE   95 (101)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>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=99.77  E-value=2.4e-20  Score=134.94  Aligned_cols=82  Identities=27%  Similarity=0.371  Sum_probs=75.7

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....++|||+|||..+++++|+++|+.||.|.++++..+.+|+++|||||+|.+.++|.+|++ |||..++|+.|+|.++
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            345668999999999999999999999999999999887789999999999999999999996 9999999999999998


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      +.+
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            753

>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=99.77  E-value=7.3e-19  Score=133.79  Aligned_cols=79  Identities=23%  Similarity=0.408  Sum_probs=73.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      .+++|||+|||..+++++|+++|++||.|++|++..+  +.++|||||+|.+.++|..|++.|||..|.|+.|+|.|+..
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            4568999999999999999999999999999999765  56789999999999999999999999999999999999864


Q ss_pred             h
Q 012257          400 K  400 (467)
Q Consensus       400 ~  400 (467)
                      .
T Consensus        84 ~   84 (114)
T d2f9da1          84 N   84 (114)
T ss_dssp             H
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=99.77  E-value=4e-19  Score=131.25  Aligned_cols=79  Identities=29%  Similarity=0.537  Sum_probs=73.7

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      ++|||+|||+.+++++|+++|++||.|.+++|+.+. ++.++|||||+|.+.++|.+|++ ++|..|+|+.|.|++|.++
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECccc
Confidence            479999999999999999999999999999999986 57889999999999999999996 7999999999999998875


Q ss_pred             H
Q 012257          401 E  401 (467)
Q Consensus       401 ~  401 (467)
                      .
T Consensus       100 e  100 (103)
T d1x4ba1         100 E  100 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.77  E-value=8.4e-19  Score=128.08  Aligned_cols=78  Identities=22%  Similarity=0.517  Sum_probs=72.4

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      .+++|||+|||.++++++|+++|++||.|.+|++.++      +|||||+|.+.++|.+|+..|++..+.|+.|+|.|+.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4689999999999999999999999999999999976      3799999999999999999999999999999999987


Q ss_pred             cCcc
Q 012257          118 RDPT  121 (467)
Q Consensus       118 ~~~~  121 (467)
                      ..+.
T Consensus        91 ~~p~   94 (96)
T d1x4ga1          91 ESPD   94 (96)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            6543

>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=99.77  E-value=3.6e-19  Score=124.44  Aligned_cols=75  Identities=21%  Similarity=0.467  Sum_probs=71.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           41 SLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        41 ~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      +|||+|||++++|++|+++|+.||.|..+.+..++.++.++|||||+|.+.++|++|++ +++..|.|+.|+|.++
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            59999999999999999999999999999999999999999999999999999999997 9999999999999764

>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=99.77  E-value=4.6e-19  Score=127.92  Aligned_cols=79  Identities=28%  Similarity=0.533  Sum_probs=73.2

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      ..+|||+|||+++++++|+++|+.||.|.++++..++.  .++|||||+|.+.++|++|++.|++..+.|+.|+|.++..
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            46799999999999999999999999999999998864  4779999999999999999999999999999999998865


Q ss_pred             C
Q 012257          119 D  119 (467)
Q Consensus       119 ~  119 (467)
                      .
T Consensus        86 ~   86 (89)
T d1cvja2          86 R   86 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.76  E-value=1.9e-19  Score=124.48  Aligned_cols=74  Identities=23%  Similarity=0.385  Sum_probs=69.0

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      .|||+|||.++|+++|+++|++||.|.+|+|+.++ +++++|||||+|.+.++|.+|++ .+++.++|+.|.|+.|
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            49999999999999999999999999999999986 68999999999999999999997 4778999999999865

>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=99.76  E-value=1.6e-18  Score=122.37  Aligned_cols=75  Identities=23%  Similarity=0.439  Sum_probs=70.2

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ++|||+|||+++|+++|+++|+.||.|..+++..+. ++.++|+|||+|.+.++|.+|++ +||+.|+|+.|.|+.|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            579999999999999999999999999999999876 77899999999999999999985 8999999999999865

>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=1.3e-18  Score=127.20  Aligned_cols=80  Identities=20%  Similarity=0.300  Sum_probs=72.6

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ...++|||+|||..+++++|+++|+.||.|..+++..+  +.+++||||+|.+.++|.+|++.|||..|+|++|+|+|++
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            35568999999999999999999999999999987655  4467899999999999999999999999999999999987


Q ss_pred             hh
Q 012257          399 RK  400 (467)
Q Consensus       399 ~~  400 (467)
                      ..
T Consensus        90 ~~   91 (95)
T d1x4aa1          90 SG   91 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.76  E-value=9.5e-19  Score=129.44  Aligned_cols=82  Identities=29%  Similarity=0.503  Sum_probs=75.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhC------CcEecccc
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMN------GKMVVSKP  391 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~------g~~~~g~~  391 (467)
                      ...++|||+|||..+++++|+++|++||.|.++++..+. .+.++|||||+|.+.++|.+|++.||      |..+.|+.
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            356789999999999999999999999999999998876 67789999999999999999999886      67889999


Q ss_pred             eEEehhhhh
Q 012257          392 LYVALAQRK  400 (467)
Q Consensus       392 l~v~~~~~~  400 (467)
                      |+|+|+.++
T Consensus        86 l~v~~a~~k   94 (98)
T d1x4ha1          86 LKVDLAVTR   94 (98)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEECCCC
Confidence            999999765

>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=3.3e-19  Score=123.32  Aligned_cols=71  Identities=25%  Similarity=0.517  Sum_probs=68.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        42 l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      |||+|||+++++++|+++|+.||.|..+++.+++.++.++|+|||+|.+.++|++|++.||+..+.|+.++
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            79999999999999999999999999999999999999999999999999999999999999999998874

>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=2.6e-18  Score=125.59  Aligned_cols=81  Identities=16%  Similarity=0.339  Sum_probs=73.0

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ...++++|||+|||+++++++|+++|+.||.|..+.+..+   +.+++||||+|.+.++|++|++.|++..|.|+.|+|.
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~   86 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   86 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456789999999999999999999999999999987654   3467999999999999999999999999999999999


Q ss_pred             eccc
Q 012257          115 YSYR  118 (467)
Q Consensus       115 ~~~~  118 (467)
                      |+..
T Consensus        87 ~a~~   90 (95)
T d1x4aa1          87 FPRS   90 (95)
T ss_dssp             CCCC
T ss_pred             eccC
Confidence            9864

>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=99.76  E-value=1.1e-18  Score=129.87  Aligned_cols=84  Identities=26%  Similarity=0.474  Sum_probs=74.2

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCcee--------EEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEe
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTIT--------SCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMV  387 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~--------~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  387 (467)
                      +.....+|||+|||..+++++|+++|+.||.|.        .+.+..+. +|+++|||||+|.+.++|.+|++.|||..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            345667999999999999999999999999885        34555554 588899999999999999999999999999


Q ss_pred             cccceEEehhhhh
Q 012257          388 VSKPLYVALAQRK  400 (467)
Q Consensus       388 ~g~~l~v~~~~~~  400 (467)
                      +|+.|+|++++++
T Consensus        84 ~gr~i~V~~a~~~   96 (101)
T d2cpea1          84 QGSKLKVSLARKK   96 (101)
T ss_dssp             TTEECEEECSSCC
T ss_pred             CCEEEEEEEcCCC
Confidence            9999999999854

>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=99.76  E-value=8.5e-19  Score=125.28  Aligned_cols=75  Identities=27%  Similarity=0.461  Sum_probs=70.2

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      .++|||+|||..+++++|+++|++||.|.+|++.++     +|||||+|.+.++|.+|++.|||..++|+.|+|+||...
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            457999999999999999999999999999999865     679999999999999999999999999999999998753

>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=99.75  E-value=2.7e-18  Score=122.02  Aligned_cols=77  Identities=19%  Similarity=0.282  Sum_probs=69.8

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc-CCceeeee
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL-NGKPIRIM  114 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~-~g~~~~v~  114 (467)
                      ..++++|||+|||.++++++|+++|+.||.|.+|++.+++     +|||||+|.+.++|.+|++.|++..+ .|+.|+|.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            3457899999999999999999999999999999997654     47999999999999999999999888 56899999


Q ss_pred             ecc
Q 012257          115 YSY  117 (467)
Q Consensus       115 ~~~  117 (467)
                      |+.
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            885

>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=8.9e-19  Score=126.08  Aligned_cols=80  Identities=21%  Similarity=0.363  Sum_probs=72.3

Q ss_pred             CCCccCeEEEcCCCCCCCHHHH---HHHHhcCCCeEEEEEEecCCCCccc---cEEEEEecChHHHHHHHHHhCCcccCC
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQL---YDLFNQMGQVVSVRVCRDLSTRRSL---GYGYVNYNAAHEATRALDELNFTPLNG  108 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l---~~~f~~~G~v~~v~i~~~~~~~~~~---g~afV~f~~~~~A~~A~~~l~~~~~~g  108 (467)
                      +-...++|||+|||+++++++|   +++|++||.|.+|.+.+++.++.++   |||||+|.+.++|.+|++.||+..+.|
T Consensus         4 Rviq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~g   83 (89)
T d2cpia1           4 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   83 (89)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             eEEecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECC
Confidence            3445778999999999999999   6789999999999999998776554   899999999999999999999999999


Q ss_pred             ceeeee
Q 012257          109 KPIRIM  114 (467)
Q Consensus       109 ~~~~v~  114 (467)
                      +.|++.
T Consensus        84 r~lkvS   89 (89)
T d2cpia1          84 RTLKAS   89 (89)
T ss_dssp             EEEEEE
T ss_pred             EEEEEC
Confidence            999873

>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=99.75  E-value=1.3e-18  Score=131.97  Aligned_cols=82  Identities=13%  Similarity=0.201  Sum_probs=73.9

Q ss_pred             CCCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           32 GDARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        32 ~~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      .....+.+++|||+|||+++++++|+++|+.||.|..|.|.+      ++|||||+|.+.++|.+|++.||+..|.|+.|
T Consensus         3 ~~~~~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l   76 (111)
T d1whxa_           3 SGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPL   76 (111)
T ss_dssp             GGGTSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeE
Confidence            345667789999999999999999999999999999998843      45799999999999999999999999999999


Q ss_pred             eeeecccC
Q 012257          112 RIMYSYRD  119 (467)
Q Consensus       112 ~v~~~~~~  119 (467)
                      +|.|+...
T Consensus        77 ~v~~a~~~   84 (111)
T d1whxa_          77 YLEWAPIG   84 (111)
T ss_dssp             EEEEEETT
T ss_pred             EEEECCCC
Confidence            99997654

>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=99.75  E-value=7.9e-19  Score=122.69  Aligned_cols=74  Identities=23%  Similarity=0.391  Sum_probs=69.6

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      .|||+|||.++|+++|+++|+.||.|..+.+..+. ++.++|+|||+|.+.++|.+|++ +||+.|+|+.|+|++|
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            38999999999999999999999999999998876 67899999999999999999996 9999999999999875

>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=99.75  E-value=2.7e-19  Score=133.32  Aligned_cols=83  Identities=22%  Similarity=0.267  Sum_probs=78.5

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .++++|||+|||.++++++|+++|+.||.|..+.+..+..+|+++|||||+|.+.++|.+|++.|++..|.|+.|+|.|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            35789999999999999999999999999999999998888999999999999999999999999999999999999998


Q ss_pred             ccC
Q 012257          117 YRD  119 (467)
Q Consensus       117 ~~~  119 (467)
                      ...
T Consensus        96 k~k   98 (102)
T d2cpxa1          96 KNK   98 (102)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            754

>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=99.75  E-value=1.4e-18  Score=124.68  Aligned_cols=79  Identities=22%  Similarity=0.371  Sum_probs=72.7

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeE-EEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITS-CKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~-v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      +....|||+|||..+++++|+++|+.||.|.. +.+..+.+|.++|+|||+|.+.++|.+|++.|||..++|++|+|+++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34557999999999999999999999999876 57778889999999999999999999999999999999999999875

>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=99.75  E-value=1.1e-18  Score=122.66  Aligned_cols=74  Identities=34%  Similarity=0.527  Sum_probs=68.4

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      .+++|||+|++  +|+++|+++|++||.|.++++.++     +|||||+|.+.++|.+|++.|||..++|+.|+|+|+++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   76 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            45689999996  899999999999999999999764     67999999999999999999999999999999999975


Q ss_pred             h
Q 012257          400 K  400 (467)
Q Consensus       400 ~  400 (467)
                      +
T Consensus        77 ~   77 (79)
T d2bz2a1          77 Q   77 (79)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.75  E-value=5.9e-18  Score=125.96  Aligned_cols=83  Identities=17%  Similarity=0.175  Sum_probs=75.7

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      +..+|||+|||++++|++|+++|+.+|.|..+.++.+..+++++|+|||+|.+.++|++|++ +++..|.||.|+|.++.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECC
Confidence            46689999999999999999999999999887788887899999999999999999999996 89999999999999887


Q ss_pred             cCcc
Q 012257          118 RDPT  121 (467)
Q Consensus       118 ~~~~  121 (467)
                      ..+.
T Consensus        93 ~~~~   96 (104)
T d1wg5a_          93 RAEV   96 (104)
T ss_dssp             TTTS
T ss_pred             HHHh
Confidence            6543

>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=1.8e-18  Score=126.89  Aligned_cols=84  Identities=17%  Similarity=0.321  Sum_probs=74.1

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCC-eEEEEEEecC-CCCccccEEEEEecChHHHHHHHHHhCC--cccCCceeeee
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQ-VVSVRVCRDL-STRRSLGYGYVNYNAAHEATRALDELNF--TPLNGKPIRIM  114 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~-v~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~~--~~~~g~~~~v~  114 (467)
                      +|+|||+|||.++++++|+++|+.||+ |.+|++.++. .+++++|||||+|.+.++|.+|++.|++  ..+.|+.|+|.
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            478999999999999999999999995 9999999875 4688999999999999999999998864  45579999999


Q ss_pred             ecccCccc
Q 012257          115 YSYRDPTI  122 (467)
Q Consensus       115 ~~~~~~~~  122 (467)
                      |+.+....
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99765443

>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=99.75  E-value=1.9e-18  Score=124.56  Aligned_cols=78  Identities=23%  Similarity=0.326  Sum_probs=70.3

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEe-cccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV-VSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~-~g~~l~v~~~  397 (467)
                      +++++|||+|||..+++++|+++|++||.|.++++...   +++|+|||+|.+.++|.+|+..|||..+ .|+.|+|+|+
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            45779999999999999999999999999988877654   3468999999999999999999999998 5899999999


Q ss_pred             hh
Q 012257          398 QR  399 (467)
Q Consensus       398 ~~  399 (467)
                      ++
T Consensus        85 k~   86 (88)
T d2adca2          85 KS   86 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            75

>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=2.5e-18  Score=122.83  Aligned_cols=76  Identities=26%  Similarity=0.548  Sum_probs=70.7

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      .++|||+|||.++++++|+++|++||.|.+|++.+++      |||||+|.+.++|.+|++.|++..+.|+.|+|.|+..
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k------~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTT------TEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeeccc------ceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            5689999999999999999999999999999998664      6999999999999999999999999999999999875


Q ss_pred             Cc
Q 012257          119 DP  120 (467)
Q Consensus       119 ~~  120 (467)
                      ..
T Consensus        82 ~~   83 (86)
T d2cpja1          82 SA   83 (86)
T ss_dssp             CS
T ss_pred             cC
Confidence            53

>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=3.7e-18  Score=124.98  Aligned_cols=76  Identities=21%  Similarity=0.445  Sum_probs=68.2

Q ss_pred             CCccCeEEEcCCC-CCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           36 QFVSTSLYVGDLD-LSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        36 ~~~~~~l~v~nLp-~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ....++|||+||| ..+++++|+++|++||.|.+|+|        ++|||||+|.+.++|++|++.|++..+.|+.|+|.
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   83 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN   83 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3446789999997 56888999999999999999998        34799999999999999999999999999999999


Q ss_pred             ecccC
Q 012257          115 YSYRD  119 (467)
Q Consensus       115 ~~~~~  119 (467)
                      ++...
T Consensus        84 ~a~~~   88 (98)
T d1wf2a_          84 LAAEP   88 (98)
T ss_dssp             ETTSC
T ss_pred             ECCCC
Confidence            98654

>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=99.74  E-value=1.7e-18  Score=124.55  Aligned_cols=76  Identities=21%  Similarity=0.381  Sum_probs=68.5

Q ss_pred             CCceEEEecCCCCCCHHHH---HHhhccCCceeEEEEeeCCC-C---CccceEEEEcCCHHHHHHHHHHhCCcEecccce
Q 012257          320 EGLNLYVKNLDDSISDDKL---KELFSEFGTITSCKVMRDPN-G---ISRGSGFVAFSTAEEASKALTEMNGKMVVSKPL  392 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l---~~~F~~~G~v~~v~i~~~~~-~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l  392 (467)
                      ...+|||+|||+.+++++|   +++|++||.|.+|++.+++. +   ..+|||||+|.+.++|.+|++.|||..++|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4457999999999999999   67899999999999998862 2   345899999999999999999999999999999


Q ss_pred             EEe
Q 012257          393 YVA  395 (467)
Q Consensus       393 ~v~  395 (467)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            986

>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=99.74  E-value=2.9e-19  Score=129.13  Aligned_cols=82  Identities=18%  Similarity=0.293  Sum_probs=74.3

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ....+++|||+|||+++++++|+++|+.||.|.++++..+ .+|+++|||||+|.+.++|++|++ +++..+.|+.|+|.
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEE
Confidence            3445779999999999999999999999999999988755 589999999999999999999996 99999999999999


Q ss_pred             eccc
Q 012257          115 YSYR  118 (467)
Q Consensus       115 ~~~~  118 (467)
                      ++..
T Consensus        87 ~ak~   90 (91)
T d1fjeb1          87 KPKG   90 (91)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            8753

>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=99.74  E-value=3.5e-19  Score=132.70  Aligned_cols=83  Identities=28%  Similarity=0.396  Sum_probs=77.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      .++++|||+|||..+++++|+++|+.||.|..+.+..+. +|.++|||||+|.+.++|.+|++.|||..|.|+.|+|+|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            456799999999999999999999999999998887765 7889999999999999999999999999999999999999


Q ss_pred             hhhH
Q 012257          398 QRKE  401 (467)
Q Consensus       398 ~~~~  401 (467)
                      ++++
T Consensus        96 k~k~   99 (102)
T d2cpxa1          96 KNKK   99 (102)
T ss_dssp             CCCS
T ss_pred             CCcc
Confidence            8754

>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=4.4e-18  Score=122.03  Aligned_cols=76  Identities=32%  Similarity=0.431  Sum_probs=69.8

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ..++|||+|||..+++++|+++|++||.|..+++.+     ++|||||+|.+.++|.+|+..|||..|+|+.|+|+|++|
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-----~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP   81 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKP   81 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-----ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccC
Confidence            346899999999999999999999999998887755     478999999999999999999999999999999999986


Q ss_pred             h
Q 012257          400 K  400 (467)
Q Consensus       400 ~  400 (467)
                      .
T Consensus        82 ~   82 (86)
T d2cpda1          82 V   82 (86)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.74  E-value=1.2e-18  Score=120.43  Aligned_cols=70  Identities=30%  Similarity=0.504  Sum_probs=66.6

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC-CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceE
Q 012257          324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP-NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLY  393 (467)
Q Consensus       324 l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  393 (467)
                      |||+|||..+++++|+++|++||.|..+++..+. ++.++|+|||+|.+.++|.+|++.|||..+.|+.|+
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            7999999999999999999999999999998886 688999999999999999999999999999999874

>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=99.74  E-value=6.1e-18  Score=126.19  Aligned_cols=83  Identities=23%  Similarity=0.432  Sum_probs=72.9

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecC-CCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDL-STRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      .+.++|||+|||++++|++|+++|+.|| +.++.++.+. .+++++|||||+|.+.++|++|++ +++..|.|+.|+|.+
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 6677777655 468899999999999999998885 999999999999999


Q ss_pred             cccCcc
Q 012257          116 SYRDPT  121 (467)
Q Consensus       116 ~~~~~~  121 (467)
                      +.....
T Consensus        91 a~~~~~   96 (104)
T d1wi8a_          91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.74  E-value=1.7e-18  Score=125.52  Aligned_cols=80  Identities=26%  Similarity=0.527  Sum_probs=71.8

Q ss_pred             CccCeEEEcCCCCCCCHHHHH----HHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLY----DLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIR  112 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~----~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~  112 (467)
                      +|+++|||+|||+++++++|+    ++|++||+|.+|++.+   +++++|||||+|.+.++|.+|++.+++..+.|+.|+
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~   77 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   77 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            468999999999999999886    4689999999998754   456889999999999999999999999999999999


Q ss_pred             eeecccC
Q 012257          113 IMYSYRD  119 (467)
Q Consensus       113 v~~~~~~  119 (467)
                      |.|+..+
T Consensus        78 v~~ak~~   84 (91)
T d1nu4a_          78 IQYAKTD   84 (91)
T ss_dssp             EEECSSC
T ss_pred             EEEeCCC
Confidence            9998754

>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=99.74  E-value=5.5e-18  Score=122.09  Aligned_cols=78  Identities=23%  Similarity=0.274  Sum_probs=69.5

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc-CCceeeeee
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL-NGKPIRIMY  115 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~-~g~~~~v~~  115 (467)
                      .++++|||+|||+++++++|+++|++||.|..+.+..+    +++|||||+|.+.++|.+|+..|++..+ .|+.|+|.|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            35889999999999999999999999999988877644    3467999999999999999999999887 689999999


Q ss_pred             ccc
Q 012257          116 SYR  118 (467)
Q Consensus       116 ~~~  118 (467)
                      ++.
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            864

>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=99.73  E-value=7.1e-18  Score=124.93  Aligned_cols=86  Identities=12%  Similarity=0.225  Sum_probs=75.0

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ..+....+|||+|||++++|++|+++|+.||. .+|.++.+. +++++|||||+|.+.++|++|++ +++..|.||.|+|
T Consensus        10 ~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V   86 (102)
T d1weza_          10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVEL   86 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEE
T ss_pred             CcCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEE
Confidence            34455679999999999999999999999985 478888775 68899999999999999999997 8999999999999


Q ss_pred             eecccCccc
Q 012257          114 MYSYRDPTI  122 (467)
Q Consensus       114 ~~~~~~~~~  122 (467)
                      .++...+..
T Consensus        87 ~~s~~~~~~   95 (102)
T d1weza_          87 FLNSTAGTS   95 (102)
T ss_dssp             EEECCCCCC
T ss_pred             EEcCCCCCC
Confidence            998765443

>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=99.73  E-value=3e-18  Score=125.53  Aligned_cols=74  Identities=24%  Similarity=0.524  Sum_probs=67.5

Q ss_pred             CCCceEEEecCC-CCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          319 FEGLNLYVKNLD-DSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       319 ~~~~~l~V~nlp-~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      ....+|||+||+ ..+++++|+++|++||.|.++++       ++|||||+|.+.++|.+|++.|||..|+|+.|+|+|+
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 57888999999999999999998       3579999999999999999999999999999999998


Q ss_pred             hh
Q 012257          398 QR  399 (467)
Q Consensus       398 ~~  399 (467)
                      ++
T Consensus        86 ~~   87 (98)
T d1wf2a_          86 AE   87 (98)
T ss_dssp             TS
T ss_pred             CC
Confidence            64

>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=99.73  E-value=1.2e-18  Score=122.70  Aligned_cols=74  Identities=26%  Similarity=0.431  Sum_probs=68.2

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCc-EecccceEEehhhhhH
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGK-MVVSKPLYVALAQRKE  401 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~-~~~g~~l~v~~~~~~~  401 (467)
                      +|||+|||.++++++|+++|++||.|.++++...     +|||||+|.+.++|.+|++.|||. .++|+.|+|+|+.++.
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-----rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~   77 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE-----TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc-----cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcC
Confidence            6999999999999999999999999988777664     789999999999999999999996 6999999999998753

>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=99.73  E-value=1.2e-17  Score=122.22  Aligned_cols=80  Identities=23%  Similarity=0.210  Sum_probs=71.6

Q ss_pred             CCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           34 ARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        34 ~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      ...+..++|||+|||+++++++|+++|+.||.|+++++.+       +|||||+|.+.++|++|++.||+..|.|+.|+|
T Consensus        10 ~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v   82 (98)
T d1wg4a_          10 PTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGET   82 (98)
T ss_dssp             CCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEE
Confidence            3445678999999999999999999999999999999864       379999999999999999999999999999999


Q ss_pred             eecccCc
Q 012257          114 MYSYRDP  120 (467)
Q Consensus       114 ~~~~~~~  120 (467)
                      .+....+
T Consensus        83 ~~~~~~~   89 (98)
T d1wg4a_          83 SYIRVYP   89 (98)
T ss_dssp             EEEEEEC
T ss_pred             EEEecCC
Confidence            8875443

>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=99.73  E-value=3.3e-18  Score=122.74  Aligned_cols=78  Identities=18%  Similarity=0.281  Sum_probs=70.0

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ..++|||+|||+++++++|+++|+.||.+....++.+..+++++|+|||+|.+.++|++|++.+++..+.|+.|+|..
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            356799999999999999999999999887644444556899999999999999999999999999999999999975

>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=99.73  E-value=2.7e-18  Score=125.91  Aligned_cols=80  Identities=14%  Similarity=0.199  Sum_probs=71.9

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCc-eeEEEEeeCC--CCCccceEEEEcCCHHHHHHHHHHhCCc--EecccceEEeh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGT-ITSCKVMRDP--NGISRGSGFVAFSTAEEASKALTEMNGK--MVVSKPLYVAL  396 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~-v~~v~i~~~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~--~~~g~~l~v~~  396 (467)
                      +.|||+|||..+++++|+++|+.||. |.++++.++.  .|+++|||||+|.+.++|.+|++.|++.  .++|+.|+|+|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            57999999999999999999999995 9999999875  4788999999999999999999999754  55799999999


Q ss_pred             hhhhH
Q 012257          397 AQRKE  401 (467)
Q Consensus       397 ~~~~~  401 (467)
                      |+++.
T Consensus        82 A~p~~   86 (96)
T d2disa1          82 AEPEI   86 (96)
T ss_dssp             SCSSC
T ss_pred             cCCCC
Confidence            98653

>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=99.73  E-value=7e-18  Score=118.51  Aligned_cols=76  Identities=21%  Similarity=0.369  Sum_probs=69.3

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      +.+++|||+||+  ++|++|+++|++||.|.+|++.+++      |||||+|.+.++|.+|++.|++..+.|+.|+|.|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~------~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTT------TEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCC------CEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            567899999986  8999999999999999999997553      69999999999999999999999999999999999


Q ss_pred             ccCc
Q 012257          117 YRDP  120 (467)
Q Consensus       117 ~~~~  120 (467)
                      ...|
T Consensus        75 ~~~P   78 (79)
T d2bz2a1          75 RKQP   78 (79)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            7553

>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=99.73  E-value=5.8e-18  Score=123.96  Aligned_cols=82  Identities=16%  Similarity=0.395  Sum_probs=72.8

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIM  114 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~  114 (467)
                      ..+++++|||+|||+++++++|+++|+.||.|..++     .+++++|||||+|.+.++|++|++.|++..+.|+.|+|.
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~   86 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            345689999999999999999999999999876654     367889999999999999999999999999999999999


Q ss_pred             ecccCcc
Q 012257          115 YSYRDPT  121 (467)
Q Consensus       115 ~~~~~~~  121 (467)
                      |+.....
T Consensus        87 ~a~~k~~   93 (96)
T d1fjca_          87 YTGEKGG   93 (96)
T ss_dssp             ECSSSCC
T ss_pred             EeCCCCC
Confidence            9876543

>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=99.72  E-value=2.1e-17  Score=121.12  Aligned_cols=80  Identities=21%  Similarity=0.441  Sum_probs=71.4

Q ss_pred             CCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC--ceee
Q 012257           35 RQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG--KPIR  112 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g--~~~~  112 (467)
                      .+.++++|||+|||+++++++|+++|++||.|..+++.+++      +||||+|.+.++|++|++.|++..|.|  +.|+
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~------~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~   86 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSS------CCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccc------cEEEeccCCHHHHHHHHHHhCCCEeCCCceEEE
Confidence            44578999999999999999999999999999999997653      699999999999999999999999976  4789


Q ss_pred             eeecccCc
Q 012257          113 IMYSYRDP  120 (467)
Q Consensus       113 v~~~~~~~  120 (467)
                      |.|+...+
T Consensus        87 v~~ak~~~   94 (97)
T d1whya_          87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEeCCCCC
Confidence            98887554

>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=99.72  E-value=4.2e-18  Score=128.52  Aligned_cols=74  Identities=23%  Similarity=0.468  Sum_probs=68.8

Q ss_pred             CceEEEecCCC-CCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          321 GLNLYVKNLDD-SISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       321 ~~~l~V~nlp~-~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      +++|||+||++ .+++++|+++|++||.|++|+++++.    +|+|||+|.+.++|.+|++.|||..|+|+.|+|+|++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            35899999964 69999999999999999999999873    6799999999999999999999999999999999986

>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=2.1e-18  Score=125.02  Aligned_cols=80  Identities=34%  Similarity=0.564  Sum_probs=71.6

Q ss_pred             CCceEEEecCCCCCCHHHHHH----hhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          320 EGLNLYVKNLDDSISDDKLKE----LFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~----~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ++++|||+|||..+++++|++    +|++||.|.+|++..  ++.++|||||+|.+.++|.+|++.|||..++|+.|+|+
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            356899999999999998864    689999999998754  46678999999999999999999999999999999999


Q ss_pred             hhhhhH
Q 012257          396 LAQRKE  401 (467)
Q Consensus       396 ~~~~~~  401 (467)
                      |++++.
T Consensus        80 ~ak~~~   85 (91)
T d1nu4a_          80 YAKTDS   85 (91)
T ss_dssp             ECSSCC
T ss_pred             EeCCCc
Confidence            998654

>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=5.3e-18  Score=121.67  Aligned_cols=74  Identities=22%  Similarity=0.363  Sum_probs=65.4

Q ss_pred             CceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          321 GLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       321 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      +.+|||+|||..+++++|+++|++|| ++.+++.     .++|||||+|.+.++|.+|++.|||..+.|++|+|+|++.+
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~-----~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee-----ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            45799999999999999999999999 3334443     35789999999999999999999999999999999998654

>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=99.72  E-value=9.9e-18  Score=116.09  Aligned_cols=73  Identities=23%  Similarity=0.257  Sum_probs=67.8

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      +|||+|||+.+++++|+++|+.||.|.++++..+.++. +++|||+|.+.++|.+|+. +|++.|+|+.|.|+.+
T Consensus         2 tv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~-~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           2 TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             EEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            79999999999999999999999999999999988665 5799999999999999985 8999999999999754

>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=99.72  E-value=4.1e-18  Score=129.14  Aligned_cols=76  Identities=24%  Similarity=0.296  Sum_probs=69.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ..++|||+|||..+++++|+++|++||.|.+|.|.+     ++|||||+|.+.++|.+|++.|||..|.|+.|.|+|+..
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~-----~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec-----cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            345899999999999999999999999999998854     478999999999999999999999999999999999864


Q ss_pred             h
Q 012257          400 K  400 (467)
Q Consensus       400 ~  400 (467)
                      .
T Consensus        84 ~   84 (111)
T d1whxa_          84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.72  E-value=3.9e-18  Score=124.91  Aligned_cols=77  Identities=27%  Similarity=0.435  Sum_probs=70.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      +.++|||+|||..+++++|+++|+.||.|..++.    ++.++|||||+|.+.++|.+|++.|||..++|+.|+|.|+.+
T Consensus        15 ~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~   90 (96)
T d1fjca_          15 AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            4568999999999999999999999999877653    567899999999999999999999999999999999999986


Q ss_pred             h
Q 012257          400 K  400 (467)
Q Consensus       400 ~  400 (467)
                      +
T Consensus        91 k   91 (96)
T d1fjca_          91 K   91 (96)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.72  E-value=7.2e-18  Score=125.77  Aligned_cols=80  Identities=21%  Similarity=0.421  Sum_probs=71.2

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCC--CCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDP--NGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .+.++|||+|||..+++++|+++|+.|| |.+++++.+.  ++.++|||||+|.+.++|.+|+ .||+..|+|+.|+|.+
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-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEE
Confidence            3567999999999999999999999999 7788887764  6788999999999999998766 5999999999999999


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      +.++
T Consensus        91 a~~~   94 (104)
T d1wi8a_          91 ADQA   94 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>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=99.72  E-value=1.2e-17  Score=115.69  Aligned_cols=73  Identities=19%  Similarity=0.357  Sum_probs=67.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeee
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMY  115 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~  115 (467)
                      ++|||+|||+++++++|+++|+.||.|.+|++..++..  .++||||+|.+.++|++|++ +++..|+|+.|.|..
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~   73 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSH   73 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEE
Confidence            58999999999999999999999999999999998754  34799999999999999996 899999999999864

>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=99.71  E-value=1.1e-17  Score=124.43  Aligned_cols=85  Identities=18%  Similarity=0.279  Sum_probs=75.0

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeE-EEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITS-CKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~-v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      ...+|||+|||+.+++++|+++|+.||.|.. +.+..+.+|.++|+|||+|.+.++|.+|+. |||..|+|+.|.|.++.
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            3457999999999999999999999999876 566677789999999999999999999996 89999999999999987


Q ss_pred             hhHHHHH
Q 012257          399 RKEERRA  405 (467)
Q Consensus       399 ~~~~~~~  405 (467)
                      ..+....
T Consensus        86 ~~~~~~~   92 (103)
T d2cpya1          86 LEDMREI   92 (103)
T ss_dssp             HHHHHHH
T ss_pred             HHHhhhh
Confidence            6655433

>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=99.71  E-value=6.3e-18  Score=125.21  Aligned_cols=81  Identities=17%  Similarity=0.259  Sum_probs=73.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      .....+|||+|||+++|+++|+++|+.|| |.+++++.+.++.++|||||+|.+.++|.+|++ +|+..|+||.|+|.++
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            34566899999999999999999999997 558899999999999999999999999999986 8999999999999988


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ...
T Consensus        90 ~~~   92 (102)
T d1weza_          90 STA   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            744

>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=99.71  E-value=1.2e-17  Score=122.48  Aligned_cols=76  Identities=21%  Similarity=0.325  Sum_probs=70.0

Q ss_pred             CCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecc--cceEEeh
Q 012257          319 FEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVS--KPLYVAL  396 (467)
Q Consensus       319 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v~~  396 (467)
                      .++++|||+|||..+++++|+++|++||.|..+++.++     +++|||+|.+.++|.+|++.|||..|.|  ++|+|+|
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            45679999999999999999999999999999999765     6799999999999999999999999976  5899999


Q ss_pred             hhh
Q 012257          397 AQR  399 (467)
Q Consensus       397 ~~~  399 (467)
                      ++.
T Consensus        90 ak~   92 (97)
T d1whya_          90 AKS   92 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            975

>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=99.71  E-value=1.6e-17  Score=125.30  Aligned_cols=76  Identities=30%  Similarity=0.416  Sum_probs=70.1

Q ss_pred             cCeEEEcCCCC-CCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           39 STSLYVGDLDL-SVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        39 ~~~l~v~nLp~-~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      +++|||+|||+ .++|++|+++|+.||.|.+|+|.+++     +|||||+|.+.++|.+|++.|++..|.|+.|+|.++.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            68999999965 59999999999999999999998875     4799999999999999999999999999999999986


Q ss_pred             cC
Q 012257          118 RD  119 (467)
Q Consensus       118 ~~  119 (467)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.71  E-value=1.4e-17  Score=115.31  Aligned_cols=71  Identities=20%  Similarity=0.450  Sum_probs=64.2

Q ss_pred             EEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          324 LYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       324 l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      |||+|||.++++++|+++|++|| +..+++.     +++|+|||+|.+.++|.+|+..|||..+.|++|+|+|++..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~-----~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-----KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-----TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec-----ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 5555553     35789999999999999999999999999999999999754

>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=99.71  E-value=6.1e-18  Score=121.25  Aligned_cols=72  Identities=25%  Similarity=0.277  Sum_probs=66.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeeccc
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYR  118 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~  118 (467)
                      .+|||+|||+++++++|+++|++||.|.++++.++       |||||+|.+.++|++|++.|++..|.|+.++|.+...
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            36999999999999999999999999999998654       6999999999999999999999999999999877643

>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=99.71  E-value=3.1e-17  Score=117.97  Aligned_cols=81  Identities=17%  Similarity=0.224  Sum_probs=72.3

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHh--CCcccCCce
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL--NFTPLNGKP  110 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l--~~~~~~g~~  110 (467)
                      .....++++|||+|||+++++++|+++|++||.|.++++.+++      ++|||+|.+.++|++|++.+  ++..+.|++
T Consensus         2 ~~~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~------~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~   75 (88)
T d2cq1a1           2 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEEAAITMVNYYSAVTPHLRNQP   75 (88)
T ss_dssp             CCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTT------TEEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccc------eEEEEEeCCHHHHHHHHHHHccCCCccCCCE
Confidence            3456789999999999999999999999999999999998654      69999999999999999865  567899999


Q ss_pred             eeeeecccC
Q 012257          111 IRIMYSYRD  119 (467)
Q Consensus       111 ~~v~~~~~~  119 (467)
                      |+|.|+...
T Consensus        76 l~v~~sk~~   84 (88)
T d2cq1a1          76 IYIQYSNHK   84 (88)
T ss_dssp             CEEEECSCS
T ss_pred             EEEEECCCC
Confidence            999998644

>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=99.71  E-value=2.2e-17  Score=118.81  Aligned_cols=79  Identities=18%  Similarity=0.349  Sum_probs=71.2

Q ss_pred             cCCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHh--CCcEecccceEE
Q 012257          317 DKFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM--NGKMVVSKPLYV  394 (467)
Q Consensus       317 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l--~g~~~~g~~l~v  394 (467)
                      +..++++|||+|||..+++++|+++|++||.|.++++.++     +++|||+|.+.++|.+|++.+  ++..+.|++|+|
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            3457889999999999999999999999999999998865     579999999999999999865  577899999999


Q ss_pred             ehhhhh
Q 012257          395 ALAQRK  400 (467)
Q Consensus       395 ~~~~~~  400 (467)
                      +|++.+
T Consensus        79 ~~sk~~   84 (88)
T d2cq1a1          79 QYSNHK   84 (88)
T ss_dssp             EECSCS
T ss_pred             EECCCC
Confidence            999754

>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=99.71  E-value=4.2e-18  Score=122.13  Aligned_cols=72  Identities=28%  Similarity=0.329  Sum_probs=67.6

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      +|||+|||..+++++|+++|++||.|.++++..+      |||||+|.+.++|.+|++.|||..|.|+.|+|.+++..
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            5999999999999999999999999999998654      79999999999999999999999999999999998654

>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=99.70  E-value=9.6e-17  Score=119.20  Aligned_cols=84  Identities=17%  Similarity=0.137  Sum_probs=72.9

Q ss_pred             CCCCCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHh--CCcccCCce
Q 012257           33 DARQFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL--NFTPLNGKP  110 (467)
Q Consensus        33 ~~~~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l--~~~~~~g~~  110 (467)
                      .....++++|||+|||.+++|++|+++|++||.|..+++.+++      |+|||+|.+.++|++|++.+  +...+.|++
T Consensus         9 ~~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k------~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~   82 (104)
T d1wexa_           9 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFENIDSAKECVTFAADVPVYIAGQQ   82 (104)
T ss_dssp             CCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTT------TEEEEEESSHHHHHHHHHHHHHSCCBSSSSB
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecc------eeEEEEeCCHHHHHHHHHHHcCCCcEEeeEE
Confidence            3445679999999999999999999999999999999997654      69999999999999999977  456789999


Q ss_pred             eeeeecccCccc
Q 012257          111 IRIMYSYRDPTI  122 (467)
Q Consensus       111 ~~v~~~~~~~~~  122 (467)
                      |+|.|+...+..
T Consensus        83 l~v~~s~~~~~~   94 (104)
T d1wexa_          83 AFFNYSTSKRIT   94 (104)
T ss_dssp             CEEEECSSSSCC
T ss_pred             EEEEEcCCCccC
Confidence            999998765443

>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=2e-17  Score=120.99  Aligned_cols=75  Identities=21%  Similarity=0.250  Sum_probs=69.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ...+|||+|||..+++++|+++|++||.|+++++..      +|||||+|.+.++|.+|++.|||..|.|+.|+|.|++.
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 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRV   87 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEec
Confidence            455799999999999999999999999999999864      47999999999999999999999999999999999875


Q ss_pred             h
Q 012257          400 K  400 (467)
Q Consensus       400 ~  400 (467)
                      .
T Consensus        88 ~   88 (98)
T d1wg4a_          88 Y   88 (98)
T ss_dssp             E
T ss_pred             C
Confidence            4

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=5.7e-17  Score=116.10  Aligned_cols=76  Identities=26%  Similarity=0.393  Sum_probs=68.7

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ..++|||+|||+++++++|+++|++||.|..+.+.+      ++|||||+|.+.++|.+|+..|++..+.|+.|+|.|+.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            468999999999999999999999999988777643      45799999999999999999999999999999999986


Q ss_pred             cC
Q 012257          118 RD  119 (467)
Q Consensus       118 ~~  119 (467)
                      +.
T Consensus        81 P~   82 (86)
T d2cpda1          81 PV   82 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.70  E-value=1e-17  Score=117.88  Aligned_cols=74  Identities=30%  Similarity=0.488  Sum_probs=67.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCc-ccCCceeeeeeccc
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFT-PLNGKPIRIMYSYR  118 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~-~~~g~~~~v~~~~~  118 (467)
                      ++|||+|||.++++++|+++|++||.|.++.+.+.      +|||||+|.+.++|.+|++.|++. .+.|+.|+|.|+.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            57999999999999999999999999887777654      479999999999999999999985 69999999999875


Q ss_pred             C
Q 012257          119 D  119 (467)
Q Consensus       119 ~  119 (467)
                      +
T Consensus        76 k   76 (80)
T d2cqha1          76 K   76 (80)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=6.6e-18  Score=121.38  Aligned_cols=75  Identities=19%  Similarity=0.365  Sum_probs=67.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhhh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQR  399 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~~  399 (467)
                      ..++|||+|||..+++++|+++|++||.|.+|++..+    +++||||+|.+.++|.+|+.  +++.|+|+.|+|+++++
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~----~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCC
Confidence            4568999999999999999999999999999987654    57899999999999999985  88899999999999875


Q ss_pred             h
Q 012257          400 K  400 (467)
Q Consensus       400 ~  400 (467)
                      +
T Consensus        78 k   78 (88)
T d1wf0a_          78 K   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.69  E-value=3.2e-17  Score=122.82  Aligned_cols=78  Identities=18%  Similarity=0.160  Sum_probs=70.2

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc--CCceeeeee
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL--NGKPIRIMY  115 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~--~g~~~~v~~  115 (467)
                      +..+|||+|||++++|++|+++|++||.|.+|.+.+++    ++|+|||+|.+.++|++|++.|++..+  .|+.++|.+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            47889999999999999999999999999999999875    468999999999999999999999988  577888888


Q ss_pred             cccC
Q 012257          116 SYRD  119 (467)
Q Consensus       116 ~~~~  119 (467)
                      +...
T Consensus        82 s~~~   85 (108)
T d2adba1          82 SKLT   85 (108)
T ss_dssp             CSSC
T ss_pred             cCCc
Confidence            7654

>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=99.69  E-value=2.2e-17  Score=122.77  Aligned_cols=82  Identities=21%  Similarity=0.266  Sum_probs=72.4

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeE-EEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITS-CKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~-v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .....+|||+|||+.+|+++|+++|+.+|.|.. +.+..+.++.++|+|||+|.+.++|.+|++ +|+..|+||.|+|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            345557999999999999999999999999877 455556688999999999999999999996 899999999999998


Q ss_pred             hhhh
Q 012257          397 AQRK  400 (467)
Q Consensus       397 ~~~~  400 (467)
                      +.+.
T Consensus        91 ~~~~   94 (104)
T d1wg5a_          91 SSRA   94 (104)
T ss_dssp             ECTT
T ss_pred             CCHH
Confidence            8755

>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=99.69  E-value=3e-17  Score=117.69  Aligned_cols=76  Identities=18%  Similarity=0.225  Sum_probs=66.2

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      .+++|||+|||+++++++|+++|++||. ..+.+      ++++|||||+|.+.++|++|++.|++..+.|+.|+|.++.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcCc-eeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4689999999999999999999999993 23333      3456899999999999999999999999999999999986


Q ss_pred             cCc
Q 012257          118 RDP  120 (467)
Q Consensus       118 ~~~  120 (467)
                      .+.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.69  E-value=1.6e-17  Score=123.52  Aligned_cols=79  Identities=11%  Similarity=0.168  Sum_probs=71.7

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ..++|||+|||+++++++|+++|+.||.|..+.++.+..+|+++|+|||+|.+.++|++|++ +++..|.|+.|.|.++.
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            45789999999999999999999999998876666666789999999999999999999996 89999999999998753

>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=99.69  E-value=6e-17  Score=118.82  Aligned_cols=80  Identities=15%  Similarity=0.208  Sum_probs=70.4

Q ss_pred             CCCccCeEEEcCCCCC-CCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHH--HhCCcccCCcee
Q 012257           35 RQFVSTSLYVGDLDLS-VNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALD--ELNFTPLNGKPI  111 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~-~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~--~l~~~~~~g~~~  111 (467)
                      ...++++|||+|||.+ +++++|+++|+.||.|.+|.+.+++      |+|||+|.+.++|.+|++  .+++..+.|+.|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k------~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK------SQAFIEMETREDAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT------TEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecC------CcEEEEecchHHHHHHHHHHhcCCceECCEEE
Confidence            3456889999999985 8999999999999999999998654      699999999999999997  467888999999


Q ss_pred             eeeecccCc
Q 012257          112 RIMYSYRDP  120 (467)
Q Consensus       112 ~v~~~~~~~  120 (467)
                      +|.++....
T Consensus        88 ~V~~s~~~~   96 (99)
T d1x4fa1          88 KVDLSEKYK   96 (99)
T ss_dssp             EEEEECSCS
T ss_pred             EEEEcCCcc
Confidence            999986543

>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=99.68  E-value=2e-17  Score=123.97  Aligned_cols=78  Identities=19%  Similarity=0.321  Sum_probs=70.7

Q ss_pred             CCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEe--cccceEEehh
Q 012257          320 EGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV--VSKPLYVALA  397 (467)
Q Consensus       320 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~--~g~~l~v~~~  397 (467)
                      +..+|||+|||+.+|+++|+++|++||.|.++++..++   ++|+|||+|.+.++|.+|+..|||..|  .|++|+|.|+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~---~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s   82 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS   82 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEEC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC---CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEec
Confidence            44579999999999999999999999999999998764   478999999999999999999999998  5789999998


Q ss_pred             hhh
Q 012257          398 QRK  400 (467)
Q Consensus       398 ~~~  400 (467)
                      ++.
T Consensus        83 ~~~   85 (108)
T d2adba1          83 KLT   85 (108)
T ss_dssp             SSC
T ss_pred             CCc
Confidence            754

>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=99.68  E-value=2.2e-17  Score=118.61  Aligned_cols=78  Identities=17%  Similarity=0.276  Sum_probs=68.5

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      ..+++|||+|||++++|++|+++|++||.|.+|++..     .++|||||+|.+.++|++|+.  ++..|.|+.|+|.++
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            4589999999999999999999999999999997643     356899999999999999995  677899999999998


Q ss_pred             ccCcc
Q 012257          117 YRDPT  121 (467)
Q Consensus       117 ~~~~~  121 (467)
                      .....
T Consensus        76 ~~k~~   80 (88)
T d1wf0a_          76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            65443

>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=99.68  E-value=3.9e-17  Score=123.07  Aligned_cols=80  Identities=14%  Similarity=0.198  Sum_probs=72.6

Q ss_pred             CccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           37 FVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      .+..+|||+|||+++++++|+++|+.||.+..+.++.+..+|.++|+|||+|.+.++|++|++ +++..|.|+.|+|..+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            356799999999999999999999999998877777777789999999999999999999996 8999999999999765


Q ss_pred             c
Q 012257          117 Y  117 (467)
Q Consensus       117 ~  117 (467)
                      .
T Consensus        95 ~   95 (112)
T d1wela1          95 T   95 (112)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=8.9e-17  Score=119.37  Aligned_cols=78  Identities=19%  Similarity=0.265  Sum_probs=70.0

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhC--CcEecccceEEe
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN--GKMVVSKPLYVA  395 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~--g~~~~g~~l~v~  395 (467)
                      ..++++|||+|||..+++++|+++|++||.|.++++.++     +++|||+|.+.++|.+|+..|+  +..+.|++|+|.
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~   86 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEE
Confidence            456779999999999999999999999999999999764     6799999999999999999884  557789999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++.+
T Consensus        87 ~s~~~   91 (104)
T d1wexa_          87 YSTSK   91 (104)
T ss_dssp             ECSSS
T ss_pred             EcCCC
Confidence            99754

>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=99.67  E-value=1.8e-16  Score=109.60  Aligned_cols=71  Identities=15%  Similarity=0.264  Sum_probs=63.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecccC
Q 012257           42 LYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSYRD  119 (467)
Q Consensus        42 l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~~~  119 (467)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.++|++|++.||+..+.|+.|+|.++..+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 444444      345689999999999999999999999999999999998654

>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=99.67  E-value=6.2e-17  Score=118.74  Aligned_cols=77  Identities=22%  Similarity=0.290  Sum_probs=69.3

Q ss_pred             CCCceEEEecCCCC-CCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHH--HhCCcEecccceEEe
Q 012257          319 FEGLNLYVKNLDDS-ISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALT--EMNGKMVVSKPLYVA  395 (467)
Q Consensus       319 ~~~~~l~V~nlp~~-~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~--~l~g~~~~g~~l~v~  395 (467)
                      ..+++|||+|||.. +|+++|+++|++||.|.++++.++     +|+|||+|.+.++|.+|++  .+++..++|+.|+|+
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~   90 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   90 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEE
Confidence            45678999999975 899999999999999999999865     6799999999999999998  578889999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++.+
T Consensus        91 ~s~~~   95 (99)
T d1x4fa1          91 LSEKY   95 (99)
T ss_dssp             EECSC
T ss_pred             EcCCc
Confidence            99754

>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=99.65  E-value=1.4e-16  Score=117.59  Aligned_cols=76  Identities=18%  Similarity=0.225  Sum_probs=67.5

Q ss_pred             CCceEEEecCCCCC-CH----HHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEE
Q 012257          320 EGLNLYVKNLDDSI-SD----DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYV  394 (467)
Q Consensus       320 ~~~~l~V~nlp~~~-~~----~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  394 (467)
                      ...+|||+||+..+ ++    ++|+++|++||.|.++++++.     +++|||+|.+.++|.+|++.|||..|+|+.|+|
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v   78 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC-----CCEEEEEECCHHHHHHHHHHhcccccCCCEeEE
Confidence            45589999999876 33    569999999999999999863     679999999999999999999999999999999


Q ss_pred             ehhhhh
Q 012257          395 ALAQRK  400 (467)
Q Consensus       395 ~~~~~~  400 (467)
                      .|+++.
T Consensus        79 ~~a~~~   84 (104)
T d1weya_          79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             eecccC
Confidence            999644

>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=1.5e-16  Score=113.96  Aligned_cols=77  Identities=21%  Similarity=0.316  Sum_probs=68.9

Q ss_pred             CCCceEEEecCCCC-CCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHh--CCcEecccceEEe
Q 012257          319 FEGLNLYVKNLDDS-ISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEM--NGKMVVSKPLYVA  395 (467)
Q Consensus       319 ~~~~~l~V~nlp~~-~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l--~g~~~~g~~l~v~  395 (467)
                      ..+++|||+|||.. +|++||.++|++||.|.++++..+     +++|||+|++.++|.+|++.|  ++..+.|++|+|+
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~   80 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   80 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEE
Confidence            46678999999985 789999999999999999999875     469999999999999999966  6778999999999


Q ss_pred             hhhhh
Q 012257          396 LAQRK  400 (467)
Q Consensus       396 ~~~~~  400 (467)
                      |++..
T Consensus        81 ~s~~~   85 (89)
T d1x4da1          81 LSQKY   85 (89)
T ss_dssp             EECCC
T ss_pred             ECCCc
Confidence            98753

>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=99.64  E-value=2.3e-16  Score=113.03  Aligned_cols=79  Identities=18%  Similarity=0.250  Sum_probs=70.4

Q ss_pred             CCCccCeEEEcCCCCC-CCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHh--CCcccCCcee
Q 012257           35 RQFVSTSLYVGDLDLS-VNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL--NFTPLNGKPI  111 (467)
Q Consensus        35 ~~~~~~~l~v~nLp~~-~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l--~~~~~~g~~~  111 (467)
                      +..++++|||+|||.. ++++||+++|+.||.|.+|.+.+++      ++|||+|++.++|.+|++.+  ++..+.|++|
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l   77 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            4567999999999986 8899999999999999999998765      48999999999999999966  5677999999


Q ss_pred             eeeecccC
Q 012257          112 RIMYSYRD  119 (467)
Q Consensus       112 ~v~~~~~~  119 (467)
                      +|.|+...
T Consensus        78 ~V~~s~~~   85 (89)
T d1x4da1          78 RVHLSQKY   85 (89)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCc
Confidence            99998644

>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=99.64  E-value=2.1e-16  Score=119.02  Aligned_cols=85  Identities=20%  Similarity=0.349  Sum_probs=74.9

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeE-EEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEeh
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITS-CKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVAL  396 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~-v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  396 (467)
                      .....+|||+|||+.+|+++|+++|+.||.|.. +.+..+.+|.++|+|||+|.+.++|.+|++ |||..|+|+.|.|..
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            345668999999999999999999999999876 455566789999999999999999999996 899999999999999


Q ss_pred             hhhhHHH
Q 012257          397 AQRKEER  403 (467)
Q Consensus       397 ~~~~~~~  403 (467)
                      +......
T Consensus        94 ~~~~~~~  100 (112)
T d1wela1          94 ITKKGML  100 (112)
T ss_dssp             ECHHHHH
T ss_pred             cChHHHH
Confidence            8766543

>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=1.2e-17  Score=120.76  Aligned_cols=78  Identities=15%  Similarity=0.412  Sum_probs=68.4

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEE-----ecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeee
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVC-----RDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRI  113 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~-----~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v  113 (467)
                      .|+|||+|||++++|++|+++|+.||.|.++.+.     .+..+++++|||||+|.+.++|++|++ |++..+.|+.|+|
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V   79 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKI   79 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCC
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEE
Confidence            3799999999999999999999999976665553     455677899999999999999999996 9999999999999


Q ss_pred             eecc
Q 012257          114 MYSY  117 (467)
Q Consensus       114 ~~~~  117 (467)
                      ..+.
T Consensus        80 ~r~k   83 (90)
T d1u2fa_          80 RRPH   83 (90)
T ss_dssp             BCTT
T ss_pred             CCCC
Confidence            7543

>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=99.62  E-value=2.1e-17  Score=121.97  Aligned_cols=75  Identities=19%  Similarity=0.373  Sum_probs=71.0

Q ss_pred             eEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehh
Q 012257          323 NLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALA  397 (467)
Q Consensus       323 ~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~  397 (467)
                      .++|.+++..++|++|+++|++||.|++|+|.++.+|+++|+|||+|.+.++|.+|++.|||+.++|+.|+|+|.
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            377788888899999999999999999999999999999999999999999999999999999999999999985

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=3e-15  Score=110.28  Aligned_cols=77  Identities=16%  Similarity=0.185  Sum_probs=68.2

Q ss_pred             CccCeEEEcCCCCCC-CH----HHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCcee
Q 012257           37 FVSTSLYVGDLDLSV-ND----SQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPI  111 (467)
Q Consensus        37 ~~~~~l~v~nLp~~~-~e----~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~  111 (467)
                      ..+++|||+||+.++ ++    ++|+++|+.||.|.++++.+.      ++||||+|.+.++|.+|++.|++..|.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            457899999999986 33    569999999999999999854      4699999999999999999999999999999


Q ss_pred             eeeecccC
Q 012257          112 RIMYSYRD  119 (467)
Q Consensus       112 ~v~~~~~~  119 (467)
                      +|.|+...
T Consensus        77 ~v~~a~~~   84 (104)
T d1weya_          77 KLYFAQTL   84 (104)
T ss_dssp             EEECCCCS
T ss_pred             EEeecccC
Confidence            99998644

>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=99.55  E-value=4e-17  Score=118.01  Aligned_cols=76  Identities=16%  Similarity=0.317  Sum_probs=66.1

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEee------CCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEe
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMR------DPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVA  395 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~------~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~  395 (467)
                      ++|||+|||..+++++|+++|+.||.|..+.+..      ...+.++|||||+|.+.++|.+|++ |||..+.|+.|+|+
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            4799999999999999999999999887766542      2356789999999999999999985 99999999999997


Q ss_pred             hhh
Q 012257          396 LAQ  398 (467)
Q Consensus       396 ~~~  398 (467)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.52  E-value=8.6e-15  Score=107.24  Aligned_cols=73  Identities=23%  Similarity=0.395  Sum_probs=62.2

Q ss_pred             CCCCceEEEec--CCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEec-ccceEE
Q 012257          318 KFEGLNLYVKN--LDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVV-SKPLYV  394 (467)
Q Consensus       318 ~~~~~~l~V~n--lp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~-g~~l~v  394 (467)
                      ..++.+|+|.|  ||..+|+++|+++|++||.|+++++.++     ++||||+|.+.++|.+|++.|||+.+. ++.+.+
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i~~~~~~~i   89 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCCCCCCCcEE
Confidence            34567899965  9999999999999999999999998765     579999999999999999999999884 444433


Q ss_pred             e
Q 012257          395 A  395 (467)
Q Consensus       395 ~  395 (467)
                      .
T Consensus        90 ~   90 (101)
T d2cq2a1          90 T   90 (101)
T ss_dssp             E
T ss_pred             E
Confidence            3

>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=99.52  E-value=5.1e-16  Score=114.47  Aligned_cols=76  Identities=21%  Similarity=0.346  Sum_probs=71.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeec
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYS  116 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~  116 (467)
                      +.++|++++.+++|++|+++|++||.|.+|+|.++ .+++++|+|||+|.+.++|.+|++.|++..+.|+.|+|.++
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 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            56889999999999999999999999999999877 58999999999999999999999999999999999999875

>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=99.51  E-value=2.2e-14  Score=107.71  Aligned_cols=74  Identities=23%  Similarity=0.295  Sum_probs=65.4

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCH-HHHHHHHHHhCCcEecccceEEehhhhh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTA-EEASKALTEMNGKMVVSKPLYVALAQRK  400 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~-~~A~~A~~~l~g~~~~g~~l~v~~~~~~  400 (467)
                      ..+||+|||..+|+++|+++|++||.|.+|+|+++     +|||||.|.+. ++|..|+..+++..+.++.+.|.++...
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~   86 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   86 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeecc
Confidence            35699999999999999999999999999999865     68999999995 7899999999999998888777776533

>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=3.1e-14  Score=104.23  Aligned_cols=66  Identities=24%  Similarity=0.367  Sum_probs=59.1

Q ss_pred             CCCccCeEEEcC--CCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCccc
Q 012257           35 RQFVSTSLYVGD--LDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPL  106 (467)
Q Consensus        35 ~~~~~~~l~v~n--Lp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~  106 (467)
                      .+.++++|+|.|  ||.+++|++|+++|++||.|.+|.+.+++      +||||+|.+.++|.+|++.|++..+
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k------~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC------SCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCc------cEEEEEECCHHHHHHHHHHhCCCCC
Confidence            456688999955  99999999999999999999999887654      5999999999999999999999876

>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=99.46  E-value=8.6e-14  Score=101.48  Aligned_cols=83  Identities=13%  Similarity=0.153  Sum_probs=71.4

Q ss_pred             CCCCCccCeEEEcCC--CCCCC---------HHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHh
Q 012257           33 DARQFVSTSLYVGDL--DLSVN---------DSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDEL  101 (467)
Q Consensus        33 ~~~~~~~~~l~v~nL--p~~~~---------e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l  101 (467)
                      +++.+.+++|+|.||  |.++.         +++|++.|++||.|..|++..+.    .+|+|||+|.+.++|.+|++.|
T Consensus         2 p~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~----~~G~~fV~f~~~e~A~~A~~~l   77 (99)
T d2dita1           2 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTL   77 (99)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC----TTCEEEEECSCHHHHHHHHHHS
T ss_pred             CCCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC----CccEEEEEECCHHHHHHHHHHh
Confidence            567788999999999  65432         26789999999999999987653    4589999999999999999999


Q ss_pred             CCcccCCceeeeeecccC
Q 012257          102 NFTPLNGKPIRIMYSYRD  119 (467)
Q Consensus       102 ~~~~~~g~~~~v~~~~~~  119 (467)
                      ++..+.|+.|+|.+....
T Consensus        78 ng~~~~gr~i~v~~~~g~   95 (99)
T d2dita1          78 DGRWFGGRQITAQAWDGT   95 (99)
T ss_dssp             TTCEETTEECEEEECCSC
T ss_pred             CCcEECCEEEEEEEeCCc
Confidence            999999999999987544

>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=99.45  E-value=8e-14  Score=101.66  Aligned_cols=79  Identities=18%  Similarity=0.252  Sum_probs=67.2

Q ss_pred             CCCceEEEecC--CCCC---------CHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEe
Q 012257          319 FEGLNLYVKNL--DDSI---------SDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMV  387 (467)
Q Consensus       319 ~~~~~l~V~nl--p~~~---------~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  387 (467)
                      -.+++|+|.|+  |.++         .+++|++.|++||.|..|++..+   ..+|+|||+|.+.++|.+|+..|||+.+
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            35668999999  4432         13689999999999999988765   3578999999999999999999999999


Q ss_pred             cccceEEehhhhh
Q 012257          388 VSKPLYVALAQRK  400 (467)
Q Consensus       388 ~g~~l~v~~~~~~  400 (467)
                      +|+.|+|+|+.++
T Consensus        83 ~gr~i~v~~~~g~   95 (99)
T d2dita1          83 GGRQITAQAWDGT   95 (99)
T ss_dssp             TTEECEEEECCSC
T ss_pred             CCEEEEEEEeCCc
Confidence            9999999998643

>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=99.43  E-value=7.9e-14  Score=102.90  Aligned_cols=83  Identities=17%  Similarity=0.330  Sum_probs=70.5

Q ss_pred             CCCceEEEecC--CCCCC--------HHHHHHhhccCCceeEEEEeeCCCC---CccceEEEEcCCHHHHHHHHHHhCCc
Q 012257          319 FEGLNLYVKNL--DDSIS--------DDKLKELFSEFGTITSCKVMRDPNG---ISRGSGFVAFSTAEEASKALTEMNGK  385 (467)
Q Consensus       319 ~~~~~l~V~nl--p~~~~--------~~~l~~~F~~~G~v~~v~i~~~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~  385 (467)
                      .+++.|.|.|+  +..+.        .++|++.|++||.|++|+|.++..+   ...|++||+|.+.++|.+|+..|||+
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            35678999999  54443        3579999999999999999887643   34689999999999999999999999


Q ss_pred             EecccceEEehhhhhH
Q 012257          386 MVVSKPLYVALAQRKE  401 (467)
Q Consensus       386 ~~~g~~l~v~~~~~~~  401 (467)
                      .++||.|.+.|.....
T Consensus        82 ~f~gR~v~v~f~~~~~   97 (104)
T d1o0pa_          82 KFANRVVVTKYCDPDS   97 (104)
T ss_dssp             CSSSSCCEEEEECHHH
T ss_pred             EECCeEEEEEEcCHHH
Confidence            9999999999987543

>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=99.43  E-value=1.4e-13  Score=103.28  Aligned_cols=73  Identities=19%  Similarity=0.245  Sum_probs=64.3

Q ss_pred             cCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecCh-HHHHHHHHHhCCcccCCceeeeeecc
Q 012257           39 STSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAA-HEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        39 ~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~-~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      ...+||+|||.++|+++|+++|++||+|.+|.|+++      +|||||.|.+. ++|..|+..+++..+.++.+.|.+..
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            345699999999999999999999999999999865      37999999996 68999999999998888888877654

>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=99.41  E-value=2.1e-13  Score=94.74  Aligned_cols=73  Identities=16%  Similarity=0.176  Sum_probs=61.8

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccc-eEEehhhhh
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKP-LYVALAQRK  400 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~-l~v~~~~~~  400 (467)
                      +.|+|+|+|+..+++.| ++|++||+|.++++.++     ++||||+|.+.++|.+|++ +||..++|+. |.|.-+..+
T Consensus         5 ~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~-----~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1           5 TWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             GEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS-----SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             cEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC-----CCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCCh
Confidence            46999999999887655 57999999999987543     6899999999999999995 9999999985 668776655


Q ss_pred             H
Q 012257          401 E  401 (467)
Q Consensus       401 ~  401 (467)
                      .
T Consensus        78 ~   78 (81)
T d1wwha1          78 N   78 (81)
T ss_dssp             H
T ss_pred             h
Confidence            3

>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=99.38  E-value=3.9e-13  Score=93.32  Aligned_cols=72  Identities=14%  Similarity=0.104  Sum_probs=60.5

Q ss_pred             ccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCce-eeeeec
Q 012257           38 VSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKP-IRIMYS  116 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~-~~v~~~  116 (467)
                      +.+.|+|+|+|++++++ +.++|++||+|.++++.+      ++|||||+|.+.++|++|++ +|+..+.|+. +.|...
T Consensus         3 ~~~wV~V~G~p~~~~~~-il~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           3 DDTWVTVFGFPQASASY-ILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHH-HHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cccEEEEECCChHHHHH-HHHHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            46789999999998865 556899999999998754      34799999999999999996 8999999985 567665


Q ss_pred             c
Q 012257          117 Y  117 (467)
Q Consensus       117 ~  117 (467)
                      .
T Consensus        75 ~   75 (81)
T d1wwha1          75 I   75 (81)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.36  E-value=3.8e-13  Score=99.14  Aligned_cols=81  Identities=14%  Similarity=0.203  Sum_probs=69.4

Q ss_pred             CccCeEEEcCC--CCCCC--------HHHHHHHHhcCCCeEEEEEEecCCCC--ccccEEEEEecChHHHHHHHHHhCCc
Q 012257           37 FVSTSLYVGDL--DLSVN--------DSQLYDLFNQMGQVVSVRVCRDLSTR--RSLGYGYVNYNAAHEATRALDELNFT  104 (467)
Q Consensus        37 ~~~~~l~v~nL--p~~~~--------e~~l~~~f~~~G~v~~v~i~~~~~~~--~~~g~afV~f~~~~~A~~A~~~l~~~  104 (467)
                      .++++|.|.|+  |.++.        .++|++.|++||.|++|.|.++..+.  ...|++||+|.+.++|.+|++.|++.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            46899999999  55543        24689999999999999998866543  35589999999999999999999999


Q ss_pred             ccCCceeeeeecc
Q 012257          105 PLNGKPIRIMYSY  117 (467)
Q Consensus       105 ~~~g~~~~v~~~~  117 (467)
                      .+.||.|.+.+..
T Consensus        82 ~f~gR~v~v~f~~   94 (104)
T d1o0pa_          82 KFANRVVVTKYCD   94 (104)
T ss_dssp             CSSSSCCEEEEEC
T ss_pred             EECCeEEEEEEcC
Confidence            9999999998864

>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=98.14  E-value=2.9e-06  Score=53.81  Aligned_cols=60  Identities=22%  Similarity=0.298  Sum_probs=53.6

Q ss_pred             HHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEecccceEEehhh
Q 012257          337 KLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVVSKPLYVALAQ  398 (467)
Q Consensus       337 ~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~~~  398 (467)
                      .|.+.|+++|.|.++.+....+|..  .|-|...+.++|.-|+..||.+.|++++|.|+|+.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            4456789999999999988877765  78999999999999999999999999999999875

>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=97.90  E-value=1.2e-05  Score=53.77  Aligned_cols=73  Identities=15%  Similarity=0.262  Sum_probs=58.1

Q ss_pred             CCCCceEEEecCCCCC------CH---HHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhCCcEec
Q 012257          318 KFEGLNLYVKNLDDSI------SD---DKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMNGKMVV  388 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~------~~---~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~  388 (467)
                      .++.-+|.|.=.....      .|   .+|.+.|..||+|.-+|+..+       ..+|+|.+-++|.+|+. ++|..++
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al~-l~g~~v~   83 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHhc-cCCeEEc
Confidence            3444567675443222      22   477888999999999999887       89999999999999996 8999999


Q ss_pred             ccceEEehhh
Q 012257          389 SKPLYVALAQ  398 (467)
Q Consensus       389 g~~l~v~~~~  398 (467)
                      |+.|.|+...
T Consensus        84 G~~l~It~~~   93 (95)
T d1ufwa_          84 GRAVKISGPS   93 (95)
T ss_dssp             TEEEEEECCC
T ss_pred             ceEEEEecCC
Confidence            9999998643

>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=97.78  E-value=6.7e-05  Score=51.32  Aligned_cols=67  Identities=10%  Similarity=0.145  Sum_probs=55.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCc-c-ccEEEEEecChHHHHHHHHHhCCccc
Q 012257           40 TSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRR-S-LGYGYVNYNAAHEATRALDELNFTPL  106 (467)
Q Consensus        40 ~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~-~-~g~afV~f~~~~~A~~A~~~l~~~~~  106 (467)
                      ++|.|+.||+.++|+++.+.+...|.+........+.+.+ + ..-|||.|.+.++.....+..++..|
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F   70 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            6899999999999999999999999887777666544432 2 24799999999999999999888766

>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=97.76  E-value=1.5e-05  Score=53.28  Aligned_cols=69  Identities=19%  Similarity=0.358  Sum_probs=56.3

Q ss_pred             ccCeEEEcCCCCCCCH---------HHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCC
Q 012257           38 VSTSLYVGDLDLSVND---------SQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNG  108 (467)
Q Consensus        38 ~~~~l~v~nLp~~~~e---------~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g  108 (467)
                      +.-+|.|.=..++..+         .+|.+.|..||+|.-|++..+        ..+|+|.+-++|.+|++ +++..+.|
T Consensus        14 pDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G   84 (95)
T d1ufwa_          14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             CCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcc
Confidence            4567777655444333         368899999999999999876        47999999999999997 89999999


Q ss_pred             ceeeeee
Q 012257          109 KPIRIMY  115 (467)
Q Consensus       109 ~~~~v~~  115 (467)
                      +.|+|..
T Consensus        85 ~~l~It~   91 (95)
T d1ufwa_          85 RAVKISG   91 (95)
T ss_dssp             EEEEEEC
T ss_pred             eEEEEec
Confidence            9999864

>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=97.61  E-value=0.00012  Score=46.36  Aligned_cols=65  Identities=18%  Similarity=0.250  Sum_probs=53.5

Q ss_pred             CCCHHH----HHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhCCcccCCceeeeeecc
Q 012257           50 SVNDSQ----LYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELNFTPLNGKPIRIMYSY  117 (467)
Q Consensus        50 ~~~e~~----l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~~~v~~~~  117 (467)
                      .+++.+    |.+.|+++|.|+++.+.... .|..  .|-|...+.+||.-|++.|+-..|.+++|.|.++.
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~-dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHT-DYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCC-STTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEecc-CCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            345555    55788999999999998653 3333  79999999999999999999999999999997653

>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=97.61  E-value=0.00022  Score=48.72  Aligned_cols=68  Identities=9%  Similarity=0.216  Sum_probs=58.6

Q ss_pred             ceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCC--C-CccceEEEEcCCHHHHHHHHHHhCCcEecc
Q 012257          322 LNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPN--G-ISRGSGFVAFSTAEEASKALTEMNGKMVVS  389 (467)
Q Consensus       322 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~--~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  389 (467)
                      ++|.|+.||+.+|++++.+.++..|.+........+.  + ....-|+|.|.+.++.....+..+|+.+.+
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            3699999999999999999999999998888777652  1 223689999999999999999999999954

>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=96.71  E-value=0.003  Score=42.92  Aligned_cols=59  Identities=24%  Similarity=0.339  Sum_probs=49.6

Q ss_pred             CCCCceEEEecCCCCCCHHHHHHhhccCCceeEEEEeeCCCCCccceEEEEcCCHHHHHHHHHHhC
Q 012257          318 KFEGLNLYVKNLDDSISDDKLKELFSEFGTITSCKVMRDPNGISRGSGFVAFSTAEEASKALTEMN  383 (467)
Q Consensus       318 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  383 (467)
                      .+....||.-..|..|...||.++|++||.| .|-.+.+.      .|||...+.++|..++..++
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V-~VswIddT------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEETT------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCce-EEEEecCc------eEEEEecCHHHHHHHHHHhc
Confidence            4456679999999999999999999999998 55555542      89999999999998887654

>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=96.04  E-value=0.019  Score=38.86  Aligned_cols=59  Identities=17%  Similarity=0.253  Sum_probs=47.7

Q ss_pred             CCccCeEEEcCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCccccEEEEEecChHHHHHHHHHhC
Q 012257           36 QFVSTSLYVGDLDLSVNDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNYNAAHEATRALDELN  102 (467)
Q Consensus        36 ~~~~~~l~v~nLp~~~~e~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~  102 (467)
                      ......||.-..|..=...||.++|+.||.|.=-+| -|.       .|||...+.++|+.+++.+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-ddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cCc-------eEEEEecCHHHHHHHHHHhc
Confidence            445667999999999999999999999998743333 332       69999999999999987543