Citrus Sinensis ID: 009944

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520--
Protein Sequence
MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccEEEEEccccccHHHHHHHHHHHHHHHccccccccccEEEEEEEcccccEEEEEEccHHHHHHHHHccccccccEEEEEcccccccccccccccccccccccHHHHHccccccccccccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccEEEEEEcccccccccccHHHHHHHHHHHHHHHcccccEEEEEEccccccccccccccEEEEEEccHHHHHHHHHHHcccEEcccEEEEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccHHccccccccccccccccccccccccccccEEEEEccccccccHHHHHHHHHHHHHHHccccccccccEEEEEEcccccEEEEEEEcHHHHHHHHHcccEEEcccEEEEEcccccccccccccccccccccccHHccccccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHHcccEEccEEcEEEEcccccccccccccccccccHHHHHHHHHHcccccccHHccccccccccccEEEEEcccccHHHHcccHHHHHHHHHHHHHHHHcccEEEEEEcccccccccccccEEEEEEEccHHHHHHHHHHHccccccccEEEEEEEcHHHHccccccc
Coil and Loop (DISEMBL)
msgrdirydavgegsrhksswvsgrsrtgergrdrhhrdfksggddrrrdknykydregirdhdrtdrhrdynrdkerrhrhrsrshssdrfrnrskslspsrspskskrrsgfdmappaaamlpgaavpgqlpgvpsavpemaqnmlpfgatqlgafplmpvQVMTQQATRHARRvyvgglpplanEQAIATFFSQVMTaiggnsagpgdAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAvrvrrptdynptlaaalgpgqpspnlnLAAVGLasgaiggaegpdrvfvgglpyyfTETQIKELLESFgtlhgfdlvkdrdtgnskgygfcvyqdpavtDIACAALNglkmgdktLTVRRatassgqsktEQESILAQAQQHIAIQKMALQTsgmntlgggmslFGETLAKVLCLTEAITadaladdeEYEEILEDMREECgkygtlvnvviprpdqnggetpgvgKVFLEYYDAvgcataknalsgrkfggntvnafyypedkyfnkdysa
Flexible Loop (DISEMBL)
msgrdirydavgegsrhksswvsgrsrtgergrdrhhrdfksggddrrrdknykydregirdhdrtdrhrdynrdkerrhrhrsrshssdrfrnrskslspsrspskskrrsgFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATassgqskteQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNvviprpdqnggeTPGVGKVFLEYYDAVGCATAknalsgrkfggntvnafyypedkyfnkdysa
Low Complexity Region (SEG)
MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGddrrrdknykydrEGIrdhdrtdrhrdynrdKErrhrhrsrshssdrfrnrskslspsrspskskrrsGFDmappaaamlpgaavpgQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESilaqaqqhiaiqKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITadaladdeeyeeiledmreeCGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA
Disordered region (IsUnstruct)
**************************************************************************************************************************************************MLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM*************GIIFEGVAVRVRRPTDYNPTLAAAL********LNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL*************************HIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADAL*******************YGTLVNVVIP********TPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYF******
Disordered Region (DISOPRED)
*******************************************************************************************************************************************************************************RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV******************************************RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA******************************************LFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY**
Disordered Region (DISEMBL)
***********************************************RRDKNYKYDREGIRDHDRTDRHRDYN*****************************************DMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV*******************QAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA
Disordered Region (DISPRO)
****************************************************************************************************************GFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFG***L*AFPLMPV*******TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLA***********LNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFN*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA
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	522	2.2.26 [Sep-21-2011]
Q9ZR39	555	Splicing factor U2af larg	N/A	no	0.762	0.717	0.689	1e-167
Q9ZR40	573	Splicing factor U2af larg	N/A	no	0.758	0.691	0.692	1e-167
Q8L716	589	Splicing factor U2af larg	yes	no	0.756	0.670	0.686	1e-164
Q2QKB4	543	Splicing factor U2af larg	N/A	no	0.775	0.745	0.667	1e-155
O23212	573	Splicing factor U2af larg	no	no	0.768	0.699	0.660	1e-154
Q2QZL4	548	Splicing factor U2af larg	yes	no	0.756	0.720	0.666	1e-152
Q2R0Q1	574	Splicing factor U2af larg	no	no	0.722	0.656	0.637	1e-143
Q2QKB3	591	Splicing factor U2af larg	N/A	no	0.795	0.702	0.560	1e-122
Q24562	416	Splicing factor U2AF 50 k	yes	no	0.664	0.834	0.395	1e-70
P26368	475	Splicing factor U2AF 65 k	yes	no	0.754	0.829	0.399	1e-67

>sp|Q9ZR39|U2A2A_NICPL Splicing factor U2af large subunit A OS=Nicotiana plumbaginifolia GN=U2AF65A PE=2 SV=1

 Score =  588 bits (1516), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 284/412 (68%), Positives = 325/412 (78%), Gaps = 14/412 (3%)

Query: 112 SGFDMAPPAAAMLPGAA-VPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQA 170
           SGFDMAPP  A+LPGA    GQ+PG   A+P +  NM P  ++Q GA P+MPVQ MTQQA
Sbjct: 157 SGFDMAPPTTALLPGATDAAGQVPGTNPAIPGLFSNMFPLASSQFGALPMMPVQAMTQQA 216

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           TRHARRVYVGGLPP ANEQ++ATFFS VM AIGGN+AGPGDAVVNVYINHEKKFAFVEMR
Sbjct: 217 TRHARRVYVGGLPPTANEQSVATFFSHVMYAIGGNTAGPGDAVVNVYINHEKKFAFVEMR 276

Query: 231 TVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
           +VEEASNAMALDG+IFEG  V+VRRP+DYNP+LAA LGP QPSPNLNLAAVG   G+ GG
Sbjct: 277 SVEEASNAMALDGVIFEGGPVKVRRPSDYNPSLAATLGPSQPSPNLNLAAVGSTPGSSGG 336

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
            EGPDR+FVGGLPYYFTE+QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTD
Sbjct: 337 LEGPDRIFVGGLPYYFTESQIRELLESFGQLRGFDLVKDRETGNSKGYAFCVYQDVSVTD 396

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 410
           IACAALNG+KMGDKTLTVRRA   + Q   EQES+L  AQQ IA+Q+  LQ   + T   
Sbjct: 397 IACAALNGIKMGDKTLTVRRANQGTTQPNPEQESVLLHAQQQIALQRFMLQPGALAT--- 453

Query: 411 GMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGG 470
                     KVLCLTE +T D L DD++Y++ILEDMR EC K+G LVNVVIPRP+ NG 
Sbjct: 454 ----------KVLCLTEVVTVDELNDDDDYQDILEDMRTECEKFGALVNVVIPRPNPNGV 503

Query: 471 ETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 522
            TPG+GKVFLEY D  G + A+  L+GRKFGGN V A +YPE+K+   DY A
Sbjct: 504 PTPGLGKVFLEYADVDGSSKARQGLNGRKFGGNQVVAVFYPENKFSEGDYEA 555

Necessary for the splicing of pre-mRNA. Binds to the U -enriched regions of plant introns.
Nicotiana plumbaginifolia (taxid: 4092)

>sp|Q9ZR40|U2A2B_NICPL Splicing factor U2af large subunit B OS=Nicotiana plumbaginifolia GN=U2AF65B PE=2 SV=1

 Score =  588 bits (1515), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 284/410 (69%), Positives = 328/410 (80%), Gaps = 14/410 (3%)

Query: 112 SGFDMAPPAAAMLPG-AAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQA 170
           SGFDMAPP +AMLPG  A  GQ+PG    +P M  NM P  + Q GA P+MP+Q MTQQA
Sbjct: 175 SGFDMAPPTSAMLPGITAAAGQVPGTNPPIPGMFPNMFPLASGQFGALPVMPIQAMTQQA 234

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           TRHARRVYVGGLP  ANEQ++ATFFS VM+AIGGN+AGPGDAVVNVYIN+EKKFAFVEMR
Sbjct: 235 TRHARRVYVGGLPAHANEQSVATFFSHVMSAIGGNTAGPGDAVVNVYINYEKKFAFVEMR 294

Query: 231 TVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
           +VEEASNAMALDGIIFEG   +VRRP+DYNP+LAA LGP QP+PNLNLAAVGL+ G+ GG
Sbjct: 295 SVEEASNAMALDGIIFEGAPCKVRRPSDYNPSLAATLGPSQPNPNLNLAAVGLSPGSAGG 354

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
            EGPDR+FVGGLPYYFTE QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTD
Sbjct: 355 LEGPDRIFVGGLPYYFTEAQIRELLESFGPLRGFDLVKDRETGNSKGYAFCVYQDVSVTD 414

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 410
           IACAALNG+KMGDKTLTVRRA   + Q K EQES+L  AQQ IA+Q++ LQ + + T   
Sbjct: 415 IACAALNGIKMGDKTLTVRRANQGTTQPKPEQESVLLHAQQQIALQRLMLQPATLAT--- 471

Query: 411 GMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGG 470
                     KVL LTE I+AD L DDE+Y++ILEDMR ECGK+G+LVNVVIPRP  NG 
Sbjct: 472 ----------KVLSLTEVISADELNDDEDYQDILEDMRTECGKFGSLVNVVIPRPSPNGE 521

Query: 471 ETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
            TPGVGKVFLEY D    + A+ +L+GRKFGGN V A +YPE+K++  DY
Sbjct: 522 PTPGVGKVFLEYADVDSSSKARQSLNGRKFGGNQVVAVFYPENKFYEGDY 571

Necessary for the splicing of pre-mRNA. Binds to the U -enriched regions of plant introns.

Nicotiana plumbaginifolia (taxid: 4092)

>sp|Q8L716|U2A2B_ARATH Splicing factor U2af large subunit B OS=Arabidopsis thaliana GN=U2AF65B PE=2 SV=2

 Score =  577 bits (1487), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 282/411 (68%), Positives = 323/411 (78%), Gaps = 16/411 (3%)

Query: 113 GFDMAPPAAAMLPGAAVPGQLPGVPSA--VPEMAQNMLPF-GATQLGAFPLMPVQVMTQQ 169
           GFDMAPP        A  GQ+P VP+   +P M  NM P     QLGA P++PVQ MTQQ
Sbjct: 190 GFDMAPPDMLAATAVAAAGQVPSVPTTATIPGMFSNMFPMVPGQQLGALPVLPVQAMTQQ 249

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           ATRHARRVYVGGLPP ANEQ+++TFFSQVM+AIGGN+AGPGDAVVNVYINHEKKFAFVEM
Sbjct: 250 ATRHARRVYVGGLPPTANEQSVSTFFSQVMSAIGGNTAGPGDAVVNVYINHEKKFAFVEM 309

Query: 230 RTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 289
           R+VEEASNAMALDGII EGV V+VRRPTDYNP+LAA LGP QP+PNLNL AVGL+SG+ G
Sbjct: 310 RSVEEASNAMALDGIILEGVPVKVRRPTDYNPSLAATLGPSQPNPNLNLGAVGLSSGSTG 369

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G EGPDR+FVGGLPYYFTE QI+ELLESFG L GF+LVKDR+TGNSKGY FCVYQDP+VT
Sbjct: 370 GLEGPDRIFVGGLPYYFTEVQIRELLESFGPLRGFNLVKDRETGNSKGYAFCVYQDPSVT 429

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG 409
           DIACAALNG+KMGDKTLTVRRA   + Q K EQE +L  AQQ IA+Q++  Q  G     
Sbjct: 430 DIACAALNGIKMGDKTLTVRRAIQGAIQPKPEQEEVLLYAQQQIALQRLMFQPGG----- 484

Query: 410 GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG 469
                   T  K++CLT+ +TAD L DDEEY EI+EDMR+E GK+G LVNVVIPRP+ + 
Sbjct: 485 --------TPTKIVCLTQVVTADDLRDDEEYAEIMEDMRQEGGKFGNLVNVVIPRPNPDH 536

Query: 470 GETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
             TPGVGKVFLEY D  G + A++ ++GRKFGGN V A YYPEDKY   DY
Sbjct: 537 DPTPGVGKVFLEYADVDGSSKARSGMNGRKFGGNQVVAVYYPEDKYAQGDY 587

Necessary for the splicing of pre-mRNA.

Arabidopsis thaliana (taxid: 3702)

>sp|Q2QKB4|U2A2B_WHEAT Splicing factor U2af large subunit B OS=Triticum aestivum GN=U2AF65B PE=2 SV=1

 Score =  548 bits (1411), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 283/424 (66%), Positives = 325/424 (76%), Gaps = 19/424 (4%)

Query: 102 SRSPSKSKRRSGFDMAPPAAAMLP---GAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAF 158
           SRS SKSKR SGFD+ P A ++LP       P QLPG  S++P M  NMLPF   Q+   
Sbjct: 134 SRSHSKSKRVSGFDLGPTAQSVLPQFPTIPTPSQLPG--SSIPGMFPNMLPFADGQINPL 191

Query: 159 PLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI 218
            + P Q MTQQATRHARRVYVGGLPP ANEQ++A +F+QVM AIGGN+AGPGDAV+NVYI
Sbjct: 192 VMQP-QAMTQQATRHARRVYVGGLPPSANEQSVAIYFNQVMAAIGGNTAGPGDAVLNVYI 250

Query: 219 NHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNL 278
           NH+KKFAFVEMR+VEEASNAMALDGI+FEG  V+VRRPTDYNP+LAAALGP QPS NLNL
Sbjct: 251 NHDKKFAFVEMRSVEEASNAMALDGILFEGAPVKVRRPTDYNPSLAAALGPSQPSSNLNL 310

Query: 279 AAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY 338
           AAVGL  G+ GG EGPDR+FVGGLPYYFTE Q++ELLESFG L GFDLVKDR+TGNSKGY
Sbjct: 311 AAVGLTPGSAGGLEGPDRIFVGGLPYYFTEAQVRELLESFGPLRGFDLVKDRETGNSKGY 370

Query: 339 GFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKM 398
            FCVYQD  VTDIACAALNG+KMGDKTLTVRRA   S Q + EQE+IL QAQQ + +QK+
Sbjct: 371 AFCVYQDLNVTDIACAALNGIKMGDKTLTVRRANQGSAQPRPEQENILLQAQQQVQLQKL 430

Query: 399 ALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLV 458
             Q   + T             KV+CLT+ +TAD L DDEEYE+I+EDMR E GKYG LV
Sbjct: 431 VYQVGALPT-------------KVVCLTQVVTADELKDDEEYEDIMEDMRLEAGKYGNLV 477

Query: 459 NVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNK 518
            VVIPRP  +G    GVGKVFLEY D  G   AK A+ GRKFGGN V A +YPE+K+ ++
Sbjct: 478 KVVIPRPHPSGEPVSGVGKVFLEYADVDGSTKAKTAMHGRKFGGNPVVAVFYPENKFADE 537

Query: 519 DYSA 522
           DY A
Sbjct: 538 DYDA 541

Necessary for the splicing of pre-mRNA.

Triticum aestivum (taxid: 4565)

>sp|O23212|U2A2A_ARATH Splicing factor U2af large subunit A OS=Arabidopsis thaliana GN=U2AF65A PE=2 SV=2

 Score =  545 bits (1405), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 276/418 (66%), Positives = 318/418 (76%), Gaps = 17/418 (4%)

Query: 109 KRRSGFDMAPPAAAMLPGAA-VPGQLPGVPSAVPE--MAQNMLPFGATQ-LGAFPLMPVQ 164
           +R SGFDMAPPA+AML   A V GQ+P  P  +P   M  NM P    Q  G   +MP+Q
Sbjct: 169 QRVSGFDMAPPASAMLAAGAAVTGQVPPAPPTLPGAGMFPNMFPLPTGQSFGGLSMMPIQ 228

Query: 165 VMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKF 224
            MTQQATRHARRVYVGGL P ANEQ++ATFFSQVM A+GGN+AGPGDAVVNVYINHEKKF
Sbjct: 229 AMTQQATRHARRVYVGGLSPTANEQSVATFFSQVMAAVGGNTAGPGDAVVNVYINHEKKF 288

Query: 225 AFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLA 284
           AFVEMR+VEEASNAM+LDGIIFEG  V+VRRP+DYNP+LAA LGP QPSP+LNLAAVGL 
Sbjct: 289 AFVEMRSVEEASNAMSLDGIIFEGAPVKVRRPSDYNPSLAATLGPSQPSPHLNLAAVGLT 348

Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
            GA GG EGPDR+FVGGLPYYFTE+Q++ELLESFG L GFDLVKDR+TGNSKGY FCVYQ
Sbjct: 349 PGASGGLEGPDRIFVGGLPYYFTESQVRELLESFGGLKGFDLVKDRETGNSKGYAFCVYQ 408

Query: 345 DPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSG 404
           D +VTDIACAALNG+KMGDKTLTVRRA   +   K EQE++L  AQQ IA Q++ LQ   
Sbjct: 409 DLSVTDIACAALNGIKMGDKTLTVRRANQGTMLQKPEQENVLLHAQQQIAFQRVMLQPGA 468

Query: 405 MNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPR 464
           + T              V+CLT+ +T D L DDEEY +I+EDMR+E GK+G L NVVIPR
Sbjct: 469 VATT-------------VVCLTQVVTEDELRDDEEYGDIMEDMRQEGGKFGALTNVVIPR 515

Query: 465 PDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 522
           P  NG    G+GKVFL+Y D  G   A+  ++GRKFGGN V A YYPEDK+   DY A
Sbjct: 516 PSPNGEPVAGLGKVFLKYADTDGSTRARFGMNGRKFGGNEVVAVYYPEDKFEQGDYGA 573

Necessary for the splicing of pre-mRNA.

Arabidopsis thaliana (taxid: 3702)

>sp|Q2QZL4|U2A2B_ORYSJ Splicing factor U2af large subunit B OS=Oryza sativa subsp. japonica GN=U2AF65B PE=2 SV=2

 Score =  540 bits (1390), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 276/414 (66%), Positives = 318/414 (76%), Gaps = 19/414 (4%)

Query: 112 SGFDMAPPAAAMLP---GAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQ 168
           SGFDMAPPA A++P       P Q PG  +A+P M  NMLP G  Q     + P Q MTQ
Sbjct: 151 SGFDMAPPAQAVVPQFPAIPTPSQFPG--TAIPGMFPNMLPMGVGQFNPLVIQP-QAMTQ 207

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
           QATRHARRVYVGGLPP ANEQ++A +F+QVM AIGGN+AGPGDAV+NVYINH+KKFAFVE
Sbjct: 208 QATRHARRVYVGGLPPTANEQSVAIYFNQVMAAIGGNTAGPGDAVLNVYINHDKKFAFVE 267

Query: 229 MRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAI 288
           MR+VEEASNAMALDGI+FEG  V+VRRPTDYNP+LAAALGP QPSPNLNLAAVGL  G+ 
Sbjct: 268 MRSVEEASNAMALDGILFEGAPVKVRRPTDYNPSLAAALGPSQPSPNLNLAAVGLTPGSA 327

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           GG EGPDR+FVGGLPYYFTE Q++ELLESFG L GFDLVKDR+TGNSKGY FCVYQD  V
Sbjct: 328 GGLEGPDRIFVGGLPYYFTEAQVRELLESFGPLRGFDLVKDRETGNSKGYAFCVYQDLNV 387

Query: 349 TDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTL 408
           TDIACAALNG+KMGDKTLTVRRA   + Q + EQESIL QAQQ + +QK+  Q   + T 
Sbjct: 388 TDIACAALNGIKMGDKTLTVRRANQGAAQPRPEQESILLQAQQQVQLQKLVYQVGALPT- 446

Query: 409 GGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQN 468
                       KV+CLT+ ++AD L DDEEYE+I+EDMR E GKYG L+ VVIPRPD +
Sbjct: 447 ------------KVVCLTQVVSADELKDDEEYEDIMEDMRLEAGKYGNLIKVVIPRPDPS 494

Query: 469 GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 522
           G    GVGKVFLEY D  G   AK A+ GRKFGGN V A +YPE+K+ + +Y A
Sbjct: 495 GLPVAGVGKVFLEYADVDGATKAKTAMHGRKFGGNPVVAVFYPENKFSSAEYDA 548

Necessary for the splicing of pre-mRNA.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q2R0Q1|U2A2A_ORYSJ Splicing factor U2af large subunit A OS=Oryza sativa subsp. japonica GN=U2AF65A PE=2 SV=2

 Score =  508 bits (1307), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 248/389 (63%), Positives = 288/389 (74%), Gaps = 12/389 (3%)

Query: 132 QLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAI 191
           Q+P V  A+  M  NM     T      + P Q MTQQATRHARRVYVGGLPP ANE  +
Sbjct: 196 QVPVVAPAISGMLPNMFNLTQTPFTPLVIQP-QAMTQQATRHARRVYVGGLPPTANEHTV 254

Query: 192 ATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV 251
           A +F+QVM A+GGN+AGPGDAV+NVYINH+KKFAFVEMR+VEEASNAMALDGI+FEG  V
Sbjct: 255 AVYFNQVMAAVGGNTAGPGDAVLNVYINHDKKFAFVEMRSVEEASNAMALDGIMFEGAPV 314

Query: 252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQI 311
           +VRRPTDYNP+LAAALGP QP+PNLNLAAVGL  G+ GG EGPDR+FVGGLPYYFTE Q+
Sbjct: 315 KVRRPTDYNPSLAAALGPSQPNPNLNLAAVGLTPGSAGGLEGPDRIFVGGLPYYFTEAQV 374

Query: 312 KELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
           +ELLESFG L GFDLVKDR+TGNSKGY FCVYQD  VTDIACAALNG+KMGDKTLTVRRA
Sbjct: 375 RELLESFGPLRGFDLVKDRETGNSKGYAFCVYQDLNVTDIACAALNGIKMGDKTLTVRRA 434

Query: 372 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITA 431
              + Q + EQES+L   QQ   +QK+  Q  G           G    KV+CLT+ ++ 
Sbjct: 435 NQGASQPRPEQESMLLHVQQQAQMQKLMFQVGG-----------GALPTKVVCLTQVVSP 483

Query: 432 DALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATA 491
           D L DDEEYE+I++DMREE  +YG LV VVIPRPD +G    GVG+VFLE+ D      A
Sbjct: 484 DELRDDEEYEDIVQDMREEGCRYGNLVKVVIPRPDPSGAPVAGVGRVFLEFADVESSTKA 543

Query: 492 KNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
           KN + GRKF  N V A +YPEDK+    Y
Sbjct: 544 KNGMHGRKFANNQVVAVFYPEDKFAEGQY 572

Necessary for the splicing of pre-mRNA.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q2QKB3|U2A2A_WHEAT Splicing factor U2af large subunit A OS=Triticum aestivum GN=U2AF65A PE=2 SV=1

 Score =  440 bits (1131), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 249/444 (56%), Positives = 296/444 (66%), Gaps = 29/444 (6%)

Query: 29  GERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRSHS 88
           G R R+RHHRD + G  DR R   +  D     +        D    +    R   R   
Sbjct: 131 GSRDRERHHRDHREGSRDRER---HHRDHRERSERREHRDRSDDRDYRRSCDRDAERRDR 187

Query: 89  SDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAA-AMLPGAAVPGQLPGVPSAVPEMAQNM 147
                 R +S SP RS S+SKR SGFD  P  A  +L   A P QLP +P+A P M  NM
Sbjct: 188 DRDGHRRHRSRSPLRSESQSKRMSGFDQRPSEAIPILAPDATPSQLPELPAANPGMFPNM 247

Query: 148 LP--FGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGN 205
           LP       LG  PL     MTQQATRHARRVYVGGLPP+ANEQ +A FF+QVM AIGGN
Sbjct: 248 LPNLVNVPALGQ-PL----AMTQQATRHARRVYVGGLPPIANEQTVAVFFNQVMAAIGGN 302

Query: 206 SAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAA 265
           +   G AVVNVYINH+KKFAFVEMR+VEEASNAMALDGI+FEG  V+VRRPTDYNP+ AA
Sbjct: 303 TFALGHAVVNVYINHDKKFAFVEMRSVEEASNAMALDGIMFEGAPVKVRRPTDYNPSQAA 362

Query: 266 ALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD 325
           ALGP QP+PNLNLAAVGL  GA GG EGPDR+FVGGLPYYFTE Q++ELLE+FG L GFD
Sbjct: 363 ALGPSQPNPNLNLAAVGLTPGAGGGLEGPDRIFVGGLPYYFTEAQVRELLETFGPLRGFD 422

Query: 326 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESI 385
           +VKD++TGNSKGY FC+Y+D  VTDIACAALNG+++GD+TLTVRRA     + + EQE+I
Sbjct: 423 IVKDKETGNSKGYAFCLYKDGTVTDIACAALNGIQLGDRTLTVRRAN-QGAEPRPEQENI 481

Query: 386 LAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETL-AKVLCLTEAITADALADDEEYEEIL 444
           L QAQQ   ++++  +              G TL  KV+CLT+ ++AD L DDEEY +IL
Sbjct: 482 LLQAQQEAQMKRLVYEV-------------GRTLTTKVVCLTQVVSADDLRDDEEYNDIL 528

Query: 445 EDMREECGKY---GTLVNVVIPRP 465
           EDM  E  KY    T+    I RP
Sbjct: 529 EDMTLEGHKYVPHSTIAESFIIRP 552

Necessary for the splicing of pre-mRNA.

Triticum aestivum (taxid: 4565)

>sp|Q24562|U2AF2_DROME Splicing factor U2AF 50 kDa subunit OS=Drosophila melanogaster GN=U2af50 PE=2 SV=1

 Score =  268 bits (684), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 156/394 (39%), Positives = 221/394 (56%), Gaps = 47/394 (11%)

Query: 131 GQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQA 190
           GQ+P   S VP+  Q  +P               V+    TR ARR+YVG +P    E+ 
Sbjct: 66  GQIPA--SVVPDTPQTAVP---------------VVGSTITRQARRLYVGNIPFGVTEEE 108

Query: 191 IATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA 250
           +  FF+Q M  +G   A  G  V+   IN +K FAF+E R+++E + AMA DGI  +G +
Sbjct: 109 MMEFFNQQMHLVGLAQAA-GSPVLACQINLDKNFAFLEFRSIDETTQAMAFDGINLKGQS 167

Query: 251 VRVRRPTDYNPTLAAALGPG-QPSPNLNLAAVGLASGAIGGA--EGPDRVFVGGLPYYFT 307
           +++RRP DY P       PG   +P +  A V  +SG I     + P ++F+GGLP Y  
Sbjct: 168 LKIRRPHDYQPM------PGITDTPAIKPAVV--SSGVISTVVPDSPHKIFIGGLPNYLN 219

Query: 308 ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT 367
           + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D ++TD + A LNG+++GDK L 
Sbjct: 220 DDQVKELLLSFGKLRAFNLVKDAATGLSKGYAFCEYVDLSITDQSIAGLNGMQLGDKKLI 279

Query: 368 VRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGM-NTLGGGMSLFGETLAKVLCLT 426
           V+RA+  +  ++    +           Q + LQ  G+ N +  G         +VLCL 
Sbjct: 280 VQRASVGAKNAQNAANT----------TQSVMLQVPGLSNVVTSGPP------TEVLCLL 323

Query: 427 EAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAV 486
             +T D L D+EEYE+ILED++EEC KYG + +V IPRP + G E PG GKVF+E+   +
Sbjct: 324 NMVTPDELRDEEEYEDILEDIKEECTKYGVVRSVEIPRPIE-GVEVPGCGKVFVEFNSVL 382

Query: 487 GCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
            C  A+ AL+GRKF    V   Y+  DKY  +++
Sbjct: 383 DCQKAQQALTGRKFSDRVVVTSYFDPDKYHRREF 416

Necessary for the splicing of pre-mRNA. Binds to the polypyrimidine tract of introns early during spliceosome assembly.

Drosophila melanogaster (taxid: 7227)

>sp|P26368|U2AF2_HUMAN Splicing factor U2AF 65 kDa subunit OS=Homo sapiens GN=U2AF2 PE=1 SV=4

 Score =  257 bits (657), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 168/421 (39%), Positives = 232/421 (55%), Gaps = 27/421 (6%)

Query: 103 RSP---SKSKRRSGFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFP 159
           RSP    K K R  +D+ PP    +     P Q   + +A    A  +LP       A  
Sbjct: 78  RSPRHEKKKKVRKYWDVPPPGFEHI----TPMQYKAMQAAGQIPATALLPTMTPDGLAVT 133

Query: 160 LMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN 219
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN
Sbjct: 134 PTPVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQIN 192

Query: 220 HEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLA 279
            +K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++ 
Sbjct: 193 QDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVY 245

Query: 280 AVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYG 339
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY 
Sbjct: 246 VPGVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 303

Query: 340 FCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMA 399
           FC Y D  VTD A A LNG+++GDK L V+RA+  +      + + L      I    + 
Sbjct: 304 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSPPSTINQTPVT 357

Query: 400 LQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVN 459
           LQ  G+ +    M   G    +VLCL   +  + L DDEEYEEI+ED+R+EC KYG + +
Sbjct: 358 LQVPGLMSSQVQM---GGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKS 414

Query: 460 VVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKD 519
           + IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D
Sbjct: 415 IEIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRD 473

Query: 520 Y 520
           +
Sbjct: 474 F 474

Necessary for the splicing of pre-mRNA. Induces cardiac troponin-T (TNNT2) pre-mRNA exon inclusion in muscle. Regulates the TNNT2 exon 5 inclusion through competition with MBNL1. Binds preferentially to a single-stranded structure within the polypyrimidine tract of TNNT2 intron 4 during spliceosome assembly. Required for the export of mRNA out of the nucleus, even if the mRNA is encoded by an intron-less gene. Represses the splicing of MAPT/Tau exon 10.

Homo sapiens (taxid: 9606)

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	522
388520789	527	unknown [Lotus japonicus]	0.931	0.922	0.653	1e-176
359497050	410	PREDICTED: splicing factor U2af large su	0.703	0.895	0.749	1e-174
156070760	553	unknown [Solanum melongena]	0.829	0.783	0.659	1e-166
188998293	554	U2 snRNP auxiliary factor large subunit	0.829	0.781	0.659	1e-166
75338883	555	RecName: Full=Splicing factor U2af large	0.762	0.717	0.689	1e-165
75338884	573	RecName: Full=Splicing factor U2af large	0.758	0.691	0.692	1e-165
156070776	551	unknown [Capsicum frutescens]	0.762	0.722	0.684	1e-165
156070797	558	unknown [Solanum bulbocastanum]	0.758	0.709	0.686	1e-164
297840477	589	hypothetical protein ARALYDRAFT_475241 [	0.756	0.670	0.690	1e-163
356509477	600	PREDICTED: splicing factor U2af large su	0.758	0.66	0.691	1e-162

>gi|388520789|gb|AFK48456.1| unknown [Lotus japonicus]

 Score =  625 bits (1613), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 328/502 (65%), Positives = 389/502 (77%), Gaps = 16/502 (3%)

Query: 25  RSRTGERG--RDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRH 82
           R + GER    DRHHRD+K GG + R D+   Y+R   RD+DR   H D  +D ERRH++
Sbjct: 34  RKQDGERRDFHDRHHRDYKDGGFNGR-DRYNSYNRHRSRDYDR---HNDRVKDGERRHKY 89

Query: 83  RSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPGAAVPGQLPGVPSAVPE 142
            + S    R R  S+S S S S S+SKR SGFDMAPP+A     +AV GQ  G+      
Sbjct: 90  EAHS---KRSRGESRSPSRSPSRSESKRVSGFDMAPPSADGT--SAVSGQTLGINHLNQG 144

Query: 143 MAQNMLPFGATQ--LGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMT 200
            AQN   FG +Q  +GA  LM VQ MTQQATRHARRVY+GGLPPL NEQ+IATFFS VMT
Sbjct: 145 TAQNFSLFGISQPQIGALSLMQVQPMTQQATRHARRVYIGGLPPLTNEQSIATFFSHVMT 204

Query: 201 AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYN 260
           AIGGNSAG GD+VVNVYINHEKKFAF+EMRTVEEASNAM+LDGI+FEGV+VRVRRPTDYN
Sbjct: 205 AIGGNSAGAGDSVVNVYINHEKKFAFLEMRTVEEASNAMSLDGIVFEGVSVRVRRPTDYN 264

Query: 261 PTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT 320
           PTLAAALGP QPSP LNL+AVGL+ G IGG +G DR+FVGGLPYYF E QI+ELL++FG 
Sbjct: 265 PTLAAALGPCQPSPYLNLSAVGLSGGTIGGTDGLDRIFVGGLPYYFAEEQIRELLQAFGP 324

Query: 321 LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKT 380
           L  FDLV+D++TGNSKGYGFC+YQDPAVTD+ACA+LNGLK+GDKTLTVRRAT  SG SKT
Sbjct: 325 LRSFDLVRDKETGNSKGYGFCIYQDPAVTDMACASLNGLKVGDKTLTVRRATV-SGHSKT 383

Query: 381 EQESILAQAQQHIAIQKMALQTSGMNTLGGGM--SLFGETLAKVLCLTEAITADALADDE 438
           EQE I AQAQQ+I +QK+AL+  G+N  G     +   E+  KVLCLTEAIT D L D+ 
Sbjct: 384 EQEHIFAQAQQNITMQKVALEVVGLNIPGVERVPTTIDESATKVLCLTEAITTDELMDNG 443

Query: 439 EYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGR 498
           EYEEI+EDMR+ECGK+GTL+NVVIPRP+ +G +TPG+GKVFLEY D      AK+AL+GR
Sbjct: 444 EYEEIVEDMRDECGKFGTLMNVVIPRPNPSGEQTPGIGKVFLEYSDTAASFAAKSALNGR 503

Query: 499 KFGGNTVNAFYYPEDKYFNKDY 520
           KFGGN V A+YYPE+K+ N ++
Sbjct: 504 KFGGNMVTAYYYPEEKFHNMEF 525

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359497050|ref|XP_002267854.2| PREDICTED: splicing factor U2af large subunit B-like, partial [Vitis vinifera]

 Score =  617 bits (1591), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 308/411 (74%), Positives = 330/411 (80%), Gaps = 44/411 (10%)

Query: 112 SGFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQAT 171
           SGFDMAPP AA+LPGAAVPG+LPGVP  VP M QNM PFGATQLGA PLMPVQ MTQQAT
Sbjct: 44  SGFDMAPPVAALLPGAAVPGELPGVPQMVPGMIQNMFPFGATQLGALPLMPVQAMTQQAT 103

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
           RHARRVYVGGLPPLANEQ IATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR+
Sbjct: 104 RHARRVYVGGLPPLANEQTIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRS 163

Query: 232 VEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGA 291
           VEEASNAMALDGI+FEGV+VRVRRPTDYNP+LAAALGP QPSP+LNLAAVGL  G IGGA
Sbjct: 164 VEEASNAMALDGIMFEGVSVRVRRPTDYNPSLAAALGPSQPSPHLNLAAVGLMPGVIGGA 223

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           EGPDR+FVGGLPYYFTE QI+ELLESFG L GFDLVKDRDTGNSKGYGFCVYQDPAVTDI
Sbjct: 224 EGPDRIFVGGLPYYFTEEQIRELLESFGPLRGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 283

Query: 352 ACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGG 411
           ACAALNGLKMGDKTLTVRRAT  SGQ+K+EQ++ILAQAQQHIAIQK+ALQ  G+N  G  
Sbjct: 284 ACAALNGLKMGDKTLTVRRATVGSGQAKSEQDNILAQAQQHIAIQKIALQAGGLNLPGA- 342

Query: 412 MSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGE 471
                                                      G LV+VVIPRP  NG  
Sbjct: 343 -------------------------------------------GALVHVVIPRPSPNGDL 359

Query: 472 TPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 522
            PGVGKVFLEY D  G ++A+NALSGRKFGGN V+A YYPEDKY++ DY A
Sbjct: 360 IPGVGKVFLEYSDTAGSSSARNALSGRKFGGNVVSAVYYPEDKYYDGDYGA 410

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|156070760|gb|ABU45175.1| unknown [Solanum melongena]

 Score =  592 bits (1525), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 302/458 (65%), Positives = 353/458 (77%), Gaps = 25/458 (5%)

Query: 67  DRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPG 126
           DR R+ ++D+E RHRH+  S +  R          SRSPSKSKR SGFDMAPP +A+L G
Sbjct: 117 DRRRNNDKDREDRHRHKPSSRARSR----------SRSPSKSKRISGFDMAPPTSALLSG 166

Query: 127 AA-VPGQLPGVPS-AVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPP 184
           A  V GQ+PG+ + ++P M  NM P  A Q GA P+MPVQ MTQQATRHARRVYVGGLPP
Sbjct: 167 ATDVAGQVPGITNPSIPGMFSNMFPVAAGQFGALPVMPVQAMTQQATRHARRVYVGGLPP 226

Query: 185 LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGI 244
            ANEQ++ATFFS VM AIGGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDG+
Sbjct: 227 TANEQSVATFFSHVMYAIGGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGV 286

Query: 245 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPY 304
           IFEG  V+VRRP+DYNP+LAA LGP QPSPNLNLAAVGL  G+ GG EGPDR+FVGGLPY
Sbjct: 287 IFEGGPVKVRRPSDYNPSLAATLGPSQPSPNLNLAAVGLTPGSSGGLEGPDRIFVGGLPY 346

Query: 305 YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK 364
           YFTE+QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTDIACAALNG+KMGDK
Sbjct: 347 YFTESQIRELLESFGQLRGFDLVKDRETGNSKGYAFCVYQDVSVTDIACAALNGIKMGDK 406

Query: 365 TLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLC 424
           TLTVRRA     Q   EQES+L  AQQ IA+Q+  LQ   + T             K+LC
Sbjct: 407 TLTVRRANQGITQPNPEQESVLLHAQQQIALQRFMLQPGALAT-------------KILC 453

Query: 425 LTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYD 484
           LT+ ++ D L DD++Y++ILEDMR ECGK+G L+NVVIPRP+ NG  TPG+GKVFLEY D
Sbjct: 454 LTQVVSVDELKDDDDYQDILEDMRIECGKFGALLNVVIPRPNPNGEPTPGLGKVFLEYAD 513

Query: 485 AVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 522
               + A+  L+GRKFGGN V A +YPE+K+   DY A
Sbjct: 514 VDSSSKARQGLNGRKFGGNQVIAVFYPENKFSEGDYEA 551

Source: Solanum melongena

Species: Solanum melongena

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|188998293|gb|ACD67872.1| U2 snRNP auxiliary factor large subunit [Solanum melongena]

 Score =  592 bits (1525), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 302/458 (65%), Positives = 353/458 (77%), Gaps = 25/458 (5%)

Query: 67  DRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPG 126
           DR R+ ++D+E RHRH+  S +  R          SRSPSKSKR SGFDMAPP +A+L G
Sbjct: 118 DRRRNNDKDREDRHRHKPSSRARSR----------SRSPSKSKRISGFDMAPPTSALLSG 167

Query: 127 AA-VPGQLPGVPS-AVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPP 184
           A  V GQ+PG+ + ++P M  NM P  A Q GA P+MPVQ MTQQATRHARRVYVGGLPP
Sbjct: 168 ATDVAGQVPGITNPSIPGMFSNMFPVAAGQFGALPVMPVQAMTQQATRHARRVYVGGLPP 227

Query: 185 LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGI 244
            ANEQ++ATFFS VM AIGGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDG+
Sbjct: 228 TANEQSVATFFSHVMYAIGGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGV 287

Query: 245 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPY 304
           IFEG  V+VRRP+DYNP+LAA LGP QPSPNLNLAAVGL  G+ GG EGPDR+FVGGLPY
Sbjct: 288 IFEGGPVKVRRPSDYNPSLAATLGPSQPSPNLNLAAVGLTPGSSGGLEGPDRIFVGGLPY 347

Query: 305 YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK 364
           YFTE+QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTDIACAALNG+KMGDK
Sbjct: 348 YFTESQIRELLESFGQLRGFDLVKDRETGNSKGYAFCVYQDVSVTDIACAALNGIKMGDK 407

Query: 365 TLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLC 424
           TLTVRRA     Q   EQES+L  AQQ IA+Q+  LQ   + T             K+LC
Sbjct: 408 TLTVRRANQGITQPNPEQESVLLHAQQQIALQRFMLQPGALAT-------------KILC 454

Query: 425 LTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYD 484
           LT+ ++ D L DD++Y++ILEDMR ECGK+G L+NVVIPRP+ NG  TPG+GKVFLEY D
Sbjct: 455 LTQVVSVDELKDDDDYQDILEDMRIECGKFGALLNVVIPRPNPNGEPTPGLGKVFLEYAD 514

Query: 485 AVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 522
               + A+  L+GRKFGGN V A +YPE+K+   DY A
Sbjct: 515 VDSSSKARQGLNGRKFGGNQVIAVFYPENKFSEGDYEA 552

Source: Solanum melongena

Species: Solanum melongena

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|75338883|sp|Q9ZR39.1|U2A2A_NICPL RecName: Full=Splicing factor U2af large subunit A; AltName: Full=NpU2AF65a; AltName: Full=U2 auxiliary factor 65 kDa subunit A; AltName: Full=U2 small nuclear ribonucleoprotein auxiliary factor large subunit A; Short=U2 snRNP auxiliary factor large subunit A gi|3850823|emb|CAA77136.1| U2 snRNP auxiliary factor, large subunit [Nicotiana plumbaginifolia]

 Score =  588 bits (1516), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 284/412 (68%), Positives = 325/412 (78%), Gaps = 14/412 (3%)

Query: 112 SGFDMAPPAAAMLPGAA-VPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQA 170
           SGFDMAPP  A+LPGA    GQ+PG   A+P +  NM P  ++Q GA P+MPVQ MTQQA
Sbjct: 157 SGFDMAPPTTALLPGATDAAGQVPGTNPAIPGLFSNMFPLASSQFGALPMMPVQAMTQQA 216

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           TRHARRVYVGGLPP ANEQ++ATFFS VM AIGGN+AGPGDAVVNVYINHEKKFAFVEMR
Sbjct: 217 TRHARRVYVGGLPPTANEQSVATFFSHVMYAIGGNTAGPGDAVVNVYINHEKKFAFVEMR 276

Query: 231 TVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
           +VEEASNAMALDG+IFEG  V+VRRP+DYNP+LAA LGP QPSPNLNLAAVG   G+ GG
Sbjct: 277 SVEEASNAMALDGVIFEGGPVKVRRPSDYNPSLAATLGPSQPSPNLNLAAVGSTPGSSGG 336

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
            EGPDR+FVGGLPYYFTE+QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTD
Sbjct: 337 LEGPDRIFVGGLPYYFTESQIRELLESFGQLRGFDLVKDRETGNSKGYAFCVYQDVSVTD 396

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 410
           IACAALNG+KMGDKTLTVRRA   + Q   EQES+L  AQQ IA+Q+  LQ   + T   
Sbjct: 397 IACAALNGIKMGDKTLTVRRANQGTTQPNPEQESVLLHAQQQIALQRFMLQPGALAT--- 453

Query: 411 GMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGG 470
                     KVLCLTE +T D L DD++Y++ILEDMR EC K+G LVNVVIPRP+ NG 
Sbjct: 454 ----------KVLCLTEVVTVDELNDDDDYQDILEDMRTECEKFGALVNVVIPRPNPNGV 503

Query: 471 ETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 522
            TPG+GKVFLEY D  G + A+  L+GRKFGGN V A +YPE+K+   DY A
Sbjct: 504 PTPGLGKVFLEYADVDGSSKARQGLNGRKFGGNQVVAVFYPENKFSEGDYEA 555

Source: Nicotiana plumbaginifolia

Species: Nicotiana plumbaginifolia

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|75338884|sp|Q9ZR40.1|U2A2B_NICPL RecName: Full=Splicing factor U2af large subunit B; AltName: Full=NpU2AF65b; AltName: Full=U2 auxiliary factor 65 kDa subunit B; AltName: Full=U2 small nuclear ribonucleoprotein auxiliary factor large subunit B; Short=U2 snRNP auxiliary factor large subunit B gi|3850821|emb|CAA77135.1| U2 snRNP auxiliary factor, large subunit [Nicotiana plumbaginifolia]

 Score =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 284/410 (69%), Positives = 328/410 (80%), Gaps = 14/410 (3%)

Query: 112 SGFDMAPPAAAMLPG-AAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQA 170
           SGFDMAPP +AMLPG  A  GQ+PG    +P M  NM P  + Q GA P+MP+Q MTQQA
Sbjct: 175 SGFDMAPPTSAMLPGITAAAGQVPGTNPPIPGMFPNMFPLASGQFGALPVMPIQAMTQQA 234

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           TRHARRVYVGGLP  ANEQ++ATFFS VM+AIGGN+AGPGDAVVNVYIN+EKKFAFVEMR
Sbjct: 235 TRHARRVYVGGLPAHANEQSVATFFSHVMSAIGGNTAGPGDAVVNVYINYEKKFAFVEMR 294

Query: 231 TVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
           +VEEASNAMALDGIIFEG   +VRRP+DYNP+LAA LGP QP+PNLNLAAVGL+ G+ GG
Sbjct: 295 SVEEASNAMALDGIIFEGAPCKVRRPSDYNPSLAATLGPSQPNPNLNLAAVGLSPGSAGG 354

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
            EGPDR+FVGGLPYYFTE QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTD
Sbjct: 355 LEGPDRIFVGGLPYYFTEAQIRELLESFGPLRGFDLVKDRETGNSKGYAFCVYQDVSVTD 414

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 410
           IACAALNG+KMGDKTLTVRRA   + Q K EQES+L  AQQ IA+Q++ LQ + + T   
Sbjct: 415 IACAALNGIKMGDKTLTVRRANQGTTQPKPEQESVLLHAQQQIALQRLMLQPATLAT--- 471

Query: 411 GMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGG 470
                     KVL LTE I+AD L DDE+Y++ILEDMR ECGK+G+LVNVVIPRP  NG 
Sbjct: 472 ----------KVLSLTEVISADELNDDEDYQDILEDMRTECGKFGSLVNVVIPRPSPNGE 521

Query: 471 ETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
            TPGVGKVFLEY D    + A+ +L+GRKFGGN V A +YPE+K++  DY
Sbjct: 522 PTPGVGKVFLEYADVDSSSKARQSLNGRKFGGNQVVAVFYPENKFYEGDY 571

Source: Nicotiana plumbaginifolia

Species: Nicotiana plumbaginifolia

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|156070776|gb|ABU45190.1| unknown [Capsicum frutescens]

 Score =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 282/412 (68%), Positives = 328/412 (79%), Gaps = 14/412 (3%)

Query: 112 SGFDMAPPAAAMLPGAA-VPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQA 170
           SGFDMAPP +A+LPGA  V GQ+PG   ++P M  NM P  A Q GA P+MPVQ MTQQA
Sbjct: 153 SGFDMAPPTSALLPGATDVTGQVPGANPSIPGMFSNMFPLAAGQFGALPIMPVQAMTQQA 212

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           TRHARRVYVGGLPP ANEQ++ATFFS VM AIGGN+AGPGDAVVNVYINHEKKFAFVEMR
Sbjct: 213 TRHARRVYVGGLPPTANEQSVATFFSHVMYAIGGNTAGPGDAVVNVYINHEKKFAFVEMR 272

Query: 231 TVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
           +VEEASNAMALDG+IFEG  V+VRRP+DYNP+LAA LGP QPSPNLNLAAVGL  G+ GG
Sbjct: 273 SVEEASNAMALDGVIFEGGPVKVRRPSDYNPSLAATLGPSQPSPNLNLAAVGLTPGSSGG 332

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
            EGPDR+FVGGLPYYFTE+QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTD
Sbjct: 333 LEGPDRIFVGGLPYYFTESQIRELLESFGQLRGFDLVKDRETGNSKGYAFCVYQDVSVTD 392

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 410
           IACAALNG+KMGDKTLTVRRA   + Q   EQES+L  AQQ IA+Q+  LQ   + T   
Sbjct: 393 IACAALNGIKMGDKTLTVRRANQGTNQPNPEQESVLLHAQQQIALQRFMLQPGALAT--- 449

Query: 411 GMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGG 470
                     KVLCLT+ ++ D L DD++Y++ILEDMR ECGK+G+L+NVVIPRP+ +G 
Sbjct: 450 ----------KVLCLTQVVSVDELNDDDDYQDILEDMRVECGKFGSLLNVVIPRPNPSGE 499

Query: 471 ETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 522
            TPG+GKVFLEY D    + A+  L+GRKFGGN V A +YPE+K+   +Y A
Sbjct: 500 PTPGLGKVFLEYADVESSSRARQGLNGRKFGGNEVIAVFYPENKFSEGEYEA 551

Source: Capsicum frutescens

Species: Capsicum frutescens

Genus: Capsicum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|156070797|gb|ABU45209.1| unknown [Solanum bulbocastanum]

 Score =  583 bits (1503), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 282/411 (68%), Positives = 326/411 (79%), Gaps = 15/411 (3%)

Query: 112 SGFDMAPPAAAMLPGAA-VPGQLPGVPS-AVPEMAQNMLPFGATQLGAFPLMPVQVMTQQ 169
           SGFDMAPP +A+L GA  V GQ+PG  + ++P M  NM P  A Q GA P+MPVQ MTQQ
Sbjct: 159 SGFDMAPPTSALLSGATDVAGQVPGTTNPSIPGMFSNMFPLAAGQFGALPIMPVQAMTQQ 218

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           ATRHARRVYVGGLPP ANEQ++ATFFS VM AIGGN+AGPGDAVVNVYINHEKKFAFVEM
Sbjct: 219 ATRHARRVYVGGLPPTANEQSVATFFSHVMYAIGGNTAGPGDAVVNVYINHEKKFAFVEM 278

Query: 230 RTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 289
           R+VEEASNAMALDG++FEG  V+VRRP+DYNP+LAA LGP QPSPNLNLAAVGL  G+ G
Sbjct: 279 RSVEEASNAMALDGVVFEGGPVKVRRPSDYNPSLAATLGPSQPSPNLNLAAVGLTPGSSG 338

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G EGPDR+FVGGLPYYFTE+QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VT
Sbjct: 339 GLEGPDRIFVGGLPYYFTESQIRELLESFGQLRGFDLVKDRETGNSKGYAFCVYQDVSVT 398

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG 409
           DIACAALNG+KMGDKTLTVRRA   + Q   EQES+L  AQQ IA+Q+  LQ   + T  
Sbjct: 399 DIACAALNGIKMGDKTLTVRRANQGTTQPNPEQESVLLHAQQQIALQRFMLQPGALAT-- 456

Query: 410 GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG 469
                      KVLCLTE ++ D L DD++Y++ILEDMR ECGK+G L+NVVIPRP+ NG
Sbjct: 457 -----------KVLCLTEVVSVDELKDDDDYQDILEDMRIECGKFGALLNVVIPRPNPNG 505

Query: 470 GETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
             TPG+GKVFLEY D    + A+  L+GRKFGGN V A +YPE+K+   DY
Sbjct: 506 EPTPGLGKVFLEYADVDSSSKARQGLNGRKFGGNQVIAVFYPENKFSEGDY 556

Source: Solanum bulbocastanum

Species: Solanum bulbocastanum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297840477|ref|XP_002888120.1| hypothetical protein ARALYDRAFT_475241 [Arabidopsis lyrata subsp. lyrata] gi|297333961|gb|EFH64379.1| hypothetical protein ARALYDRAFT_475241 [Arabidopsis lyrata subsp. lyrata]

 Score =  582 bits (1499), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 284/411 (69%), Positives = 324/411 (78%), Gaps = 16/411 (3%)

Query: 113 GFDMAPPAAAMLPGAAVPGQLPGVPSA--VPEMAQNMLPF-GATQLGAFPLMPVQVMTQQ 169
           GFDMAPP        A  GQ+P VP+   +P M  NM P     QLGA P++PVQ MTQQ
Sbjct: 190 GFDMAPPDMLAATAVAAAGQVPSVPTTATIPGMFPNMFPMVPGQQLGALPVLPVQAMTQQ 249

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           ATRHARRVYVGGLPP ANEQ++ATFFSQVM+AIGGN+AGPGDAVVNVYINHEKKFAFVEM
Sbjct: 250 ATRHARRVYVGGLPPTANEQSVATFFSQVMSAIGGNTAGPGDAVVNVYINHEKKFAFVEM 309

Query: 230 RTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 289
           R+VEEASNAMALDGII EGV V+VRRPTDYNP+LAA LGP QP+PNLNLAAVGL+SG+ G
Sbjct: 310 RSVEEASNAMALDGIILEGVPVKVRRPTDYNPSLAATLGPSQPNPNLNLAAVGLSSGSTG 369

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G EGPDR+FVGGLPYYFTE QI+ELLESFG L GF+LVKDR+TGNSKGY FCVYQDP+VT
Sbjct: 370 GLEGPDRIFVGGLPYYFTEVQIRELLESFGPLRGFNLVKDRETGNSKGYAFCVYQDPSVT 429

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG 409
           DIACAALNG+KMGDKTLTVRRA     Q K EQE +L  AQQ IA+Q++ LQ  G     
Sbjct: 430 DIACAALNGIKMGDKTLTVRRAIQGVIQPKPEQEEVLLHAQQQIALQRLMLQPGG----- 484

Query: 410 GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG 469
                   T  K++CLT+ +TAD L DDEEY +I+EDMR+E GK+G LVNVVIPRP+ + 
Sbjct: 485 --------TPTKIVCLTQVVTADDLRDDEEYADIMEDMRQEGGKFGNLVNVVIPRPNPDH 536

Query: 470 GETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
             TPGVGKVFLEY D  G + A++ ++GRKFGGN V A YYPEDKY   DY
Sbjct: 537 DPTPGVGKVFLEYADVDGSSKARSGMNGRKFGGNQVVAVYYPEDKYLQGDY 587

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509477|ref|XP_003523474.1| PREDICTED: splicing factor U2af large subunit B-like [Glycine max]

 Score =  578 bits (1491), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 287/415 (69%), Positives = 326/415 (78%), Gaps = 19/415 (4%)

Query: 112 SGFDMAPPAAAMLPGA-AVPGQLPGVPSAVPEMAQNMLPFGATQL---GAFPLMPVQVMT 167
           SGFDMAPPA+AML GA AV GQ+ G    +P M  NM P   +Q+    A P+MPVQ MT
Sbjct: 197 SGFDMAPPASAMLTGASAVAGQITGANPTIPGMFPNMFPLATSQMQQFSALPVMPVQAMT 256

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           QQATRHARRVYVGGLPP ANEQ++ATFFSQVM  IGGN+AGPGDAVVNVYINH+KKFAFV
Sbjct: 257 QQATRHARRVYVGGLPPTANEQSVATFFSQVMAKIGGNTAGPGDAVVNVYINHDKKFAFV 316

Query: 228 EMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGA 287
           EMR+VEEASNAMALDGIIFEG  V+VRRPTDYNP+LAA LGP QP+PNLNL AVGL  G+
Sbjct: 317 EMRSVEEASNAMALDGIIFEGAPVKVRRPTDYNPSLAATLGPSQPNPNLNLGAVGLTPGS 376

Query: 288 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 347
            GG +GPDRVFVGGLPYYFTETQI+ELLE+FG L GFDLVKDR+TGNSKGY FCVYQD A
Sbjct: 377 AGGLDGPDRVFVGGLPYYFTETQIRELLETFGPLRGFDLVKDRETGNSKGYAFCVYQDLA 436

Query: 348 VTDIACAALNGLKMGDKTLTVRRAT--ASSGQSKTEQESILAQAQQHIAIQKMALQTSGM 405
           VTDIACAALNG+KMGDKTLTVRRA   A+  Q K EQESIL  AQQ IA+QK+ LQ + +
Sbjct: 437 VTDIACAALNGIKMGDKTLTVRRANQGANPQQPKPEQESILMHAQQQIALQKLMLQPALV 496

Query: 406 NTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRP 465
            T             KV+CLT A+++D L DDE+YEEIL+DMR+EC K+GTLVNVVIPRP
Sbjct: 497 AT-------------KVVCLTHAVSSDELKDDEDYEEILDDMRQECSKFGTLVNVVIPRP 543

Query: 466 DQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
             +G    GVGKVFLEY D  G   A+  L+GRKF GN V A +YPE+K+   DY
Sbjct: 544 PSDGEPAAGVGKVFLEYVDIDGATKARAGLNGRKFDGNQVVAVFYPENKFAQGDY 598

Source: Glycine max

Species: Glycine max

Genus: Glycine

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	522
TAIR|locus:2206001	589	AT1G60900 [Arabidopsis thalian	0.756	0.670	0.618	4.7e-133
TAIR|locus:2115280	573	ATU2AF65A [Arabidopsis thalian	0.760	0.692	0.586	4e-123
UNIPROTKB|Q24JZ8	475	U2AF2 "Uncharacterized protein	0.649	0.713	0.381	1.1e-60
MGI|MGI:98886	475	U2af2 "U2 small nuclear ribonu	0.649	0.713	0.378	4.8e-60
RGD|1597319	475	LOC690372 "similar to U2 (RNU2	0.649	0.713	0.378	4.8e-60
UNIPROTKB|P26368	475	U2AF2 "Splicing factor U2AF 65	0.649	0.713	0.378	6.1e-60
UNIPROTKB|E2R0G3	471	U2AF2 "Uncharacterized protein	0.641	0.711	0.378	2.6e-59
FB|FBgn0005411	416	U2af50 "U2 small nuclear ribop	0.691	0.867	0.365	6.9e-59
ZFIN|ZDB-GENE-050706-131	470	u2af2a "U2 small nuclear RNA a	0.653	0.725	0.373	1.1e-58
WB|WBGene00006697	496	uaf-1 [Caenorhabditis elegans	0.442	0.465	0.394	7.8e-54

TAIR|locus:2206001 AT1G60900 [Arabidopsis thaliana (taxid:3702)]

 Score = 1268 (451.4 bits), Expect = 4.7e-133, Sum P(2) = 4.7e-133
 Identities = 254/411 (61%), Positives = 291/411 (70%)

Query:   113 GFDXXXXXXXXXXXXXXXXQLPGVPSA--VPEMAQNMLPF-GATQLGAFPLMPVQVMTQQ 169
             GFD                Q+P VP+   +P M  NM P     QLGA P++PVQ MTQQ
Sbjct:   190 GFDMAPPDMLAATAVAAAGQVPSVPTTATIPGMFSNMFPMVPGQQLGALPVLPVQAMTQQ 249

Query:   170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
             ATRHARRVYVGGLPP ANEQ+++TFFSQVM+AIGGN+AGPGDAVVNVYINHEKKFAFVEM
Sbjct:   250 ATRHARRVYVGGLPPTANEQSVSTFFSQVMSAIGGNTAGPGDAVVNVYINHEKKFAFVEM 309

Query:   230 RTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 289
             R+VEEASNAMALDGII EGV V+VRRPTDYNP+LAA LGP QP+PNLNL AVGL+SG+ G
Sbjct:   310 RSVEEASNAMALDGIILEGVPVKVRRPTDYNPSLAATLGPSQPNPNLNLGAVGLSSGSTG 369

Query:   290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
             G EGPDR+FVGGLPYYFTE QI+ELLESFG L GF+LVKDR+TGNSKGY FCVYQDP+VT
Sbjct:   370 GLEGPDRIFVGGLPYYFTEVQIRELLESFGPLRGFNLVKDRETGNSKGYAFCVYQDPSVT 429

Query:   350 DIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQTSGMNTLG 409
             DIACAALNG+KMGDKTLTVRRA   + Q K EQE             ++  Q  G  T  
Sbjct:   430 DIACAALNGIKMGDKTLTVRRAIQGAIQPKPEQEEVLLYAQQQIALQRLMFQPGGTPT-- 487

Query:   410 GGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVVIPRPDQNG 469
                        K++CLT+ +T                     GK+G LVNVVIPRP+ + 
Sbjct:   488 -----------KIVCLTQVVTADDLRDDEEYAEIMEDMRQEGGKFGNLVNVVIPRPNPDH 536

Query:   470 GETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
               TPGVGKVFLEY D  G + A++ ++GRKFGGN V A YYPEDKY   DY
Sbjct:   537 DPTPGVGKVFLEYADVDGSSKARSGMNGRKFGGNQVVAVYYPEDKYAQGDY 587

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006397 "mRNA processing" evidence=IEA

TAIR|locus:2115280 ATU2AF65A [Arabidopsis thaliana (taxid:3702)]

 Score = 1185 (422.2 bits), Expect = 4.0e-123, Sum P(2) = 4.0e-123
 Identities = 243/414 (58%), Positives = 279/414 (67%)

Query:   113 GFDXXX-XXXXXXXXXXXXXQLPGVPSAVPE--MAQNMLPFGATQ-LGAFPLMPVQVMTQ 168
             GFD                 Q+P  P  +P   M  NM P    Q  G   +MP+Q MTQ
Sbjct:   173 GFDMAPPASAMLAAGAAVTGQVPPAPPTLPGAGMFPNMFPLPTGQSFGGLSMMPIQAMTQ 232

Query:   169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
             QATRHARRVYVGGL P ANEQ++ATFFSQVM A+GGN+AGPGDAVVNVYINHEKKFAFVE
Sbjct:   233 QATRHARRVYVGGLSPTANEQSVATFFSQVMAAVGGNTAGPGDAVVNVYINHEKKFAFVE 292

Query:   229 MRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAI 288
             MR+VEEASNAM+LDGIIFEG  V+VRRP+DYNP+LAA LGP QPSP+LNLAAVGL  GA 
Sbjct:   293 MRSVEEASNAMSLDGIIFEGAPVKVRRPSDYNPSLAATLGPSQPSPHLNLAAVGLTPGAS 352

Query:   289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
             GG EGPDR+FVGGLPYYFTE+Q++ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +V
Sbjct:   353 GGLEGPDRIFVGGLPYYFTESQVRELLESFGGLKGFDLVKDRETGNSKGYAFCVYQDLSV 412

Query:   349 TDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQTSGMNTL 408
             TDIACAALNG+KMGDKTLTVRRA   +   K EQE+            ++ LQ   + T 
Sbjct:   413 TDIACAALNGIKMGDKTLTVRRANQGTMLQKPEQENVLLHAQQQIAFQRVMLQPGAVATT 472

Query:   409 GGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVVIPRPDQN 468
                          V+CLT+ +T                     GK+G L NVVIPRP  N
Sbjct:   473 -------------VVCLTQVVTEDELRDDEEYGDIMEDMRQEGGKFGALTNVVIPRPSPN 519

Query:   469 GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 522
             G    G+GKVFL+Y D  G   A+  ++GRKFGGN V A YYPEDK+   DY A
Sbjct:   520 GEPVAGLGKVFLKYADTDGSTRARFGMNGRKFGGNEVVAVYYPEDKFEQGDYGA 573

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0042742 "defense response to bacterium" evidence=IEP

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

UNIPROTKB|Q24JZ8 U2AF2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 596 (214.9 bits), Expect = 1.1e-60, Sum P(2) = 1.1e-60
 Identities = 137/359 (38%), Positives = 193/359 (53%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 401
              Y D  VTD A A LNG+++GDK L V+RA+  +      + +             + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSPLSTINQTPVTLQ 359

Query:   402 TSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVV 461
               G+  +   + + G    +VLCL   +                     CGKYG + ++ 
Sbjct:   360 VPGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECGKYGLVKSIE 416

Query:   462 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
             IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   417 IPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 474

GO:0070742 "C2H2 zinc finger domain binding" evidence=IEA

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IEA

GO:0019899 "enzyme binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:98886 U2af2 "U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2" [Mus musculus (taxid:10090)]

 Score = 590 (212.7 bits), Expect = 4.8e-60, Sum P(2) = 4.8e-60
 Identities = 136/359 (37%), Positives = 192/359 (53%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 401
              Y D  VTD A A LNG+++GDK L V+RA+  +      + +             + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSLPSTINQTPVTLQ 359

Query:   402 TSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVV 461
               G+  +   + + G    +VLCL   +                     C KYG + ++ 
Sbjct:   360 VPGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE 416

Query:   462 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
             IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   417 IPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 474

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IDA

GO:0016607 "nuclear speck" evidence=TAS

GO:0019899 "enzyme binding" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=ISO

GO:0070742 "C2H2 zinc finger domain binding" evidence=IPI

RGD|1597319 LOC690372 "similar to U2 (RNU2) small nuclear RNA auxiliary factor 2 isoform b" [Rattus norvegicus (taxid:10116)]

 Score = 590 (212.7 bits), Expect = 4.8e-60, Sum P(2) = 4.8e-60
 Identities = 136/359 (37%), Positives = 192/359 (53%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 401
              Y D  VTD A A LNG+++GDK L V+RA+  +      + +             + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSLPSTINQTPVTLQ 359

Query:   402 TSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVV 461
               G+  +   + + G    +VLCL   +                     C KYG + ++ 
Sbjct:   360 VPGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE 416

Query:   462 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
             IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   417 IPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 474

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0019899 "enzyme binding" evidence=IEA

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IEA

GO:0070742 "C2H2 zinc finger domain binding" evidence=IEA

UNIPROTKB|P26368 U2AF2 "Splicing factor U2AF 65 kDa subunit" [Homo sapiens (taxid:9606)]

 Score = 589 (212.4 bits), Expect = 6.1e-60, Sum P(2) = 6.1e-60
 Identities = 136/359 (37%), Positives = 192/359 (53%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 401
              Y D  VTD A A LNG+++GDK L V+RA+  +      + +             + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSPPSTINQTPVTLQ 359

Query:   402 TSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVV 461
               G+  +   + + G    +VLCL   +                     C KYG + ++ 
Sbjct:   360 VPGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE 416

Query:   462 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
             IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   417 IPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 474

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0070742 "C2H2 zinc finger domain binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0019899 "enzyme binding" evidence=IPI

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IDA

GO:0006397 "mRNA processing" evidence=TAS

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

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006406 "mRNA export from nucleus" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0031124 "mRNA 3'-end processing" evidence=TAS

UNIPROTKB|E2R0G3 U2AF2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 583 (210.3 bits), Expect = 2.6e-59, Sum P(2) = 2.6e-59
 Identities = 136/359 (37%), Positives = 191/359 (53%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 401
              Y D  VTD A A LNG+++GDK L V+RA+  +  +                   + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNA----------TLSTINQTPVTLQ 355

Query:   402 TSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVV 461
               G+  +   + + G    +VLCL   +                     C KYG + ++ 
Sbjct:   356 VPGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIE 412

Query:   462 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
             IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   413 IPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 470

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

FB|FBgn0005411 U2af50 "U2 small nuclear riboprotein auxiliary factor 50" [Drosophila melanogaster (taxid:7227)]

 Score = 570 (205.7 bits), Expect = 6.9e-59, Sum P(2) = 6.9e-59
 Identities = 144/394 (36%), Positives = 201/394 (51%)

Query:   134 PGVPSAVPEMAQNMLPFGATQLGAFPLMP---VQVMTQQATRHARRVYVGGLPPLANEQA 190
             PG     P   + M   G       P  P   V V+    TR ARR+YVG +P    E+ 
Sbjct:    49 PGFEHITPMQYKAMQASGQIPASVVPDTPQTAVPVVGSTITRQARRLYVGNIPFGVTEEE 108

Query:   191 IATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA 250
             +  FF+Q M  +G   A  G  V+   IN +K FAF+E R+++E + AMA DGI  +G +
Sbjct:   109 MMEFFNQQMHLVGLAQAA-GSPVLACQINLDKNFAFLEFRSIDETTQAMAFDGINLKGQS 167

Query:   251 VRVRRPTDYNPTLAAALGPG-QPSPNLNLAAVGLASGAIGGA--EGPDRVFVGGLPYYFT 307
             +++RRP DY P       PG   +P +  A V  +SG I     + P ++F+GGLP Y  
Sbjct:   168 LKIRRPHDYQPM------PGITDTPAIKPAVV--SSGVISTVVPDSPHKIFIGGLPNYLN 219

Query:   308 ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT 367
             + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D ++TD + A LNG+++GDK L 
Sbjct:   220 DDQVKELLLSFGKLRAFNLVKDAATGLSKGYAFCEYVDLSITDQSIAGLNGMQLGDKKLI 279

Query:   368 VRRATASSGQSKTEQESXXXXXXXXXXXXKMALQTSGM-NTLGGGMSLFGETLAKVLCLT 426
             V+RA+  +   K  Q +             + LQ  G+ N +  G         +VLCL 
Sbjct:   280 VQRASVGA---KNAQNAANTTQS-------VMLQVPGLSNVVTSGPP------TEVLCLL 323

Query:   427 EAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAV 486
               +T                    C KYG + +V IPRP + G E PG GKVF+E+   +
Sbjct:   324 NMVTPDELRDEEEYEDILEDIKEECTKYGVVRSVEIPRPIE-GVEVPGCGKVFVEFNSVL 382

Query:   487 GCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
              C  A+ AL+GRKF    V   Y+  DKY  +++
Sbjct:   383 DCQKAQQALTGRKFSDRVVVTSYFDPDKYHRREF 416

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;ISS;NAS;IMP

GO:0005686 "U2 snRNP" evidence=TAS

GO:0008187 "poly-pyrimidine tract binding" evidence=NAS;IDA

GO:0005681 "spliceosomal complex" evidence=ISS;NAS

GO:0000245 "spliceosomal complex assembly" evidence=NAS

GO:0046982 "protein heterodimerization activity" evidence=NAS

GO:0005634 "nucleus" evidence=IC;NAS

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0051168 "nuclear export" evidence=IMP

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IMP

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0008380 "RNA splicing" evidence=IMP

GO:0003723 "RNA binding" evidence=IMP

GO:0022008 "neurogenesis" evidence=IMP

ZFIN|ZDB-GENE-050706-131 u2af2a "U2 small nuclear RNA auxiliary factor 2a" [Danio rerio (taxid:7955)]

 Score = 575 (207.5 bits), Expect = 1.1e-58, Sum P(2) = 1.1e-58
 Identities = 134/359 (37%), Positives = 190/359 (52%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+++  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   129 PVPVVGSQMTRQARRLYVGNIPFGITEESMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 187

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P    +  P    P  +L  V
Sbjct:   188 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPG-SLP-V 245

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   246 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 303

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 401
              Y D  ++D A A LNG+++GDK L V+RA  S G   T                 + LQ
Sbjct:   304 EYVDVNISDQAIAGLNGMQLGDKKLLVQRA--SVGSKNT--------TLTGINQTPVTLQ 353

Query:   402 TSGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVV 461
               G+  +   ++  G    +VLCL   +                     C KYG + ++ 
Sbjct:   354 VPGL--MNSSVNQMGGIPTEVLCLMNMVAPEELLDDEEYEEIVEDVRDECSKYGQVKSIE 411

Query:   462 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
             IPRP  +G + PG GK+F+E+        A   L+GRKF    V   Y   D Y  +D+
Sbjct:   412 IPRP-VDGLDIPGTGKIFVEFMSVFDSQKAMQGLTGRKFANRVVVTKYCDPDAYHRRDF 469

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0046660 "female sex differentiation" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

WB|WBGene00006697 uaf-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 400 (145.9 bits), Expect = 7.8e-54, Sum P(2) = 7.8e-54
 Identities = 97/246 (39%), Positives = 140/246 (56%)

Query:   135 GVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATF 194
             G  +  P   +NM   G    G+     V V+    T  +RR+YVG +P   NE+A+  F
Sbjct:   145 GFETTTPMEYKNMQAAGQVPRGSVQ-SAVPVVGPSVTCQSRRLYVGNIPFGCNEEAMLDF 203

Query:   195 FSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVR 254
             F+Q M   G   A PG+ ++   IN +K FAF+E R+++E +  MA DGI F G  ++VR
Sbjct:   204 FNQQMHLCGLAQA-PGNPILLCQINLDKNFAFIEFRSIDETTAGMAFDGINFMGQQLKVR 262

Query:   255 RPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKEL 314
             RP DY P+        Q + ++N + + +++  +  A   +++F+GGLP Y TE Q+KEL
Sbjct:   263 RPRDYQPS--------QNTFDMN-SRMPVSTIVVDSA---NKIFIGGLPNYLTEDQVKEL 310

Query:   315 LESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS 374
             L SFG L  F L  D   GNSKGY F  Y DP +TD A A LNG+++GDK L V+ A A+
Sbjct:   311 LCSFGPLKAFSLNVDSQ-GNSKGYAFAEYLDPTLTDQAIAGLNGMQLGDKQLVVQLACAN 369

Query:   375 SGQSKT 380
               +  T
Sbjct:   370 QQRHNT 375

GO:0003723 "RNA binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0002119 "nematode larval development" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

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

GO:0040007 "growth" evidence=IMP

GO:0042127 "regulation of cell proliferation" evidence=IMP

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0040022 "feminization of hermaphroditic germ-line" evidence=IMP

GO:0007281 "germ cell development" evidence=IMP

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

GO:0009790 "embryo development" evidence=IMP

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0030628 "pre-mRNA 3'-splice site binding" evidence=IDA

GO:0048589 "developmental growth" evidence=IMP

GO:0010172 "embryonic body morphogenesis" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

---

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)
Q2QZL4	U2A2B_ORYSJ	No assigned EC number	0.6666	0.7567	0.7208	yes	no
Q8L716	U2A2B_ARATH	No assigned EC number	0.6861	0.7567	0.6706	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	522
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-174
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-41
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	2e-39
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	7e-37
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-27
cd12465	88	cd12465, RRM_UHMK1, RNA recognition motif found in	9e-20
smart00360	73	smart00360, RRM, RNA recognition motif	1e-18
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	6e-16
cd12374	85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	9e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-15
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-14
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	5e-14
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	3e-13
cd12648	98	cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 i	4e-13
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-13
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-12
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-12
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	6e-12
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	7e-12
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	8e-12
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	1e-11
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	1e-11
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-11
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	6e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-10
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-10
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-10
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-10
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-10
cd12647	96	cd12647, RRM_UHM_SPF45, RNA recognition motif in U	3e-10
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-10
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-10
smart00360	73	smart00360, RRM, RNA recognition motif	7e-10
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-09
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	1e-09
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	3e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-09
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-09
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	6e-09
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	9e-09
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-08
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-08
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-08
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-08
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	3e-08
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	4e-08
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-07
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-07
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	1e-07
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-07
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-07
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-07
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	2e-07
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-07
cd12282	91	cd12282, RRM2_TatSF1_like, RNA recognition motif 2	3e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	3e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	4e-07
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	4e-07
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	7e-07
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	7e-07
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	7e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	8e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	9e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	1e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	1e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-06
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	1e-06
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-06
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-06
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-06
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	3e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	5e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	7e-06
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	7e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	8e-06
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	8e-06
smart00360	73	smart00360, RRM, RNA recognition motif	9e-06
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	9e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-05
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	1e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	1e-05
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-05
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	2e-05
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	2e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	2e-05
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-05
cd12287	102	cd12287, RRM_U2AF35_like, RNA recognition motif in	2e-05
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-05
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	3e-05
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	3e-05
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	3e-05
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	3e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-05
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	3e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-05
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	5e-05
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	5e-05
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	5e-05
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	5e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	5e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	5e-05
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	6e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	6e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	6e-05
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	6e-05
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	7e-05
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	7e-05
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	8e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	8e-05
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	8e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	8e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	9e-05
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	9e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-04
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	1e-04
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	1e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	1e-04
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	1e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-04
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	1e-04
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	1e-04
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-04
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	1e-04
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	2e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	2e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-04
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	2e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-04
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	2e-04
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	2e-04
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	3e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	3e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-04
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-04
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	4e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	4e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	4e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	5e-04
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	5e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	5e-04
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	5e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	6e-04
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	6e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	6e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	6e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	7e-04
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	7e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	7e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	7e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	7e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	7e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	8e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	9e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	9e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	0.001
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.001
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	0.001
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	0.001
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	0.001
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	0.002
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.002
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.002
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.002
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	0.002
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.002
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	0.002
smart00361	70	smart00361, RRM_1, RNA recognition motif	0.002
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	0.003
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.003
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	0.003
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	0.004
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.004
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.004
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	0.004
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	0.004

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score =  501 bits (1292), Expect = e-174
 Identities = 207/504 (41%), Positives = 264/504 (52%), Gaps = 29/504 (5%)

Query: 25  RSRTGERGRDRHHR--DFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRH 82
           RSR   R RDRH R  +     D R RD+  +YD    R    +   R        R R 
Sbjct: 27  RSRDRSRFRDRHRRSRERSYREDSRPRDR-RRYDSRSPRSLRYSSVRRS-------RDRP 78

Query: 83  RSRSHSSDRF---RNRSKSLSPSRSPSKS-KRRSGFDMAPPA-AAMLPGAAVPGQLPGVP 137
           R RS S       R R +  SPS    K  K+RS +D+ PP    +    A   Q+  VP
Sbjct: 79  RRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDIKPPGYELVTADQAKASQVFSVP 138

Query: 138 SAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQ 197
              P  A         +      +PV    QQATR ARR+YVGG+PP   E+A+  FF+ 
Sbjct: 139 GTAPRPAMTDPEKLLAEGSIITPLPVLPYQQQATRQARRLYVGGIPPEFVEEAVVDFFND 198

Query: 198 VMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPT 257
           +M A G + A  G  V +V IN EK FAF+E RTVEEA+ AMALD II+  V +++RRP 
Sbjct: 199 LMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKIRRPH 258

Query: 258 DYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLES 317
           DY P         Q +P+ N   V     +    +  DR+++G LP Y  E QIKELLES
Sbjct: 259 DYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLES 318

Query: 318 FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQ 377
           FG L  F+L+KD  TG SKGY FC Y+DP+VTD+A AALNG   GD  L V+RA   + Q
Sbjct: 319 FGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQ 378

Query: 378 SKTEQESILAQ-AQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALAD 436
           +  +  + +A       A+ +  LQ              G    KV+ LT  +T D L D
Sbjct: 379 ATIDTSNGMAPVTLLAKALSQSILQI-------------GGKPTKVVQLTNLVTGDDLMD 425

Query: 437 DEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS 496
           DEEYEEI ED++ E  KYG L+N+VIPRP+ +   TPGVGKVFLEY D      A   ++
Sbjct: 426 DEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMN 485

Query: 497 GRKFGGNTVNAFYYPEDKYFNKDY 520
           GRKF    V A +Y ED Y   DY
Sbjct: 486 GRKFNDRVVVAAFYGEDCYKAGDY 509

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|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 =  143 bits (363), Expect = 1e-41
 Identities = 49/77 (63%), Positives = 61/77 (79%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           +++F+GGLP Y +E Q+KELLESFG L  F+LVKD  TG SKGY FC Y DP+VTD A A
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

Query: 355 ALNGLKMGDKTLTVRRA 371
            LNG+++GDK LTV+RA
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|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 =  137 bits (348), Expect = 2e-39
 Identities = 48/83 (57%), Positives = 61/83 (73%), Gaps = 1/83 (1%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG LPP   E+ +  FF+Q M A G N   PG+ V++V IN EK FAFVE RTVE
Sbjct: 1   ARRLYVGNLPPGITEEELVDFFNQAMLAAGLN-QAPGNPVLSVQINPEKNFAFVEFRTVE 59

Query: 234 EASNAMALDGIIFEGVAVRVRRP 256
           EA+ A+ALDGIIF+G  +++RRP
Sbjct: 60  EATAALALDGIIFKGQPLKIRRP 82

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|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 =  131 bits (331), Expect = 7e-37
 Identities = 50/85 (58%), Positives = 64/85 (75%)

Query: 421 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFL 480
           +VLCL   +T + L DDEEYEEILED++EECGKYG +++VVIPRP+  G + PGVGKVF+
Sbjct: 2   RVLCLLNMVTPEELEDDEEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFV 61

Query: 481 EYYDAVGCATAKNALSGRKFGGNTV 505
           E+ D      A+ AL+GRKF G TV
Sbjct: 62  EFADVEDAQKAQLALAGRKFDGRTV 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score =  114 bits (287), Expect = 2e-27
 Identities = 123/551 (22%), Positives = 182/551 (33%), Gaps = 157/551 (28%)

Query: 25  RSRTGERGRDRHHRDFKSGGDDRRRDK--NYKYDREGIRDHDRTDRHRDYNRDKERRHRH 82
           R R  ERGR    R+     D RR DK       R   RD  R  R RDY R +  R R 
Sbjct: 1   RYRDRERGR---LRN-----DTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRS 52

Query: 83  RSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPGAAVPGQLPGVPSAVPE 142
           RS +        R +     R   +   R+                              
Sbjct: 53  RSPNR-----YYRPRGDRSYRRDDRRSGRN------------------------------ 77

Query: 143 MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAI 202
                                + +T+ A R  R V+V  L   A E+ +  FFS+V    
Sbjct: 78  -------------------TKEPLTE-AERDDRTVFVLQLALKARERDLYEFFSKV---- 113

Query: 203 GGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRP 256
                G    V +V           K  A+VE   VE    A+AL G +  G  + V+  
Sbjct: 114 -----GK---VRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQ-S 164

Query: 257 TDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLE 316
           +      AA     QP                G      +++VG L +  TE +++++ E
Sbjct: 165 SQAEKNRAAKAATHQP----------------GDIPNFLKLYVGNLHFNITEQELRQIFE 208

Query: 317 SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG 376
            FG +    L +D +TG SKG+GF  + D      A   +NG ++  + + V  A  S+ 
Sbjct: 209 PFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTY 268

Query: 377 QSKT--EQESILAQAQQHIAI----------------QKMALQTSGMNTLGGGMSLFGE- 417
                   E I  Q Q    +                    L   G  +    M      
Sbjct: 269 LLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRD 328

Query: 418 ----TLAKVLCLTEAITADAL------------------------ADDEE---YEEILED 446
                       T A+   A                         A +EE     EIL+D
Sbjct: 329 GIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDD 388

Query: 447 MREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVN 506
           ++EEC KYG +V++ +   +         GK++L++        A  AL+GR FGG  + 
Sbjct: 389 VKEECSKYGGVVHIYVDTKNSA-------GKIYLKFSSVDAALAAFQALNGRYFGGKMIT 441

Query: 507 AFYYPEDKYFN 517
           A +   D Y  
Sbjct: 442 AAFVVNDVYDM 452

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|240911 cd12465, RRM_UHMK1, RNA recognition motif found in U2AF homology motif kinase 1 (UHMK1) and similar proteins

 Score = 83.5 bits (206), Expect = 9e-20
 Identities = 39/90 (43%), Positives = 57/90 (63%), Gaps = 6/90 (6%)

Query: 422 VLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLE 481
           VL L   +    L ++EEYE+I+ED++EEC KYG +V+++IP+      E PG G+VF+E
Sbjct: 5   VLRLLNVLDDAHLQNEEEYEDIIEDIKEECQKYGPVVSLLIPK------ENPGKGQVFVE 58

Query: 482 YYDAVGCATAKNALSGRKFGGNTVNAFYYP 511
           Y +A     A+  L+GR F G  V A +YP
Sbjct: 59  YANAGDSKAAQKLLTGRIFDGKFVVATFYP 88

This subgroup corresponds to the RRM of UHMK1. UHMK1, also termed kinase interacting with stathmin (KIS) or P-CIP2, is a serine/threonine protein kinase functionally related to RNA metabolism and neurite outgrowth. It contains an N-terminal kinase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), with high homology to the corresponding motif of the mammalian U2 small nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65 or U2AF2). UHMK1 targets two key regulators of cell proliferation and migration, the cyclin-dependent kinase (CDK) inhibitor p27Kip1 and the microtubule-destabilizing protein stathmin. It plays a critical role during vascular wound repair by preventing excessive vascular smooth muscle cell (VSMC) migration into the vascular lesion. Moreover, UHMK1 may control cell migration and neurite outgrowth by interacting with and phosphorylating the splicing factor SF1, thereby probably contributing to the control of protein expression. Furthermore, UHMK1 may be functionally related to microtubule dynamics and axon development. It localizes to RNA granules, interacts with three proteins found in RNA granules (KIF3A, NonO, and eEF1A), and further enhances the local translation. UHMK1 is highly expressed in regions of the brain implicated in schizophrenia and may play a role in susceptibility to schizophrenia. Length = 88

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

 Score = 79.6 bits (197), Expect = 1e-18
 Identities = 27/73 (36%), Positives = 42/73 (57%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FVG LP   TE +++EL   FG +    LV+D++TG SKG+ F  ++     + A  A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 356 LNGLKMGDKTLTV 368
           LNG ++  + L V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>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 = 72.3 bits (178), Expect = 6e-16
 Identities = 32/72 (44%), Positives = 40/72 (55%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG +PY  TE Q+ E+    G +  F LV DRDTG  KGYGFC ++D      A   L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 357 NGLKMGDKTLTV 368
           NG +   + L V
Sbjct: 61  NGYEFNGRALRV 72

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

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

 Score = 72.3 bits (178), Expect = 9e-16
 Identities = 30/91 (32%), Positives = 48/91 (52%), Gaps = 7/91 (7%)

Query: 421 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFL 480
           K+L L   +T       E  E++ +++ EEC KYG ++NV++     +      V ++F+
Sbjct: 2   KILVLRNMVTPG-----EIDEDLKDEIEEECEKYGKVLNVIV-HEVASSEADDAV-RIFV 54

Query: 481 EYYDAVGCATAKNALSGRKFGGNTVNAFYYP 511
           E+ DA     A  AL+GR FGG  V A +Y 
Sbjct: 55  EFSDADEAIKAVRALNGRFFGGRKVTARFYD 85

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

 Score = 70.8 bits (174), Expect = 2e-15
 Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FVG LP   TE  ++EL   FG +    +V+D+D G SKG+ F  ++ P   + A  AL
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKALEAL 59

Query: 357 NGLKMGDKTLTVR 369
           NG ++  + L V 
Sbjct: 60  NGKELDGRKLKVS 72

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

>gnl|CDD|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 = 69.8 bits (171), Expect = 4e-15
 Identities = 33/75 (44%), Positives = 43/75 (57%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC Y+D      A   L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 357 NGLKMGDKTLTVRRA 371
           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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 67.2 bits (165), Expect = 3e-14
 Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FVG LP   TE  +K+L   FG +    +V+D  TG SKG+ F  ++D    + A  AL
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 357 NGLKMGDKTLT 367
           NG ++G + L 
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 = 67.3 bits (165), Expect = 4e-14
 Identities = 29/76 (38%), Positives = 42/76 (55%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++VG LPY  TE  +K+L   FG +    ++ DR+TG S+G+GF   +     + A   
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 356 LNGLKMGDKTLTVRRA 371
           LNG   G +TLTV  A
Sbjct: 61  LNGTDFGGRTLTVNEA 76

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

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 67.3 bits (165), Expect = 5e-14
 Identities = 28/72 (38%), Positives = 44/72 (61%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +++GGLPY  TE  I  +   +G +   +LV+D+ TG SKG+ F  Y+D   T +A   L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 357 NGLKMGDKTLTV 368
           NG+K+  +T+ 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|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 64.5 bits (158), Expect = 3e-13
 Identities = 22/73 (30%), Positives = 39/73 (53%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V++G LP+ F E ++++    FGT+    L + + TG SKGY F  ++ P V  I    +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 357 NGLKMGDKTLTVR 369
           N   + ++ L  +
Sbjct: 62  NNYLLFERLLKCK 74

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

>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins

 Score = 64.7 bits (158), Expect = 4e-13
 Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 441 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGV-GKVFLEYYDAVGCATAKNALSGRK 499
           +++  ++ EECGK+G +  V+I +  Q   E   +  K+F+E+        A  AL+GR 
Sbjct: 17  DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSLPSEAEKAIQALNGRW 76

Query: 500 FGGNTVNAFYYPEDKYFNKDYS 521
           FGG  V A  Y + K+   D S
Sbjct: 77  FGGRKVKAELYDQTKFDASDLS 98

This subgroup corresponds to the RRM3 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), 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. The research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 98

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

 Score = 69.6 bits (169), Expect = 5e-13
 Identities = 33/111 (29%), Positives = 56/111 (50%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FVG LPY  TE  ++EL + FG +    LV+DR+TG S+G+ F  ++     + A   
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE 176

Query: 356 LNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMN 406
           LNG ++  + L V++A  +S        ++ A   + ++  K  L     N
Sbjct: 177 LNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDN 227

Length = 306

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

 Score = 63.3 bits (154), Expect = 1e-12
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +++G LP+ F E ++K+    FGT+    + + + TGNSK YGF  + +P V  IA  ++
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 357 NGLKMGDKTLTVR 369
           N   +  K L V 
Sbjct: 62  NNYLLMGKVLQVH 74

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

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

 Score = 62.4 bits (152), Expect = 2e-12
 Identities = 25/67 (37%), Positives = 36/67 (53%)

Query: 302 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM 361
           LP   T+ +++ L E+ G +    +V+DR TG S GYGF  Y D      A   LNG ++
Sbjct: 8   LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEI 67

Query: 362 GDKTLTV 368
            +K L V
Sbjct: 68  RNKRLKV 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|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 61.4 bits (150), Expect = 6e-12
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 7/82 (8%)

Query: 430 TADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCA 489
                 +DE  +EI ED+ EEC K+G + ++ +        +    G V++++       
Sbjct: 11  DPAEETEDEWDDEIKEDVLEECSKFGPVEHIKVD-------KNSPEGVVYVKFKTVEAAQ 63

Query: 490 TAKNALSGRKFGGNTVNAFYYP 511
               AL+GR F G  + A Y  
Sbjct: 64  KCIQALNGRWFDGRQITAEYVD 85

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

 Score = 60.9 bits (148), Expect = 7e-12
 Identities = 28/70 (40%), Positives = 40/70 (57%)

Query: 302 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM 361
           LP   T+ +I+ L  S G +    L++D+ TG S GYGF  Y DP   + A   LNGL++
Sbjct: 9   LPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRL 68

Query: 362 GDKTLTVRRA 371
            +KT+ V  A
Sbjct: 69  QNKTIKVSYA 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|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 60.7 bits (148), Expect = 8e-12
 Identities = 30/75 (40%), Positives = 38/75 (50%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN 357
            VG LP  FT+ Q +EL+  FG +    LV    TG SKGYGF  Y   A    A   L+
Sbjct: 3   CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 358 GLKMGDKTLTVRRAT 372
           G ++G + L V  A 
Sbjct: 63  GKQIGGRKLQVDWAD 77

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

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

 Score = 60.3 bits (147), Expect = 1e-11
 Identities = 30/73 (41%), Positives = 42/73 (57%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VFVG +P   ++  I++LLE  G +  +  VKD  TG  K +GFC ++DP     A   
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61

Query: 356 LNGLKMGDKTLTV 368
           LNGL++G K L V
Sbjct: 62  LNGLELGGKKLLV 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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 60.5 bits (146), Expect = 1e-11
 Identities = 34/79 (43%), Positives = 42/79 (53%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ + K L  S G +    LV+D+ TG S GYGF  Y DP   D A   L
Sbjct: 6   LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65

Query: 357 NGLKMGDKTLTVRRATASS 375
           NGLK+  KT+ V  A  SS
Sbjct: 66  NGLKLQTKTIKVSYARPSS 84

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

 Score = 59.6 bits (145), Expect = 2e-11
 Identities = 26/76 (34%), Positives = 41/76 (53%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R++V  +    +E  IK + E+FG +    L  D +TG  KGYGF  Y++P     A A+
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61

Query: 356 LNGLKMGDKTLTVRRA 371
           +N   +G + L V +A
Sbjct: 62  MNLFDLGGQQLRVGKA 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|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 57.8 bits (140), Expect = 6e-11
 Identities = 28/76 (36%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGLP   TE + KE    FG +    L++D DTG S+G+GF  +   +  +   +A
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 356 LNGLKMGDKTLTVRRA 371
              L++G K + V+RA
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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 24/71 (33%), Positives = 37/71 (52%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN 357
           +VG L +  TE  ++ + E FG +    L +D +TG SKGYGF  + D      A   LN
Sbjct: 2   YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 358 GLKMGDKTLTV 368
           G ++  + + V
Sbjct: 62  GFELAGRPIKV 72

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

>gnl|CDD|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 = 26/78 (33%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           P+R+FVGG+P   TE ++++    FG++    ++ DR  G SKGYGF  ++     +   
Sbjct: 2   PNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRA-GVSKGYGFVTFETQEDAEKIL 60

Query: 354 AALNGLKMGDKTLTVRRA 371
           A  N L    K L +  A
Sbjct: 61  AMGN-LNFRGKKLNIGPA 77

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|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 = 56.5 bits (137), Expect = 2e-10
 Identities = 25/79 (31%), Positives = 43/79 (54%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
            +++FV GL    TE +++ L   FG +    L+KD +TG S+G+GF  ++     D A 
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 354 AALNGLKMGDKTLTVRRAT 372
             LNG ++  + + V +A 
Sbjct: 61  RDLNGKELEGRVIKVEKAK 79

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

>gnl|CDD|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 = 56.0 bits (135), Expect = 3e-10
 Identities = 23/79 (29%), Positives = 45/79 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +++P     A  A
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 356 LNGLKMGDKTLTVRRATAS 374
           +NG  +  + + V +A  S
Sbjct: 62  MNGKSVDGRQIRVDQAGKS 80

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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 56.3 bits (135), Expect = 3e-10
 Identities = 31/79 (39%), Positives = 42/79 (53%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ + + L  S G +    LV+D+ TG S GYGF  Y DP   + A   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 357 NGLKMGDKTLTVRRATASS 375
           NGL++  KT+ V  A  SS
Sbjct: 65  NGLRLQTKTIKVSYARPSS 83

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|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 4/83 (4%)

Query: 437 DEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS 496
           DE+ E    +++EEC KYG +  V+I        +   V ++F+E+        A   L+
Sbjct: 17  DEDLEP---EVKEECSKYGKVTKVLIFEIPGASPDDEAV-RIFVEFERVESAIKAVVDLN 72

Query: 497 GRKFGGNTVNAFYYPEDKYFNKD 519
           GR FGG TV A +Y E+++   D
Sbjct: 73  GRFFGGRTVKASFYDEERFRRND 95

This subgroup corresponds to the RRM of SPF45, also termed RNA-binding motif protein 17 (RBM17), 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. . Length = 96

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 55.9 bits (134), Expect = 4e-10
 Identities = 30/75 (40%), Positives = 41/75 (54%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ ++K L  S G +    LV+D+ TG S GYGF  Y DP   + A   L
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 357 NGLKMGDKTLTVRRA 371
           NGL++  KT+ V  A
Sbjct: 67  NGLRLQTKTIKVSYA 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 60.7 bits (147), Expect = 6e-10
 Identities = 31/78 (39%), Positives = 43/78 (55%)

Query: 302 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM 361
           LP   T+ +I+ L  S G +    LV+D+ TG S GYGF  Y  P   + A  +LNGL++
Sbjct: 11  LPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRL 70

Query: 362 GDKTLTVRRATASSGQSK 379
            +KT+ V  A  SS   K
Sbjct: 71  QNKTIKVSYARPSSDSIK 88

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|214636 smart00360, RRM, RNA recognition motif

 Score = 54.9 bits (133), Expect = 7e-10
 Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 19/85 (22%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEM 229
            ++VG LPP   E+ +   FS+          G    V +V +  +K+      FAFVE 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKF---------GK---VESVRLVRDKETGKSKGFAFVEF 48

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
            + E+A  A+ AL+G   +G  ++V
Sbjct: 49  ESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

>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 = 54.5 bits (132), Expect = 1e-09
 Identities = 21/58 (36%), Positives = 33/58 (56%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           F+GGL +  TE  ++E    +G +    ++KD  TG S+G+GF  + DP+  D   AA
Sbjct: 2   FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 59

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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V+VGG+PYY TE +I+      G +   DL+   DTG  +G  F  ++       A  AL
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRA-LAL 59

Query: 357 NGLKMGDKTLTVR 369
           +G  MG + L V 
Sbjct: 60  DGEDMGGRFLKVE 72

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

 Score = 60.1 bits (145), Expect = 1e-09
 Identities = 34/92 (36%), Positives = 53/92 (57%), Gaps = 4/92 (4%)

Query: 434 LADDEEYEEILE-DMREECGKYGTLVNVVIPRPDQNGGETPG--VGKVFLEYYDAVGCAT 490
           +   ++ +E LE ++REECGK+G  V+ VI   ++ G E     + K+F+E+ D++    
Sbjct: 522 MVTPQDIDEFLEGEIREECGKFGV-VDRVIINFEKQGEEEDAEIIVKIFVEFSDSMEVDR 580

Query: 491 AKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 522
           AK AL GR FGG TV A  Y +  + + D S 
Sbjct: 581 AKAALDGRFFGGRTVVAEAYDQILFDHADLSG 612

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

 Score = 53.2 bits (128), Expect = 3e-09
 Identities = 20/75 (26%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++FV GLP+  T+ ++++L +  G +    LV +R +G  KG  +  Y++ +    A 
Sbjct: 2   KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAV 60

Query: 354 AALNGLKMGDKTLTV 368
             ++G ++ +KT++V
Sbjct: 61  LKMDGTEIKEKTISV 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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 26/80 (32%), Positives = 39/80 (48%), Gaps = 5/80 (6%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VF+  LP+  TE ++KEL   FG +    +VKD+ TG+SKG  F  ++          A 
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 357 N-----GLKMGDKTLTVRRA 371
           +     GL +  + L V  A
Sbjct: 63  DNAEDSGLSLDGRRLIVTLA 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 52.7 bits (127), Expect = 4e-09
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 18/84 (21%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRT 231
           ++VG LPP   E+ +   FS+          G    + +V I        K FAFVE  +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKF---------GE---IESVRIVRDKDGKSKGFAFVEFES 48

Query: 232 VEEASNAM-ALDGIIFEGVAVRVR 254
            E+A  A+ AL+G   +G  ++V 
Sbjct: 49  PEDAEKALEALNGKELDGRKLKVS 72

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

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

 Score = 57.6 bits (138), Expect = 4e-09
 Identities = 40/187 (21%), Positives = 69/187 (36%), Gaps = 24/187 (12%)

Query: 161 MPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH 220
                  Q++      ++VG LP    E+ +   F +               V  V +  
Sbjct: 102 SESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGP------------VKRVRLVR 149

Query: 221 EKK------FAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPS 273
           +++      FAFVE  + E A  A+  L+G   EG  +RV++    +   +        +
Sbjct: 150 DRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSEL-----SN 204

Query: 274 PNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG 333
                 A  L+ G     E  D ++VG LP    E ++ +L +S G +    L   +D  
Sbjct: 205 NLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGK 264

Query: 334 NSKGYGF 340
             K   F
Sbjct: 265 IPKSRSF 271

Length = 306

>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 = 52.9 bits (128), Expect = 4e-09
 Identities = 22/63 (34%), Positives = 34/63 (53%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVG LP   TE  ++ L E +G +    +++D+DTG SKG  F  +        A  A
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 356 LNG 358
           L+G
Sbjct: 61  LHG 63

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|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 = 52.3 bits (126), Expect = 6e-09
 Identities = 23/63 (36%), Positives = 36/63 (57%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FV  LP+  TE +++EL E+FG +    L  D++T  SKG+ F  +  P     A + 
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 356 LNG 358
           L+G
Sbjct: 61  LDG 63

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

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

 Score = 51.8 bits (125), Expect = 9e-09
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG LP+   E ++++  E  G +    +V+DR TG  KG+G+ +++      +A   L
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KL 60

Query: 357 NGLKMGDKTLTV 368
           NG+K+  + + 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 23/62 (37%), Positives = 37/62 (59%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGLPY+ T+  +++    FG +    ++ DR TG S+GYGF  ++D    + AC  
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 356 LN 357
            N
Sbjct: 62  PN 63

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

>gnl|CDD|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 = 24/79 (30%), Positives = 35/79 (44%), Gaps = 13/79 (16%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           VYVG LP    E+ +   FS            P  A+  V +  +K +AFV   T E A+
Sbjct: 3   VYVGNLPHGLTEEELQRTFS------------PFGAIEEVRVFKDKGYAFVRFDTHEAAA 50

Query: 237 NAM-ALDGIIFEGVAVRVR 254
            A+ A++G    G  V+  
Sbjct: 51  TAIVAVNGTSINGQTVKCS 69

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

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V+V  L     + ++KEL   +G +    ++KD D G SKG+GF  +++      A   L
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 357 NGLKMGDKTLTVRRA 371
           NG ++  K L V RA
Sbjct: 63  NGKEVNGKKLYVGRA 77

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

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

 Score = 55.8 bits (134), Expect = 3e-08
 Identities = 53/212 (25%), Positives = 84/212 (39%), Gaps = 31/212 (14%)

Query: 164 QVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---INH 220
           Q   QQA     RVYVG +     E  I   F            GP  ++   +      
Sbjct: 97  QQQRQQALAIMCRVYVGSISFELREDTIRRAFDPF---------GPIKSINMSWDPATGK 147

Query: 221 EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLA 279
            K FAFVE    E A  A+  ++G +  G  ++V RP++            Q  P +++ 
Sbjct: 148 HKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM----------PQAQPIIDMV 197

Query: 280 AVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYG 339
                      A+  +R++V  +    +ET IK + E+FG +    L +       KGYG
Sbjct: 198 Q--------EEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYG 249

Query: 340 FCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
           F  Y +      A A++N   +G + L V + 
Sbjct: 250 FIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 50.5 bits (121), Expect = 3e-08
 Identities = 21/63 (33%), Positives = 36/63 (57%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FVG L +   +  +K   E FGT+ G  ++ DR+TG S+G+G+  ++ P     A  A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 356 LNG 358
           ++G
Sbjct: 61  MDG 63

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|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 = 50.6 bits (121), Expect = 3e-08
 Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 293 GPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           GP+   +F+  LP  F + ++ ++   FG +    +  DR T  SK +GF  + +PA   
Sbjct: 1   GPEGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQ 60

Query: 351 IACAALNGLKMGDKTLTVR 369
            A  A+NG ++G K L V+
Sbjct: 61  AAIQAMNGFQIGMKRLKVQ 79

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

 Score = 50.5 bits (120), Expect = 4e-08
 Identities = 26/78 (33%), Positives = 41/78 (52%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y +    + A   L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 357 NGLKMGDKTLTVRRATAS 374
           NGL++  KT+ V  A  S
Sbjct: 64  NGLRLQSKTIKVSYARPS 81

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 18/78 (23%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-----KKFAFVEMRT 231
           ++VG LPP   E+ +   FS+          GP   + ++ I  +     K FAFVE   
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKF---------GP---IESIRIVRDETGRSKGFAFVEFED 48

Query: 232 VEEASNAM-ALDGIIFEG 248
            E+A  A+ AL+G    G
Sbjct: 49  EEDAEKALEALNGKELGG 66

(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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 17/60 (28%), Positives = 30/60 (50%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL    TE  ++E    +G +   ++V D++TG  +G+ F  + D    D     
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

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|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 48.7 bits (116), Expect = 1e-07
 Identities = 25/71 (35%), Positives = 36/71 (50%)

Query: 299 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 358
           V  LP  FT  + +EL+ ++G +    LV    TG+SKGYGF  Y        A   L G
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63

Query: 359 LKMGDKTLTVR 369
            ++G+ TL  +
Sbjct: 64  KQLGESTLFAQ 74

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

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 22/67 (32%), Positives = 35/67 (52%)

Query: 302 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM 361
           LP   T+ + + L  + G +    +V+D+ TG S G+GF  YQ       A   LNGL++
Sbjct: 8   LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQL 67

Query: 362 GDKTLTV 368
            +K + V
Sbjct: 68  QNKRIKV 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|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 13/80 (16%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           R++VG LP    E+     FS+            G+ V  V++N EK F F+ + T   A
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKY-----------GE-VSEVFLNKEKGFGFIRLDTRTNA 50

Query: 236 SNA-MALDGIIFEGVAVRVR 254
             A   LDGI+ +G  +RVR
Sbjct: 51  EKAKAELDGIMRKGRQLRVR 70

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

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

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 19/75 (25%), Positives = 33/75 (44%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  LPY  T+ Q++E     G +    +VKD+ +   +G+G+  +        A    
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 357 NGLKMGDKTLTVRRA 371
              K G + + V  A
Sbjct: 62  KKTKFGGRKIHVEFA 76

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|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 = 48.0 bits (115), Expect = 2e-07
 Identities = 25/72 (34%), Positives = 39/72 (54%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +F+  LP  FT+  + +L   FG +    +  D++TG SK +GF  Y +P     A  A+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 357 NGLKMGDKTLTV 368
           NG ++G 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|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G EG + +F+  LP  FT+T + +    FG +    +  D+ T  SK +GF  Y +P   
Sbjct: 1   GPEGCN-LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSA 59

Query: 350 DIACAALNGLKMGDKTLTVR 369
             A  A+NG ++G K L V+
Sbjct: 60  QAAIQAMNGFQIGTKRLKVQ 79

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

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 22/75 (29%), Positives = 37/75 (49%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           RV+VG + +   E  I++    FG +   D+  D  T   KG+ F  Y+ P    +A   
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 356 LNGLKMGDKTLTVRR 370
           +NG+ +G + + V R
Sbjct: 62  MNGVMLGGRNIKVGR 76

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|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 48.4 bits (116), Expect = 3e-07
 Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 13/82 (15%)

Query: 432 DALADDEEYEEILEDMREECGKYGTLVNVVI-PR-PDQNGGETPGVGKV-FLEYYDAVGC 488
           +   D     E+ +D+REEC K+G +  VV+  R PD       GV  V F E  +A   
Sbjct: 14  EFEEDPTLINELRDDLREECEKFGQVKKVVVFDRHPD-------GVASVKFKEPEEA--- 63

Query: 489 ATAKNALSGRKFGGNTVNAFYY 510
                AL+GR F G  + A  +
Sbjct: 64  DRCIEALNGRWFAGRQLEAERW 85

This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 91

>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 = 47.6 bits (113), Expect = 3e-07
 Identities = 16/55 (29%), Positives = 31/55 (56%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           +F+GGL +  T+  ++E    FG +    +++D  TG S+G+GF  ++ P   + 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNE 55

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

 Score = 47.3 bits (113), Expect = 4e-07
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FVG L    TE  + EL    G L G  + KD + G  K + F  ++       A   L
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 357 NGLKMGDKTLTVR 369
           NG+++  + L ++
Sbjct: 63  NGIRLFGRELRIK 75

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

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 47.3 bits (112), Expect = 4e-07
 Identities = 27/70 (38%), Positives = 37/70 (52%)

Query: 299 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 358
           +  LP  +T+ Q +EL+  FG L    LV    TG+SKGYGF  Y        A + L G
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 359 LKMGDKTLTV 368
            ++G +TL 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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 46.7 bits (111), Expect = 7e-07
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           P+R+FVGG+ +   E  +++    +GT+    +V DR  G SKGYGF  ++         
Sbjct: 2   PNRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKIL 60

Query: 354 AALNGLKMGDKTLTVRRA 371
              N L   DK L + +A
Sbjct: 61  QEANRLCFRDKKLNIGQA 78

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

 Score = 46.7 bits (111), Expect = 7e-07
 Identities = 21/52 (40%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF  + D
Sbjct: 5   PNTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYD 55

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

 Score = 46.6 bits (111), Expect = 7e-07
 Identities = 20/50 (40%), Positives = 27/50 (54%)

Query: 299 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           V GLP+  TE  +K+   +FG L    + KD  TG SKG+GF  + D   
Sbjct: 4   VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYED 53

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

 Score = 46.5 bits (111), Expect = 8e-07
 Identities = 25/84 (29%), Positives = 34/84 (40%), Gaps = 15/84 (17%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEMRT 231
            +YVG LP    E+ +   F Q                  V  + E    + F FVEM T
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTS----------ARVITDRETGRSRGFGFVEMET 50

Query: 232 VEEASNAM-ALDGIIFEGVAVRVR 254
            EEA+ A+  L+G  F G  + V 
Sbjct: 51  AEEANAAIEKLNGTDFGGRTLTVN 74

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

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

 Score = 46.0 bits (110), Expect = 9e-07
 Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 17/77 (22%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEK----KFAFVEMRTV 232
           +YV  LPP   E+ +  FFS            P   V  V +   K     FAFVE  + 
Sbjct: 1   LYVRNLPPSVTEEDLREFFS------------PYGKVEGVRLVRNKDRPRGFAFVEFASP 48

Query: 233 EEASNAMA-LDGIIFEG 248
           E+A  A+  L+G++ +G
Sbjct: 49  EDAEAALKKLNGLVLDG 65

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

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

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++V  LP   TE  ++E    +G + G  LV+++D    +G+ F  +  P   + A   L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 357 NGLKMGDKTL 366
           NGL +  +TL
Sbjct: 59  NGLVLDGRTL 68

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

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

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FV  LPY   E  +++L   FG L    +  D+ +G SKG+ + ++ DP   + A  A
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDP---EDAVKA 60

Query: 356 LNGL 359
              L
Sbjct: 61  YKEL 64

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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGLP   TET +++    FGT+    ++ D +    +G+GF  ++     D     
Sbjct: 4   KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV-N 62

Query: 356 LNGLKMGDKTLTVRRA 371
            +   +  K + V+RA
Sbjct: 63  EHFHDINGKKVEVKRA 78

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

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 23/74 (31%), Positives = 34/74 (45%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V+VG L    TE  + EL    G +    + KDR T   +GYGF  +      D A   +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 357 NGLKMGDKTLTVRR 370
           N +K+  K + V +
Sbjct: 61  NMIKLYGKPIRVNK 74

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

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           G   +F+  L        + +   +FG +    +  D + G SKGYGF  ++       A
Sbjct: 1   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRA 59

Query: 353 CAALNGLKMGDKTLTV 368
              +NG+ + DK + V
Sbjct: 60  IEKVNGMLLNDKKVFV 75

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

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

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 4/65 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTDIAC 353
           R+F+  L Y  TE  +++L   +G L    L  D+ T   KG+ F  Y  P  AV   A 
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVK--AF 61

Query: 354 AALNG 358
           A L+G
Sbjct: 62  AELDG 66

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+ V  LP Y TE +++E  ES G +    +++ RD G S+ +GF  ++       A   
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQAVKY 60

Query: 356 LNGLKMGDKTLTVRRA 371
            N   +    ++V  A
Sbjct: 61  FNKTFIDTSKISVELA 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|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV---YQDPAVTDIAC 353
           +FV  LP    E+ + +L   FG +    +++D  T   KGYGF     Y++      A 
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYS---AI 60

Query: 354 AALNGLKMGDKTLTV 368
           A+LNG ++G + L V
Sbjct: 61  ASLNGYRLGGRVLQV 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|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +F+G L     E  + +   +FG  L    +++D DTGNSKG+ F  Y     +D A  A
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 356 LNGLKMGDKTLTVRRA 371
           +NG  + ++ +TV  A
Sbjct: 64  MNGQYLCNRPITVSYA 79

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 21/75 (28%), Positives = 36/75 (48%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V+V  LP+  T   + ++   +G +    +VKD++T  SKG  F ++ D         AL
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 357 NGLKMGDKTLTVRRA 371
           N  ++  +TL    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|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 20/64 (31%), Positives = 31/64 (48%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V++ GLP   T+  +++L + FG +     + D+ T   KGYGF  +  P     A   L
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 357 NGLK 360
           NG  
Sbjct: 63  NGRG 66

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|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 44.1 bits (105), Expect = 5e-06
 Identities = 16/45 (35%), Positives = 28/45 (62%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           R+FVGGL    TE+ ++E    FGT+   +++K +D G  +G+ +
Sbjct: 1   RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAY 45

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

 Score = 44.2 bits (105), Expect = 7e-06
 Identities = 20/71 (28%), Positives = 35/71 (49%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN 357
           FV  L Y  TE++++   E +G +    LV+D+ TG  +GY F  ++       A    +
Sbjct: 5   FVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYAD 64

Query: 358 GLKMGDKTLTV 368
           G K+  + + V
Sbjct: 65  GKKIDGRRVLV 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|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 45.6 bits (108), Expect = 7e-06
 Identities = 33/92 (35%), Positives = 42/92 (45%), Gaps = 10/92 (10%)

Query: 23  SGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKE----R 78
             RSR+  R R R  R       +RRR++     R   RD  R  R R  +R +     R
Sbjct: 3   RSRSRSPRRSR-RRGRSRSRDRRERRRER----SRSRERDRRRRSRSRSPHRSRRSRSPR 57

Query: 79  RHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKR 110
           RHR RSRS S  R R R +    +R P K +R
Sbjct: 58  RHRSRSRSPSRRRDRKRERD-KDAREPKKRER 88

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

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

 Score = 42.9 bits (102), Expect = 8e-06
 Identities = 10/63 (15%), Positives = 20/63 (31%), Gaps = 8/63 (12%)

Query: 448 REECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNA 507
            +    +G +  + + +              F+E+        A   L+G  FGG  +  
Sbjct: 2   YKLFSPFGNVEKIKLLKKKPG--------FAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53

Query: 508 FYY 510
            Y 
Sbjct: 54  DYS 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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 43.9 bits (103), Expect = 8e-06
 Identities = 23/76 (30%), Positives = 40/76 (52%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  L     E+ + +L   FG ++   +++D +T   KG+GF    +     +A A+L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 357 NGLKMGDKTLTVRRAT 372
           NG ++GD+ L V   T
Sbjct: 66  NGYRLGDRVLQVSFKT 81

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|214636 smart00360, RRM, RNA recognition motif

 Score = 43.4 bits (103), Expect = 9e-06
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 504
           E++RE   K+G + +V + R D+  G++ G    F+E+        A  AL+G++  G  
Sbjct: 14  EELRELFSKFGKVESVRLVR-DKETGKSKGFA--FVEFESEEDAEKALEALNGKELDGRP 70

Query: 505 VN 506
           + 
Sbjct: 71  LK 72

Length = 73

>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 = 43.9 bits (103), Expect = 9e-06
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 292 EGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           EGP+   +F+  LP  F +  + ++   FG +    +  D+ T  SK +GF  Y +P   
Sbjct: 3   EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 62

Query: 350 DIACAALNGLKMGDKTLTVR 369
             A  A+NG ++G K L V+
Sbjct: 63  QAAIQAMNGFQIGMKRLKVQ 82

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

 Score = 46.9 bits (111), Expect = 1e-05
 Identities = 27/103 (26%), Positives = 42/103 (40%), Gaps = 6/103 (5%)

Query: 272 PSPNLNLAAVGLASGAIGGAEGPDR------VFVGGLPYYFTETQIKELLESFGTLHGFD 325
                  A  G  +G   GA+          +FV  L     ET + +L   FG +    
Sbjct: 241 AQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVK 300

Query: 326 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV 368
           +++D  T   KGYGF    +     +A  +LNG  +G++ L V
Sbjct: 301 IIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQV 343

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

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V + AC  
Sbjct: 1   QIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVRFESPEVAERACRM 58

Query: 356 LNGLKMGDKTLTVR 369
           +NG K+  + + VR
Sbjct: 59  MNGYKLNGREIDVR 72

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|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 294 PD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           PD  ++FVG LP+  TE ++KE  + FG +    +      G    +GF V+ DP     
Sbjct: 1   PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQK 60

Query: 352 ACAALNGLKMGDKTLTV 368
             A       GD  L V
Sbjct: 61  ILANKPIYFRGDHRLNV 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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           R+FV  +P  +TE  ++E  + FG +    +VKD++TG SKG+G+  +  P+   +A
Sbjct: 3   RLFVV-IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVA 58

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL Y  T+  +K     +G +    ++KD +T  S+G+GF  +   +  D A  A
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 356 LNGLKMGDKTLTVRRATA 373
               K+  + +  +RA  
Sbjct: 61  -RPHKVDGREVEPKRAVP 77

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 21/70 (30%), Positives = 33/70 (47%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FVG L        ++     FG +    +VKD  TG SKGYGF  +      + A  ++
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 357 NGLKMGDKTL 366
           NG  +G + +
Sbjct: 62  NGQWLGGRAI 71

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

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

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE + KEL   +G +    L K+      KG+GF         + A A 
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAE 56

Query: 356 LNGLKMGDKTLTVR 369
           L+G+    + L VR
Sbjct: 57  LDGIMRKGRQLRVR 70

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 43.2 bits (102), Expect = 2e-05
 Identities = 26/91 (28%), Positives = 33/91 (36%), Gaps = 9/91 (9%)

Query: 1  MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGI 60
              +   D      + +     GR     R R R  R         R+ +  + DR+  
Sbjct: 13 EEESEEEEDDEEIRRKAERDVDRGRRSPRRRTRRRSRR-----RKRSRKRRRRRRDRDRA 67

Query: 61 RDHDRTDRHRDYNRDKERRHRHRSRSHSSDR 91
          R  DR DR RD       R R RSRS S DR
Sbjct: 68 RYRDRDDRDRDR----YDRSRSRSRSRSRDR 94

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>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 = 42.8 bits (101), Expect = 2e-05
 Identities = 21/65 (32%), Positives = 33/65 (50%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVG +P    E  ++ L E FG ++   ++KD+ TG  KG  F  Y        A +A
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66

Query: 356 LNGLK 360
           L+  K
Sbjct: 67  LHEQK 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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 42.8 bits (100), Expect = 2e-05
 Identities = 22/79 (27%), Positives = 40/79 (50%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  L     E+ + ++   FG +    +++D +T   KG+GF    +     +A A+L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 357 NGLKMGDKTLTVRRATASS 375
           NG ++GD+ L V   T  +
Sbjct: 66  NGYRLGDRVLQVSFKTNKT 84

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

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  L Y     ++KE+ +  G +   D+ +D++ G S+G G   ++ P     A +  
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59

Query: 357 NGLKMGDKTLTVR 369
           NG  + D+ + V+
Sbjct: 60  NGQMLFDRPMRVK 72

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

>gnl|CDD|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 = 18/57 (31%), Positives = 30/57 (52%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           ++FVGGL     E  + E    FG +   +++ D+ TG  +G+GF  +Q+    D A
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 23/79 (29%), Positives = 40/79 (50%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +F+  L     E  + ++   FG +    +++D +T   KG+GF    +     +A A+L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 357 NGLKMGDKTLTVRRATASS 375
           NG ++GDK L V   T+ S
Sbjct: 64  NGYRLGDKILQVSFKTSKS 82

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

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 18/51 (35%), Positives = 29/51 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
           ++FVG LP+     ++KE    FG +   ++  D++TG SKGYGF  +   
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR 51

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|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 4/86 (4%)

Query: 426 TEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDA 485
              +T       E ++E  ED+  E  ++G + ++V+     N G+   +G V++++   
Sbjct: 21  QGVLTLSEEEIQEHFDEFYEDVFLELSRFGEIEDLVVC---DNLGDHL-LGNVYVKFETE 76

Query: 486 VGCATAKNALSGRKFGGNTVNAFYYP 511
                A  AL+GR + G  +     P
Sbjct: 77  EDAEAALQALNGRYYAGRPLYPELSP 102

This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35 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. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF (U2AF65 or U2AF2). Although the biological role of U2AF35B remains unclear, it shows high sequence homolgy to U2AF35, which 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 segment interrupted by glycines. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants. . Length = 102

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

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 17/85 (20%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-----KKFAFVEMR 230
           R++VGG+PP   E+ +  FFS+              +V +V I  +     K + FV   
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRF------------GSVKDVKIITDRAGVSKGYGFVTFE 51

Query: 231 TVEEASNAMALDGIIFEGVAVRVRR 255
           T E+A   +A+  + F G  + +  
Sbjct: 52  TQEDAEKILAMGNLNFRGKKLNIGP 76

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|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 44.1 bits (104), Expect = 3e-05
 Identities = 28/88 (31%), Positives = 37/88 (42%), Gaps = 7/88 (7%)

Query: 31  RGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRSHSSD 90
           R R R  R  +  G  R RD+    +R   R   R +R R   R + R      RS S  
Sbjct: 3   RSRSRSPRRSRRRGRSRSRDRR---ERRRERSRSR-ERDRR-RRSRSRSPHRSRRSRS-- 55

Query: 91  RFRNRSKSLSPSRSPSKSKRRSGFDMAP 118
             R+RS+S SPSR   + + R      P
Sbjct: 56  PRRHRSRSRSPSRRRDRKRERDKDAREP 83

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 42.8 bits (101), Expect = 3e-05
 Identities = 19/86 (22%), Positives = 26/86 (30%), Gaps = 1/86 (1%)

Query: 21  WVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRH 80
                    +    R        G    R +  +  R   R   R  R RD +R + R  
Sbjct: 13  EEESEEEEDDEEIRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRRRRDRDRARYRDR 72

Query: 81  RHRSRSHSSDRFRNRSKSLSPSRSPS 106
             R R       R+RS+S S  R   
Sbjct: 73  DDRDRDRYDRS-RSRSRSRSRDRRRR 97

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>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 = 42.0 bits (99), Expect = 3e-05
 Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 16/83 (19%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMR 230
           R ++VGG+    +E  +  FFS      G         V  V +     H  +FAFVE  
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFS----NCG--------EVTRVRLCGDRQHSARFAFVEFA 48

Query: 231 TVEEASNAMALDGIIFEGVAVRV 253
             E A +A+ L G +  G  +RV
Sbjct: 49  DAESALSALNLSGTLLGGHPLRV 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|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE   K+L E +G      + +DR      G+GF   +   + +IA A 
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAE 56

Query: 356 LNGLKMGDKTLTVR 369
           L+G  + ++ L +R
Sbjct: 57  LDGTILKNRPLRIR 70

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 42.1 bits (100), Expect = 3e-05
 Identities = 17/52 (32%), Positives = 26/52 (50%)

Query: 307 TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 358
            E  ++EL   FG +    L KD++TG S+G+ F  +      + A   LNG
Sbjct: 12  DEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 41.9 bits (98), Expect = 3e-05
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           ++FVGG+     E  +++  E +G +   ++++DR +G  +G+ F  + D    D
Sbjct: 2   KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVD 56

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

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 6/75 (8%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++VGGL     E  +      FG +    +  D +T   +G+ F  +++P   + A AA+
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEP---EDAAAAI 57

Query: 357 ---NGLKMGDKTLTV 368
              N  ++  +T+ V
Sbjct: 58  DNMNESELFGRTIRV 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 4/63 (6%)

Query: 445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 504
           ED+RE   K+G + +V I R      +    G  F+E+        A  AL+G++  G  
Sbjct: 13  EDLRELFSKFGEIESVRIVRDKDGKSK----GFAFVEFESPEDAEKALEALNGKELDGRK 68

Query: 505 VNA 507
           +  
Sbjct: 69  LKV 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|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 41.4 bits (98), Expect = 5e-05
 Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 19/86 (22%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMR 230
           VYVG L     E+ +   F Q         AGP   VVNV+I         + + FVE  
Sbjct: 1   VYVGNLDEKVTEELLWELFIQ---------AGP---VVNVHIPKDRVTQAHQGYGFVEFL 48

Query: 231 TVEEASNAMA-LDGIIFEGVAVRVRR 255
           + E+A  A+  ++ I   G  +RV +
Sbjct: 49  SEEDADYAIKIMNMIKLYGKPIRVNK 74

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|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 43.3 bits (102), Expect = 5e-05
 Identities = 28/71 (39%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 44  GDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRS---HSSDRFRNRSKSLS 100
           G  R R       R   R  DR +R R+ +R +ER  R RSRS   H S R R+  +  S
Sbjct: 2   GRSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRS 61

Query: 101 PSRSPSKSKRR 111
            SRSPS+ + R
Sbjct: 62  RSRSPSRRRDR 72

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 41.3 bits (97), Expect = 5e-05
 Identities = 19/58 (32%), Positives = 30/58 (51%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           ++FVGGL    TE  +K+    FG +    L+ D+ T   +G+GF  ++   V D  C
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVC 58

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

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 8/76 (10%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           RV++G LPY   E  ++   + +G +        R+     G+GF  ++DP   D A   
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRI--------REINLKNGFGFVEFEDPRDADDAVYE 52

Query: 356 LNGLKMGDKTLTVRRA 371
           LNG ++  + + V  A
Sbjct: 53  LNGKELCGERVIVEHA 68

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|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 = 16/55 (29%), Positives = 33/55 (60%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           ++FVGGL +  ++  +K+    FG +    +  D +TG S+G+GF +++D +  +
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVE 55

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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 41.8 bits (98), Expect = 6e-05
 Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 3/72 (4%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  LPY  TE  +      FG++     V D+ TG +KG GF  ++D    +   A L
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYN---ACL 60

Query: 357 NGLKMGDKTLTV 368
                   T  +
Sbjct: 61  KNAPAAGSTSLL 72

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|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 41.2 bits (96), Expect = 6e-05
 Identities = 26/76 (34%), Positives = 35/76 (46%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG L    T   IK     FG +    +VKD  TG SKGYGF  + +    + A   +
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 357 NGLKMGDKTLTVRRAT 372
            G  +G + +    AT
Sbjct: 64  GGQWLGGRQIRTNWAT 79

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|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 41.2 bits (97), Expect = 6e-05
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLV-KDRDTGNSKGYGFCVYQDPAVTDIACA 354
           R+ V  +P+ F +  ++++   FG +   +++  +R    SKG+GF  + + A  D A  
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNER---GSKGFGFVTFANSADADRARE 58

Query: 355 ALNGLKMGDKTLTVRRAT 372
            L+G  +  + + V  AT
Sbjct: 59  KLHGTVVEGRKIEVNNAT 76

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 41.2 bits (96), Expect = 6e-05
 Identities = 23/82 (28%), Positives = 41/82 (50%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  L     E+ + +L   FG +    +++D  T   KG+GF    +     +A A+L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 357 NGLKMGDKTLTVRRATASSGQS 378
           NG ++GD+ L V   T+   ++
Sbjct: 64  NGYRLGDRVLQVSFKTSKQHKA 85

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|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 40.7 bits (95), Expect = 7e-05
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 295 DR-VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           DR +FVG L     E  + EL    G L    + KD++ G  K +GF  ++       A 
Sbjct: 1   DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAI 59

Query: 354 AALNGLKMGDKTLTVR 369
           A LNG+++  + + V 
Sbjct: 60  ALLNGIRLYGRPIKVH 75

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

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

 Score = 40.5 bits (95), Expect = 7e-05
 Identities = 15/75 (20%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+ G  P  F  + +K L E+ G +    ++          + F  +++     +A   
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQ----PHAFITFENLEAAQLAIET 56

Query: 356 LNGLKMGDKTLTVRR 370
           LNG  +    + V+R
Sbjct: 57  LNGASVDGNCIKVQR 71

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

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 40.8 bits (95), Expect = 8e-05
 Identities = 21/50 (42%), Positives = 27/50 (54%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           +VFVGGL    TE QIKE   +FG +   +L  D  T   +G+ F  Y D
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTD 50

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 40.7 bits (96), Expect = 8e-05
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VF  GL  Y TE  ++E+   +G +    +V D+ TG S+G+GF  ++       A   L
Sbjct: 4   VF--GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 357 NGLKMGDKTLTV 368
           NG+++  + + V
Sbjct: 62  NGMEIDGRRIRV 73

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

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

 Score = 40.6 bits (95), Expect = 8e-05
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKG--YGFCVYQDPAVTDIACA 354
           ++VG L    TE  +K++ +  G +    ++ D+   N+KG  YGF  Y      +IA  
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK---NNKGVNYGFVEYHQSHDAEIALQ 57

Query: 355 ALNGLKMGDKTLTVRRA 371
            LNG ++ +  + V  A
Sbjct: 58  TLNGRQIENNEIRVNWA 74

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|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 40.8 bits (95), Expect = 8e-05
 Identities = 26/76 (34%), Positives = 35/76 (46%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG L    T   IK     FG +    +VKD  TG SKGYGF  + +    + A   +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 357 NGLKMGDKTLTVRRAT 372
            G  +G + +    AT
Sbjct: 64  GGQWLGGRQIRTNWAT 79

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

 Score = 41.1 bits (97), Expect = 9e-05
 Identities = 19/49 (38%), Positives = 27/49 (55%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           +FVG L    TE  ++E+   +G +    LV+D  TG SKGY F  Y+ 
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEH 54

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

 Score = 40.3 bits (95), Expect = 9e-05
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  LP+  T   +K+L    G +   D+  D D G SKG+G  +++ P     A    
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59

Query: 357 NGLKMGDKTLTVR 369
           NG  +  + L VR
Sbjct: 60  NGYDLEGRELEVR 72

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

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

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 18/69 (26%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGP-GDAV-VNVYINHEKK----FAFVEMR 230
           +YVGGL    +E+ +   F             P GD   + + +++E +    FAFVE  
Sbjct: 1   LYVGGLAEEVDEKVLHAAFI------------PFGDIKDIQIPLDYETQKHRGFAFVEFE 48

Query: 231 TVEEASNAM 239
             E+A+ A+
Sbjct: 49  EPEDAAAAI 57

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

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 40.7 bits (95), Expect = 1e-04
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 3/79 (3%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVG +P   TE +++ + E  G +    ++KD+ TG+ +G  F  Y      D A  A
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 356 LNG---LKMGDKTLTVRRA 371
           L+    L  G   + VR A
Sbjct: 61  LHNQRTLPGGASPVQVRYA 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|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 42.3 bits (99), Expect = 1e-04
 Identities = 19/85 (22%), Positives = 42/85 (49%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +   +  +++    FG +    ++ DR+TG S+G+GF  + D      A + 
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 356 LNGLKMGDKTLTVRRATASSGQSKT 380
           ++G ++  + + V  A       + 
Sbjct: 96  MDGKELNGRHIRVNPANDRPSAPRA 120

Length = 144

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL    +++ ++     +G L    ++ D +T  S+G+GF  +      D     
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEAD-EAME 62

Query: 356 LNGLKMGDKTLTVRRA 371
                +    + ++RA
Sbjct: 63  AQPHSIDGNQIELKRA 78

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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE ++++L E +G      + KD      KG+GF   +   + +IA A 
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKAE 56

Query: 356 LNGLKMGDKTLTVR 369
           L+ + +  K L VR
Sbjct: 57  LDNMPLRGKQLRVR 70

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 21/70 (30%), Positives = 38/70 (54%)

Query: 299 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 358
           V GL  Y TE  ++E+   +G L G ++V D+ TG S+G+ F  ++    +  A    NG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 359 LKMGDKTLTV 368
           +++  + + V
Sbjct: 64  MELDGRRIRV 73

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 19/54 (35%), Positives = 31/54 (57%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           +FVGGL +  T+  +KE    FG +    +  D  TG S+G+GF +++D A  +
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVE 54

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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 40.5 bits (94), Expect = 1e-04
 Identities = 20/60 (33%), Positives = 34/60 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  T+  ++E  E +GTL    +++D  T  S+G+GF  Y      D A +A
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63

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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 16/55 (29%), Positives = 31/55 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           ++F+GGL +  +   +++    FG +    +++D  T  S+G+GF  + DPA  D
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVD 55

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FVG + Y  T  +++E  +S GT++   ++ D+ TG  KG+ +  + D +  + A   L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LL 60

Query: 357 NGLKMGDKTLTV 368
           N  +   + + 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|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 17/58 (29%), Positives = 30/58 (51%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           ++FVGGL    T   +K+  E FG +    L+ D+ T   +G+GF  ++   + +  C
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC 58

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|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 = 40.2 bits (94), Expect = 2e-04
 Identities = 13/46 (28%), Positives = 28/46 (60%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
           ++FVG +P  ++E  ++EL E +G ++  ++++DR     +  G C
Sbjct: 3   KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCC 48

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|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP-AVTDI 351
           ++FVGGL    TE +I+E    FG +   +L  D+ T   +G+ F  +     V  I
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKI 57

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|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 = 2e-04
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 297 VFVGGLPYYFTETQIKELLES-FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +FVG L    T+  ++E   + + ++ G  +V D  TG SKGYGF  + D    D A   
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 356 LNGLKMGDKTLTVRRAT 372
           +NG+    + + V  AT
Sbjct: 64  MNGVYCSSRPMRVSPAT 80

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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 17/82 (20%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKF---AFVEMRT 231
           VYV G P  A    I  FF +               V N+ +  + +KKF    FVE +T
Sbjct: 2   VYVKGFPKDATLDDIQEFFEKFGK------------VNNIRMRRDLDKKFKGSVFVEFKT 49

Query: 232 VEEASNAMALDGIIFEGVAVRV 253
            E+A   +  + + ++   + V
Sbjct: 50  EEDAKKFLEKEKLKYKEKELTV 71

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 19/60 (31%), Positives = 33/60 (55%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  T+  ++   E +GTL    +++D +T  S+G+GF  Y      D A  A
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG +P    E ++  L E  G ++   L+ D   G ++GY F  Y +      A   L
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFS-GLNRGYAFVTYTNKEAAQRAVKQL 62

Query: 357 NGLKM-GDKTLTV 368
           +  ++   K L V
Sbjct: 63  HNYEIRPGKRLGV 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|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 13/50 (26%), Positives = 28/50 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D
Sbjct: 2   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 51

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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 19/55 (34%), Positives = 27/55 (49%)

Query: 306 FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK 360
            T+ Q+  L +    L   DL +D  TG SKG+ +  Y +PA    A   LNG +
Sbjct: 11  VTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNGFE 65

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

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 9/81 (11%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSK---GYGFCVYQDPAVTDIAC 353
           ++V  L +   E  ++ +   FG +    + K +D    +   G+ F  ++D +      
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDAS------ 56

Query: 354 AALNGLKMGDKTLTVRRATAS 374
           +A N L++    L  R+ + S
Sbjct: 57  SAENALQLNGTELGGRKISVS 77

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

>gnl|CDD|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 = 16/63 (25%), Positives = 28/63 (44%)

Query: 299 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 358
           +G L  +  E  I       G +    +++++ TG S GYGF  +      + A  +LNG
Sbjct: 4   MGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNG 63

Query: 359 LKM 361
             +
Sbjct: 64  KPI 66

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

 Score = 39.1 bits (92), Expect = 3e-04
 Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 15/82 (18%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK----FAFVEMRTV 232
           +YVG L     E+ I   FS+          G    ++ + ++   K    F FVE  T 
Sbjct: 1   LYVGNLSFYTTEEQIYELFSR---------CGDIKRII-MGLDRFTKTPCGFCFVEYYTR 50

Query: 233 EEASNAMA-LDGIIFEGVAVRV 253
           E+A NA+  L+G   +   +RV
Sbjct: 51  EDAENAVKYLNGTKLDDRIIRV 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  L        + +    FG +    +  D + G S+GYGF  ++       A   +
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 357 NGLKMGDKTLTVRR 370
           NG+ + DK + V R
Sbjct: 150 NGMLLNDKEVYVGR 163

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

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 14/80 (17%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 234
           +VYVG L P A ++ +   F +          GP   + +V++      FAFVE     +
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKY---------GP---LRSVWVARNPPGFAFVEFEDPRD 48

Query: 235 ASNAM-ALDGIIFEGVAVRV 253
           A +A+ ALDG    G  VRV
Sbjct: 49  AEDAVRALDGRRICGNRVRV 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|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 = 38.8 bits (91), Expect = 4e-04
 Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 19/84 (22%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE------KKFAFVEMR 230
           V+VG +P  A E+ +   FS+V         GP   VV+  +  +      K + F E  
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEV---------GP---VVSFRLVTDRDTGKPKGYGFCEFE 48

Query: 231 TVEEASNAM-ALDGIIFEGVAVRV 253
            +E A++A+  L+G  F G A+RV
Sbjct: 49  DIETAASAIRNLNGYEFNGRALRV 72

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

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

 Score = 42.5 bits (100), Expect = 4e-04
 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 10/94 (10%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++V  L     E +++EL   FG +    ++KD  +G S+G+ F  ++       A   +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 357 NGLKMGD----KTLTVRRATASSGQSKTEQESIL 386
           NG K+G     K L V RA     Q + E+E+ L
Sbjct: 240 NGKKIGLAKEGKKLYVGRA-----QKRAEREAEL 268

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 39.0 bits (91), Expect = 4e-04
 Identities = 18/53 (33%), Positives = 29/53 (54%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           F+GGL +  T   ++E    FG +    +++D  T  S+G+GF  + DPA  D
Sbjct: 2   FIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVD 54

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

 Score = 38.9 bits (91), Expect = 4e-04
 Identities = 17/56 (30%), Positives = 24/56 (42%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           +FVG LPY  T   +    ++ G      L+ D+ TG SKG  F  +        A
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKA 58

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

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR---DTGNSKGYGFCVYQDPAVTDIA 352
           R+++G L    TE  + +L   +G +  FD +  +     G  +GY F  ++     + A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 353 CAALNGLKMGDKTLTVRRA 371
             +LNG     K L VR 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|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  ++  + E L  FG +    +  D  TG S+G+GF +++D A  D     
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVD-KVLE 59

Query: 356 LNGLKMGDKTLTVRRA 371
           L   K+  K +  +RA
Sbjct: 60  LKEHKLDGKLIDPKRA 75

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

 Score = 38.7 bits (90), Expect = 5e-04
 Identities = 19/77 (24%), Positives = 32/77 (41%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  L +  T+  + +       +    +V D +TG S+GYGF  +        A A L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 357 NGLKMGDKTLTVRRATA 373
              K+  + L +  A  
Sbjct: 62  KNKKLHGRILRLDIAER 78

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|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE + K+L   +G      + K       KG+GF   +  A+ +IA A 
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGEPGEVFINK------GKGFGFIKLESRALAEIAKAE 56

Query: 356 LNGLKMGDKTLTVR 369
           L+   M  + L VR
Sbjct: 57  LDDTPMRGRQLRVR 70

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

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

 Score = 39.2 bits (92), Expect = 5e-04
 Identities = 27/89 (30%), Positives = 37/89 (41%), Gaps = 21/89 (23%)

Query: 173 HARRVYVGGLPP-LANEQAIATFFSQVMT------AIGGNSAGPGDAVVNVYINHEKKFA 225
           H+R ++V  LP    +   +   FSQV        AI   +  P              FA
Sbjct: 1   HSRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIA-PNGQPRG------------FA 47

Query: 226 FVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           FVE  T E+A  A  AL+G   +G  +RV
Sbjct: 48  FVEYATAEDAEEAQQALNGHSLQGSPIRV 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|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 5/79 (6%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
            +V +  LP Y    Q+K+ L+       F   K +     + + F  ++       A  
Sbjct: 6   FKVEIKNLPKYIGFKQLKKFLKK----QLFKPHKIKLLKR-QDFAFVTFRSEEERQKALE 60

Query: 355 ALNGLKMGDKTLTVRRATA 373
            L+G K   + L+ R A  
Sbjct: 61  ILDGFKWKGRVLSARLAKP 79

This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. . Length = 79

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

 Score = 38.3 bits (90), Expect = 6e-04
 Identities = 18/73 (24%), Positives = 37/73 (50%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + VG L     +  +KE+  ++GT+   DL  DR+    +GY +  ++ P   + A   +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 357 NGLKMGDKTLTVR 369
           +G ++  + +TV 
Sbjct: 61  DGGQIDGQEVTVE 73

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

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

 Score = 38.5 bits (89), Expect = 6e-04
 Identities = 14/50 (28%), Positives = 29/50 (58%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           ++FVGG+     E  +++  E +G +   +++ DR +G  +G+GF  + D
Sbjct: 2   KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDD 51

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

 Score = 38.4 bits (89), Expect = 6e-04
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++V GLP   T+ ++++L   +G +    +++D+ TG S+G GF  +      + A   L
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 357 NGLKM--GDKTLTVRRA 371
           NG K     + +TV+ A
Sbjct: 63  NGQKPEGASEPITVKFA 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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 38.6 bits (89), Expect = 6e-04
 Identities = 18/60 (30%), Positives = 32/60 (53%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  TE  ++   E +G L    +++D  +  S+G+GF  +      D A AA
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63

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

 Score = 41.5 bits (97), Expect = 7e-04
 Identities = 32/110 (29%), Positives = 48/110 (43%), Gaps = 6/110 (5%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +S +I GA     ++V GLP   T+ +++ +   FG +    ++ D  TG SKG GF  +
Sbjct: 83  SSDSIKGAN----LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRF 138

Query: 344 QDPAVTDIACAALNGLKMGDKT--LTVRRATASSGQSKTEQESILAQAQQ 391
                 D A   LNG      T  +TV+ A   S  +     S L   Q 
Sbjct: 139 DKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQN 188

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|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 38.6 bits (90), Expect = 7e-04
 Identities = 19/78 (24%), Positives = 29/78 (37%), Gaps = 3/78 (3%)

Query: 4  RDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDH 63
           +IR  A  +  R + S      R   R +    R  +    DR R ++        RD 
Sbjct: 23 EEIRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRRRRDRDRARYRDRDDRD---RDR 79

Query: 64 DRTDRHRDYNRDKERRHR 81
              R R  +R ++RR R
Sbjct: 80 YDRSRSRSRSRSRDRRRR 97

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

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

 Score = 38.3 bits (89), Expect = 7e-04
 Identities = 18/62 (29%), Positives = 35/62 (56%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++V  LP   TE +++++ E++G +   +L++D+ TG  +G  F  Y        A ++L
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 357 NG 358
           NG
Sbjct: 63  NG 64

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 38.2 bits (89), Expect = 7e-04
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 296 RVFVGGLPYYFTETQIKELL-ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           RVF+  +PY      +K+L  E  G +   +L KD + G S+G G   ++D      A  
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKD-EEGKSRGCGVVEFKDKESVQKALE 59

Query: 355 ALNGLKMGDKTLTVR 369
            +N  ++  + L V+
Sbjct: 60  TMNRYELKGRKLVVK 74

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

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++V GLP   T+ +++ L   +G +    ++ D  TG S+G GF  +      + A  AL
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 357 NGLKMGDKT--LTVRRA 371
           NG      T  +TV+ A
Sbjct: 63  NGTIPPGATEPITVKFA 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|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 37.7 bits (88), Expect = 7e-04
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FVG L +   E  I E    +G +    L  D D+G  KG+G   Y + +  + A AAL
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFG---YVEFSSQEAAQAAL 57

Query: 357 NGL 359
           + L
Sbjct: 58  DAL 60

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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 38.3 bits (88), Expect = 8e-04
 Identities = 18/60 (30%), Positives = 31/60 (51%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +++ GLP   T+  + +L + +G +     + D+ T   KGYGF  +  PA    A +AL
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 37.6 bits (88), Expect = 9e-04
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +V+VG L    T+ ++++  E +G L    + +     N  G+ F  ++DP   + A  A
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRA 55

Query: 356 LNGLKMGDKTLTV 368
           L+G ++    + V
Sbjct: 56  LDGRRICGNRVRV 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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 37.6 bits (88), Expect = 9e-04
 Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 15/79 (18%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           +++VG LP     + +   F +  T          D V        K + FV M   E+A
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVT------ECDVV--------KNYGFVHMEEEEDA 46

Query: 236 SNAM-ALDGIIFEGVAVRV 253
            +A+ AL+G  F G  + V
Sbjct: 47  EDAIKALNGYEFMGKRINV 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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 15/81 (18%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV--EMRTVE 233
           R++VG LPP   E+ +   F +   A              ++I+ +K F F+  E RT+ 
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKA------------GEIFIHKDKGFGFIRLETRTLA 50

Query: 234 EASNAMALDGIIFEGVAVRVR 254
           E + A  LD +   G  +RVR
Sbjct: 51  EIAKA-ELDNMPLRGKQLRVR 70

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 25/78 (32%), Positives = 34/78 (43%), Gaps = 12/78 (15%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVK------DRDTGNSKGYGFCVYQDPAVTD 350
           ++VG L +Y TE QI EL    G       +K      DR T    G+ F  Y      +
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGD------IKRIIMGLDRFTKTPCGFCFVEYYTREDAE 54

Query: 351 IACAALNGLKMGDKTLTV 368
            A   LNG K+ D+ + V
Sbjct: 55  NAVKYLNGTKLDDRIIRV 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|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           ++F+GGL +  T+  ++E    FG +    +++D  T  S+G+GF  + D A  D
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD 56

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

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FV  LP+  T  ++KE     G +  F  +K  + G SKG G   +  P   + AC  
Sbjct: 1   QIFVRNLPFDLTWQKLKEKFSQCGHVM-FAEIK-MENGKSKGCGTVRFDSPESAEKACRL 58

Query: 356 LNGLKMGDKTLTVR 369
           +NG+K+  + + VR
Sbjct: 59  MNGIKINGREIDVR 72

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|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 = 16/51 (31%), Positives = 31/51 (60%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
           ++FVGGL +  T+  ++     +G +    ++KD+ T  S+G+GF  ++DP
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDP 51

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 4/61 (6%)

Query: 445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 504
           ED+++   K+G + ++ I R     G + G    F+E+ D      A  AL+G++ GG  
Sbjct: 13  EDLKDLFSKFGPIESIRIVR--DETGRSKGFA--FVEFEDEEDAEKALEALNGKELGGRE 68

Query: 505 V 505
           +
Sbjct: 69  L 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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +++G L  Y  E  IK    S G T+    +++++ TG   GY F  + D A  +     
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 356 LNGL 359
           LNG 
Sbjct: 62  LNGK 65

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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 37.1 bits (85), Expect = 0.002
 Identities = 18/60 (30%), Positives = 32/60 (53%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +++ GLP   T+  + +L + +G +     + D++T   KGYGF  +  PA    A A+L
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 36.8 bits (85), Expect = 0.002
 Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 8/73 (10%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVG LP   TE +I+ L E +G +   D++K+        YGF    D    D A   
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIRN 53

Query: 356 LNGLKMGDKTLTV 368
           L+  K+    + V
Sbjct: 54  LHHYKLHGVAINV 66

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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 16/50 (32%), Positives = 27/50 (54%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           ++FVGGL    TE +I+E    FG +   +L  D  T   +G+ F  +++
Sbjct: 6   KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKE 55

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 16/81 (19%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTVE 233
           +YVG L     E  +A  FSQ+         GP   + +  +  E     +AFVE     
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQI---------GP---IKSCKLIREHGNDPYAFVEYYDHR 48

Query: 234 EASNA-MALDGIIFEGVAVRV 253
            A+ A   ++G +  G  ++V
Sbjct: 49  SAAAALQTMNGRLILGQEIKV 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|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 17/58 (29%), Positives = 30/58 (51%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           ++FVGGL        +K+  E FG +    L+ D+ T   +G+GF  +++  V +  C
Sbjct: 5   KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVC 62

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|214637 smart00361, RRM_1, RNA recognition motif

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 3/72 (4%)

Query: 436 DDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL 495
            DE++E  L++  E  G+ G +  + I        +    G V++ +  +   A A   L
Sbjct: 1   KDEDFERELKEEEEYFGEVGKINKIYIDDVGYENHK---RGNVYITFERSEDAARAIVDL 57

Query: 496 SGRKFGGNTVNA 507
           +GR F G  V A
Sbjct: 58  NGRYFDGRLVKA 69

Length = 70

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

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 18/80 (22%), Positives = 28/80 (35%), Gaps = 15/80 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV------NVYINHEKKFAFVE 228
           R +YV  L    +E  +   FS+          G  +++                FAFV 
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSK---------FGEVESIRIPKKQDEKQGRLNNGFAFVT 51

Query: 229 MRTVEEASNAMALDGIIFEG 248
            +    A NA+ L+G    G
Sbjct: 52  FKDASSAENALQLNGTELGG 71

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

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 4/79 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVG L    TE +++E+   +G +    +++D +   S+G  F  Y    +   A  A
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKA 59

Query: 356 LNGL---KMGDKTLTVRRA 371
           LNG+   +  D+ L VR A
Sbjct: 60  LNGVYTMRGCDQPLIVRFA 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|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 22/58 (37%), Positives = 25/58 (43%), Gaps = 8/58 (13%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTL-----HGFD---LVKDRDTGNSKGYGFCVYQDP 346
           VFV  LP   TE  + E   S G +      G     L KD+DTG  KG     Y DP
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDP 58

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|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 = 36.0 bits (84), Expect = 0.004
 Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 19/86 (22%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEMR 230
           ++V GL     E+ +   FS+          G    V  V +  + +      F FV   
Sbjct: 4   LFVSGLSTRTTEKELEALFSKF---------GR---VEEVLLMKDPETGESRGFGFVTFE 51

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVRR 255
           +VE+A  A+  L+G   EG  ++V +
Sbjct: 52  SVEDADAAIRDLNGKELEGRVIKVEK 77

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

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 26/84 (30%), Positives = 37/84 (44%), Gaps = 19/84 (22%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMR 230
           ++V  LPP A+E  +   F             P  AV NV +      N  K + FV M 
Sbjct: 4   IFVYNLPPDADESLLWQLF------------SPFGAVTNVKVIRDLTTNKCKGYGFVTMT 51

Query: 231 TVEEASNAMA-LDGIIFEGVAVRV 253
             EEA +A+A L+G    G  ++V
Sbjct: 52  NYEEAYSAIASLNGYRLGGRVLQV 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 39.8 bits (93), Expect = 0.004
 Identities = 53/241 (21%), Positives = 94/241 (39%), Gaps = 31/241 (12%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           +YV  L P  NE  +   F++     G  ++    AV+       + FAFV     E+A+
Sbjct: 181 LYVKNLDPSVNEDKLRELFAK----FGEITSA---AVMKDGSGRSRGFAFVNFEKHEDAA 233

Query: 237 NAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQP----SPNLNLAAVGLASGAIGGA 291
            A+  ++G                       +G  Q        L      L       A
Sbjct: 234 KAVEEMNGKKI----------GLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKA 283

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           +G + ++V  L    T+ +++EL    G +    ++ D + G S+G+GF  + +P   + 
Sbjct: 284 QGVN-LYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANR 341

Query: 352 ACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGG 411
           A   ++G  +G K L V  A     Q K ++ + L    Q + +Q    Q    + +GG 
Sbjct: 342 AVTEMHGRMLGGKPLYVALA-----QRKEQRRAHL--QDQFMQLQPRMRQLPMGSPMGGA 394

Query: 412 M 412
           M
Sbjct: 395 M 395

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

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 4/78 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG L    T+  +      + +     +V+D+ TG SKGYGF  + DP   D   A 
Sbjct: 8   RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPN--DYLKAM 65

Query: 356 --LNGLKMGDKTLTVRRA 371
             +NG  +G++ + +R++
Sbjct: 66  KEMNGKYVGNRPIKLRKS 83

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|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 17/54 (31%), Positives = 30/54 (55%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           +F+GGL +  T+  +K+    FG +    L  D  TG S+G+GF ++++    D
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVD 54

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	522
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	100.0
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	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
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	100.0
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	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,	99.97
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.97
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.97
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.97
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.97
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.96
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.95
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.95
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.94
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.94
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.94
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.92
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.92
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.91
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.9
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.9
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.89
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.89
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.88
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.88
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.88
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.87
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.85
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.85
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.83
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.82
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.81
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.8
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.79
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.78
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.77
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.76
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.74
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.72
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.72
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.68
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.67
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.67
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.66
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.64
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.61
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.6
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.59
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.59
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.57
KOG0122	270	consensus Translation initiation factor 3, subunit	99.55
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.54
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.52
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.51
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.5
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.5
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.5
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.49
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.47
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.47
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.46
PLN03120	260	nucleic acid binding protein; Provisional	99.46
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.46
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.46
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.44
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.43
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.43
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.41
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.39
PLN03213	759	repressor of silencing 3; Provisional	99.39
smart00362	72	RRM_2 RNA recognition motif.	99.38
PLN03121	243	nucleic acid binding protein; Provisional	99.37
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.37
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.36
smart00360	71	RRM RNA recognition motif.	99.35
PLN03120	260	nucleic acid binding protein; Provisional	99.33
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.32
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.31
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.3
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.3
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.29
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.29
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.29
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.28
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.28
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.27
smart00361	70	RRM_1 RNA recognition motif.	99.26
smart00361	70	RRM_1 RNA recognition motif.	99.25
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.24
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.22
KOG0122	270	consensus Translation initiation factor 3, subunit	99.21
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.2
PLN03121	243	nucleic acid binding protein; Provisional	99.19
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.19
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.16
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.13
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.09
smart00362	72	RRM_2 RNA recognition motif.	99.05
PLN03213	759	repressor of silencing 3; Provisional	99.05
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.04
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.02
KOG0226	290	consensus RNA-binding proteins [General function p	99.02
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.02
smart00360	71	RRM RNA recognition motif.	99.02
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.0
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.98
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.95
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.94
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.93
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.91
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.91
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.9
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.88
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.86
KOG4210	285	consensus Nuclear localization sequence binding pr	98.84
KOG1996	378	consensus mRNA splicing factor [RNA processing and	98.82
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.81
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.78
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.78
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.77
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.74
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.73
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.71
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.67
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.64
KOG0226	290	consensus RNA-binding proteins [General function p	98.56
KOG4210	285	consensus Nuclear localization sequence binding pr	98.56
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.52
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.52
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	98.45
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.45
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.42
KOG0151	877	consensus Predicted splicing regulator, contains R	98.37
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.3
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.24
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.21
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.19
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.13
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.12
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.09
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.04
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.04
KOG0151	877	consensus Predicted splicing regulator, contains R	98.02
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.01
PF06495	182	Transformer: Fruit fly transformer protein; InterP	97.97
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.88
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.86
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.71
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.63
KOG2314	698	consensus Translation initiation factor 3, subunit	97.54
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.53
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.51
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.51
KOG2314	698	consensus Translation initiation factor 3, subunit	97.48
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.39
KOG2888	453	consensus Putative RNA binding protein [General fu	97.38
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.34
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.31
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.26
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.17
KOG3152	278	consensus TBP-binding protein, activator of basal	97.15
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.13
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.03
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.96
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.75
KOG2548	653	consensus SWAP mRNA splicing regulator [RNA proces	96.7
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.66
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.65
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.58
KOG2135	526	consensus Proteins containing the RNA recognition	96.5
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.41
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.36
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.35
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.29
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.01
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.91
KOG3263	196	consensus Nucleic acid binding protein [General fu	95.71
KOG3152	278	consensus TBP-binding protein, activator of basal	95.69
KOG2591	684	consensus c-Mpl binding protein, contains La domai	95.64
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.46
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.41
KOG1847	878	consensus mRNA splicing factor [RNA processing and	95.32
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.78
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.62
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.59
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.55
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	94.22
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.17
KOG2135	526	consensus Proteins containing the RNA recognition	93.8
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.52
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.01
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	92.86
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	92.78
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	92.53
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	92.26
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	91.43
KOG2591	684	consensus c-Mpl binding protein, contains La domai	91.4
KOG2891	445	consensus Surface glycoprotein [General function p	91.22
KOG2891	445	consensus Surface glycoprotein [General function p	90.76
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	90.69
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	90.59
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	90.54
KOG0670	752	consensus U4/U6-associated splicing factor PRP4 [R	90.07
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	89.68
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	89.4
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	89.07
KOG4246	1194	consensus Predicted DNA-binding protein, contains	87.22
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	86.3
KOG2812	426	consensus Uncharacterized conserved protein [Funct	85.77
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	84.86
KOG2318	650	consensus Uncharacterized conserved protein [Funct	82.05
KOG1882	293	consensus Transcriptional regulator SNIP1, contain	81.63
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	80.33
PF15513	62	DUF4651: Domain of unknown function (DUF4651)	80.09

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

Probab=100.00  E-value=9.4e-61  Score=498.53  Aligned_cols=395  Identities=44%  Similarity=0.684  Sum_probs=293.1

Q ss_pred             CCCCCCCCCCccCCCCCCC----CCCCCCCCCCCCCccccCCCCCCCCcCCCCCCCcccccchhhhcccceeEEeCCCcc
Q 009944          110 RRSGFDMAPPAAAMLPGAA----VPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPL  185 (522)
Q Consensus       110 ~~~~~d~~~~~~~~~~~~~----~~g~~p~~~p~~p~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~nlp~~  185 (522)
                      +...|+.+++++..+...+    ....+|+..+ .|++.+......  ....+..++...+.+..+...++|||+|||+.
T Consensus       110 ~~~~~d~~p~~~~~~~~~~~~~~~~~~~p~~~~-~p~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~r~lyVgnLp~~  186 (509)
T TIGR01642       110 KRSLWDIKPPGYELVTADQAKASQVFSVPGTAP-RPAMTDPEKLLA--EGSIITPLPVLPYQQQATRQARRLYVGGIPPE  186 (509)
T ss_pred             cccccccCCCcccccchHHHhhccccCCCCCCC-CCCCCCcccccc--cccccCCccccccCccCCccccEEEEeCCCCC
Confidence            4556888888776655432    1113333222 223222222111  11111122222345567788899999999999


Q ss_pred             CcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEEEecCCCCCccccc
Q 009944          186 ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAA  265 (522)
Q Consensus       186 ~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~v~~~~~~~~~~~~  265 (522)
                      +|+++|.++|..++...+.....++.+|..+.+...+|||||+|.+.++|+.||+|+|+.|.|+.|+|.++..+......
T Consensus       187 ~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~l~g~~~~g~~l~v~r~~~~~~~~~~  266 (509)
T TIGR01642       187 FVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQI  266 (509)
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhcCCCeEeeCceeEecCccccCCcccc
Confidence            99999999999998877765555577899999999999999999999999999999999999999999988877643222


Q ss_pred             cCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcC
Q 009944          266 ALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD  345 (522)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~  345 (522)
                      ........+....................++|||+|||..+++++|.++|+.||.|..+.|+.+..+|.++|||||+|.+
T Consensus       267 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~  346 (509)
T TIGR01642       267 TPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKD  346 (509)
T ss_pred             CCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECC
Confidence            11111111111111111111222234566899999999999999999999999999999999998899999999999999


Q ss_pred             hHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHH-HHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEE
Q 009944          346 PAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESI-LAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLC  424 (522)
Q Consensus       346 ~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~  424 (522)
                      .++|..||..|+|..|+|+.|.|.++.............. ..........             ..........++.|++
T Consensus       347 ~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~s~v~~  413 (509)
T TIGR01642       347 PSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKAL-------------SQSILQIGGKPTKVVQ  413 (509)
T ss_pred             HHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccc-------------hhhhccccCCCceEEE
Confidence            9999999999999999999999999876543322211110 0000000000             0000112236789999


Q ss_pred             eeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeE
Q 009944          425 LTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT  504 (522)
Q Consensus       425 l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~  504 (522)
                      |.|+++.++|.++.+|++|.++|+++|++||.|+.|.|+++..++....|+|+|||+|.++++|.+||.+|||+.|+|++
T Consensus       414 l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~  493 (509)
T TIGR01642       414 LTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRV  493 (509)
T ss_pred             eccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeE
Confidence            99999999999999999999999999999999999999987555555577899999999999999999999999999999


Q ss_pred             EEEEEeCCcccccccC
Q 009944          505 VNAFYYPEDKYFNKDY  520 (522)
Q Consensus       505 l~v~~~~~~~~~~~~~  520 (522)
                      |.|.|++++.|.++.|
T Consensus       494 v~~~~~~~~~~~~~~~  509 (509)
T TIGR01642       494 VVAAFYGEDCYKAGDY  509 (509)
T ss_pred             EEEEEeCHHHhhccCC
Confidence            9999999999999987

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

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

Probab=100.00  E-value=1.7e-51  Score=422.89  Aligned_cols=318  Identities=26%  Similarity=0.409  Sum_probs=237.4

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCce
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~  250 (522)
                      ....++|||+|||..+++++|+++|..||.|...      .++.+..++.++|||||+|.+.++|.+||.++|..|.|++
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v------~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~  159 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDV------QCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRP  159 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEE------EEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCee
Confidence            4456799999999999999999999999975321      1122233466799999999999999999999999999999


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCC
Q 009944          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (522)
Q Consensus       251 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~  330 (522)
                      |.|.++...........                 ...........+|||+|||..+++++|.++|++||.|..|.|+.++
T Consensus       160 i~v~~~~~~~~~~~~~~-----------------~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~  222 (457)
T TIGR01622       160 IIVQSSQAEKNRAAKAA-----------------THQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDP  222 (457)
T ss_pred             eEEeecchhhhhhhhcc-----------------cccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC
Confidence            99986543221110000                 0000011225789999999999999999999999999999999998


Q ss_pred             CCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHH-----------HHHHHHHHHHHHHHH
Q 009944          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES-----------ILAQAQQHIAIQKMA  399 (522)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~  399 (522)
                      .+|.++|||||+|.+.++|.+|+..|+|..|.|+.|.|.|+.............           ..........++.+.
T Consensus       223 ~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  302 (457)
T TIGR01622       223 ETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLD  302 (457)
T ss_pred             CCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhc
Confidence            899999999999999999999999999999999999999976432111000000           000000000011100


Q ss_pred             hhc--cCC-----------------------ccC--------------CCCcCCCCCCcceEEEeeCCCCcCcCCChHHH
Q 009944          400 LQT--SGM-----------------------NTL--------------GGGMSLFGETLAKVLCLTEAITADALADDEEY  440 (522)
Q Consensus       400 ~~~--~~~-----------------------~~~--------------g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~  440 (522)
                      ...  ...                       ..+              ....+.....++.|++|.|++++.++..+.++
T Consensus       303 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~  382 (457)
T TIGR01622       303 RDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFD  382 (457)
T ss_pred             cCCCCccccCCCccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHH
Confidence            000  000                       000              00001113367889999999999998999999


Q ss_pred             HHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcccccc
Q 009944          441 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNK  518 (522)
Q Consensus       441 ~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~~~~  518 (522)
                      +++++||+++|++||.|+.|.|....       ..|+|||+|.++++|.+|+++|||+.|+|+.|.+.|++++.|...
T Consensus       383 ~~~~~dv~~e~~k~G~v~~v~v~~~~-------~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~~~~~~  453 (457)
T TIGR01622       383 NEILDDVKEECSKYGGVVHIYVDTKN-------SAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDVYDMS  453 (457)
T ss_pred             HHHHHHHHHHHHhcCCeeEEEEeCCC-------CceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHHHHHhh
Confidence            99999999999999999999997532       248899999999999999999999999999999999999988653

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.

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

Probab=100.00  E-value=2.7e-47  Score=370.32  Aligned_cols=387  Identities=46%  Similarity=0.770  Sum_probs=314.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCccCCCCCC--------CCCCCCCCCCCCCCccccCCCCCCCCcCCCCCCCcccccchhhhc
Q 009944          101 PSRSPSKSKRRSGFDMAPPAAAMLPGA--------AVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATR  172 (522)
Q Consensus       101 rs~~~~r~r~~~~~d~~~~~~~~~~~~--------~~~g~~p~~~p~~p~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~  172 (522)
                      +++++...+....|+.++++++..++.        .+.|+.|+.........            ..+..|.+.+..+.+.
T Consensus       106 ~~~~~~~~r~~~~~~~~~~~fe~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~t~  173 (500)
T KOG0120|consen  106 RSRSRRYSRKRSLWDVPPEGFETITPDGAKLYKNFNATGQVPGDLSNPKKSL------------KLPQLPTPPMDSQATR  173 (500)
T ss_pred             cccccccccchhhhcCCCCCCcccCchhhhhhhhccccCCCCCCcccccccc------------ccccCCCCccCcchhh
Confidence            344455566778899999999887772        23444443321111100            0333445556677888


Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~  252 (522)
                      ..+.++|+++|+.++++.+..+|..-..+.+++....+..+..+.++..++|||++|.+.++|..|+.+++..+.|.+++
T Consensus       174 q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~nfa~ie~~s~~~at~~~~~~~~~f~g~~~~  253 (500)
T KOG0120|consen  174 QARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEKNFAFIEFRSISEATEAMALDGIIFEGRPLK  253 (500)
T ss_pred             hhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccccceeEEecCCCchhhhhcccchhhCCCCce
Confidence            89999999999999999999999999888898887778899999999999999999999999999999999999999999


Q ss_pred             EecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCC
Q 009944          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (522)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~  332 (522)
                      +..+..+...........+      +...+...........+..+||++||..+++.++.++...||.+....++.+..+
T Consensus       254 ~~r~~d~~~~p~~~~~~~~------~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~  327 (500)
T KOG0120|consen  254 IRRPHDYQPVPGITLSPSQ------LGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSAT  327 (500)
T ss_pred             ecccccccCCccchhhhcc------ccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeeccccc
Confidence            9988887765544443333      2233444455566777889999999999999999999999999999999999999


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCc
Q 009944          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGM  412 (522)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  412 (522)
                      |.++||||++|.+......|+..|||..+++..|.|..|............   ..+.+...+....             
T Consensus       328 g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~---~~~~~~~~i~~~~-------------  391 (500)
T KOG0120|consen  328 GNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFN---ISQSQVPGIPLLM-------------  391 (500)
T ss_pred             ccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCC---ccccccccchhhh-------------
Confidence            999999999999999999999999999999999999998765433333222   0000001111111             


Q ss_pred             CCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHH
Q 009944          413 SLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAK  492 (522)
Q Consensus       413 ~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai  492 (522)
                      -.....++.|++|.|++++++|.++++|++|.++|+..|.+||.|..|.|+++..++.+..|.|.+||+|++.++|++|+
T Consensus       392 ~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~  471 (500)
T KOG0120|consen  392 TQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAM  471 (500)
T ss_pred             cccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHH
Confidence            12234889999999999999999999999999999999999999999999999667777889999999999999999999


Q ss_pred             HHHhCCccCCeEEEEEEeCCcccccccCC
Q 009944          493 NALSGRKFGGNTVNAFYYPEDKYFNKDYS  521 (522)
Q Consensus       493 ~~lng~~~~Gr~l~v~~~~~~~~~~~~~~  521 (522)
                      ++|+|++|+||+|.++|+++++|.+++|+
T Consensus       472 ~~L~GrKF~nRtVvtsYydeDkY~~r~~~  500 (500)
T KOG0120|consen  472 EELTGRKFANRTVVASYYDEDKYHAREFE  500 (500)
T ss_pred             HHccCceeCCcEEEEEecCHHHhhccccC
Confidence            99999999999999999999999999985

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

Probab=100.00  E-value=2.2e-43  Score=337.21  Aligned_cols=320  Identities=26%  Similarity=0.371  Sum_probs=240.3

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecC
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g  248 (522)
                      ..+...++||+.-|+..+++-+|.+||+.+|+|.+      +.+|.+-....++|.|||+|.+.+....|+.|.|+.+.|
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrd------VriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg  247 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRD------VRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLG  247 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcce------eEeeccccchhhcceeEEEEecccchhhHhhhcCCcccC
Confidence            35667889999999999999999999999998532      333444555678999999999999999999999999999


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCe-EEEcCCCCCCCHHHHHHHHHhcCCceEEEEe
Q 009944          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDR-VFVGGLPYYFTETQIKELLESFGTLHGFDLV  327 (522)
Q Consensus       249 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~  327 (522)
                      .+|.|+.+...... .+..++.               ........+.. |||+||.+++++++|+.+|++||.|..|.++
T Consensus       248 ~pv~vq~sEaeknr-~a~~s~a---------------~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~  311 (549)
T KOG0147|consen  248 VPVIVQLSEAEKNR-AANASPA---------------LQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLT  311 (549)
T ss_pred             ceeEecccHHHHHH-HHhcccc---------------ccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeec
Confidence            99999864322111 1110000               00011122233 9999999999999999999999999999999


Q ss_pred             eCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchH-----HH----HHHH--HHHHHHHHH
Q 009944          328 KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTE-----QE----SILA--QAQQHIAIQ  396 (522)
Q Consensus       328 ~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~-----~~----~~~~--~~~~~~~~~  396 (522)
                      ++.+||.++||+||+|.+.++|.+|+..|||+.|.|+.|+|...+.........     .+    ..+.  ..-....+.
T Consensus       312 ~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~  391 (549)
T KOG0147|consen  312 KDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMA  391 (549)
T ss_pred             cccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHH
Confidence            998899999999999999999999999999999999999998766543222110     00    0000  000000111


Q ss_pred             HHHhhc--------------------cCCccCCCCcCC-CCC-------CcceEEEeeCCCCcCcCCChHHHHHHHHHHH
Q 009944          397 KMALQT--------------------SGMNTLGGGMSL-FGE-------TLAKVLCLTEAITADALADDEEYEEILEDMR  448 (522)
Q Consensus       397 ~~~~~~--------------------~~~~~~g~~~~~-~~~-------~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~  448 (522)
                      ++....                    .....+++.+.. .+.       .++.|+.|.|++++.+.....|-.+|.+||.
T Consensus       392 kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~  471 (549)
T KOG0147|consen  392 KLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVI  471 (549)
T ss_pred             HHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHH
Confidence            110000                    000001111111 111       6788999999999999999999999999999


Q ss_pred             HHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcccccc
Q 009944          449 EECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNK  518 (522)
Q Consensus       449 ~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~~~~  518 (522)
                      +.|++||+|..|.+.+..        .|++||.|.+.+.|..|+.+|||++|.|+.|.+.|++...|...
T Consensus       472 Eec~k~g~v~hi~vd~ns--------~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~~~~Y~~~  533 (549)
T KOG0147|consen  472 EECGKHGKVCHIFVDKNS--------AGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLPLERYHSK  533 (549)
T ss_pred             HHHHhcCCeeEEEEccCC--------CceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEeehhhhhhh
Confidence            999999999999997754        38999999999999999999999999999999999999887653

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

Probab=100.00  E-value=7.8e-42  Score=345.10  Aligned_cols=323  Identities=26%  Similarity=0.375  Sum_probs=236.9

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++|||+|||+.+++++|+++|..||.|..+.      ++.+..+++++|||||+|.+.++|..|+ .|||..|.|+
T Consensus       104 ~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~------I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR  177 (612)
T TIGR01645       104 LAIMCRVYVGSISFELREDTIRRAFDPFGPIKSIN------MSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGR  177 (612)
T ss_pred             hcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEE------EeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecc
Confidence            35678999999999999999999999999864321      2333345778999999999999999999 6999999999


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeC
Q 009944          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (522)
Q Consensus       250 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~  329 (522)
                      .|+|.++.......        +  ...        .........++|||+|||+.+++++|+++|+.||.|..+.|+.+
T Consensus       178 ~IkV~rp~~~p~a~--------~--~~~--------~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D  239 (612)
T TIGR01645       178 NIKVGRPSNMPQAQ--------P--IID--------MVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARA  239 (612)
T ss_pred             eeeecccccccccc--------c--ccc--------cccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEec
Confidence            99998754332110        0  000        00011223468999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCc--------h-HHHH----HHHHHHHHHHHH
Q 009944          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK--------T-EQES----ILAQAQQHIAIQ  396 (522)
Q Consensus       330 ~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~--------~-~~~~----~~~~~~~~~~~~  396 (522)
                      +.+|.++|||||+|.+.++|.+||+.|||..|+|+.|.|.++..+.....        + ....    .....+......
T Consensus       240 ~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP~~~~~pa~~~~~p~aaa~Aaaaa~a~~~a~~~~~  319 (612)
T TIGR01645       240 PTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVA  319 (612)
T ss_pred             CCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCccccCCCCCCCCCchHHHHHHHHhhhhhhhhhhhh
Confidence            98999999999999999999999999999999999999999876432210        0 0000    000000000000


Q ss_pred             H-HHhh------------------------------------------------c---cCCccCC-----------CCcC
Q 009944          397 K-MALQ------------------------------------------------T---SGMNTLG-----------GGMS  413 (522)
Q Consensus       397 ~-~~~~------------------------------------------------~---~~~~~~g-----------~~~~  413 (522)
                      . ....                                                .   .+...+|           ...|
T Consensus       320 ~~a~~g~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  399 (612)
T TIGR01645       320 GAAVLGPRAQSPATPSSSLPTDIGNKAVVSSAKKEAEEVPPLPQAAPAVVKPGPMEIPTPVPPPGLAIPSLVAPPGLVAP  399 (612)
T ss_pred             cccccccccCCCccccccccccccccccccccCCcccCCCCCccccccccCCCCcccccCCCCccccccccCCCccccCC
Confidence            0 0000                                                0   0000000           0000


Q ss_pred             --------------------------------------------------------------------------------
Q 009944          414 --------------------------------------------------------------------------------  413 (522)
Q Consensus       414 --------------------------------------------------------------------------------  413 (522)
                                                                                                      
T Consensus       400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  479 (612)
T TIGR01645       400 TEINPSFLASPRKKMKREKLPVTFGALDDTLAWKEPSKEDQTSEDGKMLAIMGEAAAALALEPKKKKKEKEGEELQPKLV  479 (612)
T ss_pred             CcCchhhhcCcccccccccccccccccccchhccccchhhhhhhhhhhcccchhhHHHHhhhhhHHhhhhhhhhhccccc
Confidence                                                                                            


Q ss_pred             ----------------------------CCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCC
Q 009944          414 ----------------------------LFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRP  465 (522)
Q Consensus       414 ----------------------------~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~  465 (522)
                                                  ...+..++|++|.|+++.+++.     +++++||++.|++||.|++|.|...
T Consensus       480 ~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~rp~~S~vVvL~NMv~~~eld-----edl~eDV~eEC~K~G~V~~v~I~~~  554 (612)
T TIGR01645       480 MNSEDASLASQEGMSIRGNSARHLVMQKLMRTNRSNVIVLRNMVTPQDID-----EFLEGEIREECGKFGVVDRVIINFE  554 (612)
T ss_pred             ccccccccccccccccccchhhHHHHHhhcCCCCCCEEEEeCCCChHHhH-----HHHHHHHHHHhhcCceeEEEEEecC
Confidence                                        0012357899999999988653     4577899999999999999999875


Q ss_pred             CCC-CCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcccccccCCC
Q 009944          466 DQN-GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA  522 (522)
Q Consensus       466 ~~~-g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~~~~~~~~  522 (522)
                      ... ...-.+.|.+||+|.+.++|.+|+..|||++|+||+|.+.|+++.+|..++|+.
T Consensus       555 ~~~~~~~~~~~g~VfV~F~~~~~A~~A~~~LnGR~F~GR~V~a~~yd~~~f~~~~l~~  612 (612)
T TIGR01645       555 KQGEEEDAEIIVKIFVEFSDSMEVDRAKAALDGRFFGGRTVVAEAYDQILFDHADLSG  612 (612)
T ss_pred             CCCccccccceEEEEEEECCHHHHHHHHHHhcCCeECCeEEEEEEcCHHHhhccccCC
Confidence            422 111123567899999999999999999999999999999999999999999974

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=100.00  E-value=6.3e-42  Score=340.37  Aligned_cols=289  Identities=20%  Similarity=0.277  Sum_probs=211.7

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~  252 (522)
                      ..+|||+|||+.+|+++|+++|..||+|..+.      ++.+...+.++|||||+|.+.++|.+|+ .|+|..|.|++|+
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~------i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~   76 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCK------LVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIK   76 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEE------EEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEE
Confidence            56899999999999999999999999864321      1223334678899999999999999999 6999999999999


Q ss_pred             EecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCC
Q 009944          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (522)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~  332 (522)
                      |.++.....                             .....+|||+|||..+++++|.++|+.||.|..+.++.+..+
T Consensus        77 v~~a~~~~~-----------------------------~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~  127 (352)
T TIGR01661        77 VSYARPSSD-----------------------------SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVT  127 (352)
T ss_pred             EEeeccccc-----------------------------ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCC
Confidence            987543221                             112357999999999999999999999999999999998888


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCccCC--eEEEEEEccCCCCCCchHHHHHHHHH---------------------
Q 009944          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASSGQSKTEQESILAQA---------------------  389 (522)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~~~~~~~~~~~~~~~~~~~---------------------  389 (522)
                      +.++|||||+|.+.++|+.|++.|||..+.|  .+|.|.++..................                     
T Consensus       128 ~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  207 (352)
T TIGR01661       128 GLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGP  207 (352)
T ss_pred             CCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCC
Confidence            9999999999999999999999999998877  67899998755421110000000000                     


Q ss_pred             -------------------HHHHHHHHHHh-----hccCCcc--------CCCCcCCCCCC---cceEEEeeCCCCcCcC
Q 009944          390 -------------------QQHIAIQKMAL-----QTSGMNT--------LGGGMSLFGET---LAKVLCLTEAITADAL  434 (522)
Q Consensus       390 -------------------~~~~~~~~~~~-----~~~~~~~--------~g~~~~~~~~~---~~~v~~l~~~~~~~~l  434 (522)
                                         ...........     .......        .+...+. ...   .+.|.+|+..+     
T Consensus       208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~lfV~NL~~~~-----  281 (352)
T TIGR01661       208 MHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAA-SDGAGYCIFVYNLSPDT-----  281 (352)
T ss_pred             ccCcccccccCcchhhhhhhhhhhhcccccccccccCCCccccccccccccCCCCCC-CCCCCcEEEEeCCCCCC-----
Confidence                               00000000000     0000000        0000000 011   13333333332     


Q ss_pred             CChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          435 ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       435 ~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                              .+++|.++|++||.|+.|+|+.+..++..   +|+|||+|.+.++|.+||++|||..|+|+.|+|.|++...
T Consensus       282 --------~e~~L~~~F~~fG~v~~v~i~~d~~t~~s---kG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       282 --------DETVLWQLFGPFGAVQNVKIIRDLTTNQC---KGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             --------CHHHHHHHHHhCCCeEEEEEeEcCCCCCc---cceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCC
Confidence                    23599999999999999999999877765   7888999999999999999999999999999999988654

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

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

Probab=100.00  E-value=5.7e-37  Score=265.14  Aligned_cols=292  Identities=18%  Similarity=0.265  Sum_probs=221.5

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      .+....|.|.-||..+|+++|+.+|...|+|.++.      .|.+..++++-||+||.|-+++||++|+ .+||..+..+
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScK------LvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~K  111 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCK------LVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNK  111 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeee------eeeccccccccccceeeecChHHHHHHHhhhcceeeccc
Confidence            44556799999999999999999999999986655      4888899999999999999999999999 7999999999


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeC
Q 009944          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (522)
Q Consensus       250 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~  329 (522)
                      .|+|.++.+....                             .....|||.+||...|..+|.++|++||.|..-+|..|
T Consensus       112 TIKVSyARPSs~~-----------------------------Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~d  162 (360)
T KOG0145|consen  112 TIKVSYARPSSDS-----------------------------IKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVD  162 (360)
T ss_pred             eEEEEeccCChhh-----------------------------hcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhh
Confidence            9999987654322                             22348999999999999999999999999988888888


Q ss_pred             CCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC--eEEEEEEccCCCCCCchHH-HHH-----------HHHHHHHH--
Q 009944          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASSGQSKTEQ-ESI-----------LAQAQQHI--  393 (522)
Q Consensus       330 ~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~~~~~~~~~~~~-~~~-----------~~~~~~~~--  393 (522)
                      ..+|.++|.+||.|...++|+.||+.|||.+-.|  .+|.|+|+..+........ .+.           +....+..  
T Consensus       163 qvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~  242 (360)
T KOG0145|consen  163 QVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRL  242 (360)
T ss_pred             cccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhcc
Confidence            8899999999999999999999999999988766  6799999987643221110 000           00000000  


Q ss_pred             ----HHHHHHhhccCCccC------CCCcCCCCC--CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEE
Q 009944          394 ----AIQKMALQTSGMNTL------GGGMSLFGE--TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVV  461 (522)
Q Consensus       394 ----~~~~~~~~~~~~~~~------g~~~~~~~~--~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~  461 (522)
                          .+........++...      |...|..+.  -+++|++|....++             .-|-++|.+||.|.+|+
T Consensus       243 ~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de-------------~~LWQlFgpFGAv~nVK  309 (360)
T KOG0145|consen  243 DNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADE-------------SILWQLFGPFGAVTNVK  309 (360)
T ss_pred             ccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEecCCCchH-------------hHHHHHhCcccceeeEE
Confidence                000001111111111      112222222  22344444333222             36889999999999999


Q ss_pred             ecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          462 IPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       462 i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      |++|..+.   +++||+||.+.+-++|..||..|||..++++.|.|+|-+.+
T Consensus       310 virD~ttn---kCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  310 VIRDFTTN---KCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             EEecCCcc---cccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            99998664   45788899999999999999999999999999999997653

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

Probab=100.00  E-value=2.3e-36  Score=317.67  Aligned_cols=273  Identities=20%  Similarity=0.316  Sum_probs=211.2

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~  252 (522)
                      ..+|||+|||.++++++|+++|+.||.|..+.       |.....++++|||||+|.+.++|..|+ ++++..+.|+.|.
T Consensus        88 ~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~-------i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~  160 (562)
T TIGR01628        88 VGNIFVKNLDKSVDNKALFDTFSKFGNILSCK-------VATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVY  160 (562)
T ss_pred             CCceEEcCCCccCCHHHHHHHHHhcCCcceeE-------eeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEE
Confidence            45799999999999999999999999865321       222234568999999999999999999 7999999999999


Q ss_pred             EecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCC
Q 009944          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (522)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~  332 (522)
                      |..........                        .......++|||+|||.++|+++|+++|+.||.|..+.++.+. +
T Consensus       161 v~~~~~~~~~~------------------------~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~-~  215 (562)
T TIGR01628       161 VGRFIKKHERE------------------------AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-S  215 (562)
T ss_pred             Eeccccccccc------------------------cccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC-C
Confidence            97543322110                        0012334689999999999999999999999999999999984 7


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCccC----CeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccC
Q 009944          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMG----DKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTL  408 (522)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~----g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  408 (522)
                      |.++|||||+|.+.++|.+|++.|+|..|.    |+.|.|.++..+..     ....+.............         
T Consensus       216 g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~e-----r~~~~~~~~~~~~~~~~~---------  281 (562)
T TIGR01628       216 GRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAE-----REAELRRKFEELQQERKM---------  281 (562)
T ss_pred             CCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhh-----hHHHHHhhHHhhhhhhhc---------
Confidence            899999999999999999999999999999    99999998865321     111111111111110000         


Q ss_pred             CCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhH
Q 009944          409 GGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGC  488 (522)
Q Consensus       409 g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A  488 (522)
                           ........|.+|+..+++             ++|+++|++||.|.+|+|+.+. +|..   +|+|||+|.+.++|
T Consensus       282 -----~~~~~~l~V~nl~~~~~~-------------~~L~~~F~~~G~i~~~~i~~d~-~g~~---~g~gfV~f~~~~~A  339 (562)
T TIGR01628       282 -----KAQGVNLYVKNLDDTVTD-------------EKLRELFSECGEITSAKVMLDE-KGVS---RGFGFVCFSNPEEA  339 (562)
T ss_pred             -----ccCCCEEEEeCCCCccCH-------------HHHHHHHHhcCCeEEEEEEECC-CCCc---CCeEEEEeCCHHHH
Confidence                 001133445555554444             4999999999999999999984 5543   68889999999999


Q ss_pred             HHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          489 ATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       489 ~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      .+|+..|||..|+|++|.|.|+..+.
T Consensus       340 ~~A~~~~~g~~~~gk~l~V~~a~~k~  365 (562)
T TIGR01628       340 NRAVTEMHGRMLGGKPLYVALAQRKE  365 (562)
T ss_pred             HHHHHHhcCCeeCCceeEEEeccCcH
Confidence            99999999999999999999988643

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

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

Probab=100.00  E-value=1.7e-36  Score=306.47  Aligned_cols=242  Identities=19%  Similarity=0.295  Sum_probs=189.8

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceec-Cce
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE-GVA  250 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~-g~~  250 (522)
                      ..++|||+|||.++++++|+++|.+||.|..+.      ++.+ ..+.++|||||+|.+.++|++|| .||+..|. |+.
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vr------l~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~  129 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELR------LMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRL  129 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEE------EEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcc
Confidence            357999999999999999999999999864321      1223 45788999999999999999999 69998885 677


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCC-ceEEEE-ee
Q 009944          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDL-VK  328 (522)
Q Consensus       251 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~-i~~v~~-~~  328 (522)
                      |.|.++.                                   ..++|||+|||..+++++|.++|++++. +..+.+ ..
T Consensus       130 l~V~~S~-----------------------------------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~  174 (578)
T TIGR01648       130 LGVCISV-----------------------------------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHS  174 (578)
T ss_pred             ccccccc-----------------------------------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEecc
Confidence            7776421                                   1358999999999999999999999864 444433 33


Q ss_pred             CCCCCCcceEEEEEEcChHHHHHHHHHHcC--CccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCc
Q 009944          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMN  406 (522)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  406 (522)
                      ....++++|||||+|.+.++|.+|+..|+.  ..+.|+.|.|.|+.+.......             .            
T Consensus       175 ~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~-------------~------------  229 (578)
T TIGR01648       175 AADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDED-------------V------------  229 (578)
T ss_pred             ccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeeccccccccc-------------c------------
Confidence            334678899999999999999999998864  4678999999999764211100             0            


Q ss_pred             cCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhcc--CCeEEEEecCCCCCCCCCCCccEEEEEecC
Q 009944          407 TLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY--GTLVNVVIPRPDQNGGETPGVGKVFLEYYD  484 (522)
Q Consensus       407 ~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~--G~I~~v~i~~~~~~g~~~~g~G~afV~F~~  484 (522)
                             ......+.|-+|+..+++             ++|+++|+.|  |.|+.|.+++           ++|||+|.+
T Consensus       230 -------~~~~k~LfVgNL~~~~te-------------e~L~~~F~~f~~G~I~rV~~~r-----------gfAFVeF~s  278 (578)
T TIGR01648       230 -------MAKVKILYVRNLMTTTTE-------------EIIEKSFSEFKPGKVERVKKIR-----------DYAFVHFED  278 (578)
T ss_pred             -------cccccEEEEeCCCCCCCH-------------HHHHHHHHhcCCCceEEEEeec-----------CeEEEEeCC
Confidence                   000022333344433333             4999999999  9999998764           688999999


Q ss_pred             hHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          485 AVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       485 ~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      .++|.+||+.|||..|+|++|.|.|+..
T Consensus       279 ~e~A~kAi~~lnG~~i~Gr~I~V~~Akp  306 (578)
T TIGR01648       279 REDAVKAMDELNGKELEGSEIEVTLAKP  306 (578)
T ss_pred             HHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            9999999999999999999999999975

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=9.7e-36  Score=312.93  Aligned_cols=254  Identities=19%  Similarity=0.341  Sum_probs=202.7

Q ss_pred             eeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEEEe
Q 009944          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR  254 (522)
Q Consensus       176 ~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~v~  254 (522)
                      +|||+|||+++|+++|.++|..||.|...      .++.+..+++++|||||+|.+.++|++|+ .+++..|.|++|+|.
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~   75 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSV------RVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIM   75 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEE------EEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEee
Confidence            69999999999999999999999985321      11222234677899999999999999999 699999999999999


Q ss_pred             cCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCC
Q 009944          255 RPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN  334 (522)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~  334 (522)
                      |+......                           ......+|||+|||.++++++|+++|+.||.|..|+++.+. +|.
T Consensus        76 ~s~~~~~~---------------------------~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~  127 (562)
T TIGR01628        76 WSQRDPSL---------------------------RRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGK  127 (562)
T ss_pred             cccccccc---------------------------cccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCC
Confidence            85321100                           01123579999999999999999999999999999999884 788


Q ss_pred             cceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCC
Q 009944          335 SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSL  414 (522)
Q Consensus       335 ~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  414 (522)
                      ++|||||+|.+.++|.+|++.|+|..+.|+.|.|.....+....                  .              ...
T Consensus       128 skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~------------------~--------------~~~  175 (562)
T TIGR01628       128 SRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHERE------------------A--------------APL  175 (562)
T ss_pred             cccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccccccc------------------c--------------ccc
Confidence            99999999999999999999999999999999998654321110                  0              000


Q ss_pred             CCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHH
Q 009944          415 FGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA  494 (522)
Q Consensus       415 ~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~  494 (522)
                      .......|.+|+..+++             ++|+++|+.||.|.+|.|+.+. +|..   +|+|||+|.+.++|.+|++.
T Consensus       176 ~~~~~l~V~nl~~~~te-------------e~L~~~F~~fG~i~~~~i~~~~-~g~~---~G~afV~F~~~e~A~~Av~~  238 (562)
T TIGR01628       176 KKFTNLYVKNLDPSVNE-------------DKLRELFAKFGEITSAAVMKDG-SGRS---RGFAFVNFEKHEDAAKAVEE  238 (562)
T ss_pred             cCCCeEEEeCCCCcCCH-------------HHHHHHHHhcCCEEEEEEEECC-CCCc---ccEEEEEECCHHHHHHHHHH
Confidence            00123344445444433             4999999999999999998875 4433   68899999999999999999


Q ss_pred             HhCCccC----CeEEEEEEeCC
Q 009944          495 LSGRKFG----GNTVNAFYYPE  512 (522)
Q Consensus       495 lng~~~~----Gr~l~v~~~~~  512 (522)
                      |||..|.    |+.|.|.++..
T Consensus       239 l~g~~i~~~~~g~~l~v~~a~~  260 (562)
T TIGR01628       239 MNGKKIGLAKEGKKLYVGRAQK  260 (562)
T ss_pred             hCCcEecccccceeeEeecccC
Confidence            9999999    99999988754

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=2.3e-35  Score=301.81  Aligned_cols=289  Identities=18%  Similarity=0.145  Sum_probs=202.3

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHH---hcCceecCce
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIFEGVA  250 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~---~~~~~~~g~~  250 (522)
                      ++.|||+|||+.+|+++|+++|..||.            |..+.+..+++||||+|.+.++|+.|+.   +++..|.|++
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~------------V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~   69 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGP------------VSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQP   69 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCC------------eeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeE
Confidence            578999999999999999999999997            6667777789999999999999999994   5889999999


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCC
Q 009944          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (522)
Q Consensus       251 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~  330 (522)
                      |.|.++.........   ..    .          ..........+|||.||++.+++++|+++|+.||.|..|.++++.
T Consensus        70 l~v~~s~~~~~~~~~---~~----~----------~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~  132 (481)
T TIGR01649        70 AFFNYSTSQEIKRDG---NS----D----------FDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN  132 (481)
T ss_pred             EEEEecCCcccccCC---CC----c----------ccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC
Confidence            999987543211000   00    0          000112233579999999999999999999999999999998763


Q ss_pred             CCCCcceEEEEEEcChHHHHHHHHHHcCCccCC--eEEEEEEccCCCCCCc-----------h----HHHHHHHH--HHH
Q 009944          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASSGQSK-----------T----EQESILAQ--AQQ  391 (522)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~~~~~~~~~-----------~----~~~~~~~~--~~~  391 (522)
                          .+|+|||+|.+.++|.+|++.|||..|.|  +.|+|.|+........           +    +.+..+..  ...
T Consensus       133 ----~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~  208 (481)
T TIGR01649       133 ----NVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQR  208 (481)
T ss_pred             ----CceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCcccccc
Confidence                24789999999999999999999999854  6899999876431100           0    00000000  000


Q ss_pred             HHHHHHHHhhccCCccC--------------------------C-----CCcC-------CCCCCcceEEEeeCCCCcCc
Q 009944          392 HIAIQKMALQTSGMNTL--------------------------G-----GGMS-------LFGETLAKVLCLTEAITADA  433 (522)
Q Consensus       392 ~~~~~~~~~~~~~~~~~--------------------------g-----~~~~-------~~~~~~~~v~~l~~~~~~~~  433 (522)
                      ....+.........+..                          .     ...+       .....+..++.+.|+.... 
T Consensus       209 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~-  287 (481)
T TIGR01649       209 QPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEK-  287 (481)
T ss_pred             ccccccCCCccCCCcccccCCCCCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCC-
Confidence            00000000000000000                          0     0000       0012244555555553211 


Q ss_pred             CCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          434 LADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       434 l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                              .++++|+++|+.||.|..|+|+++.        +|+|||+|.+.++|..||..|||..|.|++|.|.++..
T Consensus       288 --------vt~~~L~~lF~~yG~V~~vki~~~~--------~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~  350 (481)
T TIGR01649       288 --------VNCDRLFNLFCVYGNVERVKFMKNK--------KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQ  350 (481)
T ss_pred             --------CCHHHHHHHHHhcCCeEEEEEEeCC--------CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccc
Confidence                    1125999999999999999998863        37899999999999999999999999999999999754

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

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

Probab=100.00  E-value=8.4e-36  Score=277.31  Aligned_cols=244  Identities=19%  Similarity=0.338  Sum_probs=200.7

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCcee-cCc
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF-EGV  249 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~-~g~  249 (522)
                      ..-+.|||+.||.++.|++|.-+|...|+|..+.      .+.+-..+.++|||||+|.+.++|++|+ .||+..| .|+
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elR------LMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK  154 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELR------LMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGK  154 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEE------EeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCC
Confidence            4467899999999999999999999999975432      2444456788999999999999999999 7999887 478


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCC-ceEEEEee
Q 009944          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVK  328 (522)
Q Consensus       250 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~-i~~v~~~~  328 (522)
                      .|.|.-+                                   ...++|||+|||..+++++|.+.|++.+. |..|.|..
T Consensus       155 ~igvc~S-----------------------------------van~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~  199 (506)
T KOG0117|consen  155 LLGVCVS-----------------------------------VANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYP  199 (506)
T ss_pred             EeEEEEe-----------------------------------eecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEec
Confidence            8888642                                   22368999999999999999999999987 78888877


Q ss_pred             CCC-CCCcceEEEEEEcChHHHHHHHHHHc-C-CccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCC
Q 009944          329 DRD-TGNSKGYGFCVYQDPAVTDIACAALN-G-LKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGM  405 (522)
Q Consensus       329 ~~~-~g~~~g~afV~f~~~~~A~~Al~~l~-g-~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (522)
                      .+. ..+++|||||+|.+...|..|...|- | +++-|..+.|.||.+....   +.+.          +          
T Consensus       200 ~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~---ded~----------m----------  256 (506)
T KOG0117|consen  200 SPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEP---DEDT----------M----------  256 (506)
T ss_pred             CccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCC---Chhh----------h----------
Confidence            654 56789999999999999999988764 3 6789999999999874321   1111          1          


Q ss_pred             ccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecCh
Q 009944          406 NTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDA  485 (522)
Q Consensus       406 ~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~  485 (522)
                                  ...+|+.+.|+.          ..++++.|+++|+.||.|+.|+.++|           ||||.|.+.
T Consensus       257 ------------s~VKvLYVRNL~----------~~tTeE~lk~~F~~~G~veRVkk~rD-----------YaFVHf~eR  303 (506)
T KOG0117|consen  257 ------------SKVKVLYVRNLM----------ESTTEETLKKLFNEFGKVERVKKPRD-----------YAFVHFAER  303 (506)
T ss_pred             ------------hheeeeeeeccc----------hhhhHHHHHHHHHhccceEEeecccc-----------eeEEeecch
Confidence                        334555555542          23445699999999999999999874           789999999


Q ss_pred             HhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          486 VGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       486 ~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      ++|.+||+.|||..|+|..|.|++++.
T Consensus       304 ~davkAm~~~ngkeldG~~iEvtLAKP  330 (506)
T KOG0117|consen  304 EDAVKAMKETNGKELDGSPIEVTLAKP  330 (506)
T ss_pred             HHHHHHHHHhcCceecCceEEEEecCC
Confidence            999999999999999999999999875

>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=2.6e-35  Score=256.79  Aligned_cols=237  Identities=24%  Similarity=0.397  Sum_probs=184.6

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCce
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~  250 (522)
                      +...++|||+||...+||+-|..+|++.|.++.            +++         .|+                   .
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~------------~k~---------i~~-------------------e   42 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTK------------TKV---------IFD-------------------E   42 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhcccccc------------cee---------ehh-------------------h
Confidence            345689999999999999999999999998543            211         111                   4


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCC
Q 009944          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (522)
Q Consensus       251 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~  330 (522)
                      |+|.|+....         .++.+.               ......+||+.|...++.++|++.|.+||.|.+++|++|.
T Consensus        43 ~~v~wa~~p~---------nQsk~t---------------~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~   98 (321)
T KOG0148|consen   43 LKVNWATAPG---------NQSKPT---------------SNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDM   98 (321)
T ss_pred             hccccccCcc---------cCCCCc---------------cccceeEEehhcchhcchHHHHHHhccccccccceEeecc
Confidence            5555543221         111111               1123469999999999999999999999999999999999


Q ss_pred             CCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCC
Q 009944          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG  410 (522)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~  410 (522)
                      .|++++||+||.|-+.++|+.||..|||.+|+++.|+-.||+.+.......          ......+..+..+.|    
T Consensus        99 ~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~----------~ltfdeV~NQssp~N----  164 (321)
T KOG0148|consen   99 NTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGK----------PLTFDEVYNQSSPDN----  164 (321)
T ss_pred             cCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccCCC----------CccHHHHhccCCCCC----
Confidence            999999999999999999999999999999999999999998875221111          122333444433322    


Q ss_pred             CcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHH
Q 009944          411 GMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCAT  490 (522)
Q Consensus       411 ~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~  490 (522)
                             +...|-++...++++             +|++.|++||.|.+|+|.++.         |||||+|++.|.|..
T Consensus       165 -------tsVY~G~I~~~lte~-------------~mr~~Fs~fG~I~EVRvFk~q---------GYaFVrF~tkEaAah  215 (321)
T KOG0148|consen  165 -------TSVYVGNIASGLTED-------------LMRQTFSPFGPIQEVRVFKDQ---------GYAFVRFETKEAAAH  215 (321)
T ss_pred             -------ceEEeCCcCccccHH-------------HHHHhcccCCcceEEEEeccc---------ceEEEEecchhhHHH
Confidence                   444444455544443             899999999999999998875         999999999999999


Q ss_pred             HHHHHhCCccCCeEEEEEEeCCcc
Q 009944          491 AKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       491 Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ||..|||..|+|+.|+|+|-.+..
T Consensus       216 AIv~mNntei~G~~VkCsWGKe~~  239 (321)
T KOG0148|consen  216 AIVQMNNTEIGGQLVRCSWGKEGD  239 (321)
T ss_pred             HHHHhcCceeCceEEEEeccccCC
Confidence            999999999999999999987743

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

Probab=100.00  E-value=1.4e-34  Score=274.98  Aligned_cols=323  Identities=17%  Similarity=0.250  Sum_probs=222.1

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEEE
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~v  253 (522)
                      .+|||++||+.++.++|.++|+.+|+|.++.+      |.......++|||||+|.-.|+++.|+ +.++..|.|+.|.|
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~v------Vt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v   79 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVV------VTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNV   79 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEE------ecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccc
Confidence            58999999999999999999999999876432      333344567999999999999999999 79999999999999


Q ss_pred             ecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCC
Q 009944          254 RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG  333 (522)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g  333 (522)
                      ..++..........+....   .........+.......+.++|.|+|||+.+.+.+|..+|+.||.|..|.|++....+
T Consensus        80 ~~A~~R~r~e~~~~~e~~~---veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgk  156 (678)
T KOG0127|consen   80 DPAKKRARSEEVEKGENKA---VEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGK  156 (678)
T ss_pred             ccccccccchhcccccchh---hhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCC
Confidence            8766554333111110000   0000000000001112235789999999999999999999999999999999887555


Q ss_pred             CcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHH--HHHHHHH-HHHHHHHHhhc--cCCcc-
Q 009944          334 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES--ILAQAQQ-HIAIQKMALQT--SGMNT-  407 (522)
Q Consensus       334 ~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~--~~~~~~~-~~~~~~~~~~~--~~~~~-  407 (522)
                      .+ |||||+|....+|.+||+.+||..|.|++|.|.||-++..........  .+..+.. ..... .....  ...+. 
T Consensus       157 lc-GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e-~~~d~~~~~~~Ed  234 (678)
T KOG0127|consen  157 LC-GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKE-ADEDDGKDFDEED  234 (678)
T ss_pred             cc-ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcc-cccccccccchhc
Confidence            55 999999999999999999999999999999999998876544322110  0000000 00000 00000  00000 


Q ss_pred             -----------CC---------C------Cc-----CC--CCCCcceEEEeeCCCC--cCcCCChHHHHHHHHHHHHHhh
Q 009944          408 -----------LG---------G------GM-----SL--FGETLAKVLCLTEAIT--ADALADDEEYEEILEDMREECG  452 (522)
Q Consensus       408 -----------~g---------~------~~-----~~--~~~~~~~v~~l~~~~~--~~~l~~~~~~~~~~~~l~~~f~  452 (522)
                                 .|         .      .+     +.  .+.....+.++....+  ...++.|++|.+++++|.++|+
T Consensus       235 ~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fs  314 (678)
T KOG0127|consen  235 GEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFS  314 (678)
T ss_pred             ccccccccccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHH
Confidence                       00         0      00     00  0001111111111111  1224557788888899999999


Q ss_pred             ccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHH-----hC-CccCCeEEEEEEeC
Q 009944          453 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL-----SG-RKFGGNTVNAFYYP  511 (522)
Q Consensus       453 ~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~l-----ng-~~~~Gr~l~v~~~~  511 (522)
                      +||.|..+.|..++.++.+   .|+|||.|.+..+|.+||.+.     .| ..|.||.|.|..+-
T Consensus       315 kFG~v~ya~iV~~k~T~~s---kGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av  376 (678)
T KOG0127|consen  315 KFGEVKYAIIVKDKDTGHS---KGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAV  376 (678)
T ss_pred             hhccceeEEEEeccCCCCc---ccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeecc
Confidence            9999999999999999876   789999999999999999976     34 77899999998854

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

Probab=100.00  E-value=1.1e-33  Score=255.99  Aligned_cols=324  Identities=26%  Similarity=0.391  Sum_probs=240.2

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      +..-.|+|||+.|.+.+.|+.|+..|..||+|+++|.      .-+-.+++.+|||||+|+-+|.|..|+ .|||.+++|
T Consensus       109 ALaiMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInM------SWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGG  182 (544)
T KOG0124|consen  109 ALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINM------SWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGG  182 (544)
T ss_pred             HHHHhHheeeeeeEEEechHHHHhhccCCCCcceeec------ccccccccccceEEEEEeCcHHHHHHHHHhccccccC
Confidence            3455789999999999999999999999999875432      333457889999999999999999999 599999999


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEee
Q 009944          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (522)
Q Consensus       249 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~  328 (522)
                      +.|+|.++.+-....        +  -.+.        ........++|||..+.++.+++||+..|+.||+|..|.+.+
T Consensus       183 RNiKVgrPsNmpQAQ--------p--iID~--------vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr  244 (544)
T KOG0124|consen  183 RNIKVGRPSNMPQAQ--------P--IIDM--------VQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLAR  244 (544)
T ss_pred             ccccccCCCCCcccc--------h--HHHH--------HHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeec
Confidence            999999876543211        0  0000        001123457899999999999999999999999999999999


Q ss_pred             CCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCC--------chHHHH-HHHHHHHHHHHHHHH
Q 009944          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQS--------KTEQES-ILAQAQQHIAIQKMA  399 (522)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~--------~~~~~~-~~~~~~~~~~~~~~~  399 (522)
                      ++..+..+||+||+|.+..+...|+..||-+-++|..|+|..+..++..-        .+.... ....+......+...
T Consensus       245 ~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAv  324 (544)
T KOG0124|consen  245 APTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAV  324 (544)
T ss_pred             cCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHh
Confidence            99888999999999999999999999999999999999998765443211        011111 011111111111111


Q ss_pred             hhccCC-----------------------------ccCC--------------------CCcCC----------------
Q 009944          400 LQTSGM-----------------------------NTLG--------------------GGMSL----------------  414 (522)
Q Consensus       400 ~~~~~~-----------------------------~~~g--------------------~~~~~----------------  414 (522)
                      ......                             ..+|                    ...|.                
T Consensus       325 Ag~avlg~~G~~~~vSpA~~aa~p~~~l~qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeK  404 (544)
T KOG0124|consen  325 AGSAVLGTVGAPGLVSPAPRAAQPLGTLPQAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEK  404 (544)
T ss_pred             ccCCcccccCCccccCccccccCCCCCccccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhh
Confidence            111000                             0000                    00000                


Q ss_pred             ------------------------------------CCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeE
Q 009944          415 ------------------------------------FGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLV  458 (522)
Q Consensus       415 ------------------------------------~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~  458 (522)
                                                          .-...++|++|.|+++++++.+     +++.+|.+.|.+||.|.
T Consensus       405 e~eelqpkl~~~~~L~~QE~msI~G~sARhlvMqkLmR~~~S~VivLRNMV~P~DiDe-----~LegEi~EECgKfG~V~  479 (544)
T KOG0124|consen  405 EEEELQPKLERPEMLSEQEHMSISGSSARHLVMQKLMRKQESTVIVLRNMVDPKDIDE-----DLEGEITEECGKFGAVN  479 (544)
T ss_pred             hHhhhcccccCHHHhhhhhCccccCccHHHHHHHHHhccccCcEEEEeccCChhhhhh-----HHHHHHHHHHhccccee
Confidence                                                1145588999999999987643     45569999999999999


Q ss_pred             EEEecCCCCCCCCC-CCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcccccccCCC
Q 009944          459 NVVIPRPDQNGGET-PGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA  522 (522)
Q Consensus       459 ~v~i~~~~~~g~~~-~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~~~~~~~~  522 (522)
                      .|.|...+..+..- .=.-..||+|....++.+|.++|+|++|+|++|+...++...|.+++|+.
T Consensus       480 rViI~nekq~e~edaeiiVKIFVefS~~~e~~rak~ALdGRfFgGr~VvAE~YDQ~~FD~~Dlsg  544 (544)
T KOG0124|consen  480 RVIIYNEKQGEEEDAEIIVKIFVEFSIASETHRAKQALDGRFFGGRKVVAEVYDQERFDNSDLSG  544 (544)
T ss_pred             EEEEEecccccccchhhhheeeeeechhhHHHHHHHhhccceecCceeehhhhhhhcccccccCC
Confidence            99998876544210 00234799999999999999999999999999999999999999999974

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

Probab=100.00  E-value=3.8e-33  Score=258.30  Aligned_cols=172  Identities=25%  Similarity=0.386  Sum_probs=145.6

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-Hhc-Ccee
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD-GIIF  246 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~-~~~~  246 (522)
                      ..+...-++||+-||..++|.||+++|++||.+..++      ++.|..++.++|||||.|.+.++|.+|+ .|+ .++|
T Consensus        29 ~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~ein------l~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktl  102 (510)
T KOG0144|consen   29 NPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEIN------LIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTL  102 (510)
T ss_pred             CCCchhhhheeccCCccccHHHHHHHHHHhCceeEEE------eecccccCcccceEEEEeccHHHHHHHHHHhhccccc
Confidence            3445667899999999999999999999999876544      4777788899999999999999999999 554 4567


Q ss_pred             cC--ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEE
Q 009944          247 EG--VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF  324 (522)
Q Consensus       247 ~g--~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v  324 (522)
                      -|  .+|.|+++......                            .....+|||+.|+..+||.+|+++|++||.|++|
T Consensus       103 pG~~~pvqvk~Ad~E~er----------------------------~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~  154 (510)
T KOG0144|consen  103 PGMHHPVQVKYADGERER----------------------------IVEERKLFVGMLSKQCTENEVREIFSRFGHIEDC  154 (510)
T ss_pred             CCCCcceeecccchhhhc----------------------------cccchhhhhhhccccccHHHHHHHHHhhCccchh
Confidence            76  57888875433221                            1224689999999999999999999999999999


Q ss_pred             EEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcC-CccCC--eEEEEEEccCCC
Q 009944          325 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG-LKMGD--KTLTVRRATASS  375 (522)
Q Consensus       325 ~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g-~~~~g--~~l~v~~~~~~~  375 (522)
                      .|.++. .+.++|||||.|.+.+.|..||+.||| .++.|  .+|.|.||.++.
T Consensus       155 ~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqk  207 (510)
T KOG0144|consen  155 YILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQK  207 (510)
T ss_pred             hheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCC
Confidence            999995 799999999999999999999999999 45665  689999998864

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

Probab=100.00  E-value=1.4e-32  Score=281.36  Aligned_cols=300  Identities=18%  Similarity=0.195  Sum_probs=196.4

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec--CCCcEEEEEEeCHHHHHHHH-HhcCceecC--
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--HEKKFAFVEMRTVEEASNAM-ALDGIIFEG--  248 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~--~~~g~afV~f~~~~~a~~a~-~~~~~~~~g--  248 (522)
                      ..+|||+||++.+|+++|+++|..||.|            ..+.+.  ...++|||+|.+.++|.+|+ .|||..|.+  
T Consensus        96 ~~~v~v~nl~~~vt~~~L~~~F~~~G~V------------~~v~i~~~~~~~~afVef~~~~~A~~A~~~Lng~~i~~~~  163 (481)
T TIGR01649        96 VLRVIVENPMYPITLDVLYQIFNPYGKV------------LRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGC  163 (481)
T ss_pred             eEEEEEcCCCCCCCHHHHHHHHhccCCE------------EEEEEEecCCceEEEEEECCHHHHHHHHHHhcCCcccCCc
Confidence            3479999999999999999999999984            444433  23469999999999999999 699999965  


Q ss_pred             ceEEEecCCCCCcc------cc-----ccC-CC-----------CCCCC---------Ccccccc---------cC--C-
Q 009944          249 VAVRVRRPTDYNPT------LA-----AAL-GP-----------GQPSP---------NLNLAAV---------GL--A-  284 (522)
Q Consensus       249 ~~~~v~~~~~~~~~------~~-----~~~-~~-----------~~~~~---------~~~~~~~---------~~--~-  284 (522)
                      +.|+|.|++...-.      ..     ..+ +.           .++..         .......         +.  . 
T Consensus       164 ~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~  243 (481)
T TIGR01649       164 CTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGP  243 (481)
T ss_pred             eEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCcccccccCCC
Confidence            47888876532110      00     000 00           00000         0000000         00  0 


Q ss_pred             ---------------C-------CCCCCCCCCCeEEEcCCCC-CCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEE
Q 009944          285 ---------------S-------GAIGGAEGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC  341 (522)
Q Consensus       285 ---------------~-------~~~~~~~~~~~l~v~nLp~-~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV  341 (522)
                                     +       ..........+|||+|||. .+++++|.++|+.||.|..|+++.++     +|||||
T Consensus       244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV  318 (481)
T TIGR01649       244 PHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALI  318 (481)
T ss_pred             cccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEE
Confidence                           0       0000122456899999998 69999999999999999999999863     689999


Q ss_pred             EEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHh-hccCCccCCCCcCCCCCCcc
Q 009944          342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMAL-QTSGMNTLGGGMSLFGETLA  420 (522)
Q Consensus       342 ~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~  420 (522)
                      +|.+.++|..||..|||..|.|+.|.|.++...........  .+.....  ....... .......++.........++
T Consensus       319 ~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~--~~~~~~~--~~~d~~~~~~~r~~~~~~~~~~~~~~ps  394 (481)
T TIGR01649       319 EMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREG--QLDDGLT--SYKDYSSSRNHRFKKPGSANKNNIQPPS  394 (481)
T ss_pred             EECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCC--cCcCCCc--ccccccCCccccCCCcccccccccCCCC
Confidence            99999999999999999999999999999865432211100  0000000  0000000 00000001100000011233


Q ss_pred             eEEEeeCC---CCcCcCCChHHHHHHHHHHHHHhhccCC--eEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHH
Q 009944          421 KVLCLTEA---ITADALADDEEYEEILEDMREECGKYGT--LVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL  495 (522)
Q Consensus       421 ~v~~l~~~---~~~~~l~~~~~~~~~~~~l~~~f~~~G~--I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~l  495 (522)
                      .++.+.|+   +++             ++|+++|+.||.  |..|++.... ++.    .|+|||+|.+.++|.+||..|
T Consensus       395 ~~L~v~NLp~~~te-------------e~L~~lF~~~G~~~i~~ik~~~~~-~~~----~~~gfVeF~~~e~A~~Al~~l  456 (481)
T TIGR01649       395 ATLHLSNIPLSVSE-------------EDLKELFAENGVHKVKKFKFFPKD-NER----SKMGLLEWESVEDAVEALIAL  456 (481)
T ss_pred             cEEEEecCCCCCCH-------------HHHHHHHHhcCCccceEEEEecCC-CCc----ceeEEEEcCCHHHHHHHHHHh
Confidence            34444444   333             499999999998  8888886543 221    478899999999999999999


Q ss_pred             hCCccCCeE------EEEEEeCC
Q 009944          496 SGRKFGGNT------VNAFYYPE  512 (522)
Q Consensus       496 ng~~~~Gr~------l~v~~~~~  512 (522)
                      ||+.|+|+.      |+|+|++.
T Consensus       457 n~~~l~~~~~~~~~~lkv~fs~~  479 (481)
T TIGR01649       457 NHHQLNEPNGSAPYHLKVSFSTS  479 (481)
T ss_pred             cCCccCCCCCCccceEEEEeccC
Confidence            999999985      99999865

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=99.97  E-value=6.7e-30  Score=266.62  Aligned_cols=193  Identities=19%  Similarity=0.216  Sum_probs=141.3

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~  251 (522)
                      ..++|||+|||..+|+++|.++|..||.|..++      ++.+..++.++|||||+|.+.++|..|+ .|+|+.|.|+.|
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~------~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l  367 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFN------LIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKL  367 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE------EEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            457899999999999999999999999865432      2344456778999999999999999999 699999999999


Q ss_pred             EEecCCCCCccccccCCCCCCCCCcccccccCCC-CCCCCCCCCCeEEEcCCCCCC----------CHHHHHHHHHhcCC
Q 009944          252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLAS-GAIGGAEGPDRVFVGGLPYYF----------TETQIKELLESFGT  320 (522)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~v~nLp~~~----------t~~~l~~~F~~~G~  320 (522)
                      .|.++................  ........... .......+..+|+|.||...-          ..++|+++|++||.
T Consensus       368 ~v~~a~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~  445 (509)
T TIGR01642       368 HVQRACVGANQATIDTSNGMA--PVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGP  445 (509)
T ss_pred             EEEECccCCCCCCcccccccc--ccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCC
Confidence            999875432211100000000  00000000000 001122345789999996421          23689999999999


Q ss_pred             ceEEEEeeCC---CCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          321 LHGFDLVKDR---DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       321 i~~v~~~~~~---~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      |..|.|+++.   .++.+.|+|||+|.+.++|++||..|||.+|+|+.|.|.|...
T Consensus       446 v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       446 LINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             eeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            9999998752   3456789999999999999999999999999999999999743

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

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

Probab=99.97  E-value=5e-30  Score=263.77  Aligned_cols=176  Identities=23%  Similarity=0.326  Sum_probs=141.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      .+|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||. |+|..|.|++|.|.++...
T Consensus        90 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~~~  168 (457)
T TIGR01622        90 RTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQAE  168 (457)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecchh
Confidence            589999999999999999999999999999999999999999999999999999999997 9999999999999976431


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhcc
Q 009944          375 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  454 (522)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~  454 (522)
                      ....                 ....     ....+.   ......+.|-+|+..+++             ++|+++|++|
T Consensus       169 ~~~~-----------------~~~~-----~~~~~~---~p~~~~l~v~nl~~~~te-------------~~l~~~f~~~  210 (457)
T TIGR01622       169 KNRA-----------------AKAA-----THQPGD---IPNFLKLYVGNLHFNITE-------------QELRQIFEPF  210 (457)
T ss_pred             hhhh-----------------hhcc-----cccCCC---CCCCCEEEEcCCCCCCCH-------------HHHHHHHHhc
Confidence            1000                 0000     000000   001133334444443333             4999999999


Q ss_pred             CCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          455 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       455 G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      |.|..|.|+.+..+|..   +|+|||+|.+.++|.+|++.|||..|.|++|.|.|+..
T Consensus       211 G~i~~v~~~~d~~~g~~---~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       211 GDIEDVQLHRDPETGRS---KGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCeEEEEEEEcCCCCcc---ceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            99999999998876654   68999999999999999999999999999999999763

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.97  E-value=4.4e-30  Score=247.95  Aligned_cols=170  Identities=19%  Similarity=0.310  Sum_probs=146.4

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      .....++|||+|||+++|+++|+++|..||.|+.+      .++.+..++.++|||||+|.++++|++|+ +|++..|.+
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v------~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~g  176 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTC------RIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRN  176 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEE------EEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCC
Confidence            34467899999999999999999999999986432      12334456678899999999999999999 799999999


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEee
Q 009944          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (522)
Q Consensus       249 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~  328 (522)
                      ++|+|.++.....                             ....++|||+|||..+++++|+++|++||.|..|.|+.
T Consensus       177 r~i~V~~a~p~~~-----------------------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~  227 (346)
T TIGR01659       177 KRLKVSYARPGGE-----------------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILR  227 (346)
T ss_pred             ceeeeeccccccc-----------------------------ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEee
Confidence            9999998543211                             11235799999999999999999999999999999999


Q ss_pred             CCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC--eEEEEEEccCC
Q 009944          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATAS  374 (522)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~~~~  374 (522)
                      ++.+++++|||||+|.+.++|++||+.||+..|.+  ++|.|.++...
T Consensus       228 d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       228 DKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             cCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcc
Confidence            98899999999999999999999999999998865  79999998764

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).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.97  E-value=2.7e-29  Score=242.47  Aligned_cols=170  Identities=25%  Similarity=0.351  Sum_probs=146.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||.++|+++|+++|+.||.|..|+|+.+..++.++|||||+|.++++|.+||+.|+|..|.+++|+|.++
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a  184 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA  184 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHh
Q 009944          372 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  451 (522)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f  451 (522)
                      .+....                                     .....+.|-+|+..+++             ++|+++|
T Consensus       185 ~p~~~~-------------------------------------~~~~~lfV~nLp~~vte-------------e~L~~~F  214 (346)
T TIGR01659       185 RPGGES-------------------------------------IKDTNLYVTNLPRTITD-------------DQLDTIF  214 (346)
T ss_pred             cccccc-------------------------------------cccceeEEeCCCCcccH-------------HHHHHHH
Confidence            542100                                     00133445555554444             4999999


Q ss_pred             hccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCC--eEEEEEEeCCcc
Q 009944          452 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYYPEDK  514 (522)
Q Consensus       452 ~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~G--r~l~v~~~~~~~  514 (522)
                      ++||.|+.|.|+++..++.+   +|+|||+|.+.++|++||+.||+..|.|  ++|.|.|+.+..
T Consensus       215 ~~fG~V~~v~i~~d~~tg~~---kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       215 GKYGQIVQKNILRDKLTGTP---RGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             HhcCCEEEEEEeecCCCCcc---ceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCccc
Confidence            99999999999999878766   6899999999999999999999999976  799999998754

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=99.97  E-value=2.3e-29  Score=243.91  Aligned_cols=242  Identities=21%  Similarity=0.336  Sum_probs=195.1

Q ss_pred             eeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEEEe
Q 009944          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR  254 (522)
Q Consensus       176 ~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~v~  254 (522)
                      .|||+   +++|+..|.++|+.+|+++..      .++.+. +  +-|||||.|.++++|++|| ++|...+.|++|+|.
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~------rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim   70 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSI------RVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIM   70 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeE------EEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEee
Confidence            58999   899999999999999987642      223333 3  8999999999999999999 799999999999999


Q ss_pred             cCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCC
Q 009944          255 RPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN  334 (522)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~  334 (522)
                      |+..-                                  +..|||.||+++++..+|.++|+.||.|.+|++..+. .| 
T Consensus        71 ~s~rd----------------------------------~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-  114 (369)
T KOG0123|consen   71 WSQRD----------------------------------PSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-  114 (369)
T ss_pred             hhccC----------------------------------CceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-
Confidence            84321                                  1239999999999999999999999999999999995 56 


Q ss_pred             cceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCC
Q 009944          335 SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSL  414 (522)
Q Consensus       335 ~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  414 (522)
                      ++|| ||+|.++++|.+|+..+||..+.|+.|.|.....+.....+..+ .         .+.                 
T Consensus       115 ~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~-~---------~~~-----------------  166 (369)
T KOG0123|consen  115 SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLGE-Y---------KKR-----------------  166 (369)
T ss_pred             ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhcccccc-h---------hhh-----------------
Confidence            9999 99999999999999999999999999999988654322211111 0         000                 


Q ss_pred             CCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHH
Q 009944          415 FGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA  494 (522)
Q Consensus       415 ~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~  494 (522)
                        -....++++....+.             ..|.++|..||.|.++.++.+.... +   .|++||.|.++++|..|++.
T Consensus       167 --~t~v~vk~~~~~~~~-------------~~l~~~f~~~g~i~s~~v~~~~~g~-~---~~~gfv~f~~~e~a~~av~~  227 (369)
T KOG0123|consen  167 --FTNVYVKNLEEDSTD-------------EELKDLFSAYGSITSVAVMRDSIGK-S---KGFGFVNFENPEDAKKAVET  227 (369)
T ss_pred             --hhhhheeccccccch-------------HHHHHhhcccCcceEEEEeecCCCC-C---CCccceeecChhHHHHHHHh
Confidence              022333334322222             3899999999999999999987433 2   46779999999999999999


Q ss_pred             HhCCccCCeEEEEEEeCC
Q 009944          495 LSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       495 lng~~~~Gr~l~v~~~~~  512 (522)
                      |||..+++..+.|.-+..
T Consensus       228 l~~~~~~~~~~~V~~aqk  245 (369)
T KOG0123|consen  228 LNGKIFGDKELYVGRAQK  245 (369)
T ss_pred             ccCCcCCccceeeccccc
Confidence            999999999998876554

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

Probab=99.96  E-value=8.3e-29  Score=240.08  Aligned_cols=288  Identities=23%  Similarity=0.352  Sum_probs=216.8

Q ss_pred             CCCCCCcccccchhhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHH
Q 009944          156 GAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA  235 (522)
Q Consensus       156 ~~~~~~~~~~~~~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a  235 (522)
                      ..+.+.+...++.+.....  |||.||++.++..+|.++|+.||.|+++.        +.+.-..++|| ||+|.+++.|
T Consensus        60 ~~~~~~~~rim~s~rd~~~--~~i~nl~~~~~~~~~~d~f~~~g~ilS~k--------v~~~~~g~kg~-FV~f~~e~~a  128 (369)
T KOG0123|consen   60 DVLKGKPIRIMWSQRDPSL--VFIKNLDESIDNKSLYDTFSEFGNILSCK--------VATDENGSKGY-FVQFESEESA  128 (369)
T ss_pred             cccCCcEEEeehhccCCce--eeecCCCcccCcHHHHHHHHhhcCeeEEE--------EEEcCCCceee-EEEeCCHHHH
Confidence            3444556666666554443  99999999999999999999999976542        12222338999 9999999999


Q ss_pred             HHHH-HhcCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHH
Q 009944          236 SNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKEL  314 (522)
Q Consensus       236 ~~a~-~~~~~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~  314 (522)
                      .+|+ .+||..+.|++|.|..............                    . .....+.++|.+++.+++++.|.++
T Consensus       129 ~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~--------------------~-~~~~~t~v~vk~~~~~~~~~~l~~~  187 (369)
T KOG0123|consen  129 KKAIEKLNGMLLNGKKIYVGLFERKEEREAPLG--------------------E-YKKRFTNVYVKNLEEDSTDEELKDL  187 (369)
T ss_pred             HHHHHHhcCcccCCCeeEEeeccchhhhccccc--------------------c-hhhhhhhhheeccccccchHHHHHh
Confidence            9999 7999999999999976444332211000                    0 1123357999999999999999999


Q ss_pred             HHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHH
Q 009944          315 LESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIA  394 (522)
Q Consensus       315 F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~  394 (522)
                      |..||.|..+.++.+. .|.++||+||+|.+.++|.+|+..|+|..+.+..+.|..+..     +.+....+........
T Consensus       188 f~~~g~i~s~~v~~~~-~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqk-----k~e~~~~l~~~~~~~~  261 (369)
T KOG0123|consen  188 FSAYGSITSVAVMRDS-IGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQK-----KSEREAELKRKFEQEF  261 (369)
T ss_pred             hcccCcceEEEEeecC-CCCCCCccceeecChhHHHHHHHhccCCcCCccceeeccccc-----chhhHHHHhhhhHhhh
Confidence            9999999999999985 677999999999999999999999999999999999998855     2222333332222222


Q ss_pred             HHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCC
Q 009944          395 IQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPG  474 (522)
Q Consensus       395 ~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g  474 (522)
                      .+....              .....+.+-++...++.             +.|.++|+.||+|.+++|+.+.. |.   .
T Consensus       262 ~~~~~~--------------~~~~nl~vknld~~~~~-------------e~L~~~f~~~GeI~s~kv~~~~~-g~---s  310 (369)
T KOG0123|consen  262 AKRSVS--------------LQGANLYVKNLDETLSD-------------EKLRKIFSSFGEITSAKVMVDEN-GK---S  310 (369)
T ss_pred             hhcccc--------------ccccccccccCccccch-------------hHHHHHHhcccceeeEEEEeccC-CC---c
Confidence            222111              01133334444333333             38999999999999999998873 33   3


Q ss_pred             ccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          475 VGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       475 ~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      +|++||+|.+.++|.+|+..+||..++|+.|.|.++..
T Consensus       311 kG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr  348 (369)
T KOG0123|consen  311 KGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQR  348 (369)
T ss_pred             cceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhh
Confidence            67889999999999999999999999999999987653

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

Probab=99.95  E-value=8.4e-27  Score=236.29  Aligned_cols=176  Identities=20%  Similarity=0.372  Sum_probs=143.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||+.+++++|+++|+.||.|..|.|+.++.+|+++|||||+|.+.++|.+||..|||..|.|+.|+|.+...
T Consensus       107 ~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~  186 (612)
T TIGR01645       107 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  186 (612)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccccc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999996543


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhc
Q 009944          374 SSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGK  453 (522)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~  453 (522)
                      .......     ..         ..            .........++|.+|+..++.+             +|+++|+.
T Consensus       187 ~p~a~~~-----~~---------~~------------~~~~~~~~rLfVgnLp~~vtee-------------dLk~lFs~  227 (612)
T TIGR01645       187 MPQAQPI-----ID---------MV------------QEEAKKFNRIYVASVHPDLSET-------------DIKSVFEA  227 (612)
T ss_pred             ccccccc-----cc---------cc------------cccccccceEEeecCCCCCCHH-------------HHHHHHhh
Confidence            2111000     00         00            0000011344555565554444             99999999


Q ss_pred             cCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          454 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       454 ~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                      ||.|.+|.|+++..++..   +|||||+|.+.++|.+||..|||..|+|+.|+|.++.
T Consensus       228 FG~I~svrl~~D~~tgks---KGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       228 FGEIVKCQLARAPTGRGH---KGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             cCCeeEEEEEecCCCCCc---CCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            999999999998876654   6888999999999999999999999999999999865

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.

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

Probab=99.95  E-value=6.6e-27  Score=204.40  Aligned_cols=182  Identities=18%  Similarity=0.331  Sum_probs=151.3

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~  252 (522)
                      .-.|||+.|...++.++|++.|.+||+|..      ..+|.|..++++||||||.|.+.++|+.|+ .|||.-|++|.|+
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~------akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IR  135 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSD------AKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIR  135 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhcccccccc------ceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceee
Confidence            456999999999999999999999999865      456999999999999999999999999999 7999999999999


Q ss_pred             EecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCC
Q 009944          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (522)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~  332 (522)
                      -.|+........      ..  .+     .............++|||+||+..++|++|++.|+.||.|.+|++.++   
T Consensus       136 TNWATRKp~e~n------~~--~l-----tfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~---  199 (321)
T KOG0148|consen  136 TNWATRKPSEMN------GK--PL-----TFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD---  199 (321)
T ss_pred             ccccccCccccC------CC--Cc-----cHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc---
Confidence            999765541110      00  00     000001112344578999999999999999999999999999999987   


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCch
Q 009944          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKT  380 (522)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~  380 (522)
                         +|||||.|.+.|.|.+||..+||..++|..|++.|.+........
T Consensus       200 ---qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~~~~  244 (321)
T KOG0148|consen  200 ---QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDGINN  244 (321)
T ss_pred             ---cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCCCCc
Confidence               589999999999999999999999999999999998765444333

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.94  E-value=2.4e-26  Score=228.60  Aligned_cols=166  Identities=26%  Similarity=0.409  Sum_probs=142.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+++++|+++|+.||+|..|+|+.++.+|.++|||||+|.+.++|.+||+.|+|..|.|+.|.|.|+.+
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhc
Q 009944          374 SSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGK  453 (522)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~  453 (522)
                      .....                                     ....+.|.+|+..+++             ++|.++|++
T Consensus        83 ~~~~~-------------------------------------~~~~l~v~~l~~~~~~-------------~~l~~~f~~  112 (352)
T TIGR01661        83 SSDSI-------------------------------------KGANLYVSGLPKTMTQ-------------HELESIFSP  112 (352)
T ss_pred             ccccc-------------------------------------ccceEEECCccccCCH-------------HHHHHHHhc
Confidence            21100                                     0133444455555444             499999999


Q ss_pred             cCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCC--eEEEEEEeCC
Q 009944          454 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYYPE  512 (522)
Q Consensus       454 ~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~G--r~l~v~~~~~  512 (522)
                      ||.|..+.++.+..++..   +|+|||+|.+.++|..||+.|||..+.|  .+|.|.|+..
T Consensus       113 ~G~i~~~~~~~~~~~~~~---~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~  170 (352)
T TIGR01661       113 FGQIITSRILSDNVTGLS---KGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANN  170 (352)
T ss_pred             cCCEEEEEEEecCCCCCc---CcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCC
Confidence            999999999988766644   6888999999999999999999999988  6788888754

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

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

Probab=99.94  E-value=7.9e-26  Score=223.00  Aligned_cols=289  Identities=19%  Similarity=0.254  Sum_probs=206.8

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....+-|+|+|||..+..++|..+|..||.            |..+.+....--|+|+|.++.+|.+|+ .|....+...
T Consensus       382 ~rs~~vil~kNlpa~t~~~elt~~F~~fG~------------i~rvllp~~G~~aiv~fl~p~eAr~Afrklaysr~k~~  449 (725)
T KOG0110|consen  382 ERSDTVILVKNLPAGTLSEELTEAFLRFGE------------IGRVLLPPGGTGAIVEFLNPLEARKAFRKLAYSRFKSA  449 (725)
T ss_pred             hhhcceeeeccCccccccHHHHHHhhcccc------------cceeecCcccceeeeeecCccchHHHHHHhchhhhccC
Confidence            344577999999999999999999999997            444555544446999999999999999 6898888888


Q ss_pred             eEEEecCCCCCcc-------ccccCCCC-CCCCCcccccc------cCC----CC---CCCCCCCCCeEEEcCCCCCCCH
Q 009944          250 AVRVRRPTDYNPT-------LAAALGPG-QPSPNLNLAAV------GLA----SG---AIGGAEGPDRVFVGGLPYYFTE  308 (522)
Q Consensus       250 ~~~v~~~~~~~~~-------~~~~~~~~-~~~~~~~~~~~------~~~----~~---~~~~~~~~~~l~v~nLp~~~t~  308 (522)
                      ++.+.|+....-.       ........ ..++.......      ...    ..   ........++|||.||+++++.
T Consensus       450 plyle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~  529 (725)
T KOG0110|consen  450 PLYLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTL  529 (725)
T ss_pred             ccccccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccch
Confidence            8888775321111       00000000 00000000000      000    00   0011122344999999999999


Q ss_pred             HHHHHHHHhcCCceEEEEeeCCCC---CCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHH
Q 009944          309 TQIKELLESFGTLHGFDLVKDRDT---GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESI  385 (522)
Q Consensus       309 ~~l~~~F~~~G~i~~v~~~~~~~~---g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~  385 (522)
                      ++|...|.++|.|..+.|...+..   -.|.|||||+|.++++|+.|+..|+|..|.|+.|.|.++..+......     
T Consensus       530 e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~g-----  604 (725)
T KOG0110|consen  530 EDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVG-----  604 (725)
T ss_pred             hHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccc-----
Confidence            999999999999999988775422   235699999999999999999999999999999999998621110000     


Q ss_pred             HHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCC
Q 009944          386 LAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRP  465 (522)
Q Consensus       386 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~  465 (522)
                                                ........+          ...|+.|++|+.+..+|+++|..||.|.+|.|++.
T Consensus       605 --------------------------K~~~~kk~~----------tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK  648 (725)
T KOG0110|consen  605 --------------------------KKKSKKKKG----------TKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKK  648 (725)
T ss_pred             --------------------------ccccccccc----------ceeeeeccchHHHHHHHHHHHhcccceeeeccchh
Confidence                                      000000111          12244566788888999999999999999999987


Q ss_pred             CCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          466 DQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       466 ~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      ...+   -++|+|||+|-++.+|.+|+.+|.+..|-||.|++.|+..+..
T Consensus       649 ~~k~---a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~~  695 (725)
T KOG0110|consen  649 IGKG---AHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDNT  695 (725)
T ss_pred             hcch---hhccceeeeccCcHHHHHHHHhhcccceechhhheehhccchH
Confidence            3333   3367889999999999999999999999999999999987653

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

Probab=99.94  E-value=5.6e-26  Score=210.97  Aligned_cols=172  Identities=26%  Similarity=0.401  Sum_probs=142.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCC-ccCC--eEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL-KMGD--KTLTV  368 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~-~~~g--~~l~v  368 (522)
                      ...-+|||+-||..++|.||+++|++||.|.+|.|++|+.+|.++|||||.|.+.++|.+|+.+||+. +|-|  .+|.|
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            33457999999999999999999999999999999999999999999999999999999999999984 4544  78999


Q ss_pred             EEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHH
Q 009944          369 RRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMR  448 (522)
Q Consensus       369 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~  448 (522)
                      .||....       +..                             ..+...+|-.|....++.             +|+
T Consensus       112 k~Ad~E~-------er~-----------------------------~~e~KLFvg~lsK~~te~-------------evr  142 (510)
T KOG0144|consen  112 KYADGER-------ERI-----------------------------VEERKLFVGMLSKQCTEN-------------EVR  142 (510)
T ss_pred             cccchhh-------hcc-----------------------------ccchhhhhhhccccccHH-------------HHH
Confidence            9985411       000                             011445566666666655             999


Q ss_pred             HHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCc-cCC--eEEEEEEeCCcccc
Q 009944          449 EECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRK-FGG--NTVNAFYYPEDKYF  516 (522)
Q Consensus       449 ~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~-~~G--r~l~v~~~~~~~~~  516 (522)
                      ++|++||.|++|.|+++. .+..   +|||||+|.+.+.|..||++|||.. +.|  .+|+|-|++..+-.
T Consensus       143 ~iFs~fG~Ied~~ilrd~-~~~s---RGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk  209 (510)
T KOG0144|consen  143 EIFSRFGHIEDCYILRDP-DGLS---RGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDK  209 (510)
T ss_pred             HHHHhhCccchhhheecc-cccc---cceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCc
Confidence            999999999999999988 4443   7999999999999999999999986 566  78999999976543

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

Probab=99.92  E-value=5e-25  Score=181.73  Aligned_cols=165  Identities=28%  Similarity=0.464  Sum_probs=142.1

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEEeCHHHHHHHH-HhcCce
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGII  245 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~a~-~~~~~~  245 (522)
                      ...+|||+||+..++++.|.++|-+.|+            |+++.+      ...+|||||+|.++|+|+-|+ -||...
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagp------------Vv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~Vk   75 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGP------------VVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVK   75 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCc------------eeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHH
Confidence            3468999999999999999999999997            555544      446899999999999999999 599999


Q ss_pred             ecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceE-E
Q 009944          246 FEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG-F  324 (522)
Q Consensus       246 ~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~-v  324 (522)
                      |.|++|+|..+......                            .....+|||+||.+.++|..|.+.|+.||+|.. -
T Consensus        76 LYgrpIrv~kas~~~~n----------------------------l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P  127 (203)
T KOG0131|consen   76 LYGRPIRVNKASAHQKN----------------------------LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPP  127 (203)
T ss_pred             hcCceeEEEeccccccc----------------------------ccccccccccccCcchhHHHHHHHHHhccccccCC
Confidence            99999999875422111                            112258999999999999999999999999764 4


Q ss_pred             EEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCC
Q 009944          325 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQ  377 (522)
Q Consensus       325 ~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~  377 (522)
                      ++++++.||.++|||||.|.+.+.+.+|+..+||..+..++|+|.++..+...
T Consensus       128 ~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  128 KIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTK  180 (203)
T ss_pred             cccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCC
Confidence            78889889999999999999999999999999999999999999999776543

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

Probab=99.92  E-value=3.9e-24  Score=185.75  Aligned_cols=168  Identities=26%  Similarity=0.427  Sum_probs=146.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      .+..+.|.|.-||...|+++|+.+|...|.|++|++++|+.+|.+-||+||.|.++++|++|+..|||..+..++|+|.|
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            34556799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHH
Q 009944          371 ATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREE  450 (522)
Q Consensus       371 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~  450 (522)
                      +.+....-                                     ...+.+|-.|+..++..             +|.++
T Consensus       118 ARPSs~~I-------------------------------------k~aNLYvSGlPktMtqk-------------elE~i  147 (360)
T KOG0145|consen  118 ARPSSDSI-------------------------------------KDANLYVSGLPKTMTQK-------------ELEQI  147 (360)
T ss_pred             ccCChhhh-------------------------------------cccceEEecCCccchHH-------------HHHHH
Confidence            97732111                                     12556677777766665             89999


Q ss_pred             hhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCC--eEEEEEEeC
Q 009944          451 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYYP  511 (522)
Q Consensus       451 f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~G--r~l~v~~~~  511 (522)
                      |++||.|..-.|+.+..+|..   +|++||.|....+|+.||+.|||..-.|  .+|.|-|+.
T Consensus       148 Fs~fGrIItSRiL~dqvtg~s---rGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFan  207 (360)
T KOG0145|consen  148 FSPFGRIITSRILVDQVTGLS---RGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFAN  207 (360)
T ss_pred             HHHhhhhhhhhhhhhccccee---cceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecC
Confidence            999999999999999988875   4556999999999999999999999877  578888865

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

Probab=99.91  E-value=2.7e-24  Score=177.42  Aligned_cols=171  Identities=21%  Similarity=0.303  Sum_probs=144.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ....+|||+||+..++++.|.++|-+.|+|..|.++++..++..+|||||+|.+.|+|+-|++.||...|.|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            34569999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             cCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHh
Q 009944          372 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  451 (522)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f  451 (522)
                      ..-. ...                                   ......++.+|...+++             ..|.+.|
T Consensus        87 s~~~-~nl-----------------------------------~vganlfvgNLd~~vDe-------------~~L~dtF  117 (203)
T KOG0131|consen   87 SAHQ-KNL-----------------------------------DVGANLFVGNLDPEVDE-------------KLLYDTF  117 (203)
T ss_pred             cccc-ccc-----------------------------------cccccccccccCcchhH-------------HHHHHHH
Confidence            5210 000                                   00144556566554433             3889999


Q ss_pred             hccCCeEEE-EecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          452 GKYGTLVNV-VIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       452 ~~~G~I~~v-~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      +.||.|... +|++++.+|++   .|++||.|.+.+.+.+|+..|||..+++++|.|+|+..+.
T Consensus       118 safG~l~~~P~i~rd~~tg~~---~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~  178 (203)
T KOG0131|consen  118 SAFGVLISPPKIMRDPDTGNP---KGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKD  178 (203)
T ss_pred             HhccccccCCcccccccCCCC---CCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecC
Confidence            999998875 88888888875   5777999999999999999999999999999999987543

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

Probab=99.90  E-value=1.8e-23  Score=201.10  Aligned_cols=178  Identities=21%  Similarity=0.278  Sum_probs=140.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      +++|+--|+..+++.+|.++|+.+|.|..|.++.+..++.++|.|||+|.+.+....||. |.|..+.|.+|.|..... 
T Consensus       180 Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~sEa-  257 (549)
T KOG0147|consen  180 RTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLSEA-  257 (549)
T ss_pred             HHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecccHH-
Confidence            355555566667789999999999999999999999999999999999999999999985 999999999999997522 


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHHhhccCCcc-CCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhc
Q 009944          375 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNT-LGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGK  453 (522)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~  453 (522)
                            ++          +.    .....++.. .+...|.   ..++|-+|+..+++.             +|+..|++
T Consensus       258 ------ek----------nr----~a~~s~a~~~k~~~~p~---~rl~vgnLHfNite~-------------~lr~ifep  301 (549)
T KOG0147|consen  258 ------EK----------NR----AANASPALQGKGFTGPM---RRLYVGNLHFNITED-------------MLRGIFEP  301 (549)
T ss_pred             ------HH----------HH----HHhccccccccccccch---hhhhhcccccCchHH-------------HHhhhccC
Confidence                  00          00    001111111 1111122   116677777666665             99999999


Q ss_pred             cCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          454 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       454 ~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ||.|+.|.++++..+|..   +||+||+|.+.++|.+|++.|||..+.|+.|+|..+++.
T Consensus       302 fg~Ie~v~l~~d~~tG~s---kgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  302 FGKIENVQLTKDSETGRS---KGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             cccceeeeeccccccccc---cCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            999999999999888874   455599999999999999999999999999999998764

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

Probab=99.90  E-value=9.9e-23  Score=206.67  Aligned_cols=198  Identities=20%  Similarity=0.229  Sum_probs=147.6

Q ss_pred             HHHHHHHH-HhcCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHH
Q 009944          232 VEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQ  310 (522)
Q Consensus       232 ~~~a~~a~-~~~~~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~  310 (522)
                      .++|.+|| ++++..+........+..+..              .+.          .......++|||+|||.+++|++
T Consensus        19 ~~~a~~a~~~~~gy~~~~~~g~r~~g~Pp~--------------~~~----------~~~p~~~~~lFVgnLp~~~tEd~   74 (578)
T TIGR01648        19 DEAALKALLERTGYTLVQENGQRKYGGPPP--------------GWS----------GVQPGRGCEVFVGKIPRDLYEDE   74 (578)
T ss_pred             cHHHHHHHHHhhCccccccCCcccCCCCCC--------------ccc----------CCCCCCCCEEEeCCCCCCCCHHH
Confidence            57788888 788888766655554422110              000          00122347899999999999999


Q ss_pred             HHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC-CeEEEEEEccCCCCCCchHHHHHHHHH
Q 009944          311 IKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRATASSGQSKTEQESILAQA  389 (522)
Q Consensus       311 l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~~~~~~~~~~~~~~~~~~~~  389 (522)
                      |.++|++||.|..|+|+++ .+|.++|||||+|.+.++|++||+.||+..|. |+.|.|..+..                
T Consensus        75 L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~~----------------  137 (578)
T TIGR01648        75 LVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVD----------------  137 (578)
T ss_pred             HHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccccc----------------
Confidence            9999999999999999999 79999999999999999999999999998884 77777765421                


Q ss_pred             HHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCC-eEEEEec-CCCC
Q 009944          390 QQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGT-LVNVVIP-RPDQ  467 (522)
Q Consensus       390 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~-I~~v~i~-~~~~  467 (522)
                                                 ...+.|-+|+...+.             ++|.++|++++. |+.+.+. ....
T Consensus       138 ---------------------------~~rLFVgNLP~~~Te-------------eeL~eeFskv~egvv~vIv~~~~~~  177 (578)
T TIGR01648       138 ---------------------------NCRLFVGGIPKNKKR-------------EEILEEFSKVTEGVVDVIVYHSAAD  177 (578)
T ss_pred             ---------------------------CceeEeecCCcchhh-------------HHHHHHhhcccCCceEEEEeccccc
Confidence                                       134445555554444             489999999864 4444443 2222


Q ss_pred             CCCCCCCccEEEEEecChHhHHHHHHHHhC--CccCCeEEEEEEeCCc
Q 009944          468 NGGETPGVGKVFLEYYDAVGCATAKNALSG--RKFGGNTVNAFYYPED  513 (522)
Q Consensus       468 ~g~~~~g~G~afV~F~~~~~A~~Ai~~lng--~~~~Gr~l~v~~~~~~  513 (522)
                      .+   +..|+|||+|.++++|..|+..|+.  ..+.|+.|.|.|+..+
T Consensus       178 kg---KnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~  222 (578)
T TIGR01648       178 KK---KNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPE  222 (578)
T ss_pred             cC---ccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeeccc
Confidence            22   3468999999999999999998864  3578999999998754

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.

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

Probab=99.89  E-value=1.3e-22  Score=189.76  Aligned_cols=164  Identities=22%  Similarity=0.325  Sum_probs=138.6

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-------cCCCcEEEEEEeCHHHHHHHH-H-
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVEMRTVEEASNAM-A-  240 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~-------~~~~g~afV~f~~~~~a~~a~-~-  240 (522)
                      .+...++|||+|||.+.++++|.+.|++.++           -|++|.+       .+++|||||+|.+...|..|- . 
T Consensus       160 ~Svan~RLFiG~IPK~k~keeIlee~~kVte-----------GVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl  228 (506)
T KOG0117|consen  160 VSVANCRLFIGNIPKTKKKEEILEEMKKVTE-----------GVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKL  228 (506)
T ss_pred             EeeecceeEeccCCccccHHHHHHHHHhhCC-----------CeeEEEEecCccccccccceEEEEeecchhHHHHHhhc
Confidence            4566889999999999999999999999865           3666654       356899999999999999888 4 


Q ss_pred             hcC-ceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcC
Q 009944          241 LDG-IIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG  319 (522)
Q Consensus       241 ~~~-~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G  319 (522)
                      +++ +++.|..+.|.|+.+......                        ........|||+||+.+||++.|+++|+.||
T Consensus       229 ~~g~~klwgn~~tVdWAep~~e~de------------------------d~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G  284 (506)
T KOG0117|consen  229 MPGKIKLWGNAITVDWAEPEEEPDE------------------------DTMSKVKVLYVRNLMESTTEETLKKLFNEFG  284 (506)
T ss_pred             cCCceeecCCcceeeccCcccCCCh------------------------hhhhheeeeeeeccchhhhHHHHHHHHHhcc
Confidence            444 668999999999775542210                        0123446899999999999999999999999


Q ss_pred             CceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCC
Q 009944          320 TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  376 (522)
Q Consensus       320 ~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~  376 (522)
                      .|+.|+.++|        ||||.|.+.++|.+||+.+||..|.|..|.|.+|++..+
T Consensus       285 ~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k  333 (506)
T KOG0117|consen  285 KVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDK  333 (506)
T ss_pred             ceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhh
Confidence            9999998866        999999999999999999999999999999999987543

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

Probab=99.89  E-value=5.9e-23  Score=196.19  Aligned_cols=190  Identities=18%  Similarity=0.306  Sum_probs=145.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      .||||++||+.++.++|.++|+.+|+|..+.++.++.++.++||+||.|.-.++++.|+..+.+..|.|+.|.|.++...
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            59999999999999999999999999999999999989999999999999999999999999999999999999999775


Q ss_pred             CCCCchH--HHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhh
Q 009944          375 SGQSKTE--QESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  452 (522)
Q Consensus       375 ~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~  452 (522)
                      .-....+  ..........+....+...             .....-+.|-+|+..+..             .+|+.+|+
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v-------------~~~k~rLIIRNLPf~~k~-------------~dLk~vFs  139 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKV-------------DLPKWRLIIRNLPFKCKK-------------PDLKNVFS  139 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhc-------------cCccceEEeecCCcccCc-------------HHHHHHHh
Confidence            4222100  0000000000000000000             000122233344444444             49999999


Q ss_pred             ccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          453 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       453 ~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      .||.|..|.||+....+..    |||||+|....+|.+||+.+||..|+||+|-|.|+-..+
T Consensus       140 ~~G~V~Ei~IP~k~dgklc----GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  140 NFGKVVEIVIPRKKDGKLC----GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             hcceEEEEEcccCCCCCcc----ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence            9999999999988765554    899999999999999999999999999999999965544

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

Probab=99.88  E-value=2.7e-22  Score=177.45  Aligned_cols=148  Identities=24%  Similarity=0.431  Sum_probs=129.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      .+|||+|||..+++.+|+.+|++||+|.+|.|+++        ||||..++...|..||..|||.+|.|..|.|.-++.+
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            47999999999999999999999999999999986        8999999999999999999999999999999988764


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhcc
Q 009944          375 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  454 (522)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~  454 (522)
                      .+..                                       +...|-++....+.             ++|+..|++|
T Consensus        75 sk~s---------------------------------------tkl~vgNis~tctn-------------~ElRa~fe~y  102 (346)
T KOG0109|consen   75 SKAS---------------------------------------TKLHVGNISPTCTN-------------QELRAKFEKY  102 (346)
T ss_pred             CCCc---------------------------------------cccccCCCCccccC-------------HHHhhhhccc
Confidence            2111                                       23334444444333             3899999999


Q ss_pred             CCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          455 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       455 G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      |.|.+|.|.+           +++||.|.-.++|..|+..|+|+.|.|++++|.+.+..
T Consensus       103 gpviecdivk-----------dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen  103 GPVIECDIVK-----------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             CCceeeeeec-----------ceeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence            9999999987           58899999999999999999999999999999998753

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

Probab=99.88  E-value=2.7e-21  Score=175.42  Aligned_cols=206  Identities=21%  Similarity=0.338  Sum_probs=158.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCce--------EEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeE
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT  365 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~--------~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~  365 (522)
                      .+.|||.|||.++|.+++.++|++||.|.        .|+|.++. .|.-+|-|+|.|.-.+++.-|++.|++..|.|+.
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            35699999999999999999999999876        38888885 5999999999999999999999999999999999


Q ss_pred             EEEEEccCCCCCCch--HHHH--HHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCCh-HHH
Q 009944          366 LTVRRATASSGQSKT--EQES--ILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADD-EEY  440 (522)
Q Consensus       366 l~v~~~~~~~~~~~~--~~~~--~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~-~~~  440 (522)
                      |+|..|.-.......  .+..  ...........+++    ..+...-  ....-.....++++.|++++.++..+ +..
T Consensus       213 ~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~----~dw~pd~--~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~  286 (382)
T KOG1548|consen  213 LRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKL----LDWRPDR--DDPSKARADRTVILKNMFTPEDFEKNPDLL  286 (382)
T ss_pred             EEEehhhhhhccCcCcccccccccccHHHHHHHHHhh----cccCCCc--cccccccCCcEEEeeecCCHHHhccCHHHH
Confidence            999988754321100  0000  01111111111111    1111000  11122355678999999999999888 558


Q ss_pred             HHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          441 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       441 ~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ..+.++|.+.|++||.|.+|.|.-.++       .|.|-|.|.+.++|..||+.|+|++|+||+|..+..+-.
T Consensus       287 ~dlkedl~eec~K~G~v~~vvv~d~hP-------dGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  287 NDLKEDLTEECEKFGQVRKVVVYDRHP-------DGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHHHHHHhCCcceEEEeccCC-------CceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            999999999999999999999976554       378899999999999999999999999999999987753

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

Probab=99.88  E-value=3.4e-22  Score=181.70  Aligned_cols=173  Identities=22%  Similarity=0.442  Sum_probs=139.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      ++|||+.|.+.+.|+.|+..|.+||+|++|.+..|+.|++.+|||||+|+-+|.|+-|++.|||..++|+.|+|.....-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999965432


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhcc
Q 009944          375 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  454 (522)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~  454 (522)
                      .+.     .......++.  ..+.                   ..++|-.++..++++             ||+..|+.|
T Consensus       194 pQA-----QpiID~vqee--Ak~f-------------------nRiYVaSvHpDLSe~-------------DiKSVFEAF  234 (544)
T KOG0124|consen  194 PQA-----QPIIDMVQEE--AKKF-------------------NRIYVASVHPDLSET-------------DIKSVFEAF  234 (544)
T ss_pred             ccc-----chHHHHHHHH--HHhh-------------------heEEeeecCCCccHH-------------HHHHHHHhh
Confidence            211     1111111110  0000                   223333344444443             999999999


Q ss_pred             CCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEE
Q 009944          455 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFY  509 (522)
Q Consensus       455 G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~  509 (522)
                      |+|.+|.+.+.+..+.+   +||+|++|.+...-..||..||-+.++|.-|+|--
T Consensus       235 G~I~~C~LAr~pt~~~H---kGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk  286 (544)
T KOG0124|consen  235 GEIVKCQLARAPTGRGH---KGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGK  286 (544)
T ss_pred             cceeeEEeeccCCCCCc---cceeeEEeccccchHHHhhhcchhhcccceEeccc
Confidence            99999999999865553   55669999999999999999999999999999854

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

Probab=99.87  E-value=4.2e-22  Score=176.25  Aligned_cols=146  Identities=25%  Similarity=0.461  Sum_probs=132.2

Q ss_pred             eeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEEEe
Q 009944          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR  254 (522)
Q Consensus       176 ~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~v~  254 (522)
                      +|||+|||..+++.+|+.+|++||+            |..+.+.  |.||||..++...|..|+ .|++.+|+|..|.|+
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygk------------VlECDIv--KNYgFVHiEdktaaedairNLhgYtLhg~nInVe   69 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGK------------VLECDIV--KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVE   69 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCc------------eEeeeee--cccceEEeecccccHHHHhhcccceecceEEEEE
Confidence            7999999999999999999999998            5666554  569999999999999999 699999999999999


Q ss_pred             cCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCC
Q 009944          255 RPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN  334 (522)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~  334 (522)
                      .++...                               ...++|+|+||.+.++.++|+..|++||+|.+++|+++     
T Consensus        70 aSksKs-------------------------------k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd-----  113 (346)
T KOG0109|consen   70 ASKSKS-------------------------------KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD-----  113 (346)
T ss_pred             eccccC-------------------------------CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc-----
Confidence            765542                               22368999999999999999999999999999999976     


Q ss_pred             cceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          335 SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       335 ~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                         |+||.|.-.++|..|+..|+|..|.|+.|+|..++..
T Consensus       114 ---y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen  114 ---YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             ---eeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence               9999999999999999999999999999999998764

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

Probab=99.85  E-value=3.2e-19  Score=166.15  Aligned_cols=187  Identities=22%  Similarity=0.317  Sum_probs=135.7

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE-----ecCCCcEEEEEEeCHHHHHHHH-HhcCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY-----INHEKKFAFVEMRTVEEASNAM-ALDGII  245 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~-----~~~~~g~afV~f~~~~~a~~a~-~~~~~~  245 (522)
                      ...+.+||.|||+++.+++|+++|....-           .|.-|.     .++.+|||.|+|+++|.+++|+ .||...
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvG-----------ev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~  110 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVG-----------EVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYE  110 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcC-----------ceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhcc
Confidence            34567999999999999999999996521           244443     3678999999999999999999 599999


Q ss_pred             ecCceEEEecCCCCCccccccC---------------------------------CCCCCCC-C------cc--------
Q 009944          246 FEGVAVRVRRPTDYNPTLAAAL---------------------------------GPGQPSP-N------LN--------  277 (522)
Q Consensus       246 ~~g~~~~v~~~~~~~~~~~~~~---------------------------------~~~~~~~-~------~~--------  277 (522)
                      +.|++|+|+.....+.......                                 +.+.... .      ..        
T Consensus       111 ~~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~  190 (608)
T KOG4212|consen  111 VNGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNN  190 (608)
T ss_pred             ccCceEEEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCcccccccccc
Confidence            9999999975443211110000                                 0000000 0      00        


Q ss_pred             ---cccccCC-----CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHH
Q 009944          278 ---LAAVGLA-----SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT  349 (522)
Q Consensus       278 ---~~~~~~~-----~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A  349 (522)
                         ....++.     +...-.+....++||.||.+.+....|++.|.-.|.|..|.+-.++ .|.++|||.++|..+-+|
T Consensus       191 ~~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idK-eG~s~G~~vi~y~hpvea  269 (608)
T KOG4212|consen  191 SSNYNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDK-EGNSRGFAVIEYDHPVEA  269 (608)
T ss_pred             chhhhcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeecc-ccccCCeeEEEecchHHH
Confidence               0000000     0001122334679999999999999999999999999999999997 579999999999999999


Q ss_pred             HHHHHHHcCCccCCeEEEEEE
Q 009944          350 DIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       350 ~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ..||..|++.-+..++..+..
T Consensus       270 vqaIsml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  270 VQAISMLDRQGLFDRRMTVRL  290 (608)
T ss_pred             HHHHHhhccCCCccccceeec
Confidence            999999998777777777766

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

Probab=99.85  E-value=4.5e-21  Score=177.23  Aligned_cols=303  Identities=16%  Similarity=0.181  Sum_probs=189.9

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHH-h--cCceecC
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-L--DGIIFEG  248 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~-~--~~~~~~g  248 (522)
                      ..++-|+++|||++++|++|.+++.+||.            |..+...+.+.-||++|.+++.|...+. .  -.-.+.|
T Consensus        26 ~pSkV~HlRnlp~e~tE~elI~Lg~pFG~------------vtn~~~lkGknQAflem~d~~sAvtmv~~y~~~~p~lr~   93 (492)
T KOG1190|consen   26 EPSKVVHLRNLPWEVTEEELISLGLPFGK------------VTNLLMLKGKNQAFLEMADEESAVTMVNYYTSVTPVLRG   93 (492)
T ss_pred             CCcceeEeccCCccccHHHHHHhcccccc------------eeeeeeeccchhhhhhhcchhhhhheeecccccCccccC
Confidence            35678999999999999999999999997            6666667777799999999999998662 2  2244788


Q ss_pred             ceEEEecCCCCC--cccccc-------CCCCCCCCCcc--cccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHh
Q 009944          249 VAVRVRRPTDYN--PTLAAA-------LGPGQPSPNLN--LAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLES  317 (522)
Q Consensus       249 ~~~~v~~~~~~~--~~~~~~-------~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~  317 (522)
                      ++|.|+++....  ......       ...........  +.......+...++..--+++|.|+-+.++-+-|..+|++
T Consensus        94 ~~~yiq~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~  173 (492)
T KOG1190|consen   94 QPIYIQYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSK  173 (492)
T ss_pred             cceeehhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhh
Confidence            999998743211  000000       00000000000  1111111122222333346789999999999999999999


Q ss_pred             cCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc--CCeEEEEEEccCCCCC----------------Cc
Q 009944          318 FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVRRATASSGQ----------------SK  379 (522)
Q Consensus       318 ~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--~g~~l~v~~~~~~~~~----------------~~  379 (522)
                      ||.|..|.-....    ..=-|+|+|.+.+.|+.|-.+|+|..|  +-+.|+|.|+....-.                +.
T Consensus       174 fG~VlKIiTF~Kn----n~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~  249 (492)
T KOG1190|consen  174 FGFVLKIITFTKN----NGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPV  249 (492)
T ss_pred             cceeEEEEEEecc----cchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCC
Confidence            9999877544321    112389999999999999999999877  3367777776532100                00


Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhccCC-----ccCCC-----Cc-CCCCCCc-ceEEEeeCCCCcCcCCChHHHHHHHHHH
Q 009944          380 TEQESILAQAQQHIAIQKMALQTSGM-----NTLGG-----GM-SLFGETL-AKVLCLTEAITADALADDEEYEEILEDM  447 (522)
Q Consensus       380 ~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~g~-----~~-~~~~~~~-~~v~~l~~~~~~~~l~~~~~~~~~~~~l  447 (522)
                      .+....+     +..+..........     ..|..     .. ....... ..++.+.|. .++.+        +.+-|
T Consensus       250 gd~~p~l-----~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnl-n~~~V--------T~d~L  315 (492)
T KOG1190|consen  250 GDGQPSL-----DQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNL-NEEAV--------TPDVL  315 (492)
T ss_pred             Ccccccc-----chhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecC-chhcc--------chhHH
Confidence            0000000     00000000000000     00000     00 0011111 233333333 33322        22489


Q ss_pred             HHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          448 REECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       448 ~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      ..+|+.||.|..|+|+.++.        -.|.|+|.+...|+-|++.|+|..+.|++|+|++..-
T Consensus       316 ftlFgvYGdVqRVkil~nkk--------d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  316 FTLFGVYGDVQRVKILYNKK--------DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             HHHHhhhcceEEEEeeecCC--------cceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            99999999999999998752        4689999999999999999999999999999999654

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

Probab=99.83  E-value=3.8e-20  Score=183.14  Aligned_cols=167  Identities=23%  Similarity=0.428  Sum_probs=139.3

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC---------CCcEEEEEEeCHHHHHHHH-HhcCc
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH---------EKKFAFVEMRTVEEASNAM-ALDGI  244 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~---------~~g~afV~f~~~~~a~~a~-~~~~~  244 (522)
                      ++|||.||++.+|.++|...|...|.            |.++.+..         +.|||||+|.++++|+.|+ .|+|.
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~------------VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgt  583 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGT------------VLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGT  583 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCe------------EEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCc
Confidence            34999999999999999999999987            44444322         3499999999999999999 79999


Q ss_pred             eecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEE
Q 009944          245 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF  324 (522)
Q Consensus       245 ~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v  324 (522)
                      .|.|..|.|+++......   ..+.                 ........+.|+|+|||+.++..+|+++|..||.|.+|
T Consensus       584 vldGH~l~lk~S~~k~~~---~~gK-----------------~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksv  643 (725)
T KOG0110|consen  584 VLDGHKLELKISENKPAS---TVGK-----------------KKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSV  643 (725)
T ss_pred             eecCceEEEEeccCcccc---cccc-----------------ccccccccceeeeeccchHHHHHHHHHHHhcccceeee
Confidence            999999999986511111   0110                 00011224689999999999999999999999999999


Q ss_pred             EEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          325 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       325 ~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .|+.-...+.++|||||+|-++.+|..|+.+|.+..|.|+.|.+.|+..
T Consensus       644 RlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~  692 (725)
T KOG0110|consen  644 RLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKS  692 (725)
T ss_pred             ccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhcc
Confidence            9998755677899999999999999999999999999999999999966

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

Probab=99.82  E-value=2.9e-19  Score=156.16  Aligned_cols=204  Identities=18%  Similarity=0.264  Sum_probs=144.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCC-ccC--CeEEEEE
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL-KMG--DKTLTVR  369 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~-~~~--g~~l~v~  369 (522)
                      ..++|||+-|...-.|+|++.+|..||.|.+|.+.+.+ .|.++|+|||.|.+..+|+.||..|||. ++-  ...|.|+
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            34689999999999999999999999999999999986 7999999999999999999999999993 443  4779999


Q ss_pred             EccCCCCC----------------Cch-------HHHHHHHHH------------------HHHHHHHHH---HhhccC-
Q 009944          370 RATASSGQ----------------SKT-------EQESILAQA------------------QQHIAIQKM---ALQTSG-  404 (522)
Q Consensus       370 ~~~~~~~~----------------~~~-------~~~~~~~~~------------------~~~~~~~~~---~~~~~~-  404 (522)
                      |+......                +..       ...+.+...                  ...-.+|.+   ...-.. 
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            98754210                000       000000000                  000011111   000000 


Q ss_pred             -C--------ccC--------C-------------------C--------------------------------------
Q 009944          405 -M--------NTL--------G-------------------G--------------------------------------  410 (522)
Q Consensus       405 -~--------~~~--------g-------------------~--------------------------------------  410 (522)
                       +        ..+        +                   .                                      
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             0        000        0                   0                                      


Q ss_pred             ----------Cc------------CCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCC
Q 009944          411 ----------GM------------SLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQN  468 (522)
Q Consensus       411 ----------~~------------~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~  468 (522)
                                ..            .....++.+|+.|+..+.+.             +|.++|-+||.|++.++..|..+
T Consensus       257 ypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDa-------------EliQmF~PFGhivSaKVFvDRAT  323 (371)
T KOG0146|consen  257 YPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDA-------------ELIQMFLPFGHIVSAKVFVDRAT  323 (371)
T ss_pred             cchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccH-------------HHHHHhccccceeeeeeeehhcc
Confidence                      00            00224556677777666665             89999999999999999888866


Q ss_pred             CCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          469 GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       469 g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      .. ++++|  ||.|.|+.+|+.||.+|||+.|+-++|+|.+--.+
T Consensus       324 NQ-SKCFG--FVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPk  365 (371)
T KOG0146|consen  324 NQ-SKCFG--FVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPK  365 (371)
T ss_pred             cc-cccee--eEecCCchhHHHHHHHhcchhhhhhhhhhhhcCcc
Confidence            65 46666  99999999999999999999999999999875443

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

Probab=99.81  E-value=7.7e-19  Score=172.02  Aligned_cols=187  Identities=16%  Similarity=0.250  Sum_probs=138.6

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++++|++||..+++.++.+++..||.+.++++      |.+..++.++||||.+|.+.-....|+ .+||+.+.++
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~l------v~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~  359 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRL------VKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDK  359 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhhee------ecccccccccceeeeeeeCCcchhhhhcccchhhhcCc
Confidence            345678999999999999999999999999988876      778888999999999999999999999 6999999999


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCCccc---ccccCCCC-CCCCCCCCCeEEEcCCC--CCC-CH-------HHHHHHH
Q 009944          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNL---AAVGLASG-AIGGAEGPDRVFVGGLP--YYF-TE-------TQIKELL  315 (522)
Q Consensus       250 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~-~~~~~~~~~~l~v~nLp--~~~-t~-------~~l~~~F  315 (522)
                      +|.|+.+-.-...         +....+.   ...+.... ......+...|.+.|+=  .+. .+       ++|+..|
T Consensus       360 ~lvvq~A~~g~~~---------~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec  430 (500)
T KOG0120|consen  360 KLVVQRAIVGASN---------ANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTEC  430 (500)
T ss_pred             eeEeehhhccchh---------ccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHh
Confidence            9999864322111         1111110   11111111 11122333445555551  111 11       4677788


Q ss_pred             HhcCCceEEEEeeC-C--CCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          316 ESFGTLHGFDLVKD-R--DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       316 ~~~G~i~~v~~~~~-~--~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ++||.|..|.++++ .  ...-..|..||+|.+.+++++|+.+|+|.+|.|++|...|..
T Consensus       431 ~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  431 AKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             cccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            89999999999887 2  223346779999999999999999999999999999999874

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

Probab=99.80  E-value=5.9e-18  Score=156.81  Aligned_cols=298  Identities=17%  Similarity=0.142  Sum_probs=193.6

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcE-EEEEEeCHHHHHHHH-HhcCceecC--c
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKF-AFVEMRTVEEASNAM-ALDGIIFEG--V  249 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~-afV~f~~~~~a~~a~-~~~~~~~~g--~  249 (522)
                      .-.++|+|+-+-++-+-|..+|+.||.+           ..-+.+.+..+| |.|+|.+.+.|..|. .|+|..|..  +
T Consensus       150 vLr~iie~m~ypVslDVLHqvFS~fG~V-----------lKIiTF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcC  218 (492)
T KOG1190|consen  150 VLRTIIENMFYPVSLDVLHQVFSKFGFV-----------LKIITFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCC  218 (492)
T ss_pred             eEEEEeccceeeeEHHHHHHHHhhccee-----------EEEEEEecccchhhhhhccchhhHHHHHHhccCCcccCcee
Confidence            4468899999999999999999999983           233344566665 999999999999999 799988765  4


Q ss_pred             eEEEecCCC--------------CCccccccCCCCCCCCC-------cccccccCCC--------------CCCCCCCCC
Q 009944          250 AVRVRRPTD--------------YNPTLAAALGPGQPSPN-------LNLAAVGLAS--------------GAIGGAEGP  294 (522)
Q Consensus       250 ~~~v~~~~~--------------~~~~~~~~~~~~~~~~~-------~~~~~~~~~~--------------~~~~~~~~~  294 (522)
                      .|+|.+++-              |..... ..+..++.-.       .+..+....+              +........
T Consensus       219 tLrId~Sklt~LnvKynndkSRDyTnp~L-P~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n  297 (492)
T KOG1190|consen  219 TLRIDFSKLTDLNVKYNNDKSRDYTNPDL-PVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSAN  297 (492)
T ss_pred             EEEeehhhcccceeeccccccccccCCCC-CCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCc
Confidence            566655431              111100 0010000000       0000000000              000001124


Q ss_pred             CeEEEcCCCC-CCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          295 DRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       295 ~~l~v~nLp~-~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      ..|.|.||.. .+|.+-|..+|..||.|..|+|..++.     --|+|+|.+...|+-|+..|+|..+.|+.|+|.+++.
T Consensus       298 ~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  298 VVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             eEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            5688999865 599999999999999999999998742     3599999999999999999999999999999999876


Q ss_pred             CCCCCchHHHH--HHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHh
Q 009944          374 SSGQSKTEQES--ILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  451 (522)
Q Consensus       374 ~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f  451 (522)
                      ...+.+.+.+.  -+...       .......-...||.-.....-.++..+.|.++...-          .+++|+.+|
T Consensus       373 ~~vqlp~egq~d~glT~d-------y~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~sv----------see~lk~~f  435 (492)
T KOG1190|consen  373 TNVQLPREGQEDQGLTKD-------YGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSV----------SEEDLKNLF  435 (492)
T ss_pred             ccccCCCCCCcccccccc-------CCCCchhhccCcccccccccCCchhheeeccCCccc----------chhHHHHhh
Confidence            65443332110  00000       000000111223333333333445555665554322          114999999


Q ss_pred             hccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCe-EEEEEEeCC
Q 009944          452 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGN-TVNAFYYPE  512 (522)
Q Consensus       452 ~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr-~l~v~~~~~  512 (522)
                      ..-|-..+....-.       ++.-+|++.++++|+|..|+..|+++.+++. .|+|+|...
T Consensus       436 ~~~g~~vkafkff~-------kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  436 QEPGGQVKAFKFFQ-------KDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             hcCCceEEeeeecC-------CCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            99887766544321       1235899999999999999999999999765 999999753

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

Probab=99.79  E-value=1.2e-17  Score=159.06  Aligned_cols=170  Identities=22%  Similarity=0.291  Sum_probs=130.5

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEEE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  253 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~v  253 (522)
                      ..-|.+.+||+++|++||.+||..++.-         ..++....++..|-|||+|.++|++++||+.+...+..+-|.|
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~I~---------~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEV   80 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCGIE---------NLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEV   80 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCcee---------EEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEE
Confidence            4468899999999999999999998531         1233334477789999999999999999999999999999999


Q ss_pred             ecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceE-EEEeeCCCC
Q 009944          254 RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDRDT  332 (522)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~-v~~~~~~~~  332 (522)
                      -.+...+....                  +.+...........|.+++||+.||++||.++|+..-.|.. |.++.+. .
T Consensus        81 f~~~~~e~d~~------------------~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-r  141 (510)
T KOG4211|consen   81 FTAGGAEADWV------------------MRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-R  141 (510)
T ss_pred             EccCCcccccc------------------ccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-C
Confidence            75433221100                  00000111123457999999999999999999998877665 4455554 6


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      +.+.|.|||+|++.+.|++||. -|...|+.+-|.|..+.
T Consensus       142 gR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  142 GRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRSS  180 (510)
T ss_pred             CCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehhH
Confidence            7899999999999999999987 56688899999998764

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

Probab=99.78  E-value=1.7e-19  Score=168.66  Aligned_cols=173  Identities=21%  Similarity=0.382  Sum_probs=145.7

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~  252 (522)
                      +.++|||++|++.++++.|+++|.+||.+..+.      +..+..++.++||+||+|++++.+.++|......|.|+.|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~------vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve   78 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCV------VMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVE   78 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEE------EeccCCCCCcccccceecCCCcchheeecccccccCCcccc
Confidence            678999999999999999999999999965432      23333457789999999999999999998888899999999


Q ss_pred             EecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCC
Q 009944          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (522)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~  332 (522)
                      +..+..........                       ......+|||++||.++++++++++|++||.|..+.++.|..+
T Consensus        79 ~k~av~r~~~~~~~-----------------------~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~  135 (311)
T KOG4205|consen   79 PKRAVSREDQTKVG-----------------------RHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTT  135 (311)
T ss_pred             ceeccCcccccccc-----------------------cccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccc
Confidence            98765543221100                       0112358999999999999999999999999999999999999


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCC
Q 009944          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (522)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (522)
                      ...+||+||.|.+.+.+.+++. ..-+.|.|+.|.|..|.++.
T Consensus       136 ~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~  177 (311)
T KOG4205|consen  136 SRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKE  177 (311)
T ss_pred             cccccceeeEeccccccceecc-cceeeecCceeeEeeccchh
Confidence            9999999999999999999876 66789999999999998754

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

Probab=99.77  E-value=1.1e-17  Score=144.50  Aligned_cols=185  Identities=21%  Similarity=0.314  Sum_probs=142.2

Q ss_pred             cceeEEeCCCccCcHHHHHH----HHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          174 ARRVYVGGLPPLANEQAIAT----FFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~----~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      ..+|||.||+..+..++|+.    +|++||.|+.         |....+.+.+|-|||.|.+.+.|..|+ .|+|..+.|
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ild---------I~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFyg   79 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILD---------ISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYG   79 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEE---------EEecCCCCccCceEEEecChhHHHHHHHHhcCCcccC
Confidence            34999999999999999888    9999998653         666667888999999999999999999 799999999


Q ss_pred             ceEEEecCCCCCccccccCCCCCC---C----------------CCcc-cccccCCCC-CCCCCCCCCeEEEcCCCCCCC
Q 009944          249 VAVRVRRPTDYNPTLAAALGPGQP---S----------------PNLN-LAAVGLASG-AIGGAEGPDRVFVGGLPYYFT  307 (522)
Q Consensus       249 ~~~~v~~~~~~~~~~~~~~~~~~~---~----------------~~~~-~~~~~~~~~-~~~~~~~~~~l~v~nLp~~~t  307 (522)
                      +.++|+|++..........+....   .                .... .......+. ......+...||+.|||..++
T Consensus        80 K~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~  159 (221)
T KOG4206|consen   80 KPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESE  159 (221)
T ss_pred             chhheecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchh
Confidence            999999988766554432210000   0                0000 000000000 011233446799999999999


Q ss_pred             HHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC-CeEEEEEEcc
Q 009944          308 ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRAT  372 (522)
Q Consensus       308 ~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~~~  372 (522)
                      .+.|..+|.+|.....|.++...     .+.|||+|.+...|..|...|+|..|- ..+|.|.++.
T Consensus       160 ~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  160 SEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            99999999999999999988653     578999999999999999999998886 8889888874

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

Probab=99.76  E-value=2e-17  Score=136.87  Aligned_cols=176  Identities=24%  Similarity=0.340  Sum_probs=129.3

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC---CcEEEEEEeCHHHHHHHH-HhcCceec
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE---KKFAFVEMRTVEEASNAM-ALDGIIFE  247 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~---~g~afV~f~~~~~a~~a~-~~~~~~~~  247 (522)
                      ...++|||+|||.++-+.+|.++|.+||.            |.++.+...   ..||||+|+++.+|+.|+ .-+|..+.
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~------------i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdyd   71 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGR------------IREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYD   71 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcc------------eEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccC
Confidence            34689999999999999999999999998            555655433   569999999999999999 69999999


Q ss_pred             CceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEe
Q 009944          248 GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLV  327 (522)
Q Consensus       248 g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~  327 (522)
                      |..|+|..+.......-....-+.....   ...+........-.....|.|.+||+..+++||++++.+.|.|....+.
T Consensus        72 g~rLRVEfprggr~s~~~~G~y~gggrg---Ggg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~  148 (241)
T KOG0105|consen   72 GCRLRVEFPRGGRSSSDRRGSYSGGGRG---GGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQ  148 (241)
T ss_pred             cceEEEEeccCCCcccccccccCCCCCC---CCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeee
Confidence            9999999876543211000000000000   0000000001112344689999999999999999999999999999888


Q ss_pred             eCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc--CCeEEEEE
Q 009944          328 KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVR  369 (522)
Q Consensus       328 ~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--~g~~l~v~  369 (522)
                      +|       |++.|+|...|+.+-|+..|....+  .|....+.
T Consensus       149 rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yir  185 (241)
T KOG0105|consen  149 RD-------GVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIR  185 (241)
T ss_pred             cc-------cceeeeeeehhhHHHHHHhhccccccCcCcEeeEE
Confidence            87       4799999999999999999987665  44444443

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

Probab=99.74  E-value=1.4e-17  Score=145.82  Aligned_cols=81  Identities=28%  Similarity=0.517  Sum_probs=77.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||-.||.+..+.+|.++|-.||.|.+.++..|+.|+.+++|+||.|.++.+|+.||.+|||+.|+-+.|+|.+..+
T Consensus       285 GCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRP  364 (371)
T KOG0146|consen  285 GCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRP  364 (371)
T ss_pred             cceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCc
Confidence            48899999999999999999999999999999999999999999999999999999999999999999999999998766


Q ss_pred             C
Q 009944          374 S  374 (522)
Q Consensus       374 ~  374 (522)
                      +
T Consensus       365 k  365 (371)
T KOG0146|consen  365 K  365 (371)
T ss_pred             c
Confidence            4

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

Probab=99.72  E-value=7.2e-17  Score=136.38  Aligned_cols=84  Identities=23%  Similarity=0.549  Sum_probs=79.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.|++..|.|+.|+|.++
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            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      ..+.
T Consensus       112 ~~~~  115 (144)
T PLN03134        112 NDRP  115 (144)
T ss_pred             CcCC
Confidence            7643

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

Probab=99.72  E-value=1.1e-16  Score=138.47  Aligned_cols=194  Identities=19%  Similarity=0.271  Sum_probs=136.0

Q ss_pred             CeEEEcCCCCCCCHHHHHH----HHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          295 DRVFVGGLPYYFTETQIKE----LLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~----~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      .||||.||+..+..++|+.    +|++||.|.+|...+   +.+.+|-|||.|.+.+.|..|+.+|+|+.|.|+.++|.|
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqy   86 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQY   86 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheec
Confidence            4999999999999998877    999999999888775   567899999999999999999999999999999999999


Q ss_pred             ccCCCCCCchHHHHHHHHHHHHHHH-------HHHHhh-----ccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChH
Q 009944          371 ATASSGQSKTEQESILAQAQQHIAI-------QKMALQ-----TSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDE  438 (522)
Q Consensus       371 ~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~-----~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~  438 (522)
                      |..+...-..... ...........       +.....     ....+.+... +.....+..++.+.++..+.      
T Consensus        87 A~s~sdii~~~~~-~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~-~~~~~ppn~ilf~~niP~es------  158 (221)
T KOG4206|consen   87 AKSDSDIIAQAPG-TFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPF-LAQMAPPNNILFLTNIPSES------  158 (221)
T ss_pred             ccCccchhhccCc-eeccccCccccccccccCCcccccccccccccccCCCCc-cccCCCCceEEEEecCCcch------
Confidence            9876532211000 00000000000       000000     0000111111 12223455565565554443      


Q ss_pred             HHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccC-CeEEEEEEeC
Q 009944          439 EYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG-GNTVNAFYYP  511 (522)
Q Consensus       439 ~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~-Gr~l~v~~~~  511 (522)
                          ..+.|..+|+.|.-...|.++...        .+.|||+|.+...|..|..+|.|..+- ..++.+.|+.
T Consensus       159 ----~~e~l~~lf~qf~g~keir~i~~~--------~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  159 ----ESEMLSDLFEQFPGFKEIRLIPPR--------SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             ----hHHHHHHHHhhCcccceeEeccCC--------CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence                235778889999988888887643        388999999999999999999999997 8999998875

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

Probab=99.68  E-value=1.3e-15  Score=126.27  Aligned_cols=178  Identities=21%  Similarity=0.298  Sum_probs=126.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||.++-+.+|.++|.+||.|..|.|...+   ...+||||+|+++-+|+.||..-+|.-+.|+.|.|.++.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            34689999999999999999999999999999887542   235799999999999999999999999999999999986


Q ss_pred             CCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCc----CC--CCCCcceEEEeeCCCCcCcCCChHHHHHHHHH
Q 009944          373 ASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGM----SL--FGETLAKVLCLTEAITADALADDEEYEEILED  446 (522)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~----~~--~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~  446 (522)
                      -........                 ......-...+...    +.  .++.-.-|-.|+...++             +|
T Consensus        82 ggr~s~~~~-----------------G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSW-------------QD  131 (241)
T KOG0105|consen   82 GGRSSSDRR-----------------GSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSW-------------QD  131 (241)
T ss_pred             CCCcccccc-----------------cccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCch-------------HH
Confidence            532110000                 00000000000000    11  11111222234444344             59


Q ss_pred             HHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCcc--CCeEEEEEEeCCc
Q 009944          447 MREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF--GGNTVNAFYYPED  513 (522)
Q Consensus       447 l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~--~Gr~l~v~~~~~~  513 (522)
                      |++++.+-|.|-...+.++          |+..|+|...|+.+.|+..|....|  .|-+..+......
T Consensus       132 LKDHmReaGdvCfadv~rD----------g~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yirv~~~~  190 (241)
T KOG0105|consen  132 LKDHMREAGDVCFADVQRD----------GVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIRVRGDE  190 (241)
T ss_pred             HHHHHHhhCCeeeeeeecc----------cceeeeeeehhhHHHHHHhhccccccCcCcEeeEEecccC
Confidence            9999999999999999886          4459999999999999999998877  4666655554443

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

Probab=99.67  E-value=1.2e-16  Score=149.55  Aligned_cols=173  Identities=22%  Similarity=0.362  Sum_probs=139.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ...+|||++|++.++++.|++.|.+||.|.++.+++++.++.++||+||+|.+++....+|.. .-+.|.|+.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            457899999999999999999999999999999999999999999999999999999988774 3488999999999987


Q ss_pred             CCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhh
Q 009944          373 ASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  452 (522)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~  452 (522)
                      +...+.......                               ......|-.|+..+++             ++++++|+
T Consensus        84 ~r~~~~~~~~~~-------------------------------~tkkiFvGG~~~~~~e-------------~~~r~yfe  119 (311)
T KOG4205|consen   84 SREDQTKVGRHL-------------------------------RTKKIFVGGLPPDTTE-------------EDFKDYFE  119 (311)
T ss_pred             Cccccccccccc-------------------------------ceeEEEecCcCCCCch-------------HHHhhhhh
Confidence            754433221100                               0012222223333333             49999999


Q ss_pred             ccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          453 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       453 ~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      +||.|..+.++.+.....+   +|++||.|.+.+...+++. ...+.|+|+.|.|--|..+.
T Consensus       120 ~~g~v~~~~~~~d~~~~~~---rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~  177 (311)
T KOG4205|consen  120 QFGKVADVVIMYDKTTSRP---RGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKE  177 (311)
T ss_pred             ccceeEeeEEeeccccccc---ccceeeEeccccccceecc-cceeeecCceeeEeeccchh
Confidence            9999999999999877665   6677999999999999887 58999999999998877654

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

Probab=99.67  E-value=2.1e-14  Score=131.84  Aligned_cols=281  Identities=19%  Similarity=0.173  Sum_probs=185.7

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHH---hcCceecCce
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIFEGVA  250 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~---~~~~~~~g~~  250 (522)
                      +--|.|.+|-..++|.+|.+.++.||+            |.-+.....+..|.|+|++.+.|+.++.   -+...+.|+.
T Consensus        31 spvvhvr~l~~~v~eadl~eal~~fG~------------i~yvt~~P~~r~alvefedi~~akn~Vnfaa~n~i~i~gq~   98 (494)
T KOG1456|consen   31 SPVVHVRGLHQGVVEADLVEALSNFGP------------IAYVTCMPHKRQALVEFEDIEGAKNCVNFAADNQIYIAGQQ   98 (494)
T ss_pred             CceEEEeccccccchhHHHHHHhcCCc------------eEEEEeccccceeeeeeccccchhhheehhccCcccccCch
Confidence            346999999999999999999999997            4445555667789999999999999983   4667788888


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCC-eEE--EcCCCCCCCHHHHHHHHHhcCCceEEEEe
Q 009944          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPD-RVF--VGGLPYYFTETQIKELLESFGTLHGFDLV  327 (522)
Q Consensus       251 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~l~--v~nLp~~~t~~~l~~~F~~~G~i~~v~~~  327 (522)
                      ..+.++....-..   .+                    .....++ .|+  |-|--+.+|-+-|..++...|+|..|.|+
T Consensus        99 Al~NyStsq~i~R---~g--------------------~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIf  155 (494)
T KOG1456|consen   99 ALFNYSTSQCIER---PG--------------------DESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIF  155 (494)
T ss_pred             hhcccchhhhhcc---CC--------------------CCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEE
Confidence            7777653221100   00                    0111222 333  44555679999999999999999999888


Q ss_pred             eCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc--CCeEEEEEEccCCCCCCc-hHHHHHHHHHHHHH-----------
Q 009944          328 KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVRRATASSGQSK-TEQESILAQAQQHI-----------  393 (522)
Q Consensus       328 ~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--~g~~l~v~~~~~~~~~~~-~~~~~~~~~~~~~~-----------  393 (522)
                      +.  +|.   -|.|||++.+.|++|-.+|||.-|  +-++|+|.||++..-... .+++. ........           
T Consensus       156 kk--ngV---QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~Dt-wDyTlp~~~~~~~~g~~~~  229 (494)
T KOG1456|consen  156 KK--NGV---QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDT-WDYTLPDLRGPYDPGRNHY  229 (494)
T ss_pred             ec--cce---eeEEeechhHHHHHHHhhcccccccccceeEEEEecCcceeeeeecCCcc-ccccCCCCCCCCCCCCCCC
Confidence            75  444   599999999999999999999766  458899999987531110 00000 10000000           


Q ss_pred             HHHH--HHhhccCCccCC--------------CCcCC---------------CCCCcceEEEeeCCCCcCcCCChHHHHH
Q 009944          394 AIQK--MALQTSGMNTLG--------------GGMSL---------------FGETLAKVLCLTEAITADALADDEEYEE  442 (522)
Q Consensus       394 ~~~~--~~~~~~~~~~~g--------------~~~~~---------------~~~~~~~v~~l~~~~~~~~l~~~~~~~~  442 (522)
                      ..+.  ......+.+..|              ...|.               ....+..|+.+..+   +...-|     
T Consensus       230 ~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGL---dh~k~N-----  301 (494)
T KOG1456|consen  230 DRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGL---DHGKMN-----  301 (494)
T ss_pred             ccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEec---cccccc-----
Confidence            0000  000000000000              00000               11122333332221   111111     


Q ss_pred             HHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          443 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       443 ~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                       .+.|..+|..||.|+.|+.++.+        -|.|.|++.+..+.++|+..||+..+-|.+|.|.+...
T Consensus       302 -~drlFNl~ClYGNV~rvkFmkTk--------~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ  362 (494)
T KOG1456|consen  302 -CDRLFNLFCLYGNVERVKFMKTK--------PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQ  362 (494)
T ss_pred             -hhhhhhhhhhcCceeeEEEeecc--------cceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccc
Confidence             15899999999999999999865        27889999999999999999999999999999987654

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.66  E-value=9.6e-16  Score=140.95  Aligned_cols=289  Identities=20%  Similarity=0.223  Sum_probs=186.7

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE-ecCCCcEEEEEEeCHHHHHHHHHhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY-INHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~-~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~  251 (522)
                      ...-|-..+||+..++.+|..||+..-..       .+..+++.. .+...|.|.|.|.+.|.-+-|++-+...+.++.|
T Consensus        59 ~~vvvRaRglpwq~Sd~~ia~ff~gl~ia-------~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryi  131 (508)
T KOG1365|consen   59 DNVVVRARGLPWQSSDQDIARFFKGLNIA-------NGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYI  131 (508)
T ss_pred             cceEEEecCCCCCcccCCHHHHHhhhhcc-------ccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCce
Confidence            34457788999999999999999876322       223344333 4556799999999999999999888888999999


Q ss_pred             EEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCC----ceEEEEe
Q 009944          252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT----LHGFDLV  327 (522)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~----i~~v~~~  327 (522)
                      .|-.+...+--..+..+...+.+..             .....--|.+++||+++++.++.++|..-..    ++.|-++
T Consensus       132 evYka~ge~f~~iagg~s~e~~~fl-------------sk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV  198 (508)
T KOG1365|consen  132 EVYKATGEEFLKIAGGTSNEAAPFL-------------SKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFV  198 (508)
T ss_pred             eeeccCchhheEecCCccccCCCCC-------------CcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEE
Confidence            9976543321111100000000000             0011224779999999999999999974333    3455555


Q ss_pred             eCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCC--
Q 009944          328 KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGM--  405 (522)
Q Consensus       328 ~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  405 (522)
                      +.+ +|+.+|-|||.|..+++|+.||. -|...|+.+-|.+..++.      .+            -.|-++......  
T Consensus       199 ~rp-dgrpTGdAFvlfa~ee~aq~aL~-khrq~iGqRYIElFRSTa------aE------------vqqvlnr~~s~pLi  258 (508)
T KOG1365|consen  199 TRP-DGRPTGDAFVLFACEEDAQFALR-KHRQNIGQRYIELFRSTA------AE------------VQQVLNREVSEPLI  258 (508)
T ss_pred             ECC-CCCcccceEEEecCHHHHHHHHH-HHHHHHhHHHHHHHHHhH------HH------------HHHHHHhhcccccc
Confidence            553 78999999999999999999997 344455555554443321      11            111111111111  


Q ss_pred             ------ccCCCCcCCCCC-CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEE---EEecCCCCCCCCCCCc
Q 009944          406 ------NTLGGGMSLFGE-TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVN---VVIPRPDQNGGETPGV  475 (522)
Q Consensus       406 ------~~~g~~~~~~~~-~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~---v~i~~~~~~g~~~~g~  475 (522)
                            -.++......++ ....|+-|...          +|+.++++|-.||..|..-+.   |.+.-+. +|.+   .
T Consensus       259 ~~~~sp~~p~~p~~~~p~~~~kdcvRLRGL----------Py~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrP---S  324 (508)
T KOG1365|consen  259 PGLTSPLLPGGPARLVPPTRSKDCVRLRGL----------PYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRP---S  324 (508)
T ss_pred             CCCCCCCCCCCccccCCCCCCCCeeEecCC----------ChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCc---C
Confidence                  111111111111 22445555443          788888999999999986433   5555443 6776   5


Q ss_pred             cEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          476 GKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       476 G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      |-|||+|.+.++|..|...-+.....+|-|.|--..-+++
T Consensus       325 GeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~eel  364 (508)
T KOG1365|consen  325 GEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVEEL  364 (508)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHHHH
Confidence            9999999999999999999888888889888866554443

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

Probab=99.64  E-value=1.1e-14  Score=124.50  Aligned_cols=180  Identities=21%  Similarity=0.294  Sum_probs=120.5

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC----CCcEEEEEEeCHHHHHHHH-HhcC
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH----EKKFAFVEMRTVEEASNAM-ALDG  243 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~----~~g~afV~f~~~~~a~~a~-~~~~  243 (522)
                      +.....++|||.|||.++...+|..+|..|--.-        ...+.. +.+    .+-+|||.|.+...|..|+ +|||
T Consensus        29 ~~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYE--------gslLK~-Tsk~~~~~~pvaFatF~s~q~A~aamnaLNG   99 (284)
T KOG1457|consen   29 DEPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYE--------GSLLKY-TSKGDQVCKPVAFATFTSHQFALAAMNALNG   99 (284)
T ss_pred             ccccccceeeeccCCcccCHHHHHHHhccCCCcc--------ceeeee-ccCCCccccceEEEEecchHHHHHHHHHhcC
Confidence            3445679999999999999999999999883211        112221 222    2479999999999999999 7999


Q ss_pred             ceec---CceEEEecCCCCCccccccCCC-CCCCCCc-------------------------ccccc-------------
Q 009944          244 IIFE---GVAVRVRRPTDYNPTLAAALGP-GQPSPNL-------------------------NLAAV-------------  281 (522)
Q Consensus       244 ~~~~---g~~~~v~~~~~~~~~~~~~~~~-~~~~~~~-------------------------~~~~~-------------  281 (522)
                      +.|+   +..|+|..++............ +.+.+..                         .+...             
T Consensus       100 vrFDpE~~stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~  179 (284)
T KOG1457|consen  100 VRFDPETGSTLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTK  179 (284)
T ss_pred             eeeccccCceeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccc
Confidence            9986   5778887655332211111000 0000000                         00000             


Q ss_pred             --------cCCC----------CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEE
Q 009944          282 --------GLAS----------GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY  343 (522)
Q Consensus       282 --------~~~~----------~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f  343 (522)
                              ...+          ....+...+.+|||.||.++++|++|+.+|+.|.....++|...  .|  -..|||+|
T Consensus       180 ~~~l~a~~~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~  255 (284)
T KOG1457|consen  180 SEALSAPDSKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADF  255 (284)
T ss_pred             hhhhhhhhhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecH
Confidence                    0000          01112334578999999999999999999999988776666532  33  35799999


Q ss_pred             cChHHHHHHHHHHcCCcc
Q 009944          344 QDPAVTDIACAALNGLKM  361 (522)
Q Consensus       344 ~~~~~A~~Al~~l~g~~~  361 (522)
                      ++.+.|..||..|+|..|
T Consensus       256 ~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  256 EEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             HHHHHHHHHHHHhhccee
Confidence            999999999999998766

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

Probab=99.61  E-value=2.9e-13  Score=124.47  Aligned_cols=294  Identities=15%  Similarity=0.163  Sum_probs=182.2

Q ss_pred             EeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-cCCCcEEEEEEeCHHHHHHHH-HhcCceecC--ceEEEe
Q 009944          179 VGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-NHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--VAVRVR  254 (522)
Q Consensus       179 v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~-~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g--~~~~v~  254 (522)
                      |-|--+.+|-+-|..+....|+            |..+.+ .+..-.|.|+|.+.+.|++|. .|||..|..  ++|+|.
T Consensus       127 IlNp~YpItvDVly~Icnp~Gk------------VlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIe  194 (494)
T KOG1456|consen  127 ILNPQYPITVDVLYTICNPQGK------------VLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIE  194 (494)
T ss_pred             eecCccccchhhhhhhcCCCCc------------eEEEEEEeccceeeEEeechhHHHHHHHhhcccccccccceeEEEE
Confidence            4455556899999999999887            444444 444457999999999999999 799988764  678887


Q ss_pred             cCCCCCcccc---------------ccCC------------------------------------CCCCCCCcccc--cc
Q 009944          255 RPTDYNPTLA---------------AALG------------------------------------PGQPSPNLNLA--AV  281 (522)
Q Consensus       255 ~~~~~~~~~~---------------~~~~------------------------------------~~~~~~~~~~~--~~  281 (522)
                      ++++..-...               ....                                    +..+.+.....  ..
T Consensus       195 yAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~  274 (494)
T KOG1456|consen  195 YAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRD  274 (494)
T ss_pred             ecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCcccccc
Confidence            7664211000               0000                                    00000000000  00


Q ss_pred             cCCCCCCCCCCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCc
Q 009944          282 GLASGAIGGAEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK  360 (522)
Q Consensus       282 ~~~~~~~~~~~~~~~l~v~nLp~~-~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~  360 (522)
                      +.......+..+...+.|-+|... ++-+.|..+|-.||.|+.|++++.+     .|.|.||+.+....++|+..||+..
T Consensus       275 ~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~  349 (494)
T KOG1456|consen  275 GRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIP  349 (494)
T ss_pred             CCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCc
Confidence            000111123345578899999876 5668899999999999999999875     4779999999999999999999999


Q ss_pred             cCCeEEEEEEccCCCCCCc-----hHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEe---eCCCCcC
Q 009944          361 MGDKTLTVRRATASSGQSK-----TEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCL---TEAITAD  432 (522)
Q Consensus       361 ~~g~~l~v~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l---~~~~~~~  432 (522)
                      +.|.+|.|.++......+.     ++.......    ....    ...-...|+...-..-..+++|+..   +..++++
T Consensus       350 lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfKd----ys~S----kNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe  421 (494)
T KOG1456|consen  350 LFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFKD----YSGS----KNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEE  421 (494)
T ss_pred             cccceEEEeeccccccccCCceecCCCCcchhh----cccc----cccccCChhHhhcccccCCcceeEEecCCCccCHH
Confidence            9999999998865432111     110000000    0000    0000001111111112245555544   3344443


Q ss_pred             cCCChHHHHHHHHHHHHHhhccCC-eEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCe------EE
Q 009944          433 ALADDEEYEEILEDMREECGKYGT-LVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGN------TV  505 (522)
Q Consensus       433 ~l~~~~~~~~~~~~l~~~f~~~G~-I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr------~l  505 (522)
                                   .|.++|...+. -.+|+|..-+..-..   -|  .++|++.++|..||..||...+.+.      +|
T Consensus       422 -------------~l~~i~nek~v~~~svkvFp~kserSs---sG--llEfe~~s~Aveal~~~NH~pi~~p~gs~Pfil  483 (494)
T KOG1456|consen  422 -------------QLIGICNEKDVPPTSVKVFPLKSERSS---SG--LLEFENKSDAVEALMKLNHYPIEGPNGSFPFIL  483 (494)
T ss_pred             -------------HHHHHhhhcCCCcceEEeecccccccc---cc--eeeeehHHHHHHHHHHhccccccCCCCCCCeee
Confidence                         77777776554 455666554422221   25  9999999999999999999998763      67


Q ss_pred             EEEEeCCccc
Q 009944          506 NAFYYPEDKY  515 (522)
Q Consensus       506 ~v~~~~~~~~  515 (522)
                      ++.|.+..-+
T Consensus       484 Klcfsts~~~  493 (494)
T KOG1456|consen  484 KLCFSTSKHM  493 (494)
T ss_pred             eeeecccccC
Confidence            7888776543

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

Probab=99.60  E-value=2.1e-15  Score=132.29  Aligned_cols=165  Identities=21%  Similarity=0.312  Sum_probs=126.5

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEEE
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~v  253 (522)
                      ..|||++||+.+.+.+|..||..||.+.            ++.+  ..||+||+|.+..+|.-|+ .+++..|.|..+.|
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~------------d~~m--k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vv   67 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIP------------DADM--KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVV   67 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccc------------ccee--ecccceeccCchhhhhcccchhcCceecceeeee
Confidence            3699999999999999999999999853            2222  4578899999999999999 79999999988888


Q ss_pred             ecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCC
Q 009944          254 RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG  333 (522)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g  333 (522)
                      .++.......    +.+..+....     .......+....+.|+|.+++..+.+.+|.+.|.++|.+....+       
T Consensus        68 e~~r~~~~~~----g~~~~g~r~~-----~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-------  131 (216)
T KOG0106|consen   68 EHARGKRRGR----GRPRGGDRRS-----DSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-------  131 (216)
T ss_pred             eccccccccc----CCCCCCCccc-----hhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh-------
Confidence            8876433222    1111100000     00011112334467999999999999999999999999955544       


Q ss_pred             CcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          334 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       334 ~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                       ..+++||+|.+.++|.+|+..|+|..+.++.|.+..
T Consensus       132 -~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  132 -RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             -hccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence             245899999999999999999999999999999943

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

Probab=99.59  E-value=3.1e-15  Score=131.22  Aligned_cols=162  Identities=21%  Similarity=0.348  Sum_probs=123.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCC
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (522)
                      .+||++||+.+.+.+|..+|..||.|..|.+..        ||+||+|.+..+|.-|+..|||..|.|..+.|.|+....
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~   74 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKR   74 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeecccccc
Confidence            699999999999999999999999999988763        689999999999999999999999999889999886421


Q ss_pred             CCCchHHHHHHHHHHHHHHHHHHHhhccCCccCC-----CCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHH
Q 009944          376 GQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG-----GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREE  450 (522)
Q Consensus       376 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g-----~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~  450 (522)
                      ...                         +...+|     ...-..+....+++++.+..+.          .-+++|.+.
T Consensus        75 ~~~-------------------------g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r----------~~~qdl~d~  119 (216)
T KOG0106|consen   75 RGR-------------------------GRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLR----------VSWQDLKDH  119 (216)
T ss_pred             ccc-------------------------CCCCCCCccchhhccCCcccccceeeeccchhh----------hhHHHHhhh
Confidence            110                         000111     0011111234445555444332          234699999


Q ss_pred             hhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          451 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       451 f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                      |.++|.+....+.           .+++||+|++.++|.+|+..|+|..+.|+.|.+....
T Consensus       120 ~~~~g~~~~~~~~-----------~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~~  169 (216)
T KOG0106|consen  120 FRPAGEVTYVDAR-----------RNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKNS  169 (216)
T ss_pred             hcccCCCchhhhh-----------ccccceeehhhhhhhhcchhccchhhcCceeeecccC
Confidence            9999999666552           2577999999999999999999999999999995433

>PF00076 RRM_1: RNA recognition motif

Probab=99.59  E-value=7.7e-15  Score=108.97  Aligned_cols=70  Identities=27%  Similarity=0.644  Sum_probs=67.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       297 l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      |||+|||..+++++|+++|+.||.|..+.+..+ .++..+|+|||+|.+.++|.+|++.|+|..++|+.|+
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            799999999999999999999999999999987 5889999999999999999999999999999999885

(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 ....

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

Probab=99.57  E-value=5.3e-14  Score=128.37  Aligned_cols=196  Identities=17%  Similarity=0.156  Sum_probs=134.5

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEE---EecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV---YINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~---~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      ....|||.|||.++|-+++.++|..||.|......  +.+-+.+   .-+.-+|=|.+.|-..+.+..|+ -|++..|.|
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t--~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQT--GEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCC--CCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            35569999999999999999999999987543221  1122222   22455899999999999999999 599999999


Q ss_pred             ceEEEecCCCCCccccccCCC----CCCCCCcc---cccccCCC--CCCCCCCCCCeEEEcCCC----CCCC-------H
Q 009944          249 VAVRVRRPTDYNPTLAAALGP----GQPSPNLN---LAAVGLAS--GAIGGAEGPDRVFVGGLP----YYFT-------E  308 (522)
Q Consensus       249 ~~~~v~~~~~~~~~~~~~~~~----~~~~~~~~---~~~~~~~~--~~~~~~~~~~~l~v~nLp----~~~t-------~  308 (522)
                      ++|+|+.++-.....-...+.    ......+.   ....+-.+  ....-....++|.|.||=    ...+       +
T Consensus       211 ~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlk  290 (382)
T KOG1548|consen  211 KKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLK  290 (382)
T ss_pred             cEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHH
Confidence            999998765221111000000    00000000   00000001  112223455789999982    2233       3


Q ss_pred             HHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          309 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       309 ~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      ++|.+.+++||.|..|.|.-.    .+.|.+-|.|.+.++|..||..|+|++|+|++|......-+
T Consensus       291 edl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  291 EDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            678888999999999988743    35788999999999999999999999999999999987543

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

Probab=99.55  E-value=1.8e-14  Score=125.23  Aligned_cols=82  Identities=29%  Similarity=0.441  Sum_probs=79.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ...+|.|.||+.+++|.+|.++|.+||.|..|.|.++++||.++|||||.|.+.++|++||+.|||+-+..-.|.|.|+.
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            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q 009944          373 AS  374 (522)
Q Consensus       373 ~~  374 (522)
                      |+
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            74

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

Probab=99.54  E-value=1.4e-13  Score=131.60  Aligned_cols=172  Identities=16%  Similarity=0.276  Sum_probs=124.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      .....|.+++||+++|++||.++|+.+ .|+.+.+.+.  +|+..|-|||+|.+.+++++||+ .+...++.+-|.|.-+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRR--NGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEecc--CCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            344578899999999999999999998 4666666654  89999999999999999999998 7778899999999987


Q ss_pred             cCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHh
Q 009944          372 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  451 (522)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f  451 (522)
                      ......-                   .. ...+      ........-+++-.|+..++.+             ||.+||
T Consensus        84 ~~~e~d~-------------------~~-~~~g------~~s~~~d~vVRLRGLPfscte~-------------dI~~FF  124 (510)
T KOG4211|consen   84 GGAEADW-------------------VM-RPGG------PNSSANDGVVRLRGLPFSCTEE-------------DIVEFF  124 (510)
T ss_pred             CCccccc-------------------cc-cCCC------CCCCCCCceEEecCCCccCcHH-------------HHHHHh
Confidence            6532100                   00 0000      0000111333444466666665             999999


Q ss_pred             hccCCeEE-EEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          452 GKYGTLVN-VVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       452 ~~~G~I~~-v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                      +..-.|.. |.++.+. .+.+   .|-|||+|++.+.|++|+.. |.+.|+-+-|.|--+.
T Consensus       125 aGL~Iv~~gi~l~~d~-rgR~---tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  125 AGLEIVPDGILLPMDQ-RGRP---TGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSS  180 (510)
T ss_pred             cCCcccccceeeeccC-CCCc---ccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhH
Confidence            98777666 4455544 5544   68999999999999999985 7777888887775433

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.52  E-value=6e-14  Score=104.02  Aligned_cols=70  Identities=27%  Similarity=0.580  Sum_probs=65.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       297 l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      |||+|||+.+++++|.++|+.||.|..+.+..++. |..+|+|||+|.+.++|.+|+..++|..|.|+.|.
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            79999999999999999999999999999999976 99999999999999999999999999999999874

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 ....

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

Probab=99.51  E-value=5.2e-14  Score=109.65  Aligned_cols=81  Identities=25%  Similarity=0.399  Sum_probs=76.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ..+++|||+||.+.++|++|.++|+++|.|..|.+-.|+.+..+-|||||+|.+.++|..||.-++|..+..++|.|.|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            34579999999999999999999999999999999999888899999999999999999999999999999999999986


Q ss_pred             c
Q 009944          372 T  372 (522)
Q Consensus       372 ~  372 (522)
                      .
T Consensus       114 ~  114 (153)
T KOG0121|consen  114 A  114 (153)
T ss_pred             c
Confidence            3

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

Probab=99.50  E-value=1.1e-13  Score=125.43  Aligned_cols=85  Identities=28%  Similarity=0.593  Sum_probs=77.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          288 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       288 ~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      ......+++|+|.|||+..-+-||+.+|.+||.|.+|.|+.+  ..-|||||||+|++.++|++|.++|||..+.|++|.
T Consensus        90 s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIE  167 (376)
T KOG0125|consen   90 SSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIE  167 (376)
T ss_pred             CCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEE
Confidence            334566789999999999999999999999999999999987  356899999999999999999999999999999999


Q ss_pred             EEEccCC
Q 009944          368 VRRATAS  374 (522)
Q Consensus       368 v~~~~~~  374 (522)
                      |..++..
T Consensus       168 Vn~ATar  174 (376)
T KOG0125|consen  168 VNNATAR  174 (376)
T ss_pred             Eeccchh
Confidence            9998765

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

Probab=99.50  E-value=4.7e-14  Score=119.30  Aligned_cols=84  Identities=24%  Similarity=0.431  Sum_probs=79.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      .+....|.|-||-+.|+.++|+.+|++||.|-+|.|+.|+.|+.++|||||.|....+|+.|+++|+|..|.|+.|.|++
T Consensus        10 v~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~   89 (256)
T KOG4207|consen   10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQM   89 (256)
T ss_pred             cccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehh
Confidence            45557899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 009944          371 ATAS  374 (522)
Q Consensus       371 ~~~~  374 (522)
                      |.-.
T Consensus        90 aryg   93 (256)
T KOG4207|consen   90 ARYG   93 (256)
T ss_pred             hhcC
Confidence            8654

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

Probab=99.50  E-value=6e-13  Score=124.76  Aligned_cols=206  Identities=17%  Similarity=0.302  Sum_probs=131.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHH-hcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          294 PDRVFVGGLPYYFTETQIKELLE-SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~-~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      .+.+||.|||+++.+++|+++|. +.|.|++|.|..| ++|+++|+|.|||+++|.++||++.||.+.+.|++|.|+-..
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            34599999999999999999998 7899999999999 589999999999999999999999999999999999998654


Q ss_pred             CCCCC----------------------------------------CchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCc
Q 009944          373 ASSGQ----------------------------------------SKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGM  412 (522)
Q Consensus       373 ~~~~~----------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  412 (522)
                      .....                                        ...+.+.... .-....+.+........+..+..+
T Consensus       123 d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr-~~~t~t~~~~~~~~~~~~lfgl~~  201 (608)
T KOG4212|consen  123 DEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSR-RNNTNTMSNDYNNSSNYNLFGLSA  201 (608)
T ss_pred             chhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCccccccccc-ccCccccccccccchhhhcccchh
Confidence            31000                                        0000000000 000000000000000000000000


Q ss_pred             CCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHH
Q 009944          413 SLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAK  492 (522)
Q Consensus       413 ~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai  492 (522)
                      .-.  .+..  ++....-+..|+.++.|.-=...|++.|.--|+|+.|.+--++ .|..   .|+|.++|.++-+|..||
T Consensus       202 ~Fl--r~~h--~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idK-eG~s---~G~~vi~y~hpveavqaI  273 (608)
T KOG4212|consen  202 SFL--RSLH--IFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDK-EGNS---RGFAVIEYDHPVEAVQAI  273 (608)
T ss_pred             hhh--hhcc--CCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeecc-cccc---CCeeEEEecchHHHHHHH
Confidence            000  0000  0011111122233333333335899999999999999877766 3443   479999999999999999


Q ss_pred             HHHhCCccCCeEEEEEE
Q 009944          493 NALSGRKFGGNTVNAFY  509 (522)
Q Consensus       493 ~~lng~~~~Gr~l~v~~  509 (522)
                      ..|++.-+..++..+.+
T Consensus       274 sml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  274 SMLDRQGLFDRRMTVRL  290 (608)
T ss_pred             HhhccCCCccccceeec
Confidence            99998777777777666

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

Probab=99.49  E-value=2e-13  Score=136.86  Aligned_cols=78  Identities=19%  Similarity=0.397  Sum_probs=71.5

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      ....++||||++|+..+++.||.++|+.||.            |..+.+...+|||||.+.+..+|.+|| +|+...+.+
T Consensus       417 isV~SrTLwvG~i~k~v~e~dL~~~feefGe------------iqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv~~  484 (894)
T KOG0132|consen  417 ISVCSRTLWVGGIPKNVTEQDLANLFEEFGE------------IQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVAD  484 (894)
T ss_pred             eeEeeeeeeeccccchhhHHHHHHHHHhccc------------ceeEeeccCCceeEEEEeehhHHHHHHHHHhcccccc
Confidence            3456789999999999999999999999998            788888999999999999999999999 899999999


Q ss_pred             ceEEEecCCCC
Q 009944          249 VAVRVRRPTDY  259 (522)
Q Consensus       249 ~~~~v~~~~~~  259 (522)
                      +.|+|.|+-.+
T Consensus       485 k~Iki~Wa~g~  495 (894)
T KOG0132|consen  485 KTIKIAWAVGK  495 (894)
T ss_pred             eeeEEeeeccC
Confidence            99999996543

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

Probab=99.47  E-value=1.2e-13  Score=113.97  Aligned_cols=75  Identities=21%  Similarity=0.431  Sum_probs=70.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+||+..+++.||..+|..||+|..|.|...+     .|||||+|+++.+|..|+..|+|..|.|..|.|.+++-
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            4689999999999999999999999999999998864     69999999999999999999999999999999999865

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

Probab=99.47  E-value=1.2e-11  Score=122.45  Aligned_cols=195  Identities=12%  Similarity=0.058  Sum_probs=137.4

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceE
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~  251 (522)
                      ...+.+-+.+++++..+.++++||...-.       ......++..-....|-++|+|.....+++|+.-|...+-.+.+
T Consensus       309 ~d~~y~~~~gm~fn~~~nd~rkfF~g~~~-------~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~  381 (944)
T KOG4307|consen  309 SDKYYNNYKGMEFNNDFNDGRKFFPGRNA-------QSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPF  381 (944)
T ss_pred             chhheeeecccccccccchhhhhcCcccc-------cccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcce
Confidence            45566778899999999999999885421       11111222222233799999999999999999988888889999


Q ss_pred             EEecCCCCCccccccCCCCCCCCCc--------ccccccCCCCCC--CCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCc
Q 009944          252 RVRRPTDYNPTLAAALGPGQPSPNL--------NLAAVGLASGAI--GGAEGPDRVFVGGLPYYFTETQIKELLESFGTL  321 (522)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~--~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i  321 (522)
                      .|..+.+.....+.......+.+..        ........++..  ....-..+|||..||..+++.++.++|...-.|
T Consensus       382 q~~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~V  461 (944)
T KOG4307|consen  382 QTGPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAV  461 (944)
T ss_pred             eecCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhh
Confidence            9987766554433322211111100        000000111111  122334689999999999999999999987777


Q ss_pred             eE-EEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          322 HG-FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       322 ~~-v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      ++ |.|...+ ++.-++.|||+|..++++.+|+..-+.++++.+.|.|.-...+
T Consensus       462 ed~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~  514 (944)
T KOG4307|consen  462 EDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADY  514 (944)
T ss_pred             hheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeechhhH
Confidence            76 6666654 7888999999999999999999888888999999999976654

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

Probab=99.46  E-value=3.4e-13  Score=120.72  Aligned_cols=81  Identities=27%  Similarity=0.511  Sum_probs=77.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      .+-+||||.-|+.+++|..|+..|+.||+|+.|.|+.+..||+++|||||+|++.-+...|.+..+|.+|.|+.|.|.+-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            55689999999999999999999999999999999999999999999999999999999999999999999999999985


Q ss_pred             c
Q 009944          372 T  372 (522)
Q Consensus       372 ~  372 (522)
                      .
T Consensus       179 R  179 (335)
T KOG0113|consen  179 R  179 (335)
T ss_pred             c
Confidence            4

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.46  E-value=3e-13  Score=121.99  Aligned_cols=76  Identities=21%  Similarity=0.347  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||+.+++++|+++|+.||.|..|.|+.+..   ++|||||+|.+.++|..||. |+|..|.|+.|.|.++..
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            36899999999999999999999999999999998753   57999999999999999996 999999999999999864

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

Probab=99.46  E-value=1e-13  Score=120.31  Aligned_cols=79  Identities=28%  Similarity=0.562  Sum_probs=73.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+||++.+..+.|+++|++||.|++..|+.|+.+|+++|||||+|.+.+.|.+|++..+ -.|+|+...|.+|..
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            4689999999999999999999999999999999999999999999999999999999998554 788999999988765

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

Probab=99.46  E-value=1.5e-14  Score=119.71  Aligned_cols=80  Identities=34%  Similarity=0.674  Sum_probs=76.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      .-|||+|||+..||.||...|++||.|..|.|++|+.||+++||||+.|++.-+..-|+..|||..|.|+.|+|......
T Consensus        36 A~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~Y  115 (219)
T KOG0126|consen   36 AYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSNY  115 (219)
T ss_pred             eEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecccc
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999987553

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

Probab=99.44  E-value=2.3e-12  Score=96.61  Aligned_cols=79  Identities=23%  Similarity=0.474  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      +...-|||.|||+.+|.+++.++|.+||.|..|+|-..+   ..+|.|||.|++..+|.+|+..|+|..+.++.|.|-|.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            344679999999999999999999999999999987654   45899999999999999999999999999999999998


Q ss_pred             cC
Q 009944          372 TA  373 (522)
Q Consensus       372 ~~  373 (522)
                      ++
T Consensus        93 q~   94 (124)
T KOG0114|consen   93 QP   94 (124)
T ss_pred             CH
Confidence            65

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

Probab=99.43  E-value=6.5e-13  Score=112.31  Aligned_cols=68  Identities=15%  Similarity=0.330  Sum_probs=62.3

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|||||+|.+.++|+.||+.|||..|+|++|+|.++.+..-
T Consensus        49 ~~L~~~F~~~G~I~~v~i~~d~~tg~~---kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~~  116 (144)
T PLN03134         49 ASLRDAFAHFGDVVDAKVIVDRETGRS---RGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS  116 (144)
T ss_pred             HHHHHHHhcCCCeEEEEEEecCCCCCc---ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCCC
Confidence            499999999999999999999877765   78999999999999999999999999999999999876543

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

Probab=99.43  E-value=2.2e-13  Score=107.05  Aligned_cols=82  Identities=27%  Similarity=0.390  Sum_probs=78.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .+-|||.++...++|++|.+.|..||.|..|.|-.|..||-.+|||+|+|.+.++|++|+.+|||..|.|..|.|.|+-.
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv  151 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFV  151 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEe
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             CC
Q 009944          374 SS  375 (522)
Q Consensus       374 ~~  375 (522)
                      +.
T Consensus       152 ~g  153 (170)
T KOG0130|consen  152 KG  153 (170)
T ss_pred             cC
Confidence            43

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

Probab=99.41  E-value=2.8e-12  Score=109.93  Aligned_cols=188  Identities=18%  Similarity=0.226  Sum_probs=120.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeC-CCCCCcceEEEEEEcChHHHHHHHHHHcCCcc---CCeEEEE
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIACAALNGLKM---GDKTLTV  368 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~-~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~---~g~~l~v  368 (522)
                      ..+||||.+||.++...+|+.+|..|-.-+...|... +.....+-+|||.|.+..+|..|+++|||..|   .+..|+|
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            3589999999999999999999999877766655443 22234467999999999999999999999998   5789999


Q ss_pred             EEccCCCCCCchH------HHHHHHH------HHHHHHHHHHHhhccC--CccCCCCc--------------------C-
Q 009944          369 RRATASSGQSKTE------QESILAQ------AQQHIAIQKMALQTSG--MNTLGGGM--------------------S-  413 (522)
Q Consensus       369 ~~~~~~~~~~~~~------~~~~~~~------~~~~~~~~~~~~~~~~--~~~~g~~~--------------------~-  413 (522)
                      .+++...+.....      ....+..      ......++.......+  ...++...                    | 
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            9987654221110      0000000      0000001110000000  00000000                    0 


Q ss_pred             ---------CC-----CCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEE
Q 009944          414 ---------LF-----GETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVF  479 (522)
Q Consensus       414 ---------~~-----~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~af  479 (522)
                               ..     .=.+.+|-+|...++++             +|+.+|+.|--...++|...       .|.-+||
T Consensus       193 a~a~l~ks~q~~~~~~acstlfianl~~~~~ed-------------~l~~~~~~~~gf~~l~~~~~-------~g~~vaf  252 (284)
T KOG1457|consen  193 ANAHLEKSSQGGSGARACSTLFIANLGPNCTED-------------ELKQLLSRYPGFHILKIRAR-------GGMPVAF  252 (284)
T ss_pred             ccchhhhhhcccccchhhhhHhhhccCCCCCHH-------------HHHHHHHhCCCceEEEEecC-------CCcceEe
Confidence                     00     00123344555555554             89999999988877777542       3446899


Q ss_pred             EEecChHhHHHHHHHHhCCcc
Q 009944          480 LEYYDAVGCATAKNALSGRKF  500 (522)
Q Consensus       480 V~F~~~~~A~~Ai~~lng~~~  500 (522)
                      |+|+..+.|..||..|+|..+
T Consensus       253 ~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  253 ADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             ecHHHHHHHHHHHHHhhccee
Confidence            999999999999999999876

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

Probab=99.39  E-value=3.6e-12  Score=123.02  Aligned_cols=80  Identities=35%  Similarity=0.710  Sum_probs=76.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      ..+|||+|||..+++++|.++|..||.|..|.+..++.+|.++|||||+|.+.++|..|+..++|..|.|+.|.|.++..
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            47999999999999999999999999999999999988999999999999999999999999999999999999999753

>PLN03213 repressor of silencing 3; Provisional

Probab=99.39  E-value=1.5e-12  Score=123.93  Aligned_cols=76  Identities=17%  Similarity=0.351  Sum_probs=71.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcCh--HHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~--~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ..+|||+||++.+++++|...|+.||.|..|.|++  ++|  +|||||+|.+.  .++.+||..|||..+.|+.|+|..|
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA   85 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA   85 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence            46899999999999999999999999999999994  477  89999999987  7899999999999999999999998


Q ss_pred             cC
Q 009944          372 TA  373 (522)
Q Consensus       372 ~~  373 (522)
                      .+
T Consensus        86 KP   87 (759)
T PLN03213         86 KE   87 (759)
T ss_pred             cH
Confidence            65

>smart00362 RRM_2 RNA recognition motif

Probab=99.38  E-value=2.8e-12  Score=95.33  Aligned_cols=72  Identities=39%  Similarity=0.691  Sum_probs=67.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEE
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (522)
                      +|+|+|||..+++++|.++|..||.|..+.+..++  +.++|+|||+|.+.++|..|+..++|..+.|+.|.|.
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            58999999999999999999999999999998875  7788999999999999999999999999999998873

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.37  E-value=3e-12  Score=113.56  Aligned_cols=76  Identities=14%  Similarity=0.249  Sum_probs=69.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      ..+|||+||++.+|+++|+++|+.||.|..|.|+.+.   ...|||||+|.++++|..|+. |+|..|.++.|.|..+..
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            3699999999999999999999999999999999873   456899999999999999995 999999999999998654

>PF13893 RRM_5: RNA recognition motif

Probab=99.37  E-value=3.1e-12  Score=89.91  Aligned_cols=56  Identities=23%  Similarity=0.438  Sum_probs=50.8

Q ss_pred             HHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEe
Q 009944          447 MREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  510 (522)
Q Consensus       447 l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~  510 (522)
                      |.++|++||+|..|.+....        .|+|||+|.+.++|..|++.|||..|+|++|+|.|+
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            67899999999999997754        379999999999999999999999999999999985

(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 ....

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

Probab=99.36  E-value=1e-12  Score=111.28  Aligned_cols=79  Identities=27%  Similarity=0.340  Sum_probs=69.0

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhC
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  497 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng  497 (522)
                      ..++|.||.+-.++             ++|+.+|++||.|-+|.|+.+..+...   .|||||.|....||+.|+++|+|
T Consensus        14 ~SLkVdNLTyRTsp-------------d~LrrvFekYG~vgDVyIPrdr~Tr~s---RgFaFVrf~~k~daedA~damDG   77 (256)
T KOG4207|consen   14 TSLKVDNLTYRTSP-------------DDLRRVFEKYGRVGDVYIPRDRYTRQS---RGFAFVRFHDKRDAEDALDAMDG   77 (256)
T ss_pred             eeEEecceeccCCH-------------HHHHHHHHHhCcccceecccccccccc---cceeEEEeeecchHHHHHHhhcc
Confidence            44555556555555             499999999999999999999999876   78999999999999999999999


Q ss_pred             CccCCeEEEEEEeCC
Q 009944          498 RKFGGNTVNAFYYPE  512 (522)
Q Consensus       498 ~~~~Gr~l~v~~~~~  512 (522)
                      .+++|+.|.|+++.-
T Consensus        78 ~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   78 AVLDGRELRVQMARY   92 (256)
T ss_pred             eeeccceeeehhhhc
Confidence            999999999998764

>smart00360 RRM RNA recognition motif

Probab=99.35  E-value=4.5e-12  Score=93.89  Aligned_cols=71  Identities=38%  Similarity=0.700  Sum_probs=66.9

Q ss_pred             EcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEE
Q 009944          299 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (522)
Q Consensus       299 v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (522)
                      |+|||..+++++|+++|+.||.|..+.+..++.++.++|+|||+|.+.++|..|+..|++..+.|+.|.|.
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            57999999999999999999999999999987788999999999999999999999999999999998873

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.33  E-value=4.8e-12  Score=114.29  Aligned_cols=76  Identities=25%  Similarity=0.358  Sum_probs=66.7

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec---CCCcEEEEEEeCHHHHHHHHHhcCceecCce
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN---HEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~---~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~  250 (522)
                      .++|||+|||+.+|+++|+++|..||.            |.++.+.   ..+|||||+|.++++|..||.|+|..|.|+.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~------------I~~V~I~~d~~~~GfAFVtF~d~eaAe~AllLnG~~l~gr~   71 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGD------------IEYVEMQSENERSQIAYVTFKDPQGAETALLLSGATIVDQS   71 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEeecCCCCCEEEEEeCcHHHHHHHHHhcCCeeCCce
Confidence            468999999999999999999999998            4444443   3579999999999999999999999999999


Q ss_pred             EEEecCCCCCc
Q 009944          251 VRVRRPTDYNP  261 (522)
Q Consensus       251 ~~v~~~~~~~~  261 (522)
                      |.|.+...+..
T Consensus        72 V~Vt~a~~~~~   82 (260)
T PLN03120         72 VTITPAEDYQL   82 (260)
T ss_pred             EEEEeccCCCC
Confidence            99998776643

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.32  E-value=1.6e-12  Score=119.98  Aligned_cols=192  Identities=20%  Similarity=0.187  Sum_probs=129.8

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE--ecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEE
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY--INHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~--~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~  252 (522)
                      -.|-+.+||++.|+.++.+||..-..+.+     ..+-|.-|.  -++..|-|||.|..+++|+.|+..+...++.+-|.
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~-----g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIE  236 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTG-----GTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIE  236 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccC-----CccceEEEECCCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHH
Confidence            35888999999999999999985544432     122344444  35567999999999999999997777777766666


Q ss_pred             EecCCCCCccccccCCCCCCCCC-cccccccCCCC-CCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCC-ceE--EEEe
Q 009944          253 VRRPTDYNPTLAAALGPGQPSPN-LNLAAVGLASG-AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHG--FDLV  327 (522)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~-i~~--v~~~  327 (522)
                      +-++...+-........+.+... .........+. .........+|.+++||+..+.++|.++|..|.. |..  |.++
T Consensus       237 lFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv  316 (508)
T KOG1365|consen  237 LFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMV  316 (508)
T ss_pred             HHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEE
Confidence            64432211110000000000000 00000000010 0111223568999999999999999999998876 333  6777


Q ss_pred             eCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          328 KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       328 ~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      .+ ..|...|.|||+|.+.+.|..|....+.....++.|.|..+.
T Consensus       317 ~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S  360 (508)
T KOG1365|consen  317 LN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCS  360 (508)
T ss_pred             Ec-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeecc
Confidence            76 478999999999999999999999999888889999998763

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

Probab=99.31  E-value=3e-11  Score=121.47  Aligned_cols=75  Identities=27%  Similarity=0.483  Sum_probs=70.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      +||||++|+..+++.||.++|+.||.|.+|.++..      +|||||.+....+|.+||.+|+...+.++.|+|.|+-.+
T Consensus       422 rTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  422 RTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            59999999999999999999999999999998764      789999999999999999999999999999999999664


Q ss_pred             C
Q 009944          375 S  375 (522)
Q Consensus       375 ~  375 (522)
                      .
T Consensus       496 G  496 (894)
T KOG0132|consen  496 G  496 (894)
T ss_pred             C
Confidence            3

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

Probab=99.30  E-value=4.7e-12  Score=98.87  Aligned_cols=80  Identities=24%  Similarity=0.404  Sum_probs=68.5

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC------CCcEEEEEEeCHHHHHHHH-Hh
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAM-AL  241 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~a~~a~-~~  241 (522)
                      .+...+++|||+||++.++|++|.++|..+|+|            ..+.++.      .-|||||+|.+.++|+.|| -+
T Consensus        31 ~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~i------------rriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryi   98 (153)
T KOG0121|consen   31 EALRKSCTVYVGNLSFYTTEEQIYELFSKCGDI------------RRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYI   98 (153)
T ss_pred             HHHhhcceEEEeeeeeeecHHHHHHHHHhccch------------heeEeccccCCcCccceEEEEEecchhHHHHHHHh
Confidence            456788999999999999999999999999984            4444443      3499999999999999999 59


Q ss_pred             cCceecCceEEEecCCCCC
Q 009944          242 DGIIFEGVAVRVRRPTDYN  260 (522)
Q Consensus       242 ~~~~~~g~~~~v~~~~~~~  260 (522)
                      ++..+..++|.|.|...+.
T Consensus        99 sgtrLddr~ir~D~D~GF~  117 (153)
T KOG0121|consen   99 SGTRLDDRPIRIDWDAGFV  117 (153)
T ss_pred             ccCcccccceeeeccccch
Confidence            9999999999999855443

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

Probab=99.30  E-value=1.6e-12  Score=110.96  Aligned_cols=83  Identities=20%  Similarity=0.402  Sum_probs=79.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||++|...++|.-|...|-+||.|..|.++.|-++++.+|||||+|.-.|+|..||..||+..|.|+.|+|.+|.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            34789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 009944          373 ASS  375 (522)
Q Consensus       373 ~~~  375 (522)
                      |..
T Consensus        89 P~k   91 (298)
T KOG0111|consen   89 PEK   91 (298)
T ss_pred             Ccc
Confidence            764

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

Probab=99.29  E-value=6.1e-12  Score=123.47  Aligned_cols=80  Identities=36%  Similarity=0.684  Sum_probs=77.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      ..|||+|||+++++++|.++|+..|.|..++++.|+++|..+|||||+|.+.++|.+|+..|||..+.|++|+|.|+...
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            68999999999999999999999999999999999999999999999999999999999999999999999999998653

>PF00076 RRM_1: RNA recognition motif

Probab=99.29  E-value=6.6e-12  Score=92.99  Aligned_cols=66  Identities=36%  Similarity=0.631  Sum_probs=56.2

Q ss_pred             eEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE---ecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEE
Q 009944          177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (522)
Q Consensus       177 v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~---~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~  252 (522)
                      |||+|||+.+|+++|+++|.+||.+..          ..+.   .+..++||||+|.+.++|..|+ .+++..+.|++|+
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 LYVGNLPPDVTEEELRDFFSQFGKIES----------IKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEE----------EEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccc----------ccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999998532          1122   2345799999999999999999 5999999999885

(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 ....

>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=99.29  E-value=3.2e-11  Score=90.07  Aligned_cols=74  Identities=38%  Similarity=0.689  Sum_probs=68.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      +|+|+|||..+++++|.++|..||.|..+.+..++.+ ...|+|||+|.+.++|..|+..+++..+.|+.|.|.+
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            4899999999999999999999999999999987643 7789999999999999999999999999999999874

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).

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

Probab=99.28  E-value=8.2e-12  Score=113.37  Aligned_cols=83  Identities=19%  Similarity=0.285  Sum_probs=69.1

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhC
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  497 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng  497 (522)
                      .-+.|-+++..+-+.             ||+.+|++||+|.+|.|+.++. |  +||+|  ||+|++++||.+|-++|||
T Consensus        97 kRLhVSNIPFrFRdp-------------DL~aMF~kfG~VldVEIIfNER-G--SKGFG--FVTmen~~dadRARa~LHg  158 (376)
T KOG0125|consen   97 KRLHVSNIPFRFRDP-------------DLRAMFEKFGKVLDVEIIFNER-G--SKGFG--FVTMENPADADRARAELHG  158 (376)
T ss_pred             ceeEeecCCccccCc-------------cHHHHHHhhCceeeEEEEeccC-C--CCccc--eEEecChhhHHHHHHHhhc
Confidence            445566666655554             9999999999999999998763 3  45555  9999999999999999999


Q ss_pred             CccCCeEEEEEEeCCcccccc
Q 009944          498 RKFGGNTVNAFYYPEDKYFNK  518 (522)
Q Consensus       498 ~~~~Gr~l~v~~~~~~~~~~~  518 (522)
                      ..+.||+|.|..++....+++
T Consensus       159 t~VEGRkIEVn~ATarV~n~K  179 (376)
T KOG0125|consen  159 TVVEGRKIEVNNATARVHNKK  179 (376)
T ss_pred             ceeeceEEEEeccchhhccCC
Confidence            999999999999998766554

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

Probab=99.28  E-value=2.1e-11  Score=117.60  Aligned_cols=168  Identities=23%  Similarity=0.294  Sum_probs=112.0

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~  252 (522)
                      ..+|||+|||..+|+++|.++|..||.+....      ++.+..++..+|||||+|.+.++|..|+ .+++..|.|+.|.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~------~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~  188 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVR------LVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLR  188 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEE------eeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeE
Confidence            68999999999999999999999999864321      1223345788999999999999999999 6999999999999


Q ss_pred             EecCCC-CCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCC
Q 009944          253 VRRPTD-YNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD  331 (522)
Q Consensus       253 v~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~  331 (522)
                      |.+... ........     .. ......................+++.+++..++..++...|..+|.+..+.+.....
T Consensus       189 v~~~~~~~~~~~~~~-----~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (306)
T COG0724         189 VQKAQPASQPRSELS-----NN-LDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKD  262 (306)
T ss_pred             eeccccccccccccc-----cc-cchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCC
Confidence            998543 10000000     00 000000000111122234456799999999999999999999999997666665543


Q ss_pred             CCCcceEEEEEEcChHHHHHHH
Q 009944          332 TGNSKGYGFCVYQDPAVTDIAC  353 (522)
Q Consensus       332 ~g~~~g~afV~f~~~~~A~~Al  353 (522)
                      ........++.+.....+..++
T Consensus       263 ~~~~~~~~~~~~~~~~~~~~~~  284 (306)
T COG0724         263 GKIPKSRSFVGNEASKDALESN  284 (306)
T ss_pred             CcccccccccchhHHHhhhhhh
Confidence            3333333444444444444333

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

Probab=99.27  E-value=7.9e-12  Score=103.40  Aligned_cols=73  Identities=32%  Similarity=0.479  Sum_probs=65.1

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCcEEEEEEeCHHHHHHHH-HhcCceecCceE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~-~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~  251 (522)
                      .++|||+||+..+++.||...|..||+            +..|++. ...|||||+|+++.+|+.|+ .|+|..|.|..|
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~------------lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~   77 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGP------------LRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRI   77 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCc------------ceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceE
Confidence            678999999999999999999999997            5666654 45799999999999999999 799999999999


Q ss_pred             EEecCCC
Q 009944          252 RVRRPTD  258 (522)
Q Consensus       252 ~v~~~~~  258 (522)
                      .|+....
T Consensus        78 rVE~S~G   84 (195)
T KOG0107|consen   78 RVELSTG   84 (195)
T ss_pred             EEEeecC
Confidence            9986543

>smart00361 RRM_1 RNA recognition motif

Probab=99.26  E-value=2.7e-11  Score=89.19  Aligned_cols=61  Identities=15%  Similarity=0.289  Sum_probs=55.0

Q ss_pred             HHHHHHHHH----hcCCceEEE-EeeCCCC--CCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEE
Q 009944          308 ETQIKELLE----SFGTLHGFD-LVKDRDT--GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (522)
Q Consensus       308 ~~~l~~~F~----~~G~i~~v~-~~~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (522)
                      +++|.++|.    +||.|..|. ++.++.+  +.++|||||+|.+.++|.+|+..|||..+.|+.|.+
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            567888888    999999995 7776666  899999999999999999999999999999999986

>smart00361 RRM_1 RNA recognition motif

Probab=99.25  E-value=2.8e-11  Score=89.16  Aligned_cols=61  Identities=26%  Similarity=0.376  Sum_probs=48.8

Q ss_pred             HHHHHHhhccCCeEEEE-ecCCCCC--CCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEE
Q 009944          445 EDMREECGKYGTLVNVV-IPRPDQN--GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF  508 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~-i~~~~~~--g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~  508 (522)
                      +.+.++|++||.|.+|. |+.+..+  +..   +|+|||+|.+.++|.+|+..|||..|.|++|.++
T Consensus         7 ~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~---rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        7 REFSEEEEYFGEVGKINKIYIDNVGYENHK---RGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             HHHHHHHHhcCCeeEEEEEEeCCCCCCCCC---cEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            34444445999999995 5555544  443   6888999999999999999999999999999873

>PF13893 RRM_5: RNA recognition motif

Probab=99.24  E-value=3.4e-11  Score=84.56  Aligned_cols=56  Identities=23%  Similarity=0.486  Sum_probs=50.8

Q ss_pred             HHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          311 IKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       311 l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      |.++|++||.|..|.+....     +++|||+|.+.++|.+|+..|||..|.|++|+|.|+
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            68999999999999987653     589999999999999999999999999999999986

(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 ....

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

Probab=99.22  E-value=8.2e-12  Score=108.59  Aligned_cols=80  Identities=19%  Similarity=0.333  Sum_probs=68.4

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCce
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~  250 (522)
                      ...-.+|||+||++.++.++|+++|++||+|+..+      +|.|..+++++|||||+|.+.+.|++|++-..-.|+|++
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eav------vitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~   82 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAV------VITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRK   82 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEE------EEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccc
Confidence            34457899999999999999999999999986533      466777899999999999999999999977777889988


Q ss_pred             EEEecC
Q 009944          251 VRVRRP  256 (522)
Q Consensus       251 ~~v~~~  256 (522)
                      .-++.+
T Consensus        83 aNcnlA   88 (247)
T KOG0149|consen   83 ANCNLA   88 (247)
T ss_pred             cccchh
Confidence            777643

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

Probab=99.21  E-value=4e-11  Score=104.66  Aligned_cols=81  Identities=21%  Similarity=0.332  Sum_probs=71.8

Q ss_pred             CCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHh
Q 009944          417 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  496 (522)
Q Consensus       417 ~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~ln  496 (522)
                      ...++|-+|+...++.             +|.++|.+||.|..|.|.++..+|..   +|||||.|.+.++|.+||..||
T Consensus       189 ~~tvRvtNLsed~~E~-------------dL~eLf~~fg~i~rvylardK~TG~~---kGFAFVtF~sRddA~rAI~~Ln  252 (270)
T KOG0122|consen  189 EATVRVTNLSEDMRED-------------DLEELFRPFGPITRVYLARDKETGLS---KGFAFVTFESRDDAARAIADLN  252 (270)
T ss_pred             cceeEEecCccccChh-------------HHHHHhhccCccceeEEEEccccCcc---cceEEEEEecHHHHHHHHHHcc
Confidence            4556676776665554             99999999999999999999999987   7899999999999999999999


Q ss_pred             CCccCCeEEEEEEeCCc
Q 009944          497 GRKFGGNTVNAFYYPED  513 (522)
Q Consensus       497 g~~~~Gr~l~v~~~~~~  513 (522)
                      |+-++.=.|.|+|..+.
T Consensus       253 G~gyd~LILrvEwskP~  269 (270)
T KOG0122|consen  253 GYGYDNLILRVEWSKPS  269 (270)
T ss_pred             CcccceEEEEEEecCCC
Confidence            99999999999998764

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

Probab=99.20  E-value=7.3e-13  Score=109.90  Aligned_cols=90  Identities=27%  Similarity=0.365  Sum_probs=80.3

Q ss_pred             cchhhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCc
Q 009944          166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI  244 (522)
Q Consensus       166 ~~~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~  244 (522)
                      .+.+....+.-|||+|||+.+||.||.-.|++||.+++.|+      |.+..+++++||||+.|++......|+ .|||.
T Consensus        27 SWH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinL------iRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGi  100 (219)
T KOG0126|consen   27 SWHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINL------IRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGI  100 (219)
T ss_pred             chhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEE------EecCCCCcccceEEEEecCccceEEEEeccCCc
Confidence            34456677888999999999999999999999999988775      888899999999999999999999999 79999


Q ss_pred             eecCceEEEecCCCCCc
Q 009944          245 IFEGVAVRVRRPTDYNP  261 (522)
Q Consensus       245 ~~~g~~~~v~~~~~~~~  261 (522)
                      .|.|+.|+|.....|..
T Consensus       101 ki~gRtirVDHv~~Yk~  117 (219)
T KOG0126|consen  101 KILGRTIRVDHVSNYKK  117 (219)
T ss_pred             eecceeEEeeecccccC
Confidence            99999999987666543

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.19  E-value=6.3e-11  Score=105.23  Aligned_cols=75  Identities=24%  Similarity=0.274  Sum_probs=65.6

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe---cCCCcEEEEEEeCHHHHHHHHHhcCceecCce
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~---~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~  250 (522)
                      ..+|||+||++.+|+++|++||+.||.|            .++.+   +..++||||+|.++++|+.|+.|+|..|.+++
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I------------~~V~I~~D~et~gfAfVtF~d~~aaetAllLnGa~l~d~~   72 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAI------------EHVEIIRSGEYACTAYVTFKDAYALETAVLLSGATIVDQR   72 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCe------------EEEEEecCCCcceEEEEEECCHHHHHHHHhcCCCeeCCce
Confidence            3589999999999999999999999984            44444   44568999999999999999999999999999


Q ss_pred             EEEecCCCCC
Q 009944          251 VRVRRPTDYN  260 (522)
Q Consensus       251 ~~v~~~~~~~  260 (522)
                      |.|.....|.
T Consensus        73 I~It~~~~y~   82 (243)
T PLN03121         73 VCITRWGQYE   82 (243)
T ss_pred             EEEEeCcccc
Confidence            9998766654

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.19  E-value=2.1e-10  Score=110.97  Aligned_cols=154  Identities=23%  Similarity=0.298  Sum_probs=113.4

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE-------ecCCCc---EEEEEEeCHHHHHHHH-
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY-------INHEKK---FAFVEMRTVEEASNAM-  239 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~-------~~~~~g---~afV~f~~~~~a~~a~-  239 (522)
                      ..-+++||||+||++++|+.|...|..||.++           ++-.       .-..+|   |+|+.|+++..+...+ 
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-----------VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~  324 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVK-----------VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLS  324 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceE-----------eecCCCccccccCCCCCcccEEEEEecchHHHHHHHH
Confidence            34578999999999999999999999999853           2222       112356   9999999999988877 


Q ss_pred             H-hc-C--cee-------cCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCH
Q 009944          240 A-LD-G--IIF-------EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTE  308 (522)
Q Consensus       240 ~-~~-~--~~~-------~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~  308 (522)
                      + .. .  ..|       ..+.|+|....-.+                    ...........++.+||||++||--++.
T Consensus       325 aC~~~~~~~yf~vss~~~k~k~VQIrPW~laD--------------------s~fv~d~sq~lDprrTVFVGgvprpl~A  384 (520)
T KOG0129|consen  325 ACSEGEGNYYFKVSSPTIKDKEVQIRPWVLAD--------------------SDFVLDHNQPIDPRRTVFVGGLPRPLTA  384 (520)
T ss_pred             HHhhcccceEEEEecCcccccceeEEeeEecc--------------------chhhhccCcccCccceEEecCCCCcchH
Confidence            2 11 1  111       12223332111110                    0111112233566689999999999999


Q ss_pred             HHHHHHHH-hcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHH
Q 009944          309 TQIKELLE-SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA  355 (522)
Q Consensus       309 ~~l~~~F~-~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~  355 (522)
                      ++|..+|+ .||.|..+-|-.|++-+-++|-|=|.|.+...-.+||.+
T Consensus       385 ~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  385 EELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             HHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            99999999 899999999999988899999999999999999999874

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.16  E-value=5.4e-11  Score=88.01  Aligned_cols=64  Identities=36%  Similarity=0.644  Sum_probs=53.3

Q ss_pred             eEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC-----CcEEEEEEeCHHHHHHHHH-hcCceecCce
Q 009944          177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-----KKFAFVEMRTVEEASNAMA-LDGIIFEGVA  250 (522)
Q Consensus       177 v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~-----~g~afV~f~~~~~a~~a~~-~~~~~~~g~~  250 (522)
                      |||+|||+++++++|.++|..+|.            |..+.+...     +++|||+|.++++|..|+. +++..|.|+.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~------------v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~   68 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGP------------VEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRK   68 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSB------------EEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCC------------cceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEE
Confidence            799999999999999999999986            555554433     6999999999999999994 6669999998


Q ss_pred             EE
Q 009944          251 VR  252 (522)
Q Consensus       251 ~~  252 (522)
                      |+
T Consensus        69 l~   70 (70)
T PF14259_consen   69 LR   70 (70)
T ss_dssp             EE
T ss_pred             cC
Confidence            74

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

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

Probab=99.13  E-value=2.3e-10  Score=85.97  Aligned_cols=63  Identities=29%  Similarity=0.503  Sum_probs=56.8

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      +++.++|.+||.|..|.|-..+.+      +|.|||.|++..+|.+|+..|+|..+.++.|.|-|+...
T Consensus        33 eemydlFGkyg~IrQIRiG~~k~T------rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   33 EEMYDLFGKYGTIRQIRIGNTKET------RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             HHHHHHhhcccceEEEEecCccCc------CceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHH
Confidence            499999999999999999665533      589999999999999999999999999999999997753

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

Probab=99.09  E-value=1e-10  Score=92.23  Aligned_cols=81  Identities=25%  Similarity=0.245  Sum_probs=71.1

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      +.+.-.|||.++...+|+++|.+.|..||+|+++++      -.+..++-.+|||+|+|.+.++|++|+ .+||..|.|+
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihL------NLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q  142 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHL------NLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQ  142 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceee------ccccccccccceeeeehHhHHHHHHHHHhccchhhhCC
Confidence            344457999999999999999999999999876554      456677788999999999999999999 7999999999


Q ss_pred             eEEEecCC
Q 009944          250 AVRVRRPT  257 (522)
Q Consensus       250 ~~~v~~~~  257 (522)
                      +|.|.|.-
T Consensus       143 ~v~VDw~F  150 (170)
T KOG0130|consen  143 NVSVDWCF  150 (170)
T ss_pred             ceeEEEEE
Confidence            99999854

>smart00362 RRM_2 RNA recognition motif

Probab=99.05  E-value=9.1e-10  Score=81.57  Aligned_cols=67  Identities=37%  Similarity=0.615  Sum_probs=57.7

Q ss_pred             eeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC----CCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH----EKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       176 ~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~----~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      +|+|+|||..+++++|+++|..||.+            ..+.+..    .+|+|||+|.+.++|+.|+ .+++..+.|+.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v------------~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~   68 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPI------------ESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRP   68 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCE------------EEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEE
Confidence            58999999999999999999999974            4444333    4699999999999999999 68999999999


Q ss_pred             EEEe
Q 009944          251 VRVR  254 (522)
Q Consensus       251 ~~v~  254 (522)
                      |.|+
T Consensus        69 i~v~   72 (72)
T smart00362       69 LRVE   72 (72)
T ss_pred             EeeC
Confidence            8873

>PLN03213 repressor of silencing 3; Provisional

Probab=99.05  E-value=4.6e-10  Score=107.28  Aligned_cols=73  Identities=19%  Similarity=0.403  Sum_probs=62.4

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec--CCCcEEEEEEeCH--HHHHHHH-HhcCceecC
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--HEKKFAFVEMRTV--EEASNAM-ALDGIIFEG  248 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~--~~~g~afV~f~~~--~~a~~a~-~~~~~~~~g  248 (522)
                      ..+||||||++.+|+++|..+|..||.|.            ++.+.  ..+|||||+|.+.  .++.+|+ .|||..|.|
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVk------------dVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKG   77 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVD------------AVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKG   77 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCee------------EEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecC
Confidence            46899999999999999999999999854            33322  2389999999987  6799999 699999999


Q ss_pred             ceEEEecCCC
Q 009944          249 VAVRVRRPTD  258 (522)
Q Consensus       249 ~~~~v~~~~~  258 (522)
                      +.|+|..+++
T Consensus        78 R~LKVNKAKP   87 (759)
T PLN03213         78 GRLRLEKAKE   87 (759)
T ss_pred             ceeEEeeccH
Confidence            9999987664

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

Probab=99.04  E-value=7.7e-10  Score=94.57  Aligned_cols=81  Identities=31%  Similarity=0.515  Sum_probs=75.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhc-CCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESF-GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~-G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ....++|..+|..+.+.+|..+|.+| |.|..+++.+++.||.++|||||+|++.+.|..|-+.||+..|.++.|.|.+.
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            34579999999999999999999998 67888999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 009944          372 TA  373 (522)
Q Consensus       372 ~~  373 (522)
                      .+
T Consensus       128 pp  129 (214)
T KOG4208|consen  128 PP  129 (214)
T ss_pred             Cc
Confidence            55

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

Probab=99.02  E-value=4.4e-11  Score=102.48  Aligned_cols=144  Identities=23%  Similarity=0.307  Sum_probs=119.4

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC----CcEEEEEEeCHHHHHHHH-HhcCce
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEMRTVEEASNAM-ALDGII  245 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~----~g~afV~f~~~~~a~~a~-~~~~~~  245 (522)
                      .+..++|||+|+...++++-|.++|-+.|+            |+.|.+...    ..||||.|.++-.+.-|+ -+||..
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGP------------V~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~   73 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGP------------VYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDD   73 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCc------------eEEEeCCCCccCCCceeeeecccccchhhhhhhcccch
Confidence            345689999999999999999999999987            666666432    349999999999999999 589999


Q ss_pred             ecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcC----CCCCCCHHHHHHHHHhcCCc
Q 009944          246 FEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGG----LPYYFTETQIKELLESFGTL  321 (522)
Q Consensus       246 ~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~n----Lp~~~t~~~l~~~F~~~G~i  321 (522)
                      +.+..++|+                                          ++.++    |...++++.+...|+..|++
T Consensus        74 l~~~e~q~~------------------------------------------~r~G~shapld~r~~~ei~~~v~s~a~p~  111 (267)
T KOG4454|consen   74 LEEDEEQRT------------------------------------------LRCGNSHAPLDERVTEEILYEVFSQAGPI  111 (267)
T ss_pred             hccchhhcc------------------------------------------cccCCCcchhhhhcchhhheeeecccCCC
Confidence            999998885                                          44455    77789999999999999999


Q ss_pred             eEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEE
Q 009944          322 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (522)
Q Consensus       322 ~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (522)
                      ..+++..+. +|.++.++|+.+......-.++....+..+.-+++.+.
T Consensus       112 ~~~R~~~~~-d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~~~~g  158 (267)
T KOG4454|consen  112 EGVRIPTDN-DGRNRNFGFVTYQRLCAVPFALDLYQGLELFQKKVTIG  158 (267)
T ss_pred             CCccccccc-cCCccCccchhhhhhhcCcHHhhhhcccCcCCCCcccc
Confidence            999999885 48888899999998888888888777765554444443

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

Probab=99.02  E-value=8.3e-10  Score=97.05  Aligned_cols=132  Identities=22%  Similarity=0.345  Sum_probs=107.4

Q ss_pred             EecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCC
Q 009944          217 YINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPD  295 (522)
Q Consensus       217 ~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  295 (522)
                      .-+.-.+++|+.|.....-.++- +-+++.+.-.+|++.....++....                       ..-.+...
T Consensus       135 ~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedPsl-----------------------~ew~~~Df  191 (290)
T KOG0226|consen  135 RPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDPSL-----------------------AEWDEDDF  191 (290)
T ss_pred             CCCccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCccc-----------------------ccCccccc
Confidence            33455789999999877777776 5677777777777765544432210                       11123446


Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      +||++.|.-+++.+.|...|.+|-.....++++++.||+++||+||.|.++.++..|+..|+|..++.++|++.-.
T Consensus       192 RIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  192 RIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             eeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            8999999999999999999999999888999999999999999999999999999999999999999999998754

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

Probab=99.02  E-value=5.3e-10  Score=102.53  Aligned_cols=84  Identities=19%  Similarity=0.388  Sum_probs=79.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ..+.+.|||--|.+-|+.+||.-+|+.||+|..|.++++..||.+-.||||+|.+.+++++|.-.|++..|..+.|+|.|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            34557899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 009944          371 ATAS  374 (522)
Q Consensus       371 ~~~~  374 (522)
                      +...
T Consensus       316 SQSV  319 (479)
T KOG0415|consen  316 SQSV  319 (479)
T ss_pred             hhhh
Confidence            8653

>smart00360 RRM RNA recognition motif

Probab=99.02  E-value=7.5e-10  Score=81.71  Aligned_cols=62  Identities=26%  Similarity=0.461  Sum_probs=55.1

Q ss_pred             HHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEE
Q 009944          444 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF  508 (522)
Q Consensus       444 ~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~  508 (522)
                      .++|+++|++||.|..+.+.....++.+   .|+|||+|.+.++|..|+..|+|..|+|++|.|.
T Consensus        10 ~~~l~~~f~~~g~v~~~~i~~~~~~~~~---~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360       10 EEELRELFSKFGKIESVRLVRDKDTGKS---KGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             HHHHHHHHHhhCCEeEEEEEeCCCCCCC---CceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            3599999999999999999887655443   6899999999999999999999999999999873

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

Probab=99.00  E-value=2e-10  Score=98.32  Aligned_cols=82  Identities=22%  Similarity=0.326  Sum_probs=71.2

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||++|...+|+.-|...|-+||.|++.      .+..+....+.+|||||+|.-.|+|..|| .||+..|.|+.
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dI------qiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~Grt   81 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDI------QIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRT   81 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhc------ccccchhcccccceeEEEeeccchhHHHhhcCchhhhccee
Confidence            346799999999999999999999999997542      23455566788999999999999999999 79999999999


Q ss_pred             EEEecCCCC
Q 009944          251 VRVRRPTDY  259 (522)
Q Consensus       251 ~~v~~~~~~  259 (522)
                      |+|.++++.
T Consensus        82 irVN~AkP~   90 (298)
T KOG0111|consen   82 IRVNLAKPE   90 (298)
T ss_pred             EEEeecCCc
Confidence            999987654

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

Probab=98.98  E-value=7e-09  Score=93.43  Aligned_cols=67  Identities=24%  Similarity=0.379  Sum_probs=62.0

Q ss_pred             HHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEE
Q 009944          440 YEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFY  509 (522)
Q Consensus       440 ~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~  509 (522)
                      |.+.+.+|+.+|+.||.|+.|.|+.+..+|++   +|||||+|+..-+...|.+..+|.+|.|+.|.|.+
T Consensus       111 ydT~EskLrreF~~YG~IkrirlV~d~vTgks---kGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen  111 YDTSESKLRREFEKYGPIKRIRLVRDKVTGKS---KGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             ccccHHHHHHHHHhcCcceeEEEeeecccCCc---cceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            44444699999999999999999999999987   89999999999999999999999999999999976

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

Probab=98.95  E-value=8.2e-09  Score=101.05  Aligned_cols=178  Identities=16%  Similarity=0.179  Sum_probs=112.0

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE-ecCCCcEEEEEEeCHHHHHHHH-HhcCcee
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY-INHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~-~~~~~g~afV~f~~~~~a~~a~-~~~~~~~  246 (522)
                      ......++|+|-|||..+++++|..+|..||+|.            .+. +....|..||+|.+..+|+.|+ +|++..+
T Consensus        70 ~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir------------~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~  137 (549)
T KOG4660|consen   70 EKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIR------------EIRETPNKRGIVFVEFYDVRDAERALKALNRREI  137 (549)
T ss_pred             cccCccceEEEEecCCcCCHHHHHHHHHhhcchh------------hhhcccccCceEEEEEeehHhHHHHHHHHHHHHh
Confidence            4455678999999999999999999999999964            232 4456899999999999999999 7999999


Q ss_pred             cCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEE
Q 009944          247 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (522)
Q Consensus       247 ~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~  326 (522)
                      .|+.|+.  +......    .+......-++.....+.....++.. ...+|+ .|++.....-+...|.-+|.+.. ..
T Consensus       138 ~~~~~k~--~~~~~~~----~~~~~~~~~~~~~~~p~a~s~pgg~~-~~~~~g-~l~P~~s~~~~~~~~~~~~~~~~-~~  208 (549)
T KOG4660|consen  138 AGKRIKR--PGGARRA----MGLQSGTSFLNHFGSPLANSPPGGWP-RGQLFG-MLSPTRSSILLEHISSVDGSSPG-RE  208 (549)
T ss_pred             hhhhhcC--CCccccc----chhcccchhhhhccchhhcCCCCCCc-CCccee-eeccchhhhhhhcchhccCcccc-cc
Confidence            9999882  1111100    00000000000000011111111111 122333 28888888777777778887754 21


Q ss_pred             eeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       327 ~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                           ++.-.---|++|.+..++..++... |..+.+....+++..+
T Consensus       209 -----~~~~~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  209 -----TPLLNHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             -----ccchhhhhhhhhccccchhhcccCC-ceecCCCCceEEecCC
Confidence                 2222224688888888886665533 6777777666666554

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

Probab=98.94  E-value=4.6e-09  Score=104.55  Aligned_cols=197  Identities=8%  Similarity=-0.013  Sum_probs=118.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      +.+-+.++++.+.+.|++++|... .|..+.|..+...+.-+|.++|+|....++++|+. -|...+-.+.+.|..+...
T Consensus       312 ~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~-rn~~~~~~R~~q~~P~g~~  389 (944)
T KOG4307|consen  312 YYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFT-RNPSDDVNRPFQTGPPGNL  389 (944)
T ss_pred             heeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHh-cCchhhhhcceeecCCCcc
Confidence            346688999999999999999743 24445555554445557889999999999999976 4556667778877765432


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHHhhccCCc-------cCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHH
Q 009944          375 SGQSKTEQESILAQAQQHIAIQKMALQTSGMN-------TLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDM  447 (522)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l  447 (522)
                      .-...+....    .+.   .+.........+       .+|..++... .-..|+.|....          +++.+.++
T Consensus       390 ~~~~a~~~~~----~~~---~~~~~~~hg~p~~~pr~~~~~gq~vp~P~-~ag~~lyv~~lP----------~~t~~~~~  451 (944)
T KOG4307|consen  390 GRNGAPPFQA----GVP---PPVIQNNHGRPIAPPRAMVRPGQNVPFPG-GAGGALYVFQLP----------VMTPIVPP  451 (944)
T ss_pred             ccccCccccc----cCC---CCcccccCCCCCCCcccccCCCCCCCCCC-CccceEEeccCC----------ccccccch
Confidence            2111000000    000   000000000011       1122211111 223333332221          11122488


Q ss_pred             HHHhhccCCeEE-EEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          448 REECGKYGTLVN-VVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       448 ~~~f~~~G~I~~-v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      .++|..--.|++ |.|..-+ ++.-   .+.|||.|.+++++.+|...-+-++++.+.|+|.-+.++.+
T Consensus       452 v~~f~~~~~Ved~I~lt~~P-~~~~---~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~~m  516 (944)
T KOG4307|consen  452 VNKFMGAAAVEDFIELTRLP-TDLL---RPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADYAM  516 (944)
T ss_pred             hhhhhhhhhhhheeEeccCC-cccc---cchhhheeccccccchhhhcccccccCceEEEeechhhHHH
Confidence            999988777777 5555444 3332   47789999999999999998888888999999988776554

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

Probab=98.93  E-value=7.2e-09  Score=106.51  Aligned_cols=161  Identities=20%  Similarity=0.350  Sum_probs=129.4

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE---ecCCCcEEEEEEeCHHHHHHHH-HhcCc
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-ALDGI  244 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~---~~~~~g~afV~f~~~~~a~~a~-~~~~~  244 (522)
                      .....+++||++||+..+++.+|+..|..+|.+.          -+++.   ++....||||.|.+...+-.|. ++.+.
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve----------~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~  436 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVE----------EVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGP  436 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhcccc----------ccccccCCCCcccchhhhhhhccccCcccchhhcCC
Confidence            3456688999999999999999999999999742          12222   3445679999999999999998 78887


Q ss_pred             eecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEE
Q 009944          245 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF  324 (522)
Q Consensus       245 ~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v  324 (522)
                      .|..-.+++.+...                               .....+.+++++|+..+....|..+|..||.|..|
T Consensus       437 ~I~~g~~r~glG~~-------------------------------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~I  485 (975)
T KOG0112|consen  437 LIGNGTHRIGLGQP-------------------------------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRII  485 (975)
T ss_pred             ccccCccccccccc-------------------------------ccccceeeccCCCCCCChHHHHHHHhhccCcceee
Confidence            77666666654211                               01233579999999999999999999999999988


Q ss_pred             EEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC--eEEEEEEccCCCC
Q 009944          325 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASSG  376 (522)
Q Consensus       325 ~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~~~~~~  376 (522)
                      .+-..      .-||||+|.+...|+.|+..|-|..|+|  +.+.|.|+.....
T Consensus       486 dy~hg------q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~~  533 (975)
T KOG0112|consen  486 DYRHG------QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPGA  533 (975)
T ss_pred             ecccC------CcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCCC
Confidence            76543      3489999999999999999999999976  7799999877543

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

Probab=98.91  E-value=1.4e-09  Score=107.05  Aligned_cols=81  Identities=27%  Similarity=0.414  Sum_probs=74.1

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEEE
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~v  253 (522)
                      +.|||||||+++++++|.++|...|.|+.+++      +.|-.+++.+||||++|.+.++|..|+ .|||..+.|++|+|
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~------v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v   92 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRL------VYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRV   92 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeee------cccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEe
Confidence            78999999999999999999999999876554      777888999999999999999999999 69999999999999


Q ss_pred             ecCCCCCc
Q 009944          254 RRPTDYNP  261 (522)
Q Consensus       254 ~~~~~~~~  261 (522)
                      .|+.....
T Consensus        93 ~~~~~~~~  100 (435)
T KOG0108|consen   93 NYASNRKN  100 (435)
T ss_pred             ecccccch
Confidence            99876554

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=98.91  E-value=8.4e-09  Score=76.74  Aligned_cols=68  Identities=37%  Similarity=0.573  Sum_probs=58.4

Q ss_pred             eeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-----CCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-----EKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       176 ~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~-----~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      +|+|+|||+.+++++|+++|..+|.+            ..+.+..     ..++|||+|.+.++|..|+ .+++..+.|+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i------------~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~   68 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKV------------ESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGR   68 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCE------------EEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            48999999999999999999999874            4443332     3799999999999999999 6999999999


Q ss_pred             eEEEec
Q 009944          250 AVRVRR  255 (522)
Q Consensus       250 ~~~v~~  255 (522)
                      .+.|.+
T Consensus        69 ~~~v~~   74 (74)
T cd00590          69 PLRVEF   74 (74)
T ss_pred             EEEEeC
Confidence            998863

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).

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.90  E-value=9.4e-11  Score=119.52  Aligned_cols=154  Identities=23%  Similarity=0.267  Sum_probs=128.3

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecC
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g  248 (522)
                      .......++||.||++.+.+.+|...|..+|.+..      +.+++.+..+.-+|+|||+|..++++.+|++++...+.|
T Consensus       662 n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~------vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  662 NEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEV------VQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             hHHHHHHHHHHhhcchhhcCchhhhhcCccchhhh------HHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            34466788999999999999999999999987532      222333444556899999999999999999877766665


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEee
Q 009944          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (522)
Q Consensus       249 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~  328 (522)
                      +                                             ..|+|.|+|+..|.++|+.+|.++|.+..+.++.
T Consensus       736 K---------------------------------------------~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt  770 (881)
T KOG0128|consen  736 K---------------------------------------------ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVT  770 (881)
T ss_pred             h---------------------------------------------hhhheeCCCCCCchHHHHhhccccCCccccchhh
Confidence            2                                             2688999999999999999999999999998887


Q ss_pred             CCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      .+ .|+++|.|||.|.+..+|.+++....+..+.-+.+.|...++.
T Consensus       771 ~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp~  815 (881)
T KOG0128|consen  771 VR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPE  815 (881)
T ss_pred             hh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCc
Confidence            75 7999999999999999999999988888887777777775553

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.88  E-value=9.2e-11  Score=119.60  Aligned_cols=234  Identities=14%  Similarity=0.104  Sum_probs=168.2

Q ss_pred             cceeEEeCCCccCcHH-HHHHHHHHHHHhhcCCCCCCCCceEEEEecC------CCcEEEEEEeCHHHHHHHHHhcCcee
Q 009944          174 ARRVYVGGLPPLANEQ-AIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAMALDGIIF  246 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~-~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~a~~a~~~~~~~~  246 (522)
                      ....++.++.+..... .+...|..+|.            |..+....      ...++++.+.....++.|....+..+
T Consensus       571 ~~e~~s~~v~p~~~~ke~~~~~~k~~~~------------vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~pa~~~~  638 (881)
T KOG0128|consen  571 RREKESTNVYPEQQKKEIQRRQFKGEGN------------VEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVPAGGAL  638 (881)
T ss_pred             hhhhcccCCCcchhhHHhhHHHhhcccc------------cccccCccccccccccchhhhhhccccchhhccccccccc
Confidence            4557777877776555 56778888876            34443332      22388999999999999998888888


Q ss_pred             cCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEE
Q 009944          247 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (522)
Q Consensus       247 ~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~  326 (522)
                      .++.+.|..+.........                   ...........++||.||+..+.+.+|...|..+|.+..+.+
T Consensus       639 a~~~~av~~ad~~~~~~~~-------------------kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi  699 (881)
T KOG0128|consen  639 ANRSAAVGLADAEEKEENF-------------------KVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQI  699 (881)
T ss_pred             CCccccCCCCCchhhhhcc-------------------CcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHH
Confidence            8887777543322210000                   000000112247899999999999999999999999888777


Q ss_pred             eeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCc
Q 009944          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMN  406 (522)
Q Consensus       327 ~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  406 (522)
                      ......+..+|+|||+|..++++.+|+....++.++...|.                                       
T Consensus       700 ~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~~v~---------------------------------------  740 (881)
T KOG0128|consen  700 VIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKISVA---------------------------------------  740 (881)
T ss_pred             HHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhhhhh---------------------------------------
Confidence            65556888999999999999999999996665555521111                                       


Q ss_pred             cCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChH
Q 009944          407 TLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAV  486 (522)
Q Consensus       407 ~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~  486 (522)
                                     +-+++...+.             +.++.+|..+|++.++.++... .|.+   +|.|||.|.+..
T Consensus       741 ---------------i~g~pf~gt~-------------e~~k~l~~~~gn~~~~~~vt~r-~gkp---kg~a~v~y~~ea  788 (881)
T KOG0128|consen  741 ---------------ISGPPFQGTK-------------EELKSLASKTGNVTSLRLVTVR-AGKP---KGKARVDYNTEA  788 (881)
T ss_pred             ---------------eeCCCCCCch-------------HHHHhhccccCCccccchhhhh-cccc---ccceeccCCCcc
Confidence                           1122222233             3899999999999999866655 6666   799999999999


Q ss_pred             hHHHHHHHHhCCccCCeEEEEEE
Q 009944          487 GCATAKNALSGRKFGGNTVNAFY  509 (522)
Q Consensus       487 ~A~~Ai~~lng~~~~Gr~l~v~~  509 (522)
                      +|..++..+.+..+.-+.+.|..
T Consensus       789 ~~s~~~~s~d~~~~rE~~~~v~v  811 (881)
T KOG0128|consen  789 DASRKVASVDVAGKRENNGEVQV  811 (881)
T ss_pred             hhhhhcccchhhhhhhcCccccc
Confidence            99999999888888776666665

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

Probab=98.86  E-value=5.5e-09  Score=89.44  Aligned_cols=65  Identities=14%  Similarity=0.296  Sum_probs=59.6

Q ss_pred             HHHHHhhcc-CCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          446 DMREECGKY-GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       446 ~l~~~f~~~-G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      .|..+|.+| |.|..+.+-++..+|+.   +|||||+|++.+.|..|.+.||++.|+|+-|.|.+++++
T Consensus        65 ~~~~~~~q~~g~v~r~rlsRnkrTGNS---KgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   65 EILNYFRQFGGTVTRFRLSRNKRTGNS---KGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             HHhhhhhhcCCeeEEEEeecccccCCc---CceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            777888877 77888888899999986   789999999999999999999999999999999999987

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.84  E-value=2.8e-09  Score=100.29  Aligned_cols=176  Identities=18%  Similarity=0.211  Sum_probs=132.5

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCc-eecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGI-IFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~-~~~g~~~  251 (522)
                      ...++|++++...+.+.++..++..+|...+.-      ....-....++|+++|.|...+.+..|+++.+. .+.+..+
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~------~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~  160 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDAR------SSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKG  160 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccch------hhhhccccccccceeeccccHHHHHHHHHhhhccccccccc
Confidence            467899999999999999999999998643211      011122345789999999999999999987775 4444444


Q ss_pred             EEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEE-EcCCCCCCCHHHHHHHHHhcCCceEEEEeeCC
Q 009944          252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVF-VGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (522)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~  330 (522)
                      ..-........                   ..............++| |++|+..+++++|+.+|..+|.|..+++..++
T Consensus       161 ~~dl~~~~~~~-------------------~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~  221 (285)
T KOG4210|consen  161 EKDLNTRRGLR-------------------PKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDE  221 (285)
T ss_pred             cCccccccccc-------------------ccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCC
Confidence            43322111100                   00000111123344666 99999999999999999999999999999999


Q ss_pred             CCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      .++.+.|||||.|.....+..++.. +...+++.++.|.+..+.
T Consensus       222 ~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  222 ESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             CccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCC
Confidence            9999999999999999999999987 889999999999998764

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

Probab=98.82  E-value=3.2e-09  Score=95.04  Aligned_cols=96  Identities=30%  Similarity=0.517  Sum_probs=78.6

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhC
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  497 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng  497 (522)
                      .+++|+.|.|++...+..+     +++.++++.|++||+|..|.|...+.....  ---..||+|+..++|.+|+-.|||
T Consensus       279 ~ptkvlllrnmVg~gevd~-----elede~keEceKyg~V~~viifeip~~p~d--eavRiFveF~r~e~aiKA~VdlnG  351 (378)
T KOG1996|consen  279 CPTKVLLLRNMVGAGEVDE-----ELEDETKEECEKYGKVGNVIIFEIPSQPED--EAVRIFVEFERVESAIKAVVDLNG  351 (378)
T ss_pred             cchHHHHhhhhcCcccccH-----HHHHHHHHHHHhhcceeeEEEEecCCCccc--hhheeeeeeccHHHHHHHHHhcCC
Confidence            7888999999988875433     345689999999999999988666433211  113479999999999999999999


Q ss_pred             CccCCeEEEEEEeCCcccccccC
Q 009944          498 RKFGGNTVNAFYYPEDKYFNKDY  520 (522)
Q Consensus       498 ~~~~Gr~l~v~~~~~~~~~~~~~  520 (522)
                      ++|+|+.|...|+++++|.+.++
T Consensus       352 RyFGGr~v~A~Fyn~ekfs~~el  374 (378)
T KOG1996|consen  352 RYFGGRVVSACFYNLEKFSNLEL  374 (378)
T ss_pred             ceecceeeeheeccHHhhhhhhh
Confidence            99999999999999999987665

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

Probab=98.81  E-value=3.4e-08  Score=96.22  Aligned_cols=82  Identities=20%  Similarity=0.387  Sum_probs=76.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||.+|...|-..+|+.+|++||.|.-.+++.+..+--.++|+||++.+.++|.+||+.||...|.|+.|.|..+..
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            46899999999999999999999999999999999877777799999999999999999999999999999999998875


Q ss_pred             CC
Q 009944          374 SS  375 (522)
Q Consensus       374 ~~  375 (522)
                      ..
T Consensus       485 Ep  486 (940)
T KOG4661|consen  485 EP  486 (940)
T ss_pred             Cc
Confidence            53

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

Probab=98.78  E-value=3.2e-09  Score=108.97  Aligned_cols=158  Identities=16%  Similarity=0.263  Sum_probs=123.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ...+||++||+..+++.+|+..|..+|.|..|.|...+ -+...-||||.|.+.+.+..|...+.+..|....+.+.+..
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            34789999999999999999999999999999887764 23344589999999999999999999988877677776654


Q ss_pred             CCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhh
Q 009944          373 ASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  452 (522)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~  452 (522)
                      ++....                                       +...+..|..+...             ..|..+|.
T Consensus       450 ~kst~t---------------------------------------tr~~sgglg~w~p~-------------~~l~r~fd  477 (975)
T KOG0112|consen  450 PKSTPT---------------------------------------TRLQSGGLGPWSPV-------------SRLNREFD  477 (975)
T ss_pred             cccccc---------------------------------------eeeccCCCCCCChH-------------HHHHHHhh
Confidence            311000                                       11112223333222             38899999


Q ss_pred             ccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCC--eEEEEEEeCC
Q 009944          453 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYYPE  512 (522)
Q Consensus       453 ~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~G--r~l~v~~~~~  512 (522)
                      .||.|..|.+-.         |--||||.|++...|+.|+..|-|..|+|  +.|.|.|+.+
T Consensus       478 ~fGpir~Idy~h---------gq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~  530 (975)
T KOG0112|consen  478 RFGPIRIIDYRH---------GQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASP  530 (975)
T ss_pred             ccCcceeeeccc---------CCcceeeecccCccchhhHHHHhcCcCCCCCcccccccccC
Confidence            999999988843         23589999999999999999999999987  7899998764

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

Probab=98.78  E-value=2.6e-08  Score=91.75  Aligned_cols=77  Identities=17%  Similarity=0.368  Sum_probs=68.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHH-cCCccCCeEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVR  369 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v~  369 (522)
                      .....+|||++|-..+++.+|+++|.+||.|..|.+...      +++|||+|.+.+.|++|.+.+ +...|.|..|.|.
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~  298 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIK  298 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEE
Confidence            344578999999999999999999999999999998865      469999999999999998765 5567899999999


Q ss_pred             EccC
Q 009944          370 RATA  373 (522)
Q Consensus       370 ~~~~  373 (522)
                      |..+
T Consensus       299 Wg~~  302 (377)
T KOG0153|consen  299 WGRP  302 (377)
T ss_pred             eCCC
Confidence            9977

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

Probab=98.77  E-value=1.6e-08  Score=93.18  Aligned_cols=80  Identities=24%  Similarity=0.365  Sum_probs=71.4

Q ss_pred             chhhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHH--hcCc
Q 009944          167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA--LDGI  244 (522)
Q Consensus       167 ~~~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~--~~~~  244 (522)
                      .+.......+|||++|-..+++.+|+++|.+||.            +..+.+-..+++|||+|.+.+.|+.|.+  ++..
T Consensus       221 epPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGe------------irsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~l  288 (377)
T KOG0153|consen  221 EPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGE------------IRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKL  288 (377)
T ss_pred             CCCcccceeEEEecccccchhHHHHHHHHhhcCC------------eeeEEeecccccceeeehhhHHHHHHHHhhccee
Confidence            3345666789999999999999999999999998            7778888888999999999999999993  8888


Q ss_pred             eecCceEEEecCCC
Q 009944          245 IFEGVAVRVRRPTD  258 (522)
Q Consensus       245 ~~~g~~~~v~~~~~  258 (522)
                      .|.|+.|+|.|...
T Consensus       289 vI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  289 VINGFRLKIKWGRP  302 (377)
T ss_pred             eecceEEEEEeCCC
Confidence            89999999999776

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

Probab=98.74  E-value=5.2e-08  Score=88.12  Aligned_cols=85  Identities=24%  Similarity=0.400  Sum_probs=76.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ..+.+|+|.|||+.|+++||+++|..||.+..+.+..++ .|.+.|.|-|.|...++|.+|++.++|..+.|..|++...
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            344689999999999999999999999999888888885 8999999999999999999999999999999999999988


Q ss_pred             cCCCCC
Q 009944          372 TASSGQ  377 (522)
Q Consensus       372 ~~~~~~  377 (522)
                      ......
T Consensus       160 ~~~~~~  165 (243)
T KOG0533|consen  160 SSPSQS  165 (243)
T ss_pred             cCcccc
Confidence            765433

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

Probab=98.73  E-value=3.7e-09  Score=90.85  Aligned_cols=159  Identities=19%  Similarity=0.281  Sum_probs=113.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      +...+|||.||-..++|+-|.++|-+.|+|..|.|..++ .++.+ ||||.|.++-...-|++.+||..+.+..+.|++-
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            344799999999999999999999999999999998885 55656 9999999999999999999999999999999875


Q ss_pred             cCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHh
Q 009944          372 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  451 (522)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f  451 (522)
                      .-....+                                              |...++.             +.+.+.|
T Consensus        85 ~G~shap----------------------------------------------ld~r~~~-------------ei~~~v~  105 (267)
T KOG4454|consen   85 CGNSHAP----------------------------------------------LDERVTE-------------EILYEVF  105 (267)
T ss_pred             cCCCcch----------------------------------------------hhhhcch-------------hhheeee
Confidence            3211110                                              0011111             2566778


Q ss_pred             hccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCC-----------ccCCeEEEEEEeCCccc
Q 009944          452 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGR-----------KFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       452 ~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~-----------~~~Gr~l~v~~~~~~~~  515 (522)
                      +.-|.|..+.+..+.. |.. ...|  ||.+.-.-..-.|+....+.           .++|..|--++.+...|
T Consensus       106 s~a~p~~~~R~~~~~d-~rn-rn~~--~~~~qr~~~~P~~~~~y~~l~~~~~~~~~ggk~Gg~~lpqsgfsPs~~  176 (267)
T KOG4454|consen  106 SQAGPIEGVRIPTDND-GRN-RNFG--FVTYQRLCAVPFALDLYQGLELFQKKVTIGGKQGGKQLPQSGFSPSAY  176 (267)
T ss_pred             cccCCCCCcccccccc-CCc-cCcc--chhhhhhhcCcHHhhhhcccCcCCCCcccccccCCCcCCcccCCcccc
Confidence            8889999999988774 332 2234  77776665555566554433           35556655555544443

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

Probab=98.71  E-value=1.4e-08  Score=99.52  Aligned_cols=175  Identities=12%  Similarity=0.044  Sum_probs=109.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      ..+|+|-|||..+++++|..+|+.||.|..|...     -...|.+||+|.++-+|+.|+++|++..|.|+.|+......
T Consensus        75 ~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t-----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~  149 (549)
T KOG4660|consen   75 QGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET-----PNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGAR  149 (549)
T ss_pred             cceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc-----cccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCccc
Confidence            4689999999999999999999999999987654     34578999999999999999999999999999998221111


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhc
Q 009944          374 SSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGK  453 (522)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~  453 (522)
                      .    .    ..+...  ..-....... ...+     ++........+..|....+..             -+.-.|..
T Consensus       150 ~----~----~~~~~~--~~~~~~~~~p-~a~s-----~pgg~~~~~~~g~l~P~~s~~-------------~~~~~~~~  200 (549)
T KOG4660|consen  150 R----A----MGLQSG--TSFLNHFGSP-LANS-----PPGGWPRGQLFGMLSPTRSSI-------------LLEHISSV  200 (549)
T ss_pred             c----c----chhccc--chhhhhccch-hhcC-----CCCCCcCCcceeeeccchhhh-------------hhhcchhc
Confidence            0    0    000000  0000010000 1111     111112333333344333331             34555667


Q ss_pred             cCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          454 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       454 ~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      +|.+.. ......        ....|++|.+..++..+...+ |..+.|.....+|...
T Consensus       201 ~~~~~~-~~~~~~--------~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  201 DGSSPG-RETPLL--------NHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             cCcccc-ccccch--------hhhhhhhhccccchhhcccCC-ceecCCCCceEEecCC
Confidence            777765 221111        124589999999997777644 7788887777776544

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

Probab=98.67  E-value=1.3e-07  Score=87.21  Aligned_cols=79  Identities=16%  Similarity=0.349  Sum_probs=69.2

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhC
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  497 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng  497 (522)
                      .+.-.++-.|.++.+            +||..+|+.||+|.+|.|+++..+|..   .-+|||+|++.+++++|.-.|.+
T Consensus       239 eNVLFVCKLNPVTtD------------eDLeiIFSrFG~i~sceVIRD~ktgds---LqyaFiEFen~escE~AyFKMdN  303 (479)
T KOG0415|consen  239 ENVLFVCKLNPVTTD------------EDLEIIFSRFGKIVSCEVIRDRKTGDS---LQYAFIEFENKESCEQAYFKMDN  303 (479)
T ss_pred             cceEEEEecCCcccc------------cchhhHHhhcccceeeeEEecccccch---hheeeeeecchhhHHHHHhhhcc
Confidence            445555566667766            399999999999999999999999876   78899999999999999999999


Q ss_pred             CccCCeEEEEEEeC
Q 009944          498 RKFGGNTVNAFYYP  511 (522)
Q Consensus       498 ~~~~Gr~l~v~~~~  511 (522)
                      ..|..+.|+|.|..
T Consensus       304 vLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  304 VLIDDRRIHVDFSQ  317 (479)
T ss_pred             eeeccceEEeehhh
Confidence            99999999999854

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.64  E-value=3.1e-07  Score=89.44  Aligned_cols=164  Identities=21%  Similarity=0.256  Sum_probs=106.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCC---CCCcce---EEEEEEcChHHHHHHHHHHcCCccCCe
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKG---YGFCVYQDPAVTDIACAALNGLKMGDK  364 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~---~g~~~g---~afV~f~~~~~A~~Al~~l~g~~~~g~  364 (522)
                      ..-.++|||++||.+++|+.|...|..||.+. |.++...+   --.++|   |+|+.|+++......|.+..- .-.+.
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~-~~~~~  333 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE-GEGNY  333 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh-cccce
Confidence            34457899999999999999999999999974 44442111   112456   999999999988877765532 11222


Q ss_pred             EEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccC------CCCcCCCCCCcceEEEeeCCCCcCcCCChH
Q 009944          365 TLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTL------GGGMSLFGETLAKVLCLTEAITADALADDE  438 (522)
Q Consensus       365 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~  438 (522)
                      -+.|.-.+.+...                      -+.-+|...      ....+.....+++|..|+-.++.+      
T Consensus       334 yf~vss~~~k~k~----------------------VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~------  385 (520)
T KOG0129|consen  334 YFKVSSPTIKDKE----------------------VQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAE------  385 (520)
T ss_pred             EEEEecCcccccc----------------------eeEEeeEeccchhhhccCcccCccceEEecCCCCcchHH------
Confidence            2333322221110                      000011100      012333334566666677777776      


Q ss_pred             HHHHHHHHHHHHhh-ccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHH
Q 009944          439 EYEEILEDMREECG-KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA  494 (522)
Q Consensus       439 ~~~~~~~~l~~~f~-~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~  494 (522)
                             +|..+|+ .||.|..|-|-.|+.-.-|   +|-+-|+|.+...=.+||.+
T Consensus       386 -------eLA~imd~lyGgV~yaGIDtD~k~KYP---kGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  386 -------ELAMIMEDLFGGVLYVGIDTDPKLKYP---KGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             -------HHHHHHHHhcCceEEEEeccCcccCCC---CCcceeeecccHHHHHHHhh
Confidence                   8999998 8999999999998755444   45559999999999999885

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

Probab=98.56  E-value=6.4e-08  Score=85.37  Aligned_cols=164  Identities=14%  Similarity=0.152  Sum_probs=113.7

Q ss_pred             EEEcCCCCCCCHHH---HHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          297 VFVGGLPYYFTETQ---IKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       297 l~v~nLp~~~t~~~---l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      +++.++-..+..+-   +...|+.|-.+...+++.+. -+.-.+++|+.|.....-.++-..-++.+++-.+|++.-.+.
T Consensus        99 p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~-p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gts  177 (290)
T KOG0226|consen   99 PFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDR-PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTS  177 (290)
T ss_pred             ccccccccccCCCCCCcchhhhccchhhhhhhhhhcC-CCccCcccccCcchhhhhhhhccccccccccCcceeeccccc
Confidence            44555544443332   35677777666666777764 466788999999988777777666667777777666654432


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhc
Q 009944          374 SSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGK  453 (522)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~  453 (522)
                      -..-...                               .-...+.-++|--|.|.++.+             -|...|.+
T Consensus       178 wedPsl~-------------------------------ew~~~DfRIfcgdlgNevnd~-------------vl~raf~K  213 (290)
T KOG0226|consen  178 WEDPSLA-------------------------------EWDEDDFRIFCGDLGNEVNDD-------------VLARAFKK  213 (290)
T ss_pred             cCCcccc-------------------------------cCccccceeecccccccccHH-------------HHHHHHHh
Confidence            1100000                               000111334444566666665             78999999


Q ss_pred             cCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEE
Q 009944          454 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF  508 (522)
Q Consensus       454 ~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~  508 (522)
                      |-.....++.++.-+|+.   +|+.||.|.++.++..|+..|+|.+++.+.|++.
T Consensus       214 fpsf~~akviRdkRTgKS---kgygfVSf~~pad~~rAmrem~gkyVgsrpiklR  265 (290)
T KOG0226|consen  214 FPSFQKAKVIRDKRTGKS---KGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLR  265 (290)
T ss_pred             ccchhhcccccccccccc---ccceeeeecCHHHHHHHHHhhcccccccchhHhh
Confidence            999999999999999875   4555999999999999999999999999999864

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.56  E-value=4.8e-08  Score=91.96  Aligned_cols=177  Identities=18%  Similarity=0.127  Sum_probs=132.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ...++|++++...+.+.++..++..+|.+....+........++|+++|.|...+.+..||.......+.++.+.....+
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            34689999999999999999999999987777776666688899999999999999999998554456666666666554


Q ss_pred             CCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCC-CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHh
Q 009944          373 ASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGE-TLAKVLCLTEAITADALADDEEYEEILEDMREEC  451 (522)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f  451 (522)
                      .........                           ......... ....+.+++...+.+             +|+.+|
T Consensus       167 ~~~~~~~n~---------------------------~~~~~~~~s~~~~~~~~~~f~~~~d-------------~~~~~~  206 (285)
T KOG4210|consen  167 RRGLRPKNK---------------------------LSRLSSGPSDTIFFVGELDFSLTRD-------------DLKEHF  206 (285)
T ss_pred             cccccccch---------------------------hcccccCccccceeecccccccchH-------------HHhhhc
Confidence            322110000                           000011111 222244455444443             888999


Q ss_pred             hccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          452 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       452 ~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ..+|.|..+.++.+..++..   .|+|||.|.+...+..|+.. +...++|+++.+.+-+..
T Consensus       207 ~~~~~i~~~r~~~~~~s~~~---kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  207 VSSGEITSVRLPTDEESGDS---KGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             cCcCcceeeccCCCCCccch---hhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCC
Confidence            99999999999999988876   67889999999999999998 999999999999887654

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

Probab=98.52  E-value=9.9e-07  Score=68.03  Aligned_cols=79  Identities=23%  Similarity=0.329  Sum_probs=69.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHh--cCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC----CeEEEE
Q 009944          295 DRVFVGGLPYYFTETQIKELLES--FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG----DKTLTV  368 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~--~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~----g~~l~v  368 (522)
                      +||.|+|||...|.++|.+++..  .|....+-++.|-.++.+.|||||-|.+++.|.+-.+.++|..+.    .+.+.|
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            58999999999999999999884  355677888999889999999999999999999999999998774    678899


Q ss_pred             EEccC
Q 009944          369 RRATA  373 (522)
Q Consensus       369 ~~~~~  373 (522)
                      .||.-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            98854

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

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.52  E-value=1.2e-07  Score=88.64  Aligned_cols=179  Identities=16%  Similarity=0.061  Sum_probs=120.4

Q ss_pred             eeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEEEec
Q 009944          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (522)
Q Consensus       176 ~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~v~~  255 (522)
                      -|.|.||.+.+|.++++.+|..+|.|..+.++..   +.++.+......|||.|.+...+..|..|..++|-++.|.|..
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~---~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p   85 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPN---VDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRP   85 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCC---CCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEe
Confidence            6899999999999999999999999876655443   3344455556789999999999999998888888888877753


Q ss_pred             CC-CCCccc--cccCCCCCCC-----CCcc--------------ccc---ccCCCCC--CCCCCCCCeEEEcCCCCCCCH
Q 009944          256 PT-DYNPTL--AAALGPGQPS-----PNLN--------------LAA---VGLASGA--IGGAEGPDRVFVGGLPYYFTE  308 (522)
Q Consensus       256 ~~-~~~~~~--~~~~~~~~~~-----~~~~--------------~~~---~~~~~~~--~~~~~~~~~l~v~nLp~~~t~  308 (522)
                      .. ...+..  ...+++....     +...              .+.   ..+.+..  ....+...+|+|.+|+..+..
T Consensus        86 ~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l  165 (479)
T KOG4676|consen   86 YGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAIL  165 (479)
T ss_pred             cCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcc
Confidence            22 111111  0011100000     0000              000   0000000  000112267999999999999


Q ss_pred             HHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC
Q 009944          309 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (522)
Q Consensus       309 ~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  362 (522)
                      .++.+.|..+|.|....+.-    |...-+|-|+|........|+. ++|..+.
T Consensus       166 ~e~~e~f~r~Gev~ya~~as----k~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  166 PESGESFERKGEVSYAHTAS----KSRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             hhhhhhhhhcchhhhhhhhc----cCCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            99999999999998776643    3345578899999988888887 6777776

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

Probab=98.45  E-value=1e-07  Score=84.69  Aligned_cols=77  Identities=21%  Similarity=0.341  Sum_probs=66.4

Q ss_pred             hHHHHHHHHHHHHHhh-ccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          437 DEEYEEILEDMREECG-KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       437 ~~~~~~~~~~l~~~f~-~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      ...+++..++|..+|+ +||+|+++.|..+-....    +|-+||.|...++|++|++.|||..|+|++|.+.|.+...|
T Consensus        75 q~~~defyEd~f~E~~~kygEiee~~Vc~Nl~~hl----~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~~  150 (260)
T KOG2202|consen   75 QRHEDEFYEDVFTELEDKYGEIEELNVCDNLGDHL----VGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTDF  150 (260)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhhhhhcccchhh----hhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCch
Confidence            4457777889999998 999999998877654444    47889999999999999999999999999999999998776


Q ss_pred             cc
Q 009944          516 FN  517 (522)
Q Consensus       516 ~~  517 (522)
                      ..
T Consensus       151 re  152 (260)
T KOG2202|consen  151 RE  152 (260)
T ss_pred             hh
Confidence            53

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

Probab=98.45  E-value=5.7e-07  Score=87.94  Aligned_cols=83  Identities=22%  Similarity=0.389  Sum_probs=71.3

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++|||.+|...+-..+|+++|++||.+++..      +|....+...+.|+||++.+.++|.+|| .|+...|.|+
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAK------VVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGr  475 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAK------VVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGR  475 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceecee------eeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcce
Confidence            44568899999999999999999999999987633      3555566667889999999999999999 6999999999


Q ss_pred             eEEEecCCCC
Q 009944          250 AVRVRRPTDY  259 (522)
Q Consensus       250 ~~~v~~~~~~  259 (522)
                      .|.|..+++.
T Consensus       476 mISVEkaKNE  485 (940)
T KOG4661|consen  476 MISVEKAKNE  485 (940)
T ss_pred             eeeeeecccC
Confidence            9999877654

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

Probab=98.42  E-value=3.3e-07  Score=83.39  Aligned_cols=80  Identities=23%  Similarity=0.411  Sum_probs=75.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ....+||+|+.+.+|.++|...|+.||.|..|.++.+...|.++|||||+|.+.+.++.|+. |+|..|.|..+.|.+..
T Consensus       100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             CCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeee
Confidence            44689999999999999999999999999999999999899999999999999999999999 99999999999999864


Q ss_pred             C
Q 009944          373 A  373 (522)
Q Consensus       373 ~  373 (522)
                      -
T Consensus       179 ~  179 (231)
T KOG4209|consen  179 T  179 (231)
T ss_pred             e
Confidence            3

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

Probab=98.37  E-value=1.4e-06  Score=87.63  Aligned_cols=84  Identities=18%  Similarity=0.304  Sum_probs=73.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCC---CCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~---~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      ....++|||+||++.++++.|...|..||+|..|+|+....   ....+-||||-|.+..+|++|++.|+|..+.+..++
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            34456799999999999999999999999999999887542   334567999999999999999999999999999999


Q ss_pred             EEEccCC
Q 009944          368 VRRATAS  374 (522)
Q Consensus       368 v~~~~~~  374 (522)
                      +.|+...
T Consensus       251 ~gWgk~V  257 (877)
T KOG0151|consen  251 LGWGKAV  257 (877)
T ss_pred             ecccccc
Confidence            9998543

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

Probab=98.30  E-value=1.4e-06  Score=85.64  Aligned_cols=79  Identities=23%  Similarity=0.394  Sum_probs=65.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      ..+|||+|||.++++.+|.++|..||.|+...|..-...+...+||||+|.+.++++.||.+- -..++++.|.|.--..
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCCeeEEEEeccc
Confidence            345999999999999999999999999998776554323444489999999999999999854 6889999999986443

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.24  E-value=2.2e-07  Score=87.62  Aligned_cols=155  Identities=19%  Similarity=0.291  Sum_probs=111.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCC-ceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcC-CccCCeEEEEEEcc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG-LKMGDKTLTVRRAT  372 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~-i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g-~~~~g~~l~v~~~~  372 (522)
                      +.||++||.+.++..+|..+|...-. ...-.++       ..||+||.+.+...|.+|++.++| ..+.|..+.|.+.-
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~-------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee-------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            36899999999999999999985421 1111122       248999999999999999999999 56899999998874


Q ss_pred             CCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhh
Q 009944          373 ASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  452 (522)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~  452 (522)
                      ++......               .                           .|.+...          ---|+-|-.+..
T Consensus        75 ~kkqrsrk---------------~---------------------------Qirnipp----------ql~wevld~Ll~  102 (584)
T KOG2193|consen   75 PKKQRSRK---------------I---------------------------QIRNIPP----------QLQWEVLDSLLA  102 (584)
T ss_pred             hHHHHhhh---------------h---------------------------hHhcCCH----------HHHHHHHHHHHh
Confidence            42111000               0                           0111100          011246778889


Q ss_pred             ccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          453 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       453 ~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      .||+|+.|........      ....-|+|.+.+.+..||..|||..+++..+++.|.+...
T Consensus       103 qyg~ve~~eqvnt~~e------tavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPdeq  158 (584)
T KOG2193|consen  103 QYGTVENCEQVNTDSE------TAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPDEQ  158 (584)
T ss_pred             ccCCHhHhhhhccchH------HHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCchhh
Confidence            9999999865432211      1344789999999999999999999999999999998654

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.21  E-value=8.5e-08  Score=90.35  Aligned_cols=151  Identities=19%  Similarity=0.325  Sum_probs=117.4

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcC-ceecCceEE
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG-IIFEGVAVR  252 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~-~~~~g~~~~  252 (522)
                      .++|++||.+.++..+|..+|...- +           -..-.+--..||+||.+.+...|.+|+ .++| ..+.|+.+.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak-~-----------~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e   69 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAK-I-----------PGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQE   69 (584)
T ss_pred             CcccccccCCCCChHHHHHHhcccc-C-----------CCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceee
Confidence            4699999999999999999998751 1           111112224689999999999999999 4776 458899998


Q ss_pred             EecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEee-CCC
Q 009944          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK-DRD  331 (522)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~-~~~  331 (522)
                      |...-...                               ...+.+-|.|+|+...++.|..++..||.+..|..+. +.+
T Consensus        70 ~~~sv~kk-------------------------------qrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e  118 (584)
T KOG2193|consen   70 VEHSVPKK-------------------------------QRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE  118 (584)
T ss_pred             ccchhhHH-------------------------------HHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH
Confidence            87532221                               1124688999999999999999999999999886543 322


Q ss_pred             CCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          332 TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       332 ~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      +    -..-|+|.+.+.+..||..|+|..|....++|.|..
T Consensus       119 t----avvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen  119 T----AVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             H----HHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence            2    223478999999999999999999999999999974

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.19  E-value=2.8e-06  Score=79.67  Aligned_cols=197  Identities=13%  Similarity=0.105  Sum_probs=119.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCC---CCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~---~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ..|-|.||.+.+|.++++.+|...|.|..+.|+....   -......|||.|.+...+..|- .|.++.|-++.|.|-..
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEec
Confidence            3799999999999999999999999999998876432   1233568999999999999885 47778888888888765


Q ss_pred             cCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCC------CCCcceEEEeeCCCCc------Cc-----C
Q 009944          372 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLF------GETLAKVLCLTEAITA------DA-----L  434 (522)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~------~~~~~~v~~l~~~~~~------~~-----l  434 (522)
                      -..   ..+... .+..    ...+...   ...-.+++.++..      ...++.++.-+.+...      ++     .
T Consensus        87 ~~~---~~p~r~-af~~----l~~~nav---prll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~  155 (479)
T KOG4676|consen   87 GDE---VIPDRF-AFVE----LADQNAV---PRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTRE  155 (479)
T ss_pred             CCC---CCccHH-HHHh----cCccccc---ccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhh
Confidence            331   222221 1110    0111100   0011111211111      1112222221111110      00     1


Q ss_pred             CChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          435 ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       435 ~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                      +.+..-.++..++.+.|..+|.|....+.-...       .-+|-|+|........|+. ++|+.|.-....+..+.
T Consensus       156 v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask~~-------s~~c~~sf~~qts~~halr-~~gre~k~qhsr~ai~k  224 (479)
T KOG4676|consen  156 VQSLISAAILPESGESFERKGEVSYAHTASKSR-------SSSCSHSFRKQTSSKHALR-SHGRERKRQHSRRAIIK  224 (479)
T ss_pred             hhcchhhhcchhhhhhhhhcchhhhhhhhccCC-------CcchhhhHhhhhhHHHHHH-hcchhhhhhhhhhhhcC
Confidence            113344556789999999999999887754331       1345699999998899988 58888775544444433

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

Probab=98.13  E-value=9.1e-06  Score=79.95  Aligned_cols=78  Identities=22%  Similarity=0.331  Sum_probs=63.5

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe--cCCCcEEEEEEeCHHHHHHHHHhcCceecCc
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~--~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~  249 (522)
                      ....+|||.|||.++++.+|.++|..||.|+..        -+.+..  +....||||+|.+.++++.|+.-+...++++
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~--------~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~  357 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEG--------GIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGR  357 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhccccccc--------ceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCe
Confidence            344569999999999999999999999998532        223332  3344899999999999999998889999999


Q ss_pred             eEEEecCC
Q 009944          250 AVRVRRPT  257 (522)
Q Consensus       250 ~~~v~~~~  257 (522)
                      +|.|+.-.
T Consensus       358 kl~Veek~  365 (419)
T KOG0116|consen  358 KLNVEEKR  365 (419)
T ss_pred             eEEEEecc
Confidence            99997533

>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=98.12  E-value=1.4e-05  Score=58.43  Aligned_cols=69  Identities=13%  Similarity=0.257  Sum_probs=47.6

Q ss_pred             CeEEEcCCCCCCCHHH----HHHHHHhcCC-ceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEE
Q 009944          295 DRVFVGGLPYYFTETQ----IKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~----l~~~F~~~G~-i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (522)
                      ..|+|.|||.+.+...    |+.++..+|. |..|.          .+.|+|.|.+.+.|.+|.+.|+|..+.|..|.|.
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----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            3699999999988764    5666667875 65541          2469999999999999999999999999999999


Q ss_pred             EccC
Q 009944          370 RATA  373 (522)
Q Consensus       370 ~~~~  373 (522)
                      |...
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            9744

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

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

Probab=98.09  E-value=1.2e-05  Score=62.14  Aligned_cols=79  Identities=11%  Similarity=0.165  Sum_probs=58.8

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceec----Cc
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE----GV  249 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~----g~  249 (522)
                      ++|+|.|||...|.++|.+++.....  +..  .-.-..+|.....+.|||||.|.+++.|.... .++|..+.    .+
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~--g~y--DF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~K   77 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFK--GKY--DFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKK   77 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhcc--Ccc--eEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCc
Confidence            58999999999999999999987621  110  00111334445667899999999999999999 69998886    35


Q ss_pred             eEEEecCC
Q 009944          250 AVRVRRPT  257 (522)
Q Consensus       250 ~~~v~~~~  257 (522)
                      .+.|.++.
T Consensus        78 vc~i~yAr   85 (97)
T PF04059_consen   78 VCEISYAR   85 (97)
T ss_pred             EEEEehhH
Confidence            67777654

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

>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=98.04  E-value=4.6e-05  Score=55.77  Aligned_cols=62  Identities=18%  Similarity=0.342  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHHHhhccC-CeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          439 EYEEILEDMREECGKYG-TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       439 ~~~~~~~~l~~~f~~~G-~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ....+...|++++.-+| +|..|.=             +.|+|.|.+++.|.+|++-|+|..+-|++|.|+|.+..
T Consensus        15 d~~~I~~RL~qLsdNCGGkVl~v~~-------------~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~~   77 (90)
T PF11608_consen   15 DPSSIKNRLRQLSDNCGGKVLSVSG-------------GTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPKN   77 (90)
T ss_dssp             -HHHHHHHHHHHHHTTT--EEE--T-------------T-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--S
T ss_pred             CHHHHHHHHHHHhhccCCEEEEEeC-------------CEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCCc
Confidence            35677789999998766 6776621             68899999999999999999999999999999998754

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

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

Probab=98.04  E-value=5.3e-06  Score=77.57  Aligned_cols=83  Identities=23%  Similarity=0.389  Sum_probs=76.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCce--------EEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCe
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK  364 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~--------~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~  364 (522)
                      ...+|||.+||..+++.+|.++|.++|.|.        .|.|.++++|++.+|-|.|.|.+...|+.|+.-+++..|.+.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            346899999999999999999999999885        478888999999999999999999999999999999999999


Q ss_pred             EEEEEEccCCC
Q 009944          365 TLTVRRATASS  375 (522)
Q Consensus       365 ~l~v~~~~~~~  375 (522)
                      +|+|.+|....
T Consensus       145 ~ikvs~a~~r~  155 (351)
T KOG1995|consen  145 TIKVSLAERRT  155 (351)
T ss_pred             Cchhhhhhhcc
Confidence            99999987643

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

Probab=98.02  E-value=1.3e-05  Score=80.98  Aligned_cols=77  Identities=23%  Similarity=0.376  Sum_probs=65.4

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe---------cCCCcEEEEEEeCHHHHHHHH-H
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---------NHEKKFAFVEMRTVEEASNAM-A  240 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~---------~~~~g~afV~f~~~~~a~~a~-~  240 (522)
                      ....+.|||+||++.++++.|...|..||+|.            .+.+         ...+.||||-|.+..+|++|+ .
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPla------------svKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~  238 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLA------------SVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKE  238 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCccc------------ceeeecccchhhhccccccceeeehhhhhHHHHHHH
Confidence            44567899999999999999999999999853            3332         123679999999999999999 7


Q ss_pred             hcCceecCceEEEecCCCC
Q 009944          241 LDGIIFEGVAVRVRRPTDY  259 (522)
Q Consensus       241 ~~~~~~~g~~~~v~~~~~~  259 (522)
                      |+|+.+.+..+++.|.+.-
T Consensus       239 lqg~iv~~~e~K~gWgk~V  257 (877)
T KOG0151|consen  239 LQGIIVMEYEMKLGWGKAV  257 (877)
T ss_pred             hcceeeeeeeeeecccccc
Confidence            9999999999999997643

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.01  E-value=2e-05  Score=72.56  Aligned_cols=87  Identities=18%  Similarity=0.321  Sum_probs=62.8

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhC
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  497 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng  497 (522)
                      .-..|++|+..+..++...-+       .--++|.+||+|..|.|.+.........+..-+||+|.+.+||.+||.+++|
T Consensus       115 NLvYVigi~pkva~Ee~~~vL-------k~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDg  187 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVL-------KRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDG  187 (480)
T ss_pred             ceeEEecCCCCCCcccccccc-------cchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcc
Confidence            345566666665555422211       3368999999999999977653322222212269999999999999999999


Q ss_pred             CccCCeEEEEEEeC
Q 009944          498 RKFGGNTVNAFYYP  511 (522)
Q Consensus       498 ~~~~Gr~l~v~~~~  511 (522)
                      ..++|+.|+++|-+
T Consensus       188 s~~DGr~lkatYGT  201 (480)
T COG5175         188 SLLDGRVLKATYGT  201 (480)
T ss_pred             ccccCceEeeecCc
Confidence            99999999999865

>PF06495 Transformer: Fruit fly transformer protein; InterPro: IPR010519 This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly)

Probab=97.97  E-value=3.8e-05  Score=63.91  Aligned_cols=16  Identities=25%  Similarity=0.378  Sum_probs=12.2

Q ss_pred             CCCCCCCCCccCCCCC
Q 009944          111 RSGFDMAPPAAAMLPG  126 (522)
Q Consensus       111 ~~~~d~~~~~~~~~~~  126 (522)
                      ...|++++++|+.+.+
T Consensus       116 ~~yv~VPp~gf~~~y~  131 (182)
T PF06495_consen  116 TKYVDVPPPGFEYAYG  131 (182)
T ss_pred             eeeccCCCcccccccC
Confidence            3479999999876654

The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster [].; GO: 0006397 mRNA processing, 0046660 female sex differentiation, 0005634 nucleus

>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=97.88  E-value=2.4e-05  Score=62.00  Aligned_cols=70  Identities=23%  Similarity=0.336  Sum_probs=45.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcC-----CccCCeEEEEEE
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG-----LKMGDKTLTVRR  370 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g-----~~~~g~~l~v~~  370 (522)
                      .|+|.|++..++.++|++.|+.||.|.+|.+....      ..|||.|.+.+.|++|+..+.-     ..+.+..+++..
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            68899999999999999999999999999987653      2699999999999999988753     466777666664


Q ss_pred             c
Q 009944          371 A  371 (522)
Q Consensus       371 ~  371 (522)
                      -
T Consensus        77 L   77 (105)
T PF08777_consen   77 L   77 (105)
T ss_dssp             -
T ss_pred             C
Confidence            3

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

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

Probab=97.86  E-value=5.2e-05  Score=68.88  Aligned_cols=67  Identities=15%  Similarity=0.253  Sum_probs=57.9

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      .||+++|+.||.+..+-+-.+. .|.+   .|+|-|.|...+||..||+.+||..+.|+.+++..+.....
T Consensus        98 ~Dl~eLF~~~~~~~r~~vhy~~-~G~s---~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~~~  164 (243)
T KOG0533|consen   98 ADLKELFAEFGELKRVAVHYDR-AGRS---LGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSPSQ  164 (243)
T ss_pred             HHHHHHHHHhccceEEeeccCC-CCCC---CccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCccc
Confidence            4999999999988888887766 5554   68899999999999999999999999999999988765443

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

Probab=97.71  E-value=7.9e-05  Score=67.97  Aligned_cols=68  Identities=15%  Similarity=0.195  Sum_probs=59.7

Q ss_pred             HHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccccc
Q 009944          446 DMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFN  517 (522)
Q Consensus       446 ~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~~~  517 (522)
                      +|..+|+.+|.|..+.|+.+...+.+   +|+|||+|.+.+.+++|+. |+|..|.|+.+.|++.--.....
T Consensus       117 ~~e~hf~~Cg~i~~~ti~~d~~~~~~---k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r~~~pg~  184 (231)
T KOG4209|consen  117 KIELHFESCGGINRVTVPKDKFRGHP---KGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKRTNVPGM  184 (231)
T ss_pred             hhhheeeccCCccceeeeccccCCCc---ceeEEEecccHhhhHHHhh-cCCcccccccceeeeeeeecCCc
Confidence            79999999999999999999877664   7899999999999999999 99999999999999865444333

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

Probab=97.63  E-value=0.00014  Score=65.83  Aligned_cols=76  Identities=14%  Similarity=0.152  Sum_probs=58.0

Q ss_pred             EEEcCC--CCCCCH---HHHHHHHHhcCCceEEEEeeCCCCCCc-ceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          297 VFVGGL--PYYFTE---TQIKELLESFGTLHGFDLVKDRDTGNS-KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       297 l~v~nL--p~~~t~---~~l~~~F~~~G~i~~v~~~~~~~~g~~-~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      |++.|+  +-.+++   +++.+.|++||.|..|.|.-.+..-.. .--.||+|...++|.+|+-.|||.+|+|+.+...|
T Consensus       284 lllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~F  363 (378)
T KOG1996|consen  284 LLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACF  363 (378)
T ss_pred             HHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeehee
Confidence            555555  233443   578999999999998877765421111 12379999999999999999999999999999998


Q ss_pred             cc
Q 009944          371 AT  372 (522)
Q Consensus       371 ~~  372 (522)
                      .+
T Consensus       364 yn  365 (378)
T KOG1996|consen  364 YN  365 (378)
T ss_pred             cc
Confidence            64

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

Probab=97.54  E-value=0.00043  Score=68.51  Aligned_cols=84  Identities=20%  Similarity=0.351  Sum_probs=65.9

Q ss_pred             ceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCc
Q 009944          420 AKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRK  499 (522)
Q Consensus       420 ~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~  499 (522)
                      -.|+++.+..-..    ..-...+..-|..+|+++|+|.++.++.++.+|+    +|++|++|++..+|+.|++.|||+.
T Consensus        58 D~vVvv~g~PvV~----~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggt----kG~lf~E~~~~~~A~~aVK~l~G~~  129 (698)
T KOG2314|consen   58 DSVVVVDGAPVVG----PARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGT----KGYLFVEYASMRDAKKAVKSLNGKR  129 (698)
T ss_pred             ceEEEECCCcccC----hhHHHHHHHHHHHHHHhhccccceeeccCccCCe----eeEEEEEecChhhHHHHHHhcccce
Confidence            3455555543222    2235556678899999999999999999987775    6999999999999999999999999


Q ss_pred             cC-CeEEEEEEeC
Q 009944          500 FG-GNTVNAFYYP  511 (522)
Q Consensus       500 ~~-Gr~l~v~~~~  511 (522)
                      |. +++..|...+
T Consensus       130 ldknHtf~v~~f~  142 (698)
T KOG2314|consen  130 LDKNHTFFVRLFK  142 (698)
T ss_pred             ecccceEEeehhh
Confidence            96 6777776654

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

Probab=97.53  E-value=0.00096  Score=55.14  Aligned_cols=61  Identities=18%  Similarity=0.394  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          441 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       441 ~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      +.+..+|.+.|..||+|.-|++.-           +..+|+|.+-+.|.+|+. |+|..++|+.|+|.+-+.+
T Consensus        47 d~l~~~ll~~~~~~GevvLvRfv~-----------~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   47 DNLMDELLQKFAQYGEVVLVRFVG-----------DTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHHHHHHCCS-ECEEEEET-----------TCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             HHHHHHHHHHHHhCCceEEEEEeC-----------CeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            345678999999999999888764           456999999999999998 8999999999999987764

; PDB: 1UFW_A 2DNR_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.51  E-value=0.00023  Score=65.73  Aligned_cols=81  Identities=17%  Similarity=0.297  Sum_probs=63.7

Q ss_pred             CCeEEEcCCCCCCCHHHH------HHHHHhcCCceEEEEeeCCCCCCc-ceE--EEEEEcChHHHHHHHHHHcCCccCCe
Q 009944          294 PDRVFVGGLPYYFTETQI------KELLESFGTLHGFDLVKDRDTGNS-KGY--GFCVYQDPAVTDIACAALNGLKMGDK  364 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l------~~~F~~~G~i~~v~~~~~~~~g~~-~g~--afV~f~~~~~A~~Al~~l~g~~~~g~  364 (522)
                      .+-+||-+||+.+..+++      .++|.+||.|..|.+-+.-.+..+ .+.  .||.|.+.++|..||.+.+|..++|+
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            356899999998877662      578999999988776543211111 222  39999999999999999999999999


Q ss_pred             EEEEEEccCC
Q 009944          365 TLTVRRATAS  374 (522)
Q Consensus       365 ~l~v~~~~~~  374 (522)
                      .|+..|.+.+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999997755

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.51  E-value=7.3e-05  Score=69.21  Aligned_cols=78  Identities=24%  Similarity=0.386  Sum_probs=69.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCC--ceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGT--LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~--i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      .++||+||-+.+|++||.+.+...|.  +.++++..+..+|+++|||+|...+.....+.|+.|-.++|.|..-.|...+
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            47999999999999999999997775  7788888898999999999999999999999999999999988776666553

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

Probab=97.48  E-value=0.00041  Score=68.62  Aligned_cols=75  Identities=25%  Similarity=0.378  Sum_probs=62.2

Q ss_pred             CeEEEcCCCCCCC------HHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc-CCeEEE
Q 009944          295 DRVFVGGLPYYFT------ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-GDKTLT  367 (522)
Q Consensus       295 ~~l~v~nLp~~~t------~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~-~g~~l~  367 (522)
                      .+|+|.|+|.--.      ..-|..+|+++|+|..+.++.+.++| .+||.|++|.+..+|+.|++.|||..| ...++.
T Consensus        59 ~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~  137 (698)
T KOG2314|consen   59 SVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFF  137 (698)
T ss_pred             eEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceEE
Confidence            5799999986432      23577899999999999999886555 899999999999999999999999887 456677


Q ss_pred             EEE
Q 009944          368 VRR  370 (522)
Q Consensus       368 v~~  370 (522)
                      |..
T Consensus       138 v~~  140 (698)
T KOG2314|consen  138 VRL  140 (698)
T ss_pred             eeh
Confidence            764

>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=97.39  E-value=0.00048  Score=54.64  Aligned_cols=58  Identities=19%  Similarity=0.288  Sum_probs=38.3

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCC-----ccCCeEEEEEEeC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGR-----KFGGNTVNAFYYP  511 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~-----~~~Gr~l~v~~~~  511 (522)
                      ++|++.|+.||.|..|.+...         --.|||.|.+++.|+.|+..+.-.     .+.+..+.+....
T Consensus        16 e~iK~~f~~~g~V~yVD~~~G---------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vLe   78 (105)
T PF08777_consen   16 EDIKEAFSQFGEVAYVDFSRG---------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVLE   78 (105)
T ss_dssp             HHHHHHT-SS--EEEEE--TT----------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE---
T ss_pred             HHHHHHHHhcCCcceEEecCC---------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEECC
Confidence            599999999999999999653         346799999999999999988654     6778888777665

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

>KOG2888 consensus Putative RNA binding protein [General function prediction only]

Probab=97.38  E-value=5.7e-05  Score=69.36  Aligned_cols=11  Identities=45%  Similarity=0.613  Sum_probs=4.4

Q ss_pred             CCCCcccccCC
Q 009944           87 HSSDRFRNRSK   97 (522)
Q Consensus        87 rsr~r~~~r~r   97 (522)
                      ||++|+++++|
T Consensus       379 RsrSRSR~~sR  389 (453)
T KOG2888|consen  379 RSRSRSRSRSR  389 (453)
T ss_pred             hhhhhhccccc
Confidence            44444443333

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

Probab=97.34  E-value=0.00057  Score=46.61  Aligned_cols=52  Identities=19%  Similarity=0.527  Sum_probs=43.5

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM  239 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~  239 (522)
                      +.|-|.|.++...+. +..+|..||.            |.++.......++||+|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGe------------I~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGE------------IVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCC------------EEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            468899998777654 5568889998            677777778899999999999999986

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

Probab=97.31  E-value=0.00012  Score=65.41  Aligned_cols=63  Identities=11%  Similarity=0.224  Sum_probs=52.9

Q ss_pred             HHHHHHHH-hcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          309 TQIKELLE-SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       309 ~~l~~~F~-~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ++|...|+ +||.|+.+.+..+. .-.-.|-+||.|...++|++|++.|||.+|.|++|...+..
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 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            56777777 99999988766542 22346889999999999999999999999999999999864

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

Probab=97.26  E-value=0.00075  Score=46.04  Aligned_cols=52  Identities=19%  Similarity=0.339  Sum_probs=41.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHH
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC  353 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al  353 (522)
                      +.|-|.|.++...+ .|...|..||.|..+.+...      .-+.||.|.+..+|++||
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            46889999877664 46669999999999887622      347999999999999985

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.17  E-value=0.001  Score=59.58  Aligned_cols=100  Identities=20%  Similarity=0.240  Sum_probs=80.3

Q ss_pred             HHHHH-HhcCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHH
Q 009944          235 ASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKE  313 (522)
Q Consensus       235 a~~a~-~~~~~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~  313 (522)
                      |..|. +|++....|+.+.|.++-.                                    ..|+|.||...+..+.|.+
T Consensus         7 ae~ak~eLd~~~~~~~~lr~rfa~~------------------------------------a~l~V~nl~~~~sndll~~   50 (275)
T KOG0115|consen    7 AEIAKRELDGRFPKGRSLRVRFAMH------------------------------------AELYVVNLMQGASNDLLEQ   50 (275)
T ss_pred             HHHHHHhcCCCCCCCCceEEEeecc------------------------------------ceEEEEecchhhhhHHHHH
Confidence            45555 6899999999999997422                                    3699999999999999999


Q ss_pred             HHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcC----CccCCeEEEEEEc
Q 009944          314 LLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG----LKMGDKTLTVRRA  371 (522)
Q Consensus       314 ~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g----~~~~g~~l~v~~~  371 (522)
                      .|+.||+|....++.| ..++..+-++|+|...-.|.+|+..+.-    .+..+.++.|...
T Consensus        51 ~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   51 AFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             hhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence            9999999987766666 3688889999999999999999988742    2345566666543

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

Probab=97.15  E-value=0.0003  Score=62.80  Aligned_cols=71  Identities=21%  Similarity=0.450  Sum_probs=60.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCC--------CCcc----eEEEEEEcChHHHHHHHHHHcCCccC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT--------GNSK----GYGFCVYQDPAVTDIACAALNGLKMG  362 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~--------g~~~----g~afV~f~~~~~A~~Al~~l~g~~~~  362 (522)
                      -.||+++||+......|+++|+.||.|-.|.|.....+        |.+.    --|.|+|.+...|..+...|||..|+
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            47999999999999999999999999999988776544        2222    23789999999999999999999999


Q ss_pred             CeE
Q 009944          363 DKT  365 (522)
Q Consensus       363 g~~  365 (522)
                      |+.
T Consensus       155 gkk  157 (278)
T KOG3152|consen  155 GKK  157 (278)
T ss_pred             CCC
Confidence            865

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

Probab=97.13  E-value=0.00054  Score=64.46  Aligned_cols=88  Identities=19%  Similarity=0.146  Sum_probs=70.4

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCC--CCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceec
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSA--GPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~--~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~  247 (522)
                      .....+|||.+||..+++++|.++|.++|.|..-.-.  ..+.+-.+..+...++-|.|.|.+...|+.|+ -+++..|.
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            4456689999999999999999999999988643322  11233444566778999999999999999999 59999999


Q ss_pred             CceEEEecCCC
Q 009944          248 GVAVRVRRPTD  258 (522)
Q Consensus       248 g~~~~v~~~~~  258 (522)
                      +.+|+|..+..
T Consensus       143 gn~ikvs~a~~  153 (351)
T KOG1995|consen  143 GNTIKVSLAER  153 (351)
T ss_pred             CCCchhhhhhh
Confidence            99999865443

>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=97.03  E-value=0.0031  Score=49.19  Aligned_cols=71  Identities=23%  Similarity=0.310  Sum_probs=51.1

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEE------------EecCCCcEEEEEEeCHHHHHHHHH
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV------------YINHEKKFAFVEMRTVEEASNAMA  240 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~------------~~~~~~g~afV~f~~~~~a~~a~~  240 (522)
                      ....|.|-|.|+. ....|.+.|++||.|           +...            ..........|+|.++.+|.+||.
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~I-----------le~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~   72 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTI-----------LEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ   72 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-E-----------ECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceE-----------EEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH
Confidence            3457999999988 455688899999985           3332            344566789999999999999999


Q ss_pred             hcCceecCceE-EEec
Q 009944          241 LDGIIFEGVAV-RVRR  255 (522)
Q Consensus       241 ~~~~~~~g~~~-~v~~  255 (522)
                      .||..|.|.-| -|.+
T Consensus        73 ~NG~i~~g~~mvGV~~   88 (100)
T PF05172_consen   73 KNGTIFSGSLMVGVKP   88 (100)
T ss_dssp             TTTEEETTCEEEEEEE
T ss_pred             hCCeEEcCcEEEEEEE
Confidence            99999998654 4554

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=96.96  E-value=0.002  Score=50.18  Aligned_cols=65  Identities=14%  Similarity=0.237  Sum_probs=44.7

Q ss_pred             HHHHHHhhccCCeEEEE-ecCCCCCC---CCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEE-EEEe
Q 009944          445 EDMREECGKYGTLVNVV-IPRPDQNG---GETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVN-AFYY  510 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~-i~~~~~~g---~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~-v~~~  510 (522)
                      ..|.++|+.||.|.+.. +.++...-   ....|.....|+|+++.+|.+||.. ||..|+|..+. |.+.
T Consensus        20 ~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~mvGV~~~   89 (100)
T PF05172_consen   20 NQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSLMVGVKPC   89 (100)
T ss_dssp             HHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCEEEEEEE-
T ss_pred             HHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcEEEEEEEc
Confidence            48999999999998875 22211000   0012346899999999999999995 99999987655 6665

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.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.75  E-value=0.0029  Score=56.68  Aligned_cols=92  Identities=20%  Similarity=0.247  Sum_probs=71.6

Q ss_pred             HHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeC
Q 009944          348 VTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTE  427 (522)
Q Consensus       348 ~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~  427 (522)
                      -|..|-..|++....|+.+.|.|+..                                            ...+|++|..
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~--------------------------------------------a~l~V~nl~~   41 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMH--------------------------------------------AELYVVNLMQ   41 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeecc--------------------------------------------ceEEEEecch
Confidence            45666677999999999999999954                                            4567777777


Q ss_pred             CCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCcc
Q 009944          428 AITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF  500 (522)
Q Consensus       428 ~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~  500 (522)
                      .++.+             .+.+.|+.||.|+..++..|. .+.+   .|-.+|+|...-.|.+|+...+-.-|
T Consensus        42 ~~snd-------------ll~~~f~~fg~~e~av~~vD~-r~k~---t~eg~v~~~~k~~a~~a~rr~~~~g~   97 (275)
T KOG0115|consen   42 GASND-------------LLEQAFRRFGPIERAVAKVDD-RGKP---TREGIVEFAKKPNARKAARRCREGGF   97 (275)
T ss_pred             hhhhH-------------HHHHhhhhcCccchheeeecc-cccc---cccchhhhhcchhHHHHHHHhccCcc
Confidence            76665             789999999999997776665 3332   35559999999999999998854444

>KOG2548 consensus SWAP mRNA splicing regulator [RNA processing and modification]

Probab=96.70  E-value=0.0032  Score=61.88  Aligned_cols=19  Identities=16%  Similarity=-0.076  Sum_probs=9.5

Q ss_pred             eCCCccCcHHHHHHHHHHH
Q 009944          180 GGLPPLANEQAIATFFSQV  198 (522)
Q Consensus       180 ~nlp~~~t~~~l~~~f~~~  198 (522)
                      ||--+.+|..+....|-++
T Consensus       555 G~~r~klt~~~~lk~rmq~  573 (653)
T KOG2548|consen  555 GNSRPKLTFFECLKSRMQF  573 (653)
T ss_pred             CCCCCcccHHHHHHHHHHH
Confidence            4555566655544444333

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.66  E-value=0.0093  Score=43.92  Aligned_cols=53  Identities=19%  Similarity=0.387  Sum_probs=40.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHc
Q 009944          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  357 (522)
Q Consensus       297 l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  357 (522)
                      ||--.+|..+...||.++|+.||.|. |.++.+-       -|||.+.+.+.|..|+..+.
T Consensus        11 VFhltFPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   11 VFHLTFPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             EEEEE--TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             EEEEeCchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            44444999999999999999999984 5566542       59999999999999999885

; 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.

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

Probab=96.65  E-value=0.0018  Score=62.11  Aligned_cols=66  Identities=14%  Similarity=0.255  Sum_probs=55.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeC---CCCC--C--------cceEEEEEEcChHHHHHHHHHHcC
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD---RDTG--N--------SKGYGFCVYQDPAVTDIACAALNG  358 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~---~~~g--~--------~~g~afV~f~~~~~A~~Al~~l~g  358 (522)
                      +.++|.+-|||.+-..+.|.++|..+|.|..|+|...   ++++  .        .+-+|||+|...+.|.+|.+.|+.
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            4579999999999999999999999999999999876   3322  1        145799999999999999998854

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

Probab=96.58  E-value=0.0099  Score=49.27  Aligned_cols=56  Identities=20%  Similarity=0.364  Sum_probs=46.1

Q ss_pred             HHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          309 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       309 ~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .+|.+.|..||.+.-|+++.+        .-+|+|.+-+.|.+|+. ++|.+++|+.|+|..-++
T Consensus        51 ~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE---
T ss_pred             HHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCc
Confidence            378888999999888887754        37999999999999988 999999999999998765

; PDB: 1UFW_A 2DNR_A.

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

Probab=96.50  E-value=0.025  Score=55.32  Aligned_cols=76  Identities=16%  Similarity=0.164  Sum_probs=62.9

Q ss_pred             hcccceeEEeCCCccC-cHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLA-NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~-t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~  249 (522)
                      ....+.|-+.-.|+.+ |-++|...|.+||.            |.++.+..+.-.|.|+|.+..+|-.|....+..|+++
T Consensus       369 ~~dhs~l~lek~~~glnt~a~ln~hfA~fG~------------i~n~qv~~~~~~a~vTF~t~aeag~a~~s~~avlnnr  436 (526)
T KOG2135|consen  369 VVDHSPLALEKSPFGLNTIADLNPHFAQFGE------------IENIQVDYSSLHAVVTFKTRAEAGEAYASHGAVLNNR  436 (526)
T ss_pred             hcccchhhhhccCCCCchHhhhhhhhhhcCc------------cccccccCchhhheeeeeccccccchhccccceecCc
Confidence            3445667777777775 77899999999998            5666666667789999999999988888999999999


Q ss_pred             eEEEecCCC
Q 009944          250 AVRVRRPTD  258 (522)
Q Consensus       250 ~~~v~~~~~  258 (522)
                      .|+|.|.+.
T Consensus       437 ~iKl~whnp  445 (526)
T KOG2135|consen  437 FIKLFWHNP  445 (526)
T ss_pred             eeEEEEecC
Confidence            999999654

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

Probab=96.41  E-value=0.0046  Score=59.45  Aligned_cols=72  Identities=15%  Similarity=0.283  Sum_probs=52.3

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCC---CCCCCCCC-------CccEEEEEecChHh
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRP---DQNGGETP-------GVGKVFLEYYDAVG  487 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~---~~~g~~~~-------g~G~afV~F~~~~~  487 (522)
                      .++++++..|+...-      .|    +.|.++|+.+|.|..|.|.+.   +.+.....       .+-||+|+|+..+.
T Consensus       229 l~srtivaenLP~Dh------~~----enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~  298 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDH------SY----ENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEA  298 (484)
T ss_pred             cccceEEEecCCcch------HH----HHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHH
Confidence            567777775553332      22    689999999999999999987   33322111       14579999999999


Q ss_pred             HHHHHHHHhCCc
Q 009944          488 CATAKNALSGRK  499 (522)
Q Consensus       488 A~~Ai~~lng~~  499 (522)
                      |.+|.+.||...
T Consensus       299 A~KA~e~~~~e~  310 (484)
T KOG1855|consen  299 ARKARELLNPEQ  310 (484)
T ss_pred             HHHHHHhhchhh
Confidence            999999886443

>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=96.36  E-value=0.0099  Score=52.21  Aligned_cols=62  Identities=15%  Similarity=0.311  Sum_probs=47.9

Q ss_pred             HHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHh--CCccCCeEEEEEEeCCcc
Q 009944          444 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS--GRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       444 ~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~ln--g~~~~Gr~l~v~~~~~~~  514 (522)
                      .+.|.++|..|+.+..+.+++.         ++-+.|.|.+.++|..|...|+  +..|.|..|+|.|+....
T Consensus         9 ~~~l~~l~~~~~~~~~~~~L~s---------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    9 LAELEELFSTYDPPVQFSPLKS---------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             HHHHHHHHHTT-SS-EEEEETT---------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             HHHHHHHHHhcCCceEEEEcCC---------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            4689999999999988877653         5889999999999999999999  999999999999985443

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.35  E-value=0.024  Score=39.63  Aligned_cols=55  Identities=20%  Similarity=0.349  Sum_probs=44.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhc---CCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHH
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL  356 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~---G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l  356 (522)
                      +..|+|.|++. .+.++|+.+|..|   .....|.++-|.       -|=|.|.+.+.|.+||.+|
T Consensus         5 peavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            35899999965 7778899999998   124467787763       3899999999999999764

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

Probab=96.29  E-value=0.0045  Score=61.93  Aligned_cols=76  Identities=25%  Similarity=0.263  Sum_probs=61.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHH-hcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc---CCeEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLE-SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM---GDKTLT  367 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~-~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~---~g~~l~  367 (522)
                      ...+.|+|.||-.-.|.-+|+.++. ..|.|...+|-+      -+..|||.|.+.++|...+.+|||..+   +++.|.
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDk------IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~  515 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDK------IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLI  515 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHHHH------hhcceeEecccHHHHHHHHHHHhccccCCCCCceeE
Confidence            4457899999999999999999999 555666653321      134699999999999999999999776   678899


Q ss_pred             EEEccC
Q 009944          368 VRRATA  373 (522)
Q Consensus       368 v~~~~~  373 (522)
                      +.|...
T Consensus       516 adf~~~  521 (718)
T KOG2416|consen  516 ADFVRA  521 (718)
T ss_pred             eeecch
Confidence            998754

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=96.01  E-value=0.0074  Score=56.30  Aligned_cols=78  Identities=15%  Similarity=0.115  Sum_probs=58.1

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHH-hcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~~  251 (522)
                      ..-++||+||-+.+|++||.+.+...|...    +...+-+.....+.++|||+|...+....++.|+ |-...|.|+.-
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~----~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P  154 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQ----FADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSP  154 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHH----HhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCC
Confidence            345799999999999999999998877531    1111112223346789999999999999999995 77788998765


Q ss_pred             EEe
Q 009944          252 RVR  254 (522)
Q Consensus       252 ~v~  254 (522)
                      .|.
T Consensus       155 ~V~  157 (498)
T KOG4849|consen  155 TVL  157 (498)
T ss_pred             eee
Confidence            553

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

Probab=95.91  E-value=0.0068  Score=60.71  Aligned_cols=82  Identities=15%  Similarity=0.235  Sum_probs=65.0

Q ss_pred             CCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhc-cCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHH
Q 009944          416 GETLAKVLCLTEAITADALADDEEYEEILEDMREECGK-YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA  494 (522)
Q Consensus       416 ~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~-~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~  494 (522)
                      -...++|+.|.|++-+..|          .+|+.++.. .|.|+...|-+-         +..|||.|.+.++|...+.+
T Consensus       440 R~~~SnvlhI~nLvRPFTl----------gQLkelL~rtgg~Vee~WmDkI---------KShCyV~yss~eEA~atr~A  500 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTL----------GQLKELLGRTGGNVEEFWMDKI---------KSHCYVSYSSVEEAAATREA  500 (718)
T ss_pred             CCCccceEeeecccccchH----------HHHHHHHhhccCchHHHHHHHh---------hcceeEecccHHHHHHHHHH
Confidence            3467889999998887744          589999984 556666644332         24689999999999999999


Q ss_pred             HhCCcc---CCeEEEEEEeCCcccc
Q 009944          495 LSGRKF---GGNTVNAFYYPEDKYF  516 (522)
Q Consensus       495 lng~~~---~Gr~l~v~~~~~~~~~  516 (522)
                      |||...   +++.|.+.|+..+.+.
T Consensus       501 lhnV~WP~sNPK~L~adf~~~deld  525 (718)
T KOG2416|consen  501 LHNVQWPPSNPKHLIADFVRADELD  525 (718)
T ss_pred             HhccccCCCCCceeEeeecchhHHH
Confidence            999986   7799999999887654

>KOG3263 consensus Nucleic acid binding protein [General function prediction only]

Probab=95.71  E-value=0.0015  Score=54.29  Aligned_cols=10  Identities=0%  Similarity=0.039  Sum_probs=4.4

Q ss_pred             HHHHHHHHHH
Q 009944          189 QAIATFFSQV  198 (522)
Q Consensus       189 ~~l~~~f~~~  198 (522)
                      ++..+++.-.
T Consensus       141 eEeiEMmk~M  150 (196)
T KOG3263|consen  141 EEEIEMMKIM  150 (196)
T ss_pred             HHHHHHHHHh
Confidence            3334554444

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

Probab=95.69  E-value=0.0075  Score=54.11  Aligned_cols=77  Identities=17%  Similarity=0.211  Sum_probs=57.2

Q ss_pred             cceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCC---------CCCCCCccEEEEEecChHhHH
Q 009944          419 LAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQN---------GGETPGVGKVFLEYYDAVGCA  489 (522)
Q Consensus       419 ~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~---------g~~~~g~G~afV~F~~~~~A~  489 (522)
                      .+=|+.|.++..-..-          ..|+++|+.||.|-.|.+-.....         |....-+--++|+|.+...|.
T Consensus        73 k~GVvylS~IPp~m~~----------~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK  142 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDP----------VRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAK  142 (278)
T ss_pred             cceEEEeccCCCccCH----------HHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHH
Confidence            3446666666544322          289999999999999998776544         332222223599999999999


Q ss_pred             HHHHHHhCCccCCeEE
Q 009944          490 TAKNALSGRKFGGNTV  505 (522)
Q Consensus       490 ~Ai~~lng~~~~Gr~l  505 (522)
                      .+...|||..|+|++=
T Consensus       143 ~iAe~Lnn~~Iggkk~  158 (278)
T KOG3152|consen  143 RIAELLNNTPIGGKKK  158 (278)
T ss_pred             HHHHHhCCCccCCCCC
Confidence            9999999999999863

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=95.64  E-value=0.037  Score=55.21  Aligned_cols=69  Identities=12%  Similarity=0.141  Sum_probs=55.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHH--hcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcC--CccCCeEEEEEE
Q 009944          295 DRVFVGGLPYYFTETQIKELLE--SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVRR  370 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~--~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v~~  370 (522)
                      +.|+|+.||..+-.++|+.+|+  .+-.+.+|.+..+.       -=||+|++..||++|.+.|..  .+|.|++|....
T Consensus       176 cIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImARI  248 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMARI  248 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhhh
Confidence            4578999999999999999998  46778888776653       159999999999999998864  567787776553

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.46  E-value=0.0067  Score=56.95  Aligned_cols=64  Identities=17%  Similarity=0.305  Sum_probs=51.1

Q ss_pred             HHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          448 REECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       448 ~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                      .+.|.+||.|.+|.+.++........+.--+||+|...++|..||...+|..+.|+.|+++|.+
T Consensus        98 ~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka~~gt  161 (327)
T KOG2068|consen   98 TEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKASLGT  161 (327)
T ss_pred             cccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHHhhCC
Confidence            5679999999999998876211111222337999999999999999999999999999888765

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.41  E-value=0.064  Score=43.79  Aligned_cols=55  Identities=13%  Similarity=0.258  Sum_probs=45.1

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEe
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  510 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~  510 (522)
                      ..|....+.||.|.+|.+.          |+-.|.|.|.+..+|-+|+.++.. ...|..+.++|-
T Consensus       105 ~sV~~~Ls~fGpI~SVT~c----------GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWq  159 (166)
T PF15023_consen  105 KSVIQRLSVFGPIQSVTLC----------GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQ  159 (166)
T ss_pred             HHHHHHHHhcCCcceeeec----------CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEeecc
Confidence            3556667899999999883          235789999999999999999877 667888888874

>KOG1847 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.32  E-value=0.0099  Score=59.98  Aligned_cols=12  Identities=17%  Similarity=0.404  Sum_probs=5.2

Q ss_pred             eEEeCCCccCcH
Q 009944          177 VYVGGLPPLANE  188 (522)
Q Consensus       177 v~v~nlp~~~t~  188 (522)
                      -|+.|-|..++.
T Consensus       848 ~~~q~~~~qvs~  859 (878)
T KOG1847|consen  848 PYLQNEPSQVSD  859 (878)
T ss_pred             cccccchhhhHH
Confidence            344444444443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.78  E-value=0.1  Score=42.62  Aligned_cols=71  Identities=14%  Similarity=0.183  Sum_probs=53.9

Q ss_pred             CeEEEcCCCCCC----CHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          295 DRVFVGGLPYYF----TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       295 ~~l~v~nLp~~~----t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      .+|.|+=|..++    +...|...++.||+|.+|.+.-.       -.|.|.|.+..+|.+|+.+++. ...|..+.+.|
T Consensus        87 sTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGr-------qsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsW  158 (166)
T PF15023_consen   87 STIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGR-------QSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSW  158 (166)
T ss_pred             eeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCC-------ceEEEEehhhHHHHHHHHhhcC-CCCCceEEeec
Confidence            477776665543    33456667789999999977532       3599999999999999999975 66778888888


Q ss_pred             ccC
Q 009944          371 ATA  373 (522)
Q Consensus       371 ~~~  373 (522)
                      -..
T Consensus       159 qqr  161 (166)
T PF15023_consen  159 QQR  161 (166)
T ss_pred             ccc
Confidence            643

>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=94.62  E-value=0.42  Score=38.12  Aligned_cols=66  Identities=12%  Similarity=0.180  Sum_probs=49.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCC-ceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~-i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  363 (522)
                      .+.+...|..++-++|..+.+.+-. |..++|+++.  ..++-.++++|.+.+.|..-...+||+.|..
T Consensus        15 ~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   15 LCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             EEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            4445555566666777766666554 7788888873  3356789999999999999999999988743

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=94.59  E-value=0.24  Score=36.64  Aligned_cols=57  Identities=16%  Similarity=0.144  Sum_probs=41.4

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHh
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  496 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~ln  496 (522)
                      ....|+.|...-...           ..||.++|++||.|.=--|- +          .-|||...+.+.|..|+..++
T Consensus         7 ~RdHVFhltFPkeWK-----------~~DI~qlFspfG~I~VsWi~-d----------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    7 SRDHVFHLTFPKEWK-----------TSDIYQLFSPFGQIYVSWIN-D----------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             SGCCEEEEE--TT-------------HHHHHHHCCCCCCEEEEEEC-T----------TEEEEEECCCHHHHHHHHHHT
T ss_pred             CcceEEEEeCchHhh-----------hhhHHHHhccCCcEEEEEEc-C----------CcEEEEeecHHHHHHHHHHhc
Confidence            445677776443222           14999999999999855552 2          468999999999999999885

; 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.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.55  E-value=0.015  Score=54.58  Aligned_cols=81  Identities=17%  Similarity=0.318  Sum_probs=63.4

Q ss_pred             CeEEEcCCCCCCCHHHHH---HHHHhcCCceEEEEeeCCC--CCC-cceEEEEEEcChHHHHHHHHHHcCCccCCeEEEE
Q 009944          295 DRVFVGGLPYYFTETQIK---ELLESFGTLHGFDLVKDRD--TGN-SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~---~~F~~~G~i~~v~~~~~~~--~g~-~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (522)
                      +-+||-+|+..+..+.+.   +.|.+||.|..|.+..+..  .+. ...-+||.|...++|..||...+|+.+.|+.|+.
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            357888999887666554   4788999999988877651  111 1123799999999999999999999999999998


Q ss_pred             EEccCCC
Q 009944          369 RRATASS  375 (522)
Q Consensus       369 ~~~~~~~  375 (522)
                      .+.+.+.
T Consensus       158 ~~gttky  164 (327)
T KOG2068|consen  158 SLGTTKY  164 (327)
T ss_pred             hhCCCcc
Confidence            8887663

>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=94.22  E-value=2.5  Score=39.36  Aligned_cols=180  Identities=8%  Similarity=0.103  Sum_probs=103.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCC-------CCCCcceEEEEEEcChHHHHHHH----HHHcC--Ccc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-------DTGNSKGYGFCVYQDPAVTDIAC----AALNG--LKM  361 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~-------~~g~~~g~afV~f~~~~~A~~Al----~~l~g--~~~  361 (522)
                      +.|...|+...++-..+...|-+||+|++|.++.+.       +.......+.+-|-+.+.+..-.    +.|+.  ..+
T Consensus        16 RSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~~L   95 (309)
T PF10567_consen   16 RSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKTKL   95 (309)
T ss_pred             HHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHHhc
Confidence            458899999999999999999999999999999864       12233457889999988765432    22322  456


Q ss_pred             CCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEe--eCCCCcCcCCChHH
Q 009944          362 GDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCL--TEAITADALADDEE  439 (522)
Q Consensus       362 ~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l--~~~~~~~~l~~~~~  439 (522)
                      ....|.|.|..-+.......+......  +......+....            .....|+.+.+  ...+..++      
T Consensus        96 ~S~~L~lsFV~l~y~~~~~~~~~~~~~--~~~~~~~L~~~i------------~~~gATRSl~IeF~~~~~~~d------  155 (309)
T PF10567_consen   96 KSESLTLSFVSLNYQKKTDPNDEEADF--SDYLVASLQYNI------------INRGATRSLAIEFKDPVDKDD------  155 (309)
T ss_pred             CCcceeEEEEEEeccccccccccccch--hhHHhhhhhhee------------ecCCcceEEEEEecCccchhH------
Confidence            788888888764322211111000000  000001111000            01123344433  33332221      


Q ss_pred             HHHHHHHHHHHhhccC----CeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCC
Q 009944          440 YEEILEDMREECGKYG----TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGR  498 (522)
Q Consensus       440 ~~~~~~~l~~~f~~~G----~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~  498 (522)
                        .+++.| .+...=+    .|+.|.|+......+ .-|..||.+.|-+...|...+.-|.-.
T Consensus       156 --l~~~kL-~fL~~~~n~RYVlEsIDlVna~~~~~-~Fp~~YaILtFlnIsMAiEV~dYlk~~  214 (309)
T PF10567_consen  156 --LIEKKL-PFLKNSNNKRYVLESIDLVNADEPSK-HFPKNYAILTFLNISMAIEVLDYLKSN  214 (309)
T ss_pred             --HHHHhh-hhhccCCCceEEEEEEEEeccCcccc-cCCcceEEEeehhHHhHHHHHHHHHhc
Confidence              222344 3333333    477788776553332 245678999999999999999887633

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.

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

Probab=94.17  E-value=0.091  Score=48.49  Aligned_cols=54  Identities=19%  Similarity=0.257  Sum_probs=45.3

Q ss_pred             HHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEE-EEE
Q 009944          446 DMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVN-AFY  509 (522)
Q Consensus       446 ~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~-v~~  509 (522)
                      -|-.+|++||+|++.....   +|      -+.+|.|.+.-+|.+||.. ||+.|+|..++ |.-
T Consensus       212 ~vL~~F~~cG~Vvkhv~~~---ng------NwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  212 IVLNLFSRCGEVVKHVTPS---NG------NWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKP  266 (350)
T ss_pred             HHHHHHHhhCeeeeeecCC---CC------ceEEEEecchhHHHHhhhh-cCeeeccceEEeeee
Confidence            6889999999999988873   33      3679999999999999995 99999998776 444

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

Probab=93.80  E-value=0.041  Score=53.90  Aligned_cols=58  Identities=10%  Similarity=0.244  Sum_probs=50.2

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      .+|-..|..||+|+.|.|--..         -.|.|+|.+..+|-.|.. .++..|+|+-|+|.|...
T Consensus       388 a~ln~hfA~fG~i~n~qv~~~~---------~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  388 ADLNPHFAQFGEIENIQVDYSS---------LHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             hhhhhhhhhcCccccccccCch---------hhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            5899999999999999885542         246999999999988876 599999999999999876

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=93.52  E-value=0.069  Score=46.85  Aligned_cols=80  Identities=14%  Similarity=0.083  Sum_probs=51.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHh-cCCc---eEEEEeeCCC-CC-CcceEEEEEEcChHHHHHHHHHHcCCccC---C-
Q 009944          294 PDRVFVGGLPYYFTETQIKELLES-FGTL---HGFDLVKDRD-TG-NSKGYGFCVYQDPAVTDIACAALNGLKMG---D-  363 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~-~G~i---~~v~~~~~~~-~g-~~~g~afV~f~~~~~A~~Al~~l~g~~~~---g-  363 (522)
                      ..+|.|++||+.+|++++.+.++. ++..   ..+.-..... .. ..-.-|||.|.+.+++..-+..++|+.|-   | 
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~   86 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN   86 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence            358999999999999999997776 5554   3333112211 11 12356999999999999999999997772   2 


Q ss_pred             -eEEEEEEccC
Q 009944          364 -KTLTVRRATA  373 (522)
Q Consensus       364 -~~l~v~~~~~  373 (522)
                       ....|.+|-.
T Consensus        87 ~~~~~VE~Apy   97 (176)
T PF03467_consen   87 EYPAVVEFAPY   97 (176)
T ss_dssp             EEEEEEEE-SS
T ss_pred             CcceeEEEcch
Confidence             4566777744

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=93.01  E-value=0.69  Score=36.89  Aligned_cols=52  Identities=12%  Similarity=0.148  Sum_probs=40.4

Q ss_pred             HHHHHhhccC-CeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCC
Q 009944          446 DMREECGKYG-TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG  502 (522)
Q Consensus       446 ~l~~~f~~~G-~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~G  502 (522)
                      +|..+.+.+- .|..++|.++....     .=.+.++|.+.++|..=....||+.|+-
T Consensus        29 ~l~~f~~~~~~~i~~~riird~~pn-----rymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   29 FLLFFGAPFREDIEHIRIIRDGTPN-----RYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             HHHHhhhcccccEEEEEEeeCCCCc-----eEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            6665555554 46778998876333     3478999999999999999999999854

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=92.86  E-value=0.28  Score=43.22  Aligned_cols=61  Identities=20%  Similarity=0.254  Sum_probs=44.9

Q ss_pred             CHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHc--CCccCCeEEEEEEccC
Q 009944          307 TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTVRRATA  373 (522)
Q Consensus       307 t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~v~~~~~  373 (522)
                      ..+.|.++|..|+.+..+.+.+.      -+-..|.|.+.++|..|...|+  +..|.|..++|.|+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            34789999999999877766543      2348999999999999999999  8999999999999854

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=92.78  E-value=0.69  Score=42.92  Aligned_cols=69  Identities=22%  Similarity=0.336  Sum_probs=56.0

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCce-EE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA-VR  252 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~-~~  252 (522)
                      ..-|-|-++|+..+ .-|..+|..||.            |++..+.....+-+|.|.+.-+|.+||..||+.|.|-. |-
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~------------Vvkhv~~~ngNwMhirYssr~~A~KALskng~ii~g~vmiG  263 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGE------------VVKHVTPSNGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIG  263 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCe------------eeeeecCCCCceEEEEecchhHHHHhhhhcCeeeccceEEe
Confidence            55688889988754 357789999998            66666677777999999999999999999999998854 45


Q ss_pred             Eec
Q 009944          253 VRR  255 (522)
Q Consensus       253 v~~  255 (522)
                      |..
T Consensus       264 Vkp  266 (350)
T KOG4285|consen  264 VKP  266 (350)
T ss_pred             eee
Confidence            654

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

Probab=92.53  E-value=0.097  Score=55.03  Aligned_cols=75  Identities=13%  Similarity=0.148  Sum_probs=62.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc--CCeEEEEEEccC
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVRRATA  373 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--~g~~l~v~~~~~  373 (522)
                      +..+.|.+...+-.-|..+|+.||.|.+++..++-      ..|.|+|.+.+.|..|+++|+|+.+  -|-+.+|.++..
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            34455666677788999999999999999987763      3699999999999999999999765  688899999876


Q ss_pred             CCC
Q 009944          374 SSG  376 (522)
Q Consensus       374 ~~~  376 (522)
                      -+.
T Consensus       374 ~~~  376 (1007)
T KOG4574|consen  374 LPM  376 (1007)
T ss_pred             ccc
Confidence            543

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=92.26  E-value=0.84  Score=32.01  Aligned_cols=54  Identities=17%  Similarity=0.239  Sum_probs=38.1

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM  239 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~  239 (522)
                      ..|+|.|+ .+++-++|+.+|..|...         .....+..-. -..|-|.|.+.+.|.+||
T Consensus         6 eavhirGv-d~lsT~dI~~y~~~y~~~---------~~~~~IEWId-DtScNvvf~d~~~A~~AL   59 (62)
T PF10309_consen    6 EAVHIRGV-DELSTDDIKAYFSEYFDE---------EGPFRIEWID-DTSCNVVFKDEETAARAL   59 (62)
T ss_pred             ceEEEEcC-CCCCHHHHHHHHHHhccc---------CCCceEEEec-CCcEEEEECCHHHHHHHH
Confidence            47999999 468889999999999211         0122232221 224889999999999998

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=91.43  E-value=0.9  Score=44.66  Aligned_cols=68  Identities=18%  Similarity=0.293  Sum_probs=58.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCC-ceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~-i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  363 (522)
                      ...|+|-.+|..++-.||..|+..+-. |..|+++++..  ..+=.++|.|.+.++|..-...+||..|..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            568999999999999999999997765 88999999642  234578999999999999999999988854

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=91.40  E-value=0.54  Score=47.29  Aligned_cols=70  Identities=13%  Similarity=0.181  Sum_probs=48.3

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhc--cCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHH
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGK--YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL  495 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~--~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~l  495 (522)
                      ...+|++|..+....          -+++|+.+|..  .-++++|...-+.          -=||+|++..||+.|.+.|
T Consensus       173 ~kRcIvilREIpett----------p~e~Vk~lf~~encPk~iscefa~N~----------nWyITfesd~DAQqAykyl  232 (684)
T KOG2591|consen  173 HKRCIVILREIPETT----------PIEVVKALFKGENCPKVISCEFAHND----------NWYITFESDTDAQQAYKYL  232 (684)
T ss_pred             cceeEEEEeecCCCC----------hHHHHHHHhccCCCCCceeeeeeecC----------ceEEEeecchhHHHHHHHH
Confidence            555666666553322          23689999974  6688888875543          1399999999999999888


Q ss_pred             hCC--ccCCeEEEE
Q 009944          496 SGR--KFGGNTVNA  507 (522)
Q Consensus       496 ng~--~~~Gr~l~v  507 (522)
                      .-.  .|-|+.|..
T Consensus       233 reevk~fqgKpImA  246 (684)
T KOG2591|consen  233 REEVKTFQGKPIMA  246 (684)
T ss_pred             HHHHHhhcCcchhh
Confidence            543  366666554

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=91.22  E-value=0.31  Score=44.37  Aligned_cols=84  Identities=21%  Similarity=0.463  Sum_probs=56.1

Q ss_pred             CCCCCeEEEcCCCCCC------------CHHHHHHHHHhcCCceEEEEeeCC-----CCCCc-----ceE---------E
Q 009944          291 AEGPDRVFVGGLPYYF------------TETQIKELLESFGTLHGFDLVKDR-----DTGNS-----KGY---------G  339 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~------------t~~~l~~~F~~~G~i~~v~~~~~~-----~~g~~-----~g~---------a  339 (522)
                      .+.+.+|++.+||..|            +++-|+..|+.||.|..|.|+...     .+|..     .||         |
T Consensus       146 gerpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipicdplr~~mn~kisgiq~~gfg~g~dlffea  225 (445)
T KOG2891|consen  146 GERPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPICDPLREEMNGKISGIQFHGFGFGGDLFFEA  225 (445)
T ss_pred             CCCCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcccchhHHHhcCccccceeeccccCcchhHHH
Confidence            3456789998888543            567899999999999998887532     13333     233         3


Q ss_pred             EEEEcChHHHHHHHHHHcCCcc----C----CeEEEEEEccCC
Q 009944          340 FCVYQDPAVTDIACAALNGLKM----G----DKTLTVRRATAS  374 (522)
Q Consensus       340 fV~f~~~~~A~~Al~~l~g~~~----~----g~~l~v~~~~~~  374 (522)
                      ||+|..-.--..||.+|.|..+    .    .-.|+|.|....
T Consensus       226 yvqfmeykgfa~amdalr~~k~akk~d~~ffqanvkvdfdrsr  268 (445)
T KOG2891|consen  226 YVQFMEYKGFAQAMDALRGMKLAKKGDDGFFQANVKVDFDRSR  268 (445)
T ss_pred             HHHHHHHHhHHHHHHHHhcchHHhhcCCcccccccccccchhh
Confidence            5666666666778888877554    2    235777776543

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=90.76  E-value=0.34  Score=44.12  Aligned_cols=76  Identities=30%  Similarity=0.440  Sum_probs=51.4

Q ss_pred             CCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCC-----CCCCC----CCCccE-------EEE
Q 009944          417 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPD-----QNGGE----TPGVGK-------VFL  480 (522)
Q Consensus       417 ~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~-----~~g~~----~~g~G~-------afV  480 (522)
                      ..|++++.|....+.+ |..       ..-|+..|+.||.|..|.|+.-.     .+|..    .+|+|+       |||
T Consensus       156 ~ip~kwf~lkedg~~d-lps-------e~rlr~a~eafg~ir~vdipicdplr~~mn~kisgiq~~gfg~g~dlffeayv  227 (445)
T KOG2891|consen  156 GIPCKWFALKEDGSED-LPS-------EDRLRKAFEAFGEIRNVDIPICDPLREEMNGKISGIQFHGFGFGGDLFFEAYV  227 (445)
T ss_pred             CCcceeeeeccccccc-CCh-------HHHHHHHHHHhccceecCCcccchhHHHhcCccccceeeccccCcchhHHHHH
Confidence            3567777766554433 221       14899999999999999886532     23332    445555       678


Q ss_pred             EecChHhHHHHHHHHhCCcc
Q 009944          481 EYYDAVGCATAKNALSGRKF  500 (522)
Q Consensus       481 ~F~~~~~A~~Ai~~lng~~~  500 (522)
                      +|..-..-..||.+|.|+.+
T Consensus       228 qfmeykgfa~amdalr~~k~  247 (445)
T KOG2891|consen  228 QFMEYKGFAQAMDALRGMKL  247 (445)
T ss_pred             HHHHHHhHHHHHHHHhcchH
Confidence            88777777888888888875

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=90.69  E-value=0.29  Score=50.40  Aligned_cols=69  Identities=14%  Similarity=0.136  Sum_probs=54.7

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ..+.-+|||+|+...+..+-++..+..+|.|..            +...   .|||..|..+..+..|+ .+....++|+
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s------------~kr~---~fgf~~f~~~~~~~ra~r~~t~~~~~~~  101 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKSGFVPS------------WKRD---KFGFCEFLKHIGDLRASRLLTELNIDDQ  101 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhCCcchh------------hhhh---hhcccchhhHHHHHHHHHHhcccCCCcc
Confidence            344568999999999999999999999987432            2211   29999999999999999 5777888888


Q ss_pred             eEEEe
Q 009944          250 AVRVR  254 (522)
Q Consensus       250 ~~~v~  254 (522)
                      .+.+.
T Consensus       102 kl~~~  106 (668)
T KOG2253|consen  102 KLIEN  106 (668)
T ss_pred             hhhcc
Confidence            77664

>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=90.59  E-value=1.4  Score=32.39  Aligned_cols=59  Identities=24%  Similarity=0.318  Sum_probs=35.9

Q ss_pred             CCCCHHHHHHHHHhcCCc-----eEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          304 YYFTETQIKELLESFGTL-----HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       304 ~~~t~~~l~~~F~~~G~i-----~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ..++..+|..++...+.|     -.|.+...        |+||+.... .|..++..|++..+.|+.|.|..|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            357888899988876554     45666543        799998755 788899999999999999999864

; PDB: 2G0C_A 3MOJ_B.

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

Probab=90.54  E-value=0.21  Score=52.68  Aligned_cols=72  Identities=13%  Similarity=0.242  Sum_probs=59.6

Q ss_pred             hHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCcc--CCeEEEEEEeCCcc
Q 009944          437 DEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF--GGNTVNAFYYPEDK  514 (522)
Q Consensus       437 ~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~--~Gr~l~v~~~~~~~  514 (522)
                      +.....+-.-|..+|..||.|.++..+++-         -.|.|+|.+.+.|..|+.+|+|+.+  .|-+.+|.|+.-..
T Consensus       305 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  305 NNAVNLTSSSLATLCSDYGSVASAWTLRDL---------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             cccccchHHHHHHHHHhhcchhhheecccc---------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            344555566899999999999999987764         5789999999999999999999985  68889999987655


Q ss_pred             ccc
Q 009944          515 YFN  517 (522)
Q Consensus       515 ~~~  517 (522)
                      +..
T Consensus       376 ~~e  378 (1007)
T KOG4574|consen  376 MYE  378 (1007)
T ss_pred             ccc
Confidence            443

>KOG0670 consensus U4/U6-associated splicing factor PRP4 [RNA processing and modification]

Probab=90.07  E-value=0.23  Score=50.02  Aligned_cols=10  Identities=30%  Similarity=0.923  Sum_probs=4.5

Q ss_pred             HHHHHHhcCC
Q 009944          311 IKELLESFGT  320 (522)
Q Consensus       311 l~~~F~~~G~  320 (522)
                      |++++.+||.
T Consensus       520 LRevLKKyG~  529 (752)
T KOG0670|consen  520 LREVLKKYGR  529 (752)
T ss_pred             HHHHHHHhCc
Confidence            4444444443

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=89.68  E-value=0.52  Score=46.24  Aligned_cols=67  Identities=18%  Similarity=0.356  Sum_probs=54.1

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccC-CeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHh
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYG-TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  496 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G-~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~ln  496 (522)
                      .-..++.+++.++..             ||..|+..|- .|..++|+++.....     =.+.|+|.+.++|..-.+.+|
T Consensus        75 ~mLcilaVP~~mt~~-------------Dll~F~~~~~~~I~~irivRd~~pnr-----ymvLIkFr~q~da~~Fy~efN  136 (493)
T KOG0804|consen   75 TMLCILAVPAYMTSH-------------DLLRFCASFIKQISDIRIVRDGMPNR-----YMVLIKFRDQADADTFYEEFN  136 (493)
T ss_pred             cEEEEEeccccccHH-------------HHHHHHHHHhhhhheeEEeecCCCce-----EEEEEEeccchhHHHHHHHcC
Confidence            556777788887776             8888888765 588899999653332     468999999999999999999


Q ss_pred             CCccCC
Q 009944          497 GRKFGG  502 (522)
Q Consensus       497 g~~~~G  502 (522)
                      |..|+-
T Consensus       137 Gk~Fn~  142 (493)
T KOG0804|consen  137 GKQFNS  142 (493)
T ss_pred             CCcCCC
Confidence            999864

>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=89.40  E-value=0.67  Score=35.12  Aligned_cols=72  Identities=19%  Similarity=0.293  Sum_probs=44.6

Q ss_pred             EEEEEeCHHHHHHHHHhcC--ceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCC
Q 009944          225 AFVEMRTVEEASNAMALDG--IIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGL  302 (522)
Q Consensus       225 afV~f~~~~~a~~a~~~~~--~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL  302 (522)
                      |+|+|..+.-|+..+.+..  ..+.+..+.|.- +++...            ......       .......++|.|.||
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v-~P~~~~------------~~~k~q-------v~~~vs~rtVlvsgi   60 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKV-SPVTLG------------HLQKFQ-------VFSGVSKRTVLVSGI   60 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEE-EeEecC------------CceEEE-------EEEcccCCEEEEeCC
Confidence            6899999999999995443  446666666642 111000            000000       001234478999999


Q ss_pred             CCCCCHHHHHHHHH
Q 009944          303 PYYFTETQIKELLE  316 (522)
Q Consensus       303 p~~~t~~~l~~~F~  316 (522)
                      |...++++|++.++
T Consensus        61 p~~l~ee~l~D~Le   74 (88)
T PF07292_consen   61 PDVLDEEELRDKLE   74 (88)
T ss_pred             CCCCChhhheeeEE
Confidence            99999999987654

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=89.07  E-value=0.46  Score=48.94  Aligned_cols=71  Identities=25%  Similarity=0.403  Sum_probs=61.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ....++||+|+-..+..+-++.+...+|.|..+....         |||++|..+.-+..|+..++-..++|..+.+...
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            3456899999999999999999999999987765543         8999999999999999999988898888777653

>KOG4246 consensus Predicted DNA-binding protein, contains SAP domain [General function prediction only]

Probab=87.22  E-value=0.29  Score=51.38  Aligned_cols=6  Identities=0%  Similarity=-0.430  Sum_probs=2.8

Q ss_pred             EEEEec
Q 009944          478 VFLEYY  483 (522)
Q Consensus       478 afV~F~  483 (522)
                      +||.|.
T Consensus       972 ~~v~~d  977 (1194)
T KOG4246|consen  972 EAVVID  977 (1194)
T ss_pred             ceeeec
Confidence            455543

>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=86.30  E-value=1.6  Score=31.19  Aligned_cols=51  Identities=18%  Similarity=0.208  Sum_probs=39.5

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEE
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNA  507 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v  507 (522)
                      ++|+..+..|+-.. |..  +. +       | -||.|.+..+|++|....+|..+.+-+|.+
T Consensus        15 ~d~K~~Lr~y~~~~-I~~--d~-t-------G-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   15 EDFKKRLRKYRWDR-IRD--DR-T-------G-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             HHHHHHHhcCCcce-EEe--cC-C-------E-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            58888888987654 222  22 2       4 499999999999999999999988877654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2812 consensus Uncharacterized conserved protein [Function unknown]

Probab=85.77  E-value=4.1  Score=38.81  Aligned_cols=14  Identities=14%  Similarity=0.090  Sum_probs=5.2

Q ss_pred             EEEEEcChHHHHHH
Q 009944          339 GFCVYQDPAVTDIA  352 (522)
Q Consensus       339 afV~f~~~~~A~~A  352 (522)
                      |||.-.+..-+..|
T Consensus       364 GYVMSGSRHrrMeA  377 (426)
T KOG2812|consen  364 GYVMSGSRHRRMEA  377 (426)
T ss_pred             ceeeccchHHHHHH
Confidence            33433333333333

>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=84.86  E-value=0.43  Score=41.86  Aligned_cols=67  Identities=16%  Similarity=0.223  Sum_probs=41.5

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHH-HHHhhcCCCCCCCCceEEEE--ecC------CCcEEEEEEeCHHHHHHHH-Hhc
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQ-VMTAIGGNSAGPGDAVVNVY--INH------EKKFAFVEMRTVEEASNAM-ALD  242 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~-~g~~~~~~~~~~~~~v~~~~--~~~------~~g~afV~f~~~~~a~~a~-~~~  242 (522)
                      ...+|.|++||+.+|++++.+.+.. ++....         ...+.  .+.      .-.-|||.|.+.+++..+. .++
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~---------w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~   76 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWD---------WYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFD   76 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE------------EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCT
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccc---------eEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcC
Confidence            3458999999999999999886665 332100         11221  111      1247999999999999998 699


Q ss_pred             CceecC
Q 009944          243 GIIFEG  248 (522)
Q Consensus       243 ~~~~~g  248 (522)
                      |..|.+
T Consensus        77 g~~F~D   82 (176)
T PF03467_consen   77 GHVFVD   82 (176)
T ss_dssp             TEEEE-
T ss_pred             CcEEEC
Confidence            987754

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.

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.05  E-value=14  Score=37.83  Aligned_cols=135  Identities=12%  Similarity=0.165  Sum_probs=79.7

Q ss_pred             hhcccceeEEeCCCcc-CcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecC
Q 009944          170 ATRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~-~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g  248 (522)
                      ....+++|-|-||.+. +...+|.-+|+.|-+        ++..|+.|.+..+.      |.-..       |..-.+.|
T Consensus       170 ~~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP--------~gGsilSV~IYpSe------FGkeR-------M~eEeV~G  228 (650)
T KOG2318|consen  170 LGEETKRLAVVNMDWDRVKAKDLFVLFNSFLP--------KGGSILSVKIYPSE------FGKER-------MKEEEVHG  228 (650)
T ss_pred             cccccceeeEeccccccccHHHHHHHHHhhcC--------CCCceeEEEechhh------hhHHH-------hhhhcccC
Confidence            3556789999999998 789999999999954        45578888775542      11111       22223344


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEee
Q 009944          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (522)
Q Consensus       249 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~  328 (522)
                      -++.+-.+......                                ..     .+....+.-.+.-+..|+ +..++.  
T Consensus       229 P~~el~~~~e~~~~--------------------------------s~-----sD~ee~~~~~~~kLR~Yq-~~rLkY--  268 (650)
T KOG2318|consen  229 PPKELFKPVEEYKE--------------------------------SE-----SDDEEEEDVDREKLRQYQ-LNRLKY--  268 (650)
T ss_pred             ChhhhccccccCcc--------------------------------cc-----cchhhhhhHHHHHHHHHH-hhhhee--
Confidence            43333211110000                                00     111111112344444453 222222  


Q ss_pred             CCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC--CeEEEEEEccC
Q 009944          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG--DKTLTVRRATA  373 (522)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~--g~~l~v~~~~~  373 (522)
                              -||.|+|.+++.|......++|..|.  +..|-+.|...
T Consensus       269 --------YyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFIPD  307 (650)
T KOG2318|consen  269 --------YYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFIPD  307 (650)
T ss_pred             --------EEEEEEecCchHHHHHHHhcCcceeccccceeeeeecCC
Confidence                    27999999999999999999999985  56677777643

>KOG1882 consensus Transcriptional regulator SNIP1, contains FHA domain [Signal transduction mechanisms]

Probab=81.63  E-value=1.5  Score=39.31  Aligned_cols=13  Identities=23%  Similarity=0.097  Sum_probs=7.2

Q ss_pred             cceEEEEEEcChH
Q 009944          335 SKGYGFCVYQDPA  347 (522)
Q Consensus       335 ~~g~afV~f~~~~  347 (522)
                      ++-.|.|+|...+
T Consensus       215 SKQHaviQyR~v~  227 (293)
T KOG1882|consen  215 SKQHAVIQYRLVE  227 (293)
T ss_pred             cccceeeeeeecc
Confidence            3445666666543

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=80.33  E-value=7.3  Score=27.80  Aligned_cols=55  Identities=20%  Similarity=0.218  Sum_probs=43.1

Q ss_pred             CCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEE
Q 009944          305 YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (522)
Q Consensus       305 ~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (522)
                      .++-++|+..+.+|+-.   +|..++ +    | =||.|.+..+|+++....+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~---~I~~d~-t----G-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD---RIRDDR-T----G-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcc---eEEecC-C----E-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            46778999999999643   333442 2    3 389999999999999999999988877654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>PF15513 DUF4651: Domain of unknown function (DUF4651)

Probab=80.09  E-value=4.4  Score=28.23  Aligned_cols=28  Identities=18%  Similarity=0.357  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHhhccCCeEEEEecCCCCC
Q 009944          441 EEILEDMREECGKYGTLVNVVIPRPDQN  468 (522)
Q Consensus       441 ~~~~~~l~~~f~~~G~I~~v~i~~~~~~  468 (522)
                      +.+..+|+++|+..|.|.-+.+.....+
T Consensus         5 e~i~~~iR~~fs~lG~I~vLYvn~~eS~   32 (62)
T PF15513_consen    5 EEITAEIRQFFSQLGEIAVLYVNPYESD   32 (62)
T ss_pred             HHHHHHHHHHHHhcCcEEEEEEcccccC
Confidence            4677899999999999998777555433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	522
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		2e-44
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		2e-42
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		2e-42
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-19
1u2f_A	90	Solution Structure Of The First Rna-Binding Domain		6e-19
2hzc_A	87	Crystal Structure Of The N-terminal Rrm Of The U2af		1e-16
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		4e-12
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		5e-10
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		6e-10
3v4m_A	105	Crystal Structure Of A Rna Binding Domain Of A U2 S		1e-09
4fxw_A	106	Structure Of Phosphorylated Sf1 Complex With U2af65		1e-09
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		1e-09
1opi_A	104	Solution Structure Of The Third Rna Recognition Mot		1e-09
1o0p_A	104	Solution Structure Of The Third Rna Recognition Mot		1e-09
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		5e-09
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		1e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		6e-09
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		7e-09
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		9e-09
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		5e-08
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		5e-08
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-07
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		8e-07
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		8e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		1e-06
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-06
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-06
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-06
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		4e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		5e-06
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		1e-05
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-05
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		1e-05
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		1e-05
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		1e-05
2khc_A	118	Bruno Rrm3+ Length = 118		2e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		2e-05
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		3e-05
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		4e-05
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-05
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		6e-05
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		6e-05
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		6e-05
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		6e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		6e-05
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		6e-05
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		8e-05
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		8e-05
3dxb_A	222	Structure Of The Uhm Domain Of Puf60 Fused To Thior		9e-05
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		1e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-04
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		1e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		2e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-04
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		2e-04
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		2e-04
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		3e-04
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		4e-04
3ue2_A	118	Crystal Structure Of A Rna Binding Domain Of Poly-U		4e-04
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		5e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		6e-04
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		7e-04

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score =  176 bits (447), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 94/200 (47%), Positives = 129/200 (64%), Gaps = 10/200 (5%)
Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 293
           E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   G+ S  +   + 
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVPGVVSTVV--PDS 113
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173
Query: 354 AALNGLKMGDKTLTVRRATA 373
           A LNG+++GDK L V+RA+ 
Sbjct: 174 AGLNGMQLGDKKLLVQRASV 193

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score =  170 bits (430), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 91/199 (45%), Positives = 121/199 (60%), Gaps = 30/199 (15%)
Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 293
           E + AMA DGIIF+G ++++RRP DY           QP P                  G
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDY-----------QPLP------------------G 93
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 94  AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
Query: 354 AALNGLKMGDKTLTVRRAT 372
           A LNG+++GDK L V+RA+
Sbjct: 154 AGLNGMQLGDKKLLVQRAS 172

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score =  169 bits (429), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 91/199 (45%), Positives = 121/199 (60%), Gaps = 30/199 (15%)
Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 293
           E + AMA DGIIF+G ++++RRP DY           QP P                  G
Sbjct: 65  ETTQAMAFDGIIFQGQSLKIRRPHDY-----------QPLP------------------G 95
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 96  AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 155
Query: 354 AALNGLKMGDKTLTVRRAT 372
           A LNG+++GDK L V+RA+
Sbjct: 156 AGLNGMQLGDKKLLVQRAS 174

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 93.6 bits (231), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 45/80 (56%), Positives = 57/80 (71%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A A 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 356 LNGLKMGDKTLTVRRATASS 375
           LNG+++GDK L V+RA+  +
Sbjct: 63  LNGMQLGDKKLLVQRASVGA 82

>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of Hu2af65 Length = 90

Iteration: 1
 Score = 92.4 bits (228), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 43/88 (48%), Positives = 62/88 (70%), Gaps = 1/88 (1%)
Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 1   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 59
Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNP 261
           E + AMA DGIIF+G ++++RRP DY P
Sbjct: 60  ETTQAMAFDGIIFQGQSLKIRRPHDYQP 87

>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large Subunit Length = 87

Iteration: 1
 Score = 84.7 bits (208), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 40/83 (48%), Positives = 59/83 (71%), Gaps = 1/83 (1%)
Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 234 EASNAMALDGIIFEGVAVRVRRP 256
           E + AMA DGIIF+G ++++RRP
Sbjct: 65  ETTQAMAFDGIIFQGQSLKIRRP 87

>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 = 69.3 bits (168), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 38/88 (43%), Positives = 50/88 (56%), Gaps = 2/88 (2%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC YQD      A   L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 357 NGLKMGDKTLTVRRATASSGQSKTEQES 384
           NG +   + L V    A+S ++K E +S
Sbjct: 71  NGREFSGRALRV--DNAASEKNKEELKS 96

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 62.4 bits (150), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 34/80 (42%), Positives = 42/80 (52%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ + K L  S G +    LV+D+ TG S GYGF  Y DP   D A   L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 357 NGLKMGDKTLTVRRATASSG 376
           NGLK+  KT+ V  A  SS 
Sbjct: 67  NGLKLQTKTIKVSYARPSSA 86

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 44/83 (53%)
Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ GP R++VG L +  TE  ++ + E FG +    L+ D +TG SKGYGF  + D    
Sbjct: 22  GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECA 81
Query: 350 DIACAALNGLKMGDKTLTVRRAT 372
             A   LNG ++  + + V   T
Sbjct: 82  KKALEQLNGFELAGRPMKVGHVT 104

>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From Mus Musculus At 1.80 A Resolution Length = 105

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 451 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 510
           C KYG + ++ IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y 
Sbjct: 36  CSKYGLVKSIEIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVVVTKYC 94
Query: 511 PEDKYFNKDY 520
             D Y  +D+
Sbjct: 95  DPDSYHRRDF 104

>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm Domain Length = 106

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 451 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 510
           C KYG + ++ IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y 
Sbjct: 37  CSKYGLVKSIEIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVVVTKYC 95
Query: 511 PEDKYFNKDY 520
             D Y  +D+
Sbjct: 96  DPDSYHRRDF 105

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/80 (42%), Positives = 42/80 (52%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ + K L  S G +    LV+D+ TG S GYGF  Y DP   D A   L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 357 NGLKMGDKTLTVRRATASSG 376
           NGLK+  KT+ V  A  SS 
Sbjct: 67  NGLKLQTKTIKVSYARPSSA 86

>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif (Rrm) Of U2af65 In Complex With An N-Terminal Sf1 Peptide Length = 104

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 451 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 510
           C KYG + ++ IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y 
Sbjct: 35  CSKYGLVKSIEIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYC 93
Query: 511 PEDKYFNKDY 520
             D Y  +D+
Sbjct: 94  DPDSYHRRDF 103

>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif (Rrm) Of U2af65 In Complex With An N-Terminal Sf1 Peptide Length = 104

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 451 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 510
           C KYG + ++ IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y 
Sbjct: 35  CSKYGLVKSIEIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYC 93
Query: 511 PEDKYFNKDY 520
             D Y  +D+
Sbjct: 94  DPDSYHRRDF 103

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 59.3 bits (142), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 43/159 (27%), Positives = 74/159 (46%), Gaps = 20/159 (12%)
Query: 215 NVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPS 273
           +V + H K FAFVE    E A  A+  ++ ++  G  ++V RP++           GQ  
Sbjct: 64  SVTMKH-KGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI----------GQAQ 112
Query: 274 PNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG 333
           P ++  A          A   +R++V  +    ++  IK + E+FG +    L +D  TG
Sbjct: 113 PIIDQLA--------EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTG 164
Query: 334 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
             KGYGF  Y+    +  A +++N   +G + L V +A 
Sbjct: 165 KHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203

>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 = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 37/77 (48%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           RV+VG + Y   E  I++    FG +   D+  D  T   KG+ F  Y+ P    +A   
Sbjct: 30  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 356 LNGLKMGDKTLTVRRAT 372
           +N + +G + + V R +
Sbjct: 90  MNSVMLGGRNIKVGRPS 106

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 43/83 (51%)
Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   ++VG L +  TE  ++ + E FG +    L+KD DTG SKGYGF  + D    
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 350 DIACAALNGLKMGDKTLTVRRAT 372
             A   LNG ++  + + V   T
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVT 83

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 58.9 bits (141), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 40/69 (57%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGLPY+ T+  +++  E FG +    ++ DR TG S+GYGF    D A  + AC  
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 356 LNGLKMGDK 364
            N +  G K
Sbjct: 79  PNPIIDGRK 87

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 58.5 bits (140), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 55/210 (26%), Positives = 91/210 (43%), Gaps = 33/210 (15%)
Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV----NVYINHEKK 223
           Q+A     RVYVG +     E  I   F+           GP  ++     +V + H K 
Sbjct: 7   QRALAIMCRVYVGSIYYELGEDTIRQAFAPF---------GPIKSIDMSWDSVTMKH-KG 56
Query: 224 FAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVG 282
           FAFVE    E A  A+  ++ ++  G  ++V RP++           GQ  P ++  A  
Sbjct: 57  FAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI----------GQAQPIIDQLA-- 104
Query: 283 LASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 342
                   A   +R++V  +    ++  IK + E+FG +    L +D  TG  KGYGF  
Sbjct: 105 ------EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIE 158
Query: 343 YQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           Y+    +  A +++N   +G + L V +A 
Sbjct: 159 YEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 188

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 45/83 (54%), Gaps = 2/83 (2%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  +P    E Q+++L E +G +    +V DR+T  S+GYGF  +Q  +    A A L
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 357 NGLKMGDKTLTVRRATASSGQSK 379
           NG  + +K L V  A A+SG  +
Sbjct: 105 NGFNILNKRLKV--ALAASGHQR 125

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 31/80 (38%), Positives = 42/80 (52%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ + + L  S G +    LV+D+ TG S GYGF  Y DP   + A   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 357 NGLKMGDKTLTVRRATASSG 376
           NGL++  KT+ V  A  SS 
Sbjct: 65  NGLRLQTKTIKVSYARPSSA 84

>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 = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/208 (25%), Positives = 85/208 (40%), Gaps = 29/208 (13%)
Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQV--MTAIGGNSAGPGDAVVNVYINHEKKFA 225
           Q+A     RVYVG +     E  I   F+    + +I        D   +      K FA
Sbjct: 6   QRALAIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSI--------DXSWDSVTXKHKGFA 57
Query: 226 FVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLA 284
           FVE    E A  A+   + +   G  ++V RP++           GQ  P ++  A    
Sbjct: 58  FVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNI----------GQAQPIIDQLA---- 103
Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
                 A   +R++V  +    ++  IK + E+FG +    L +D  TG  KGYGF  Y+
Sbjct: 104 ----EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 159
Query: 345 DPAVTDIACAALNGLKMGDKTLTVRRAT 372
               +  A ++ N   +G + L V +A 
Sbjct: 160 KAQSSQDAVSSXNLFDLGGQYLRVGKAV 187

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 42/83 (50%)
Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           G   + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y      + A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 353 CAALNGLKMGDKTLTVRRATASS 375
              LNGL++  KT+ V  A  SS
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSS 83

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 42/83 (50%)
Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           G   + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y      + A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 353 CAALNGLKMGDKTLTVRRATASS 375
              LNGL++  KT+ V  A  SS
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSS 83

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 1/88 (1%)
Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           A+ P ++F+GGL     E  +K +    G +    L+KDR T  S+G+ F  +++PA   
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAK 62
Query: 351 IACAALNGLKMGDKTLTVRRATASSGQS 378
            A   +NG  +  K + V +A   S QS
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQAKKPSFQS 90

>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 = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 43/84 (51%), Gaps = 2/84 (2%)
Query: 293 GPDR--VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           GP R  + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y      +
Sbjct: 1   GPGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 351 IACAALNGLKMGDKTLTVRRATAS 374
            A   LNGL++  KT+ V  A  S
Sbjct: 61  RAINTLNGLRLQSKTIKVSYARPS 84

>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 = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++VG L Y  T  Q+KEL   FG +    L+ DR+T   KG+GF   Q+ +V++ A A L
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAKL 62
Query: 357 NGLKMGDKTLTVRRA 371
           +      +T+ V  A
Sbjct: 63  DNTDFMGRTIRVTEA 77

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 45/80 (56%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +++      A  A
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 356 LNGLKMGDKTLTVRRATASS 375
           +NG  +  + + V +A  SS
Sbjct: 74  MNGKSVDGRQIRVDQAGKSS 93

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 293 GPDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           GP RV ++G +PY  TE QI +L  + G +    ++ D  TG SKGY F  ++D   +  
Sbjct: 1   GPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 60
Query: 352 ACAALNGLKMGDKTL 366
           A   LNG ++G + L
Sbjct: 61  AVRNLNGYQLGSRFL 75

>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 = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 282 GLASGAIGGA----EGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNS 335
           GL   +IG A    EGP+   +F+  LP  F +  + ++   FG +    +  D+ T  S
Sbjct: 7   GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS 66
Query: 336 KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR 369
           K +GF  Y +P     A  ++NG ++G K L V+
Sbjct: 67  KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ 100

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/89 (31%), Positives = 46/89 (51%), Gaps = 2/89 (2%)
Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G  ++FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V 
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVA 61
Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQS 378
           + AC  +NG+K+  + + VR    +SG S
Sbjct: 62  ERACRMMNGMKLSGREIDVRIDRNASGPS 90

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 2/85 (2%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  TE  ++E    +GT+    ++KD  TG S+G+GF  ++ P+  D     
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 356 LNGLKMGDKTLTVRRATASSGQSKT 380
            + L    K +  +RA     Q KT
Sbjct: 65  QHILD--GKVIDPKRAIPRDEQDKT 87

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 294 PDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           P RV ++G +PY  TE QI +L  + G +    ++ D  TG SKGY F  ++D   +  A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 353 CAALNGLKMGDKTL 366
              LNG ++G + L
Sbjct: 61  VRNLNGYQLGSRFL 74

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 294 PDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           P RV ++G +PY  TE QI +L  + G +    ++ D  TG SKGY F  ++D   +  A
Sbjct: 3   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 353 CAALNGLKMGDKTL 366
              LNG ++G + L
Sbjct: 63  VRNLNGYQLGSRFL 76

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 2/89 (2%)
Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   +FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V 
Sbjct: 1   GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVA 58
Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQS 378
           + AC  +NG+K+  + + VR    +SG S
Sbjct: 59  ERACRMMNGMKLSGREIDVRIDRNASGPS 87

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 292 EGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           EGP+   +F+  LP  FT+T +      FG +    +  D+ T  SK +GF  + +P   
Sbjct: 36  EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 350 DIACAALNGLKMGDKTLTVR 369
            +A  A+NG ++G K L V+
Sbjct: 96  QVAIKAMNGFQVGTKRLKVQ 115

>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 = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/78 (33%), Positives = 40/78 (51%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y      + A   L
Sbjct: 22  LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 357 NGLKMGDKTLTVRRATAS 374
           NGL++  KT+ V  A  S
Sbjct: 82  NGLRLQSKTIKVSYARPS 99

>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 = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 15  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 66
Query: 233 EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 286
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 67  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 106
Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 107 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 157
Query: 347 AVTD 350
              D
Sbjct: 158 DSVD 161

>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 = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 13  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 64
Query: 233 EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 286
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 65  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 104
Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 105 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 155
Query: 347 AVTD 350
              D
Sbjct: 156 DSVD 159

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 65
Query: 233 EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 286
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 66  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 105
Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 106 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 156
Query: 347 AVTD 350
              D
Sbjct: 157 DSVD 160

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 37/77 (48%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ Q +EL+  FG+L    LV    TG SKGYGF  Y        A + L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 357 NGLKMGDKTLTVRRATA 373
            G  +G +TL V    A
Sbjct: 158 LGKPLGPRTLYVHWTDA 174

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 37/77 (48%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ Q +EL+  FG+L    LV    TG SKGYGF  Y        A + L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 357 NGLKMGDKTLTVRRATA 373
            G  +G +TL V    A
Sbjct: 158 LGKPLGPRTLYVHWTDA 174

>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 = 45.8 bits (107), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 37/77 (48%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ Q +EL+  FG+L    LV    TG SKGYGF  Y        A + L
Sbjct: 96  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 357 NGLKMGDKTLTVRRATA 373
            G  +G +TL V    A
Sbjct: 156 LGKPLGPRTLYVHWTDA 172

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 58
Query: 233 EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 286
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 59  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 98
Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 99  ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 149
Query: 347 AVTD 350
              D
Sbjct: 150 DSVD 153

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 65
Query: 233 EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 286
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 66  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 105
Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 106 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 156
Query: 347 AVTD 350
              D
Sbjct: 157 DSVD 160

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 12  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 63
Query: 233 EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 286
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 64  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 103
Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 104 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 154
Query: 347 AVTD 350
              D
Sbjct: 155 DSVD 158

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           G+ G   +F+G L     E  + +   +FG  L    +++D DTGNSKGY F  +     
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 349 TDIACAALNGLKMGDKTLTVRRA 371
           +D A  A+NG  + ++ +TV  A
Sbjct: 61  SDAAIEAMNGQYLCNRPITVSYA 83

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC-VYQDPAVTDIA 352
           P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF   Y D  V  I 
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
Query: 353 CAALN----GLKMG 362
            + +N     LK+G
Sbjct: 68  ESQINFHGKKLKLG 81

>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin Length = 222

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 451 CGKYGTLVNVVIPRPDQNGGETPG--VGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF 508
           CGK+G  VN VI   ++ G E     + K+F+E+  A     A  AL+GR F G  V A 
Sbjct: 150 CGKFGA-VNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAE 208
Query: 509 YYPEDKYFNKDYSA 522
            Y ++++ N D SA
Sbjct: 209 VYDQERFDNSDLSA 222

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/87 (29%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           +++FVGG+P+   ET+++E  + FG +    ++ D +    +G+GF  ++D    D A  
Sbjct: 11  NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 355 ALNGLKMGDKTLTVR---RATASSGQS 378
                 MG K    R   R + SSG S
Sbjct: 71  MHFHDIMGKKVEVKRAEPRDSKSSGPS 97

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 35/77 (45%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VFVG L    T   IK     FG +    +VKD  TG SKGYGF  + +    + A   
Sbjct: 17  HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 356 LNGLKMGDKTLTVRRAT 372
           + G  +G + +    AT
Sbjct: 77  MGGQWLGGRQIRTNWAT 93

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC-VYQDPAVTDIA 352
           P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF   Y D  V  I 
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
Query: 353 CAALN----GLKMG 362
            + +N     LK+G
Sbjct: 68  ESQINFHGKKLKLG 81

>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 = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/89 (32%), Positives = 39/89 (43%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VFVG L    T   IK     FG +    +VKD  TG SKGYGF  + +    + A   
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 356 LNGLKMGDKTLTVRRATASSGQSKTEQES 384
           + G  +G + +    AT      K+  ES
Sbjct: 77  MGGQWLGGRQIRTNWATRKPPAPKSTYES 105

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE   K L E +G      + +DR      G+GF   +   + +IA A 
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAE 77
Query: 356 LNGLKMGDKTLTVRRAT 372
           L+G  +  + L +R AT
Sbjct: 78  LDGTILKSRPLRIRFAT 94

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 40/79 (50%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V+VGGL    +E  + EL    G +    + KDR TG  +GYGF  +      D A   +
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 357 NGLKMGDKTLTVRRATASS 375
           + +K+  K + V +A+A +
Sbjct: 78  DMIKLYGKPIRVNKASAHN 96

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC-VYQDPAVTDIA 352
           P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF   Y D  V  I 
Sbjct: 10  PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 68
Query: 353 CAALN 357
            + +N
Sbjct: 69  ESQIN 73

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE ++++L E +G      + KD      KG+GF   +   + +IA   
Sbjct: 24  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 356 LNGLKMGDKTLTVRRATASSG 376
           L+ + +  K L VR A  S+ 
Sbjct: 78  LDNMPLRGKQLRVRFACHSAS 98

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           P R+ V  +P+ F +  ++++   FG +   +++ +     SKG+GF  +++ A  D A 
Sbjct: 29  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAR 86
Query: 354 AALNGLKMGDKTLTVRRATA 373
             L+G  +  + + V  ATA
Sbjct: 87  EKLHGTVVEGRKIEVNNATA 106

>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 1.23 A Resolution Length = 118

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 451 CGKYGTLVNVVIPRPDQNGGETPG--VGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF 508
           CGK+G  VN VI   ++ G E     + K+F+E+  A     A  AL+GR F G  V A 
Sbjct: 46  CGKFGA-VNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAE 104
Query: 509 YYPEDKYFNKDYSA 522
            Y ++++ N D SA
Sbjct: 105 VYDQERFDNSDLSA 118

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           P R+ V  +P+ F +  ++++   FG +   +++ +     SKG+GF  +++ A  D A 
Sbjct: 15  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAR 72
Query: 354 AALNGLKMGDKTLTVRRATA 373
             L+G  +  + + V  ATA
Sbjct: 73  EKLHGTVVEGRKIEVNNATA 92

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL +  T+  ++     +G +    ++KD+ T  S+G+GF  ++DP       A+
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 356 ----LNGLKMGDKTLTVR 369
               L+G  +  K  T R
Sbjct: 78  RPHTLDGRNIDPKPCTPR 95

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 27/48 (56%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           ++FVG +P    E  +K L E FG ++   ++KDR TG  KG  F  Y
Sbjct: 17  KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTY 64

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	522
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-72
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-62
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-14
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-33
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-20
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	4e-31
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-31
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-11
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	3e-30
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	2e-29
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-28
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-17
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	9e-06
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-27
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-26
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-20
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-07
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	1e-25
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-24
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	3e-23
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-23
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-18
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-04
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-23
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	9e-10
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-23
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-22
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-18
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	9e-22
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	9e-13
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-21
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-13
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	6e-20
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-08
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	6e-20
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-19
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-18
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-14
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-18
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-18
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	9e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-18
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	7e-06
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	6e-18
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	8e-07
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-18
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	6e-18
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-08
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-17
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-17
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-10
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-17
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-08
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-17
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-08
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-17
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-07
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-17
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-08
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-16
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-16
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-08
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-16
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-07
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-16
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	8e-09
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-16
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-04
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-16
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	6e-05
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	4e-16
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	5e-06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-16
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-16
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	7e-16
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-06
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	8e-16
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-05
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	9e-16
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-07
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	9e-16
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-08
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	9e-16
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	4e-06
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-15
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-06
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-15
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-15
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	8e-06
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-15
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-07
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-15
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-09
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-15
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-07
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-15
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-06
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-15
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	4e-15
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-15
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-07
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-14
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-12
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-14
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	8e-07
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-14
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	4e-05
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-14
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-07
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-05
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-14
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-05
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-14
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-07
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	9e-07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-04
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-14
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-04
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-14
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	7e-07
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-14
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	9e-07
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-05
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-14
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	9e-11
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-14
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-05
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-14
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	7e-09
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-06
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-14
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-08
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-14
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-06
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	4e-14
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-06
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-14
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-04
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-14
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	7e-07
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-14
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-14
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	9e-05
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	7e-14
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	8e-14
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-05
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-13
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	8e-07
2div_A	99	TRNA selenocysteine associated protein; structural	1e-13
2div_A	99	TRNA selenocysteine associated protein; structural	2e-05
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-13
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-06
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-06
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-13
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-13
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	7e-05
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-13
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	5e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	3e-13
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-13
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-13
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-07
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-13
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-10
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-13
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-06
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	5e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	5e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-05
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	5e-13
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-13
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-10
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	7e-13
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	7e-13
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	9e-13
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-07
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	9e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-08
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-12
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-12
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-05
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-12
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-08
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-12
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	8e-07
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	7e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	9e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	7e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-11
1x5o_A	114	RNA binding motif, single-stranded interacting pro	6e-05
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-11
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-11
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-11
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-05
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-08
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-08
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-05
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-10
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-10
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-10
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	6e-09
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	6e-05
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-10
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	9e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-06
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-10
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	3e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-09
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-10
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	7e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	5e-10
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-09
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	5e-09
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-09
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-09
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	9e-09
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	5e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	9e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	7e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-05
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	6e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-09
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-10
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	8e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-05
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	7e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-09
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	5e-09
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-09
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-07
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-09
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-07
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	7e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-08
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	7e-09
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	9e-09
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-04
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	6e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	6e-07
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-06
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-08
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-07
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-05
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-07
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-07
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	5e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	4e-07
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	6e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	4e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	5e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	5e-07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-06
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	5e-07
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-07
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	6e-05
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	5e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	7e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	8e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-06
1x5p_A	97	Negative elongation factor E; structure genomics,	9e-07
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-04
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-06
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-06
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	4e-06
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-05
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	9e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-04
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-04

>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 =  226 bits (579), Expect = 6e-72
 Identities = 91/205 (44%), Positives = 126/205 (61%), Gaps = 10/205 (4%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 293
           E + AMA DGIIF+G ++++RRP DY P    +  P    P +    V          + 
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVV---------PDS 113

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173

Query: 354 AALNGLKMGDKTLTVRRATASSGQS 378
           A LNG+++GDK L V+RA+  +  +
Sbjct: 174 AGLNGMQLGDKKLLVQRASVGAKNA 198

>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 = 83.2 bits (206), Expect = 1e-18
 Identities = 36/216 (16%), Positives = 70/216 (32%), Gaps = 41/216 (18%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHG-----FDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           R++VG +P+  TE  + +   +   L G      + V        K + F  ++    T 
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG- 409
            A A  +G+    ++L +RR              +      ++      +     + L  
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRP-----HDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119

Query: 410 GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG 469
           GG+  +         L +                 + ++E    +G L    + + D   
Sbjct: 120 GGLPNY---------LND-----------------DQVKELLTSFGPLKAFNLVK-DSAT 152

Query: 470 GETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTV 505
           G + G    F EY D      A   L+G + G   +
Sbjct: 153 GLSKGYA--FCEYVDINVTDQAIAGLNGMQLGDKKL 186

>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 =  200 bits (511), Expect = 3e-62
 Identities = 89/199 (44%), Positives = 119/199 (59%), Gaps = 30/199 (15%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQM-RLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 293
           E + AMA DGIIF+G ++++RRP DY P                               G
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDYQPL-----------------------------PG 93

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 94  AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153

Query: 354 AALNGLKMGDKTLTVRRAT 372
           A LNG+++GDK L V+RA+
Sbjct: 154 AGLNGMQLGDKKLLVQRAS 172

>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 = 70.0 bits (172), Expect = 3e-14
 Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 6/90 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHG-----FDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           R++VG +P+  TE  + +   +   L G      + V        K + F  ++    T 
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKT 380
            A  A +G+    ++L +RR          
Sbjct: 66  QAM-AFDGIIFQGQSLKIRRPHDYQPLPGA 94

>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 = 47.6 bits (114), Expect = 1e-06
 Identities = 21/127 (16%), Positives = 42/127 (33%), Gaps = 25/127 (19%)

Query: 141 PEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQ--- 197
            +     + F         L   +    Q    A ++++GGLP   N+  +    +    
Sbjct: 61  VDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGP 120

Query: 198 -----VMT-AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVA 250
                ++  +  G S G               +AF E   +     A+A L+G+      
Sbjct: 121 LKAFNLVKDSATGLSKG---------------YAFCEYVDINVTDQAIAGLNGMQLGDKK 165

Query: 251 VRVRRPT 257
           + V+R +
Sbjct: 166 LLVQRAS 172

>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 =  126 bits (318), Expect = 5e-33
 Identities = 59/348 (16%), Positives = 97/348 (27%), Gaps = 102/348 (29%)

Query: 162 PVQVM---TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI 218
            ++     T++  R+ R++ + GLP     Q +    S                +   ++
Sbjct: 7   EIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSD----YE---------LKYCFV 53

Query: 219 NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLN 277
           +  K  AFV +   E+A  A+ A          + V+                       
Sbjct: 54  DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDA----------------- 96

Query: 278 LAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKG 337
                              + V  LP   T+ Q +EL+  FG+L    LV    TG SKG
Sbjct: 97  ------------------LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG 138

Query: 338 YGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQK 397
           YGF  Y        A + L G  +G +TL V         +     ++L      +    
Sbjct: 139 YGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT-----DAGQLTPALLHSRCLCVD--- 190

Query: 398 MALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTL 457
                                      L          D +        +        + 
Sbjct: 191 --------R------------------LPPGFN-----DVDA-------LCRALSAVHSP 212

Query: 458 VNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTV 505
               +    Q+G    G     LEY  A     A+    G   GG+ +
Sbjct: 213 TFCQLAC-GQDGQLK-GFA--VLEYETAEMAEEAQQQADGLSLGGSHL 256

>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 = 90.4 bits (225), Expect = 2e-20
 Identities = 42/235 (17%), Positives = 63/235 (26%), Gaps = 44/235 (18%)

Query: 162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---I 218
            + V  Q        + V  LPP   +Q                  G  +    VY    
Sbjct: 86  ELSVQLQP---TDALLCVANLPPSLTQQQFEELVRP---------FGSLERCFLVYSERT 133

Query: 219 NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLN 277
              K + F E    + A+ A   L G       + V                GQ +P L 
Sbjct: 134 GQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD-----------AGQLTPALL 182

Query: 278 LAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQ-IKELLESFGTLHGFDLVKDRDTGNSK 336
            +                 + V  LP  F +   +   L +  +     L      G  K
Sbjct: 183 HSR---------------CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLK 226

Query: 337 GYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQ 391
           G+    Y+   + + A    +GL +G   L V                I AQA  
Sbjct: 227 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATA 281

>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 =  115 bits (289), Expect = 4e-31
 Identities = 46/105 (43%), Positives = 62/105 (59%), Gaps = 1/105 (0%)

Query: 416 GETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGV 475
           G    +VLCL   +  + L DDEEYEEI+ED+R+EC KYG + ++ IPRP  +G E PG 
Sbjct: 1   GGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRP-VDGVEVPGC 59

Query: 476 GKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
           GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct: 60  GKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 104

>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 =  114 bits (287), Expect = 5e-31
 Identities = 39/85 (45%), Positives = 56/85 (65%), Gaps = 1/85 (1%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
             ARR+YVG +P    E+A+  FF+  M   G     PG+ V+ V IN +K FAF+E R+
Sbjct: 4   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLT-QAPGNPVLAVQINQDKNFAFLEFRS 62

Query: 232 VEEASNAMALDGIIFEGVAVRVRRP 256
           V+E + AMA DGIIF+G ++++RRP
Sbjct: 63  VDETTQAMAFDGIIFQGQSLKIRRP 87

>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 = 59.0 bits (143), Expect = 2e-11
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHG-----FDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           R++VG +P+  TE  + +   +   L G      + V        K + F  ++    T 
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 351 IACAALNGLKMGDKTLTVRR 370
               A +G+    ++L +RR
Sbjct: 68  -QAMAFDGIIFQGQSLKIRR 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 =  113 bits (284), Expect = 3e-30
 Identities = 33/136 (24%), Positives = 61/136 (44%), Gaps = 22/136 (16%)

Query: 388 QAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDM 447
            + +H+ +QK+  +                  + V+ L   +        +  +++  ++
Sbjct: 4   SSARHMVMQKLLRKQE----------------STVMVLRNMVDPK-----DIDDDLEGEV 42

Query: 448 REECGKYGTLVNVVIPRPDQNGGET-PGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVN 506
            EECGK+G +  V+I +  Q   E    + K+F+E+  A     A  AL+GR F G  V 
Sbjct: 43  TEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVV 102

Query: 507 AFYYPEDKYFNKDYSA 522
           A  Y ++++ N D SA
Sbjct: 103 AEVYDQERFDNSDLSA 118

>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 =  110 bits (278), Expect = 2e-29
 Identities = 24/98 (24%), Positives = 40/98 (40%), Gaps = 7/98 (7%)

Query: 421 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFL 480
           +   L+         +     EI +D+ EEC K+G ++++ + +           G V++
Sbjct: 8   QCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN-------SAQGNVYV 60

Query: 481 EYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNK 518
           +         A NAL GR F G  + A Y P   Y N 
Sbjct: 61  KCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNL 98

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

 Score =  110 bits (278), Expect = 4e-28
 Identities = 48/212 (22%), Positives = 83/212 (39%), Gaps = 37/212 (17%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHE 221
           Q A     RVYVG +     E  I   F+           GP   + ++ +         
Sbjct: 22  QGALAIMSRVYVGSIYYELGEDTIRQAFAP---------FGP---IKSIDMSWDSVTMKH 69

Query: 222 KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAA 280
           K FAFVE    E A  A+  ++ ++  G  ++V RP++            + +       
Sbjct: 70  KGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA----- 124

Query: 281 VGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
                         +R++V  +    ++  IK + E+FG +    L +D  TG  KGYGF
Sbjct: 125 -------------FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGF 171

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
             Y+    +  A +++N   +G + L V +A 
Sbjct: 172 IEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203

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

 Score = 80.4 bits (199), Expect = 2e-17
 Identities = 40/216 (18%), Positives = 77/216 (35%), Gaps = 46/216 (21%)

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           G      RV+VG + Y   E  I++    FG +   D+  D  T   KG+ F  Y+ P  
Sbjct: 23  GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEA 82

Query: 349 TDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTL 408
             +A   +N + +G + + V R       +  + + I+ Q  +         +    N +
Sbjct: 83  AQLALEQMNSVMLGGRNIKVGRP-----SNIGQAQPIIDQLAE---------EARAFNRI 128

Query: 409 --GGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPD 466
                             + + ++ D +             +     +G + +  + R D
Sbjct: 129 YVAS--------------VHQDLSDDDI-------------KSVFEAFGKIKSATLAR-D 160

Query: 467 QNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG 502
              G+  G G  F+EY  A     A ++++    GG
Sbjct: 161 PTTGKHKGYG--FIEYEKAQSSQDAVSSMNLFDLGG 194

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

 Score = 45.8 bits (109), Expect = 9e-06
 Identities = 18/119 (15%), Positives = 37/119 (31%), Gaps = 25/119 (21%)

Query: 162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDA 212
           P+     +  R   R+YV  +    ++  I + F          +      G   G    
Sbjct: 113 PIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKG---- 168

Query: 213 VVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPG 270
                      + F+E    + + +A+ +++     G  +RV +       L     PG
Sbjct: 169 -----------YGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATPG 216

>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 =  107 bits (269), Expect = 2e-27
 Identities = 27/210 (12%), Positives = 67/210 (31%), Gaps = 55/210 (26%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEK 222
           +     +++G L P  +   +    S+        V+    G +               +
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTN---------------R 54

Query: 223 KFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVG 282
           KF +V+  + E+   A+ L G+   G  +++ +P              +   +       
Sbjct: 55  KFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP--------------KGRDSKK----- 95

Query: 283 LASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 342
                         +    L +  TE ++KE+ E        ++      G SKG  +  
Sbjct: 96  --------VRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIE 142

Query: 343 YQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           ++  A  +       G ++  +++++    
Sbjct: 143 FKSEADAEKNLEEKQGAEIDGRSVSLYYTG 172

>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 = 49.5 bits (119), Expect = 3e-07
 Identities = 15/93 (16%), Positives = 29/93 (31%), Gaps = 20/93 (21%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQ----VMTAIGGNSAGPGDAVVNVYINHEKK 223
            +  R AR +    L     E  +   F       + +  G S G               
Sbjct: 93  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKG--------------- 137

Query: 224 FAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRR 255
            A++E ++  +A   +    G   +G +V +  
Sbjct: 138 IAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY 170

>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 =  108 bits (271), Expect = 2e-26
 Identities = 44/335 (13%), Positives = 94/335 (28%), Gaps = 101/335 (30%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEMRTV 232
           V V  LP   N+  +  +F            GP   +++V +        +FA +E    
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKH---------CGP---IIHVDVADSLKKNFRFARIEFARY 91

Query: 233 EEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAE 292
           + A  A+     +     + V   T+                                  
Sbjct: 92  DGALAAITKTHKVVGQNEIIVSHLTECT-------------------------------- 119

Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
               +++   P  +T+  I++LL+    +     +       S+ + +            
Sbjct: 120 ----LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 175

Query: 353 CAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGM 412
              LNGLK+   TL  + +       +T+  ++                         G 
Sbjct: 176 VEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLE------------------------GR 211

Query: 413 SLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGET 472
            +       +  L+  +       DE        +RE    +G++  + IP   +     
Sbjct: 212 EIM------IRNLSTELL------DE------NLLRESFEGFGSIEKINIPAGQKEHSFN 253

Query: 473 PGVGKVFLEYYDAVGCATAKNALS--GRKFGGNTV 505
                 F+ + +     +A+ AL       G   +
Sbjct: 254 NCCA--FMVFENK---DSAERALQMNRSLLGNREI 283

>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 = 91.2 bits (227), Expect = 1e-20
 Identities = 28/206 (13%), Positives = 67/206 (32%), Gaps = 42/206 (20%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRT 231
             +++   PP   ++ I      +               + +          FA++++ +
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDI---------NVVALSIRLPSLRFNTSRRFAYIDVTS 168

Query: 232 VEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
            E+A   +  L+G+  EG  +  +     NP   +            +            
Sbjct: 169 KEDARYCVEKLNGLKIEGYTLVTKV---SNPLEKSKRTDSATLEGREI------------ 213

Query: 291 AEGPDRVFVGGLPYYFT-ETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCVYQDPAV 348
                   +  L      E  ++E  E FG++   ++   +     +    F V+++   
Sbjct: 214 -------MIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENK-- 264

Query: 349 TDIACAA--LNGLKMGDKTLTVRRAT 372
            D A  A  +N   +G++ ++V  A 
Sbjct: 265 -DSAERALQMNRSLLGNREISVSLAD 289

>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 = 50.4 bits (121), Expect = 5e-07
 Identities = 14/103 (13%), Positives = 30/103 (29%), Gaps = 26/103 (25%)

Query: 167 TQQATRHARRVYVGGLPP-LANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVY 217
           T  AT   R + +  L   L +E  +   F          +      +            
Sbjct: 203 TDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEH------------ 250

Query: 218 INHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV----RRP 256
            +     AF+     + A  A+ ++  +     + V    ++P
Sbjct: 251 -SFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKKP 292

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score =   99 bits (249), Expect = 1e-25
 Identities = 32/107 (29%), Positives = 47/107 (43%), Gaps = 7/107 (6%)

Query: 415 FGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPG 474
            G+   KV+ L   + A      E  E++  + +EEC KYG +   VI      G     
Sbjct: 3   MGKCPTKVVLLRNMVGAG-----EVDEDLEVETKEECEKYGKVGKCVIFEIP--GAPDDE 55

Query: 475 VGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYS 521
             ++FLE+        A   L+GR FGG  V A +Y  DK+   D +
Sbjct: 56  AVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLDKFRVLDLA 102

>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 =  100 bits (251), Expect = 4e-24
 Identities = 38/259 (14%), Positives = 71/259 (27%), Gaps = 58/259 (22%)

Query: 159 PLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI 218
            +       ++      R++VG LP    E+     F +          G       V+I
Sbjct: 7   DIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFER---------YGE---PSEVFI 54

Query: 219 NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLN 277
           N ++ F F+ + +   A  A   LDG I +   +R+R                     L 
Sbjct: 55  NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF--------------ATHGAAL- 99

Query: 278 LAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKG 337
                                V  L    +   +++    FG +    +V D D G + G
Sbjct: 100 --------------------TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATG 138

Query: 338 YGFCVYQDPAVTDIACAALNG----LKMGDKTLTVRRATASSGQSKTEQESILAQAQQHI 393
            GF  +        A          L    + + V        +   +++ +  +  Q  
Sbjct: 139 KGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPM-----EQFDDEDGLPEKLMQKT 193

Query: 394 AIQKMALQTSGMNTLGGGM 412
                  +        G  
Sbjct: 194 QQYHKEREQPPRFAQPGTF 212

>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 = 93.6 bits (233), Expect = 3e-23
 Identities = 22/104 (21%), Positives = 37/104 (35%), Gaps = 9/104 (8%)

Query: 421 KVLCLTEAIT-ADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVF 479
           +V+ +       D   D     EI ED+R EC K+G +  +++     +G          
Sbjct: 16  RVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDG-------VAS 68

Query: 480 LEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNK-DYSA 522
           + + D          L GR FGG  + A  +     +     S 
Sbjct: 69  VSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQSGPSSG 112

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 94.9 bits (237), Expect = 4e-23
 Identities = 35/204 (17%), Positives = 71/204 (34%), Gaps = 50/204 (24%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMR 230
           + V  LP    ++   + F            G    + +  +           + FV   
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGS---------IGE---IESCKLVRDKITGQSLGYGFVNYI 52

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 289
             ++A  A+  L+G+  +   ++V                 +PS                
Sbjct: 53  DPKDAEKAINTLNGLRLQTKTIKVSYA--------------RPS---------------S 83

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
            +     ++V GLP   T+ ++++L   +G +    ++ D+ TG S+G GF  +      
Sbjct: 84  ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 143

Query: 350 DIACAALNG--LKMGDKTLTVRRA 371
           + A   LNG       + +TV+ A
Sbjct: 144 EEAIKGLNGQKPSGATEPITVKFA 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 = 81.1 bits (201), Expect = 4e-18
 Identities = 31/84 (36%), Positives = 43/84 (51%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ + + L  S G +    LV+D+ TG S GYGF  Y DP   + A   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 357 NGLKMGDKTLTVRRATASSGQSKT 380
           NGL++  KT+ V  A  SS   + 
Sbjct: 65  NGLRLQTKTIKVSYARPSSASIRD 88

>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 = 41.0 bits (97), Expect = 2e-04
 Identities = 20/108 (18%), Positives = 36/108 (33%), Gaps = 30/108 (27%)

Query: 162 PVQVMTQQATR---HARRVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGP 209
            ++V   + +        +YV GLP    ++ +   FSQ        ++   + G S G 
Sbjct: 73  TIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRG- 131

Query: 210 GDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV--AVRVR 254
                           F+      EA  A+  L+G    G    + V+
Sbjct: 132 --------------VGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK 165

>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 = 92.3 bits (230), Expect = 5e-23
 Identities = 26/89 (29%), Positives = 44/89 (49%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V++G +PY  TE QI +L  + G +    ++ D  TG SKGY F  ++D   +  A   
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 356 LNGLKMGDKTLTVRRATASSGQSKTEQES 384
           LNG ++G + L    ++ S     + +  
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVSLEHH 92

>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 = 54.5 bits (132), Expect = 9e-10
 Identities = 21/94 (22%), Positives = 43/94 (45%), Gaps = 19/94 (20%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFV 227
           +R VY+G +P    E+ I    S V         GP   V+N+ +  + +      +AF+
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNV---------GP---VINLKMMFDPQTGRSKGYAFI 49

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYN 260
           E R +E +++A+  L+G       ++    ++ +
Sbjct: 50  EFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSD 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 = 94.1 bits (235), Expect = 9e-23
 Identities = 40/204 (19%), Positives = 72/204 (35%), Gaps = 45/204 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-----FAFVEM 229
           R +YVG L     E  +  +F            GP   + N+ I  +K      +AFVE 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQV---------GGP---IANIKIMIDKNNKNVNYAFVEY 48

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAI 288
               +A+ A+  L+G   E   V++                   S   +           
Sbjct: 49  HQSHDANIALQTLNGKQIENNIVKINWA--------------FQSQQSS----------- 83

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
             ++    +FVG L     +  ++   + F +     ++ D  TG+S+GYGF  +     
Sbjct: 84  --SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDD 141

Query: 349 TDIACAALNGLKMGDKTLTVRRAT 372
              A  ++ G  +  + L +  A 
Sbjct: 142 AQNAMDSMQGQDLNGRPLRINWAA 165

>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 = 67.9 bits (167), Expect = 1e-13
 Identities = 19/89 (21%), Positives = 38/89 (42%), Gaps = 1/89 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++VG L    TE  +K+  +  G +    ++ D+    +  Y F  Y      +IA   L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 357 NGLKMGDKTLTVRRATASSGQSKTEQESI 385
           NG ++ +  + +  A  S   S  +  ++
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTFNL 90

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 93.4 bits (233), Expect = 2e-22
 Identities = 40/204 (19%), Positives = 74/204 (36%), Gaps = 50/204 (24%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMR 230
           + V  LP    ++ +   F            GP   +    I       +   +AFV+  
Sbjct: 6   LIVNYLPQDMTDRELYALFRA---------IGP---INTCRIMRDYKTGYSYGYAFVDFT 53

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 289
           +  ++  A+  L+GI      ++V            A   G+   + NL           
Sbjct: 54  SEMDSQRAIKVLNGITVRNKRLKVSY----------ARPGGESIKDTNL----------- 92

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
                   +V  LP   T+ Q+  +   +G++   ++++D+ TG  +G  F  Y      
Sbjct: 93  --------YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144

Query: 350 DIACAALNG--LKMGDKTLTVRRA 371
             A +ALN    + G + L+VR A
Sbjct: 145 QEAISALNNVIPEGGSQPLSVRLA 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 = 82.2 bits (204), Expect = 1e-18
 Identities = 46/208 (22%), Positives = 70/208 (33%), Gaps = 53/208 (25%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ ++  L  + G ++   +++D  TG S GY F  +     +  A   L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 357 NGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFG 416
           NG+ + +K L V  A       K                                 +L+ 
Sbjct: 66  NGITVRNKRLKVSYARPGGESIK-------------------------------DTNLY- 93

Query: 417 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVG 476
                V  L   IT D L                 GKYG++V   I R D+  G   GV 
Sbjct: 94  -----VTNLPRTITDDQL-------------DTIFGKYGSIVQKNILR-DKLTGRPRGVA 134

Query: 477 KVFLEYYDAVGCATAKNALSGRKFGGNT 504
             F+ Y        A +AL+     G +
Sbjct: 135 --FVRYNKREEAQEAISALNNVIPEGGS 160

>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 = 92.0 bits (229), Expect = 9e-22
 Identities = 42/209 (20%), Positives = 70/209 (33%), Gaps = 48/209 (22%)

Query: 173 HARRVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKK 223
             R++++GGL     ++++ + F Q        VM       S G               
Sbjct: 12  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG--------------- 56

Query: 224 FAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGL 283
           F FV   TVEE   AM       +G  V  +R         A        P         
Sbjct: 57  FGFVTYATVEEVDAAMNARPHKVDGRVVEPKR---------AVSREDSQRP--------- 98

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
                G      ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  +
Sbjct: 99  -----GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT 372
            D    D          +      VR+A 
Sbjct: 154 DDHDSVDKIVIQ-KYHTVNGHNCEVRKAL 181

>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 = 66.2 bits (162), Expect = 9e-13
 Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 1/88 (1%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           E   ++F+GGL +  T+  ++   E +GTL    +++D +T  S+G+GF  Y      D 
Sbjct: 11  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70

Query: 352 ACAALNGLKMGDKTLTVRRATASSGQSK 379
           A  A    K+  + +  +RA +     +
Sbjct: 71  AMNA-RPHKVDGRVVEPKRAVSREDSQR 97

>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 = 89.5 bits (223), Expect = 4e-21
 Identities = 36/204 (17%), Positives = 68/204 (33%), Gaps = 49/204 (24%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
            ++++GGL     E  +  +F +          G    V ++ I  +        F F+ 
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGK---------YGT---VTDLKIMKDPATGRSRGFGFLS 51

Query: 229 MRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAI 288
                     +    I+ +G  +  +R             P                   
Sbjct: 52  FEKPSSVDEVVKTQHIL-DGKVIDPKRAI-----------PRDEQDK------------- 86

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
                  ++FVGG+       + +E    +GT+    L+ D+DTG S+G+GF  Y     
Sbjct: 87  -----TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 349 TDIACAALNGLKMGDKTLTVRRAT 372
            D  C     +   D+ + ++RA 
Sbjct: 142 VDRVC-QNKFIDFKDRKIEIKRAE 164

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 67.6 bits (166), Expect = 1e-13
 Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  TE  ++E    +GT+    ++KD  TG S+G+GF  ++ P+  D     
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64

Query: 356 LNGLKMGDKTLTVRRATASSGQSKT 380
            +   +  K +  +RA     Q KT
Sbjct: 65  QH--ILDGKVIDPKRAIPRDEQDKT 87

>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 = 83.8 bits (208), Expect = 6e-20
 Identities = 21/90 (23%), Positives = 38/90 (42%), Gaps = 2/90 (2%)

Query: 284 ASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
            S  + G   P    V+V  LP+  T   +  +   +G +    ++KD+DT  SKG  F 
Sbjct: 4   GSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFI 63

Query: 342 VYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
           ++ D         A+N  ++  + +    A
Sbjct: 64  LFLDKDSAQNCTRAINNKQLFGRVIKASIA 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 = 51.5 bits (124), Expect = 1e-08
 Identities = 19/88 (21%), Positives = 28/88 (31%), Gaps = 19/88 (21%)

Query: 173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAF 226
               VYV  LP       +   FS+            G  VV V I  +K        AF
Sbjct: 15  SKSTVYVSNLPFSLTNNDLYRIFSKY-----------GK-VVKVTIMKDKDTRKSKGVAF 62

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           +     + A N   A++     G  ++ 
Sbjct: 63  ILFLDKDSAQNCTRAINNKQLFGRVIKA 90

>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 = 83.8 bits (208), Expect = 6e-20
 Identities = 34/76 (44%), Positives = 42/76 (55%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC YQD      A   
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 356 LNGLKMGDKTLTVRRA 371
           LNG +   + L V  A
Sbjct: 70  LNGREFSGRALRVDNA 85

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 53.0 bits (128), Expect = 4e-09
 Identities = 33/109 (30%), Positives = 50/109 (45%), Gaps = 20/109 (18%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FA 225
           R  R V+VG +P  A E+ +   FS+V         GP   VV+  + ++++      + 
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEV---------GP---VVSFRLVYDRETGKPKGYG 53

Query: 226 FVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDY-NPTLAAALGPGQP 272
           F E +  E A +AM  L+G  F G A+RV       N     +LG G P
Sbjct: 54  FCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>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 = 84.6 bits (210), Expect = 2e-19
 Identities = 39/210 (18%), Positives = 71/210 (33%), Gaps = 50/210 (23%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--------FA 225
           A +++VG +P   +E+ +   F Q          G    V  + +  ++           
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQ---------YGA---VYEINVLRDRSQNPPQSKGCC 50

Query: 226 FVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLA 284
           FV   T + A  A  AL  +                  L     P Q  P         A
Sbjct: 51  FVTFYTRKAALEAQNALHNMK----------------VLPGMHHPIQMKP---------A 85

Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
                 A    ++F+G +    TE  I+ +  SFG +    +++    G S+G  F  + 
Sbjct: 86  DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFT 144

Query: 345 DPAVTDIACAALNG---LKMGDKTLTVRRA 371
             A+   A  A++    ++     + V+ A
Sbjct: 145 TRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 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 = 71.1 bits (175), Expect = 1e-14
 Identities = 20/93 (21%), Positives = 41/93 (44%), Gaps = 2/93 (2%)

Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTD 350
              ++FVG +P  ++E  ++EL E +G ++  ++++DR      SKG  F  +       
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQE 383
            A  AL+ +K+        +   +  +     E
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVE 94

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 83.1 bits (206), Expect = 2e-18
 Identities = 42/217 (19%), Positives = 79/217 (36%), Gaps = 49/217 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
             +YVG L P   E  +   FS          AGP   ++++ +  +        +A+V 
Sbjct: 16  ASLYVGDLHPDVTEAMLYEKFSP---------AGP---ILSIRVCRDMITRRSLGYAYVN 63

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGA 287
            +   +A  A+  ++  + +G  VR+                 Q  P+L           
Sbjct: 64  FQQPADAERALDTMNFDVIKGKPVRIMWS--------------QRDPSLR---------- 99

Query: 288 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 347
                G   +F+  L        + +   +FG +    +V   D   SKGYGF  ++   
Sbjct: 100 ---KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQE 154

Query: 348 VTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
             + A   +NG+ + D+ + V R   S  + + E  +
Sbjct: 155 AAERAIEKMNGMLLNDRKVFVGRFK-SRKEREAELGA 190

>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 = 71.5 bits (176), Expect = 2e-14
 Identities = 20/89 (22%), Positives = 36/89 (40%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++VG L    TE  + E     G +    + +D  T  S GY +  +Q PA  + A   +
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77

Query: 357 NGLKMGDKTLTVRRATASSGQSKTEQESI 385
           N   +  K + +  +       K+   +I
Sbjct: 78  NFDVIKGKPVRIMWSQRDPSLRKSGVGNI 106

>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 = 80.6 bits (199), Expect = 2e-18
 Identities = 29/114 (25%), Positives = 44/114 (38%), Gaps = 2/114 (1%)

Query: 264 AAALGPGQPSPNLNLAAVGLASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTL 321
               G       L               E      + V  +P    E Q+++L E +G +
Sbjct: 10  YDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI 69

Query: 322 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS 375
               +V DR+T  S+GYGF  +Q  +    A A LNG  + +K L V  A +  
Sbjct: 70  ESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH 123

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 47.8 bits (114), Expect = 6e-07
 Identities = 28/150 (18%), Positives = 48/150 (32%), Gaps = 24/150 (16%)

Query: 131 GQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQA 190
            Q+P V    P      L     Q     + P Q          R + V  +P   +E  
Sbjct: 2   SQIPLVSQYDPYGQTAQLQ-QLQQQQQQHIPPTQ--MNPEPDVLRNLMVNYIPTTVDEVQ 58

Query: 191 IATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG 243
           +   F +     G         + +V I         + + FV+ ++   A  A+  L+G
Sbjct: 59  LRQLFER----YG--------PIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG 106

Query: 244 IIFEGVAVRVR--RPTDYNPTLAAALGPGQ 271
                  ++V         P +A A+G G 
Sbjct: 107 FNILNKRLKVALAASGHQRPGIAGAVGDGN 136

>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 = 79.1 bits (196), Expect = 3e-18
 Identities = 29/83 (34%), Positives = 43/83 (51%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   ++VG L +  TE  ++ + E FG +    L+KD DTG SKGYGF  + D    
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 350 DIACAALNGLKMGDKTLTVRRAT 372
             A   LNG ++  + + V   T
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVT 83

>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 = 46.4 bits (111), Expect = 9e-07
 Identities = 18/87 (20%), Positives = 29/87 (33%), Gaps = 19/87 (21%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFV 227
           +  +YVG L     E  +   F              G  + N+ +         K + F+
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPF-----------GK-IDNIVLMKDSDTGRSKGYGFI 52

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV 253
                E A  A+  L+G    G  +RV
Sbjct: 53  TFSDSECARRALEQLNGFELAGRPMRV 79

>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 = 78.8 bits (195), Expect = 4e-18
 Identities = 28/95 (29%), Positives = 51/95 (53%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG+ G A    ++FVGGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +
Sbjct: 2   SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQS 378
           ++      A  A+NG  +  + + V +A  SS   
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNR 96

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 43.8 bits (104), Expect = 7e-06
 Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 17/85 (20%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-VNVYINHE----KKFAFVEM 229
            +++VGGL    NEQ++   FS+            G    V V  + E    + F FV  
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKY-----------GQISEVVVVKDRETQRSRGFGFVTF 61

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
             +++A +AM A++G   +G  +RV
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRV 86

>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 = 78.5 bits (194), Expect = 6e-18
 Identities = 32/103 (31%), Positives = 51/103 (49%)

Query: 270 GQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD 329
           G    + +  A  +A+    G+ GP R++VG L +  TE  ++ + E FG +    L+ D
Sbjct: 2   GHHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMD 61

Query: 330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
            +TG SKGYGF  + D      A   LNG ++  + + V   T
Sbjct: 62  SETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVT 104

>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 = 46.9 bits (112), Expect = 8e-07
 Identities = 18/99 (18%), Positives = 33/99 (33%), Gaps = 19/99 (19%)

Query: 162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--- 218
            +    Q+ +    R+YVG L     E  +   F            G    + ++ +   
Sbjct: 14  AMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPF---------GR---IESIQLMMD 61

Query: 219 ---NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
                 K + F+     E A  A+  L+G    G  ++V
Sbjct: 62  SETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100

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

 Score = 77.6 bits (192), Expect = 6e-18
 Identities = 28/90 (31%), Positives = 46/90 (51%), Gaps = 2/90 (2%)

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
            G+ G  ++FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V
Sbjct: 3   SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEV 60

Query: 349 TDIACAALNGLKMGDKTLTVRRATASSGQS 378
            + AC  +NG+K+  + + VR    +SG S
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 = 47.6 bits (114), Expect = 2e-07
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 17/86 (19%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEM 229
           A +++V  LP     + +   F++      G+       V+   I  E    K    V+ 
Sbjct: 8   ACQIFVRNLPFDFTWKMLKDKFNEC-----GH-------VLYADIKMENGKSKGCGVVKF 55

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRVR 254
            + E A  A   ++G+   G  + VR
Sbjct: 56  ESPEVAERACRMMNGMKLSGREIDVR 81

>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 = 77.6 bits (192), Expect = 6e-18
 Identities = 18/84 (21%), Positives = 36/84 (42%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   +++ GL    T+  + +L + +G +     + D+ T   KGYGF  +  P+  
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

Query: 350 DIACAALNGLKMGDKTLTVRRATA 373
             A  AL    +  +       ++
Sbjct: 61  QKAVTALKASGVQAQMAKQSGPSS 84

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 49.8 bits (120), Expect = 4e-08
 Identities = 15/90 (16%), Positives = 28/90 (31%), Gaps = 17/90 (18%)

Query: 173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-VNVYINHE----KKFAFV 227
            +  +Y+ GL P   +Q +                  G  V     ++      K + FV
Sbjct: 4   GSSGLYIRGLQPGTTDQDLVKLCQPY-----------GKIVSTKAILDKTTNKCKGYGFV 52

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRRP 256
           +  +   A  A+ AL     +    +   P
Sbjct: 53  DFDSPSAAQKAVTALKASGVQAQMAKQSGP 82

>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 = 77.3 bits (191), Expect = 1e-17
 Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 1/95 (1%)

Query: 279 AAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY 338
            + G +       E    VFVG L     E  + EL    G L    + KDR+ G  K +
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSF 59

Query: 339 GFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA 373
           GF  ++ P     A A LNG+++  + + V   ++
Sbjct: 60  GFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSS 94

>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 = 53.4 bits (129), Expect = 3e-09
 Identities = 27/98 (27%), Positives = 36/98 (36%), Gaps = 18/98 (18%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NH 220
           M        R V+VG L     E+ +   F Q         AGP   +  V I       
Sbjct: 8   MFPAQEEADRTVFVGNLEARVREEILYELFLQ---------AGP---LTKVTICKDREGK 55

Query: 221 EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPT 257
            K F FV  +  E  S A+  L+GI   G  + V  P+
Sbjct: 56  PKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS 93

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 77.3 bits (191), Expect = 1e-17
 Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 8/86 (9%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTL--------HGFDLVKDRDTGNSKGYGFCVYQDP 346
           + +FV GL    T   + +  +  G +           +L  DR+TG  KG     + DP
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 347 AVTDIACAALNGLKMGDKTLTVRRAT 372
                A    +G +     + V  AT
Sbjct: 74  PSAKAAIDWFDGKEFSGNPIKVSFAT 99

>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 = 56.9 bits (138), Expect = 2e-10
 Identities = 22/98 (22%), Positives = 37/98 (37%), Gaps = 13/98 (13%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQ---VMTAIGGNSAGPGDAVVNVYINHE--- 221
             +      ++V GL      +++A +F Q   + T         G  ++N+Y + E   
Sbjct: 7   HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKT-----GQPMINLYTDRETGK 61

Query: 222 -KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPT 257
            K  A V       A  A+   DG  F G  ++V   T
Sbjct: 62  LKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 99

>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 = 77.7 bits (192), Expect = 1e-17
 Identities = 23/77 (29%), Positives = 34/77 (44%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FV  +     E +I+E    +G +    L  DR TG SKGY    Y+       A  A
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 356 LNGLKMGDKTLTVRRAT 372
           LNG ++  +T+ V    
Sbjct: 88  LNGAEIMGQTIQVDWCF 104

>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 = 52.3 bits (126), Expect = 1e-08
 Identities = 20/92 (21%), Positives = 37/92 (40%), Gaps = 19/92 (20%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK----- 223
           Q +     ++V  +   A E  I   F            G    + N+++N +++     
Sbjct: 21  QRSVEGWILFVTSIHEEAQEDEIQEKFCDY---------GE---IKNIHLNLDRRTGFSK 68

Query: 224 -FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
            +A VE  T ++A  A  AL+G    G  ++V
Sbjct: 69  GYALVEYETHKQALAAKEALNGAEIMGQTIQV 100

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 77.3 bits (191), Expect = 1e-17
 Identities = 25/90 (27%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 289 GGAEGPDR------VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 342
           G   GP R      +FV G+    TE  I +    +G +    L  DR TG  KGY    
Sbjct: 12  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71

Query: 343 YQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           Y+       A   LNG  +  + ++V    
Sbjct: 72  YETYKEAQAAMEGLNGQDLMGQPISVDWCF 101

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 51.5 bits (124), Expect = 2e-08
 Identities = 23/100 (23%), Positives = 42/100 (42%), Gaps = 24/100 (24%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK----- 223
           Q +     ++V G+   A E+ I   F++            G+ + N+++N +++     
Sbjct: 18  QRSVEGWILFVTGVHEEATEEDIHDKFAEY-----------GE-IKNIHLNLDRRTGYLK 65

Query: 224 -FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV-----RRP 256
            +  VE  T +EA  AM  L+G    G  + V     R P
Sbjct: 66  GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 105

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 77.3 bits (191), Expect = 1e-17
 Identities = 18/78 (23%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++F+ GLP+  T+ +++E+ ++ GT+    LV +R  G  KG  +  Y++ +    A 
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAV 75

Query: 354 AALNGLKMGDKTLTVRRA 371
             ++G+ + +  + V  +
Sbjct: 76  MKMDGMTIKENIIKVAIS 93

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 18/85 (21%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEM 229
            ++++ GLP    ++ +                G    V ++ +        K  A+VE 
Sbjct: 18  HKLFISGLPFSCTKEELEEICKAH---------GT---VKDLRLVTNRAGKPKGLAYVEY 65

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
               +AS A+  +DG+  +   ++V
Sbjct: 66  ENESQASQAVMKMDGMTIKENIIKV 90

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 78.3 bits (193), Expect = 2e-17
 Identities = 22/105 (20%), Positives = 39/105 (37%), Gaps = 4/105 (3%)

Query: 271 QPSPNLNLAAVGLASGAIGGAEGPD----RVFVGGLPYYFTETQIKELLESFGTLHGFDL 326
               N     V   SG  GG+ G       ++VGGL     +  +      FG +    +
Sbjct: 36  YTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 95

Query: 327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
             D +T   +G+ F  ++       A   +N  ++  +T+ V  A
Sbjct: 96  PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 52.9 bits (127), Expect = 1e-08
 Identities = 24/130 (18%), Positives = 46/130 (35%), Gaps = 20/130 (15%)

Query: 131 GQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQA 190
            ++  + S +PE          T+            +  +    R +YVGGL    +++ 
Sbjct: 21  DEMYEILSNLPESVA-YTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKV 79

Query: 191 IATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG 243
           +   F            G    + ++ I         + FAFVE    E+A+ A+  ++ 
Sbjct: 80  LHAAFIP---------FGD---ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE 127

Query: 244 IIFEGVAVRV 253
               G  +RV
Sbjct: 128 SELFGRTIRV 137

>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 = 74.6 bits (184), Expect = 1e-16
 Identities = 19/89 (21%), Positives = 37/89 (41%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG+ G A     ++VGGL     +  +      FG +    +  D +T   +G+ F  +
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           +       A   +N  ++  +T+ V  A 
Sbjct: 62  ELAEDAAAAIDNMNESELFGRTIRVNLAK 90

>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 = 47.2 bits (113), Expect = 4e-07
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 19/94 (20%)

Query: 167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--- 223
           +       R +YVGGL    +++ +   F            G    + ++ I  + +   
Sbjct: 5   SSGMATTKRVLYVGGLAEEVDDKVLHAAFIP---------FGD---ITDIQIPLDYETEK 52

Query: 224 ---FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
              FAFVE    E+A+ A+  ++     G  +RV
Sbjct: 53  HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 86

>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 = 73.7 bits (182), Expect = 1e-16
 Identities = 15/76 (19%), Positives = 31/76 (40%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++VGGL     +  +      FG +    +  D +T   +G+ F  ++       A   
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68

Query: 356 LNGLKMGDKTLTVRRA 371
           +N  ++  +T+ V  A
Sbjct: 69  MNESELFGRTIRVNLA 84

>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 = 51.4 bits (124), Expect = 1e-08
 Identities = 20/86 (23%), Positives = 36/86 (41%), Gaps = 19/86 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
           R +YVGGL    +++ +   F            G    + ++ I  + +      FAFVE
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIP---------FGD---ITDIQIPLDYETEKHRGFAFVE 55

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRV 253
               E+A+ A+  ++     G  +RV
Sbjct: 56  FELAEDAAAAIDNMNESELFGRTIRV 81

>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 = 73.8 bits (182), Expect = 2e-16
 Identities = 22/93 (23%), Positives = 45/93 (48%), Gaps = 3/93 (3%)

Query: 284 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G    PD    + V GL  Y TE  ++E+   +G +    +V D+ +  S+G+ F
Sbjct: 2   SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATA 373
             +++      A    NG+++  + + V   ++
Sbjct: 62  VYFENVDDAKEAKERANGMELDGRRIRVSGPSS 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 = 47.6 bits (114), Expect = 3e-07
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 19/86 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
             + V GL     E+ +   FS+          GP   + +V I ++++      FAFV 
Sbjct: 16  CCLGVFGLSLYTTERDLREVFSK---------YGP---IADVSIVYDQQSRRSRGFAFVY 63

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRV 253
              V++A  A    +G+  +G  +RV
Sbjct: 64  FENVDDAKEAKERANGMELDGRRIRV 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 = 74.2 bits (183), Expect = 2e-16
 Identities = 28/98 (28%), Positives = 44/98 (44%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG I        V+VGGL    +E  + EL    G +    + KDR TG  +GYGF  +
Sbjct: 5   SSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTE 381
                 D A   ++ +K+  K + V +A+A +      
Sbjct: 65  LSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGP 102

>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 = 52.3 bits (126), Expect = 8e-09
 Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 19/86 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
             VYVGGL    +E  +   F Q         AGP   VVN ++  ++       + FVE
Sbjct: 16  ATVYVGGLDEKVSEPLLWELFLQ---------AGP---VVNTHMPKDRVTGQHQGYGFVE 63

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRV 253
             + E+A  A+  +D I   G  +RV
Sbjct: 64  FLSEEDADYAIKIMDMIKLYGKPIRV 89

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 73.9 bits (182), Expect = 2e-16
 Identities = 27/93 (29%), Positives = 44/93 (47%), Gaps = 5/93 (5%)

Query: 285 SGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 342
           S    G +  D  ++F+G +P    E  +K L E FG ++   ++KDR TG  KG  F  
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

Query: 343 YQDPAVTDIACAALNGLKM---GDKTLTVRRAT 372
           Y +      A +AL+  K     ++ + V+ A 
Sbjct: 62  YCERESALKAQSALHEQKTLPGMNRPIQVKPAD 94

>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 = 40.0 bits (94), Expect = 2e-04
 Identities = 15/98 (15%), Positives = 33/98 (33%), Gaps = 22/98 (22%)

Query: 167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NH 220
           +      A ++++G +P   +E+ +   F +      G        +  + +        
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEF-----GK-------IYELTVLKDRFTGM 53

Query: 221 EKKFAFVEMRTVEEASNAM-ALDG---IIFEGVAVRVR 254
            K  AF+     E A  A  AL     +      ++V+
Sbjct: 54  HKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVK 91

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 74.3 bits (183), Expect = 2e-16
 Identities = 33/113 (29%), Positives = 51/113 (45%), Gaps = 1/113 (0%)

Query: 259 YNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESF 318
              + +A       S  L+ AA   A   I G EG   +F+  LP  FT+T +      F
Sbjct: 6   QFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGC-NLFIYHLPQEFTDTDLASTFLPF 64

Query: 319 GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
           G +    +  D+ T  SK +GF  + +P    +A  A+NG ++G K L V+  
Sbjct: 65  GNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 41.6 bits (98), Expect = 6e-05
 Identities = 21/131 (16%), Positives = 37/131 (28%), Gaps = 27/131 (20%)

Query: 134 PGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIAT 193
            G+P      A +  P  +  L A          Q        +++  LP    +  +A+
Sbjct: 2   AGLPQFGSASALSTSPLASVALSAAAAAAAG--KQIEGPEGCNLFIYHLPQEFTDTDLAS 59

Query: 194 FFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG 243
            F          V        S                 F FV     + A  A+ A++G
Sbjct: 60  TFLPFGNVISAKVFIDKQTSLSKC---------------FGFVSFDNPDSAQVAIKAMNG 104

Query: 244 IIFEGVAVRVR 254
                  ++V+
Sbjct: 105 FQVGTKRLKVQ 115

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 72.6 bits (179), Expect = 4e-16
 Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++VG L Y  T  Q+KEL   FG +    L+ DR+T   KG+GF   Q+ +V++ A A 
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAK 61

Query: 356 LNGLKMGDKTLTVRRA 371
           L+      +T+ V  A
Sbjct: 62  LDNTDFMGRTIRVTEA 77

>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 = 44.1 bits (105), Expect = 5e-06
 Identities = 27/87 (31%), Positives = 38/87 (43%), Gaps = 20/87 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
           R +YVG L   A  + +   FSQ            G  V NV + ++++      F FVE
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQF-----------GK-VFNVKLIYDRETKKPKGFGFVE 49

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRVR 254
           M+  E  S A+  LD   F G  +RV 
Sbjct: 50  MQE-ESVSEAIAKLDNTDFMGRTIRVT 75

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 74.6 bits (183), Expect = 5e-16
 Identities = 26/114 (22%), Positives = 43/114 (37%), Gaps = 2/114 (1%)

Query: 271 QPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD--LVK 328
           +PSP  N     +     G       V+VG   ++ T+ Q+ +++ S G     +    +
Sbjct: 32  EPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAE 91

Query: 329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQ 382
           +R  G SKGY   V             L G  +  + + VR AT  +      Q
Sbjct: 92  NRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQ 145

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 47.2 bits (112), Expect = 1e-06
 Identities = 25/121 (20%), Positives = 37/121 (30%), Gaps = 16/121 (13%)

Query: 161 MPVQVMTQQATRHAR-RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-VNVYI 218
            P  + T    R+ R  VYVG       +Q +                G  D V +    
Sbjct: 41  TPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRS---------IGVYDVVELKFAE 91

Query: 219 NHE----KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPS 273
           N      K +A V + +       +  L G +  G  V VR  T  N +   A    +  
Sbjct: 92  NRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKREC 151

Query: 274 P 274
            
Sbjct: 152 V 152

>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 = 72.1 bits (178), Expect = 5e-16
 Identities = 17/77 (22%), Positives = 33/77 (42%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FVG L     +  ++   + F +     ++ D  TG+S+GYGF  +        A  +
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 356 LNGLKMGDKTLTVRRAT 372
           + G  +  + L +  A 
Sbjct: 63  MQGQDLNGRPLRINWAA 79

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 25/88 (28%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKKFAF 226
            ++VG L    +++ +   F          VM     G+S G               + F
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG---------------YGF 47

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           V   + ++A NAM ++ G    G  +R+
Sbjct: 48  VSFTSQDDAQNAMDSMQGQDLNGRPLRI 75

>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 = 72.0 bits (177), Expect = 7e-16
 Identities = 16/90 (17%), Positives = 36/90 (40%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG+  G  GP  + V  +P+  +  +I +    +  + G   +K  + G   G     +
Sbjct: 5   SSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATA 373
           +       A   LN   +G + + +   ++
Sbjct: 65  ESRDEATAAVIDLNDRPIGSRKVKLSGPSS 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 = 44.6 bits (106), Expect = 3e-06
 Identities = 15/86 (17%), Positives = 28/86 (32%), Gaps = 13/86 (15%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTV 232
            + V  +P   +   I  FF                  V +  N +      A V   + 
Sbjct: 17  VIKVQNMPFTVSIDEILDFFYGY---------QVIPGSVCLKYNEKGMPTGEAMVAFESR 67

Query: 233 EEASNAMA-LDGIIFEGVAVRVRRPT 257
           +EA+ A+  L+        V++  P+
Sbjct: 68  DEATAAVIDLNDRPIGSRKVKLSGPS 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 = 72.3 bits (178), Expect = 8e-16
 Identities = 21/85 (24%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN---SKGYGFCVYQDP 346
           G+ G   +F+  L +  TE  +K +    G +    + K ++      S G+GF  Y+ P
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 347 AVTDIACAALNGLKMGDKTLTVRRA 371
                A   L G  +    L VR +
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRIS 85

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 16/89 (17%), Positives = 28/89 (31%), Gaps = 20/89 (22%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
            +++  L     E+ +   FS+        +                         F FV
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVL-----------LSMGFGFV 55

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRR 255
           E +  E+A  A+  L G   +G  + VR 
Sbjct: 56  EYKKPEQAQKALKQLQGHTVDGHKLEVRI 84

>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 = 74.1 bits (182), Expect = 9e-16
 Identities = 23/73 (31%), Positives = 34/73 (46%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FV  +     E +I+E    +G +    L  DR TG SKGY    Y+       A  A
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 356 LNGLKMGDKTLTV 368
           LNG ++  +T+ V
Sbjct: 134 LNGAEIMGQTIQV 146

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 49.8 bits (119), Expect = 2e-07
 Identities = 20/92 (21%), Positives = 37/92 (40%), Gaps = 19/92 (20%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK----- 223
           Q +     ++V  +   A E  I   F            G    + N+++N +++     
Sbjct: 67  QRSVEGWILFVTSIHEEAQEDEIQEKFCDY---------GE---IKNIHLNLDRRTGFSK 114

Query: 224 -FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
            +A VE  T ++A  A  AL+G    G  ++V
Sbjct: 115 GYALVEYETHKQALAAKEALNGAEIMGQTIQV 146

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

 Score = 72.4 bits (178), Expect = 9e-16
 Identities = 11/83 (13%), Positives = 25/83 (30%)

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           GG      V    L     ET +K++   +G +   +++    T    G    ++     
Sbjct: 1   GGQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRG 60

Query: 349 TDIACAALNGLKMGDKTLTVRRA 371
                  L+   +    +  +  
Sbjct: 61  AKETVKNLHLTSVMGNIIHAQLD 83

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

 Score = 51.6 bits (124), Expect = 2e-08
 Identities = 12/93 (12%), Positives = 20/93 (21%), Gaps = 19/93 (20%)

Query: 173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAF 226
             + V    L     E  +     +          G    V  V I    +       A 
Sbjct: 5   PLKEVTFARLNDNVRETFLKDMCRKY---------GE---VEEVEILLHPRTRKHLGLAR 52

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTD 258
           V   +   A   +  L      G  +  +    
Sbjct: 53  VLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIK 85

>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 = 72.4 bits (178), Expect = 9e-16
 Identities = 26/106 (24%), Positives = 39/106 (36%), Gaps = 6/106 (5%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG          VF+  L +   E  + E+L+ FG L    +V   DT +SKG  F  +
Sbjct: 5   SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF 64

Query: 344 QDPAVTDIACAALN------GLKMGDKTLTVRRATASSGQSKTEQE 383
                     AA +      GLK+  + L V  A      +     
Sbjct: 65  MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSS 110

>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 = 45.0 bits (107), Expect = 4e-06
 Identities = 18/96 (18%), Positives = 32/96 (33%), Gaps = 25/96 (26%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKF 224
               + V++  L   + E+A+     Q          G    +  V +       H K  
Sbjct: 12  VTEGKTVFIRNLSFDSEEEALGEVLQQF---------GD---LKYVRVVLHPDTEHSKGC 59

Query: 225 AFVEMRTVEEASNAMA-------LDGIIFEGVAVRV 253
           AF +  T E A   +A         G+  +G  ++V
Sbjct: 60  AFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKV 95

>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 = 71.5 bits (176), Expect = 2e-15
 Identities = 27/92 (29%), Positives = 39/92 (42%), Gaps = 3/92 (3%)

Query: 284 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G     D    + V  L     ET ++EL   FG++    L KD+ TG SKG+ F
Sbjct: 2   SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
             +        A A ++G       L V  A 
Sbjct: 62  ISFHRREDAARAIAGVSGFGYDHLILNVEWAK 93

>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 = 45.3 bits (108), Expect = 2e-06
 Identities = 17/97 (17%), Positives = 36/97 (37%), Gaps = 22/97 (22%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEM 229
            + V  L     E  +   F       G        ++  +Y+  +K       FAF+  
Sbjct: 17  TIRVTNLSEDTRETDLQELFRP----FG--------SISRIYLAKDKTTGQSKGFAFISF 64

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV---RRPTDYNPT 262
              E+A+ A+  + G  ++ + + V   +  T+  P+
Sbjct: 65  HRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPS 101

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 71.7 bits (176), Expect = 2e-15
 Identities = 18/86 (20%), Positives = 29/86 (33%), Gaps = 8/86 (9%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTL--------HGFDLVKDRDTGNSKGYGFCVYQDP 346
             ++V GL    T   + +  +  G +            +  D++TG  KG     Y+DP
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75

Query: 347 AVTDIACAALNGLKMGDKTLTVRRAT 372
                A    +G       L V  A 
Sbjct: 76  PTAKAAVEWFDGKDFQGSKLKVSLAR 101

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 54.0 bits (130), Expect = 3e-09
 Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 7/86 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEMR 230
             +YV GL        +A FF Q    +   +   G  ++++Y++ E    K  A V   
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQC--GVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 73

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVRR 255
               A  A+   DG  F+G  ++V  
Sbjct: 74  DPPTAKAAVEWFDGKDFQGSKLKVSL 99

>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 = 71.2 bits (175), Expect = 2e-15
 Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 1/94 (1%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SGA  G  GP  + V  +P+  +  +I +    +  + G   +K  + G   G     +
Sbjct: 5   SSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT-ASSG 376
           +       A   LN   +G + + +   +  SSG
Sbjct: 65  ESRDEATAAVIDLNDRPIGSRKVKLVLGSGPSSG 98

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 14/83 (16%), Positives = 26/83 (31%), Gaps = 13/83 (15%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTVE 233
           + V  +P   +   I  FF                  V +  N +      A V   + +
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGY---------QVIPGSVCLKYNEKGMPTGEAMVAFESRD 68

Query: 234 EASNAMA-LDGIIFEGVAVRVRR 255
           EA+ A+  L+        V++  
Sbjct: 69  EATAAVIDLNDRPIGSRKVKLVL 91

>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 = 71.1 bits (175), Expect = 2e-15
 Identities = 23/84 (27%), Positives = 37/84 (44%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G  R+FV  L Y  +E  +++L  ++G L       D  T   KG+ F  +  P   
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 350 DIACAALNGLKMGDKTLTVRRATA 373
             A A ++G     + L V  +T 
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTI 87

>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 = 48.4 bits (116), Expect = 1e-07
 Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 19/85 (22%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEM 229
           R++V  L   ++E+ +   FS           GP   +  ++          K FAFV  
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAY---------GP---LSELHYPIDSLTKKPKGFAFVTF 57

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
              E A  A   +DG +F+G  + V
Sbjct: 58  MFPEHAVKAYAEVDGQVFQGRMLHV 82

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 71.3 bits (175), Expect = 3e-15
 Identities = 20/87 (22%), Positives = 32/87 (36%), Gaps = 8/87 (9%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTL--------HGFDLVKDRDTGNSKGYGFCVYQD 345
            + +FV GL    T   + +  +  G +           +L  DR+TG  KG     + D
Sbjct: 7   NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 66

Query: 346 PAVTDIACAALNGLKMGDKTLTVRRAT 372
           P     A    +G +     + V  AT
Sbjct: 67  PPSAKAAIDWFDGKEFSGNPIKVSFAT 93

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 53.2 bits (128), Expect = 6e-09
 Identities = 26/104 (25%), Positives = 42/104 (40%), Gaps = 14/104 (13%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIG--GNSAGPGDAVVNVYINHE---- 221
           +Q       ++V GL      +++A +F Q    IG    +   G  ++N+Y + E    
Sbjct: 1   EQDNSDNNTIFVQGLGENVTIESVADYFKQ----IGIIKTNKKTGQPMINLYTDRETGKL 56

Query: 222 KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV---RRPTDYNP 261
           K  A V       A  A+   DG  F G  ++V    R  D+N 
Sbjct: 57  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNR 100

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 71.2 bits (175), Expect = 3e-15
 Identities = 25/90 (27%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 289 GGAEGPDR------VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 342
           G   GP R      +FV G+    TE  I +    +G +    L  DR TG  KGY    
Sbjct: 11  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70

Query: 343 YQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           Y+       A   LNG  +  + ++V    
Sbjct: 71  YETYKEAQAAMEGLNGQDLMGQPISVDWCF 100

>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 = 49.3 bits (118), Expect = 1e-07
 Identities = 23/107 (21%), Positives = 43/107 (40%), Gaps = 19/107 (17%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEM 229
            ++V G+   A E+ I   F++            G+ + N+++N +++      +  VE 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEY-----------GE-IKNIHLNLDRRTGYLKGYTLVEY 71

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPN 275
            T +EA  AM  L+G    G  + V       P      G  + S +
Sbjct: 72  ETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRS 118

>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 = 70.8 bits (174), Expect = 3e-15
 Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 1/94 (1%)

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           A+ P ++F+GGL     E  +K +    G +    L+KDR T  S+G+ F  +++PA   
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAK 62

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
            A   +NG  +  K + V +A   S QS   +  
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRP 96

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 45.4 bits (108), Expect = 3e-06
 Identities = 21/109 (19%), Positives = 38/109 (34%), Gaps = 24/109 (22%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++++GGL    NE+ +   F +        ++      S G               FAF+
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRG---------------FAFI 53

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPN 275
                 +A NA   ++G    G A++V +    +        P   S N
Sbjct: 54  TFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRN 102

>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 = 70.8 bits (174), Expect = 4e-15
 Identities = 31/117 (26%), Positives = 53/117 (45%), Gaps = 6/117 (5%)

Query: 273 SPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT 332
           S  L   ++G A     G EG   +F+  LP  F +  + ++   FG +    +  D+ T
Sbjct: 5   SSGLTQQSIGAAGSQKEGPEGA-NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 63

Query: 333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQA 389
             SK +GF  Y +P     A  ++NG ++G K L V+       +SK + +S  +  
Sbjct: 64  NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK-----RSKNDSKSGPSSG 115

>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 = 70.3 bits (172), Expect = 4e-15
 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 5/76 (6%)

Query: 437 DEEYEEILEDM-REECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL 495
            E Y+E  E++  E   KYG +  + +            VG V++++        A   L
Sbjct: 33  QEHYDEFFEEVFTEMEEKYGEVEEMNVCDN----LGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 496 SGRKFGGNTVNAFYYP 511
           + R F G  ++A   P
Sbjct: 89  NNRWFNGQPIHAELSP 104

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 70.4 bits (173), Expect = 5e-15
 Identities = 23/109 (21%), Positives = 44/109 (40%), Gaps = 6/109 (5%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SGA+        VFV  L Y     ++KE+    G +   D+++D+D G S+G G   +
Sbjct: 5   SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTF 63

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 392
           +       A +  NG  + D+ + V+       +    +       +  
Sbjct: 64  EQSIEAVQAISMFNGQLLFDRPMHVKMD-----ERALPKGDFFPPERPQ 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 = 49.2 bits (118), Expect = 1e-07
 Identities = 20/118 (16%), Positives = 31/118 (26%), Gaps = 26/118 (22%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINH 220
           QA R    V+V  L      + +   FS         ++    G S G            
Sbjct: 10  QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRG------------ 57

Query: 221 EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR--RPTDYNPTLAAALGPGQPSPN 275
                 V      EA  A+   +G +     + V+                P Q  P+
Sbjct: 58  ---IGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPS 112

>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 = 68.7 bits (169), Expect = 1e-14
 Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 290 GAEGPDR-VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           G E   R ++VG + Y  T  +++      G+++   ++ D+ +G+ KG+ +  + D   
Sbjct: 1   GMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60

Query: 349 TDIACAALNGLKMGDKTLTVRRA 371
              +  AL+      + + V   
Sbjct: 61  VRTS-LALDESLFRGRQIKVIPK 82

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 60.6 bits (148), Expect = 6e-12
 Identities = 23/88 (26%), Positives = 34/88 (38%), Gaps = 18/88 (20%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFV 227
           AR +YVG +   A  + +   F              G  V  V I       H K FA++
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGC-----------GS-VNRVTILCDKFSGHPKGFAYI 53

Query: 228 EMRTVEEASNAMALDGIIFEGVAVRVRR 255
           E    E    ++ALD  +F G  ++V  
Sbjct: 54  EFSDKESVRTSLALDESLFRGRQIKVIP 81

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 68.3 bits (168), Expect = 1e-14
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 1/84 (1%)

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVT 349
           +  P +V +G L    T+  I E+  ++G +   D+  +R     SKGY +  +++P   
Sbjct: 1   SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60

Query: 350 DIACAALNGLKMGDKTLTVRRATA 373
           + A   ++G ++  + +T     A
Sbjct: 61  EKALKHMDGGQIDGQEITATAVLA 84

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 46.0 bits (110), Expect = 8e-07
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 20/86 (23%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVE 228
           +V++G L     +  I   FS      G         +  + +       +  K +A+VE
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFST----YG--------KIKMIDMPVERMHPHLSKGYAYVE 53

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRV 253
               +EA  A+  +DG   +G  +  
Sbjct: 54  FENPDEAEKALKHMDGGQIDGQEITA 79

>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 = 68.8 bits (169), Expect = 1e-14
 Identities = 26/103 (25%), Positives = 42/103 (40%), Gaps = 8/103 (7%)

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
            G   P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF  + +   
Sbjct: 4   EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVD 62

Query: 349 TDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQ 391
                   + +    K L +  A       K    +   Q + 
Sbjct: 63  VQKIVE--SQINFHGKKLKLGPA-----IRKQNLSTYHVQPRP 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 = 41.4 bits (98), Expect = 4e-05
 Identities = 17/88 (19%), Positives = 31/88 (35%), Gaps = 24/88 (27%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
            V+VGG+    +E  I +FF++        ++T   G S G               + FV
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKG---------------YGFV 55

Query: 228 EMRTVEEASNAMALDGIIFEGVAVRVRR 255
                 +    +    I F G  +++  
Sbjct: 56  SFYNDVDVQKIVE-SQINFHGKKLKLGP 82

>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 = 68.4 bits (168), Expect = 1e-14
 Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 2/79 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFD--LVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
            +++G L ++ T+  + E + S G     +    ++R  G SKG+        A +    
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 354 AALNGLKMGDKTLTVRRAT 372
             L   ++  +   V  + 
Sbjct: 63  DLLPKRELHGQNPVVTPSN 81

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 47.6 bits (114), Expect = 3e-07
 Identities = 14/94 (14%), Positives = 29/94 (30%), Gaps = 17/94 (18%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-VNVYINHE----KKFAFVEMR 230
            +Y+G L     ++ +      +         G  D + +  + N      K FA V + 
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSL---------GVNDILEIKFFENRANGQSKGFALVGVG 53

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVR--RPTDYNP 261
           +   +   M  L      G    V      +++ 
Sbjct: 54  SEASSKKLMDLLPKRELHGQNPVVTPSNKLEHHH 87

>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 = 69.2 bits (170), Expect = 1e-14
 Identities = 20/89 (22%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +++  L    TE  +  L   F    G  +     TG  +G  F  + +  +   A   
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 356 LNGLKMGDKTLTV--------RRATASSG 376
           +NG K+  K L +        R +  SSG
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQRSSGPSSG 115

>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 = 41.9 bits (99), Expect = 4e-05
 Identities = 12/83 (14%), Positives = 28/83 (33%), Gaps = 13/83 (15%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRT 231
           + +Y+  L P   E+ + + F++                   +     +    AF+    
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARF---------QEKKGPPIQFRMMTGRMRGQAFITFPN 76

Query: 232 VEEASNAM-ALDGIIFEGVAVRV 253
            E A  A+  ++G    G  + +
Sbjct: 77  KEIAWQALHLVNGYKLYGKILVI 99

>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 = 68.9 bits (169), Expect = 1e-14
 Identities = 31/101 (30%), Positives = 42/101 (41%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG          VFVG L    T   IK     FG +    +VKD  TG SKGYGF  +
Sbjct: 5   SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
            +    + A   + G  +G + +    AT      K+  ES
Sbjct: 65  FNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYES 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 = 41.2 bits (97), Expect = 7e-05
 Identities = 24/112 (21%), Positives = 35/112 (31%), Gaps = 29/112 (25%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKKFAF 226
            V+VG L P    + I   F+         V+     G S G               + F
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKG---------------YGF 61

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRV----RRPTDYNPTLAAALGPGQPS 273
           V      +A NA+  + G    G  +R     R+P     T  +      PS
Sbjct: 62  VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPS 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 = 71.5 bits (175), Expect = 1e-14
 Identities = 35/196 (17%), Positives = 57/196 (29%), Gaps = 25/196 (12%)

Query: 177 VYVGGLPPLA-NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 234
           + V  L P     Q++   F        G+       V  V I   KK  A V+M    +
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVY-----GD-------VQRVKILFNKKENALVQMADGNQ 53

Query: 235 ASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPS------PNLNLAAVGLASGA 287
           A  AM  L+G    G  +R+      N  L       Q          L+      +   
Sbjct: 54  AQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF 113

Query: 288 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 347
                    + +  +P   +E  +K L  S G +        +D    +           
Sbjct: 114 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVE 169

Query: 348 VTDIACAALNGLKMGD 363
               A   L+   +G+
Sbjct: 170 EAVQALIDLHNHDLGE 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 = 50.7 bits (121), Expect = 2e-07
 Identities = 27/212 (12%), Positives = 52/212 (24%), Gaps = 36/212 (16%)

Query: 297 VFVGGL-PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           + V  L P   T   +  L   +G +    ++ +      K        D     +A + 
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60

Query: 356 LNGLKMGDKTLTVRRATASSGQSKTEQESILAQA----QQHIAIQKMALQTSGMNTLGGG 411
           LNG K+  K + +  +   + Q   E +             +   K     +  N     
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120

Query: 412 MSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGE 471
            +L    +   +                     ED++      G +V             
Sbjct: 121 ATLHLSNIPPSVS-------------------EEDLKVLFSSNGGVVKGFKFFQKDRKM- 160

Query: 472 TPGVGKVFLEYYDAVGCATAKNALSGRKFGGN 503
                   ++         A   L     G N
Sbjct: 161 ------ALIQMGSVEEAVQALIDLHNHDLGEN 186

>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 = 48.7 bits (116), Expect = 9e-07
 Identities = 26/124 (20%), Positives = 46/124 (37%), Gaps = 13/124 (10%)

Query: 132 QLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAI 191
           Q   +P    E       +G + L  F   P     Q     +  +++  +PP  +E+ +
Sbjct: 79  QNVQLPREGQEDQGLTKDYGNSPLHRFKK-PGSKNFQNIFPPSATLHLSNIPPSVSEEDL 137

Query: 192 ATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI-IFEGV 249
              FS             G      +   ++K A ++M +VEEA  A+  L    + E  
Sbjct: 138 KVLFSSN----------GGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENH 187

Query: 250 AVRV 253
            +RV
Sbjct: 188 HLRV 191

>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 = 71.3 bits (174), Expect = 2e-14
 Identities = 30/204 (14%), Positives = 48/204 (23%), Gaps = 25/204 (12%)

Query: 177 VYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 234
           + V GL     N   +   F        GN       V  V     K   A VEM     
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLY-----GN-------VEKVKFMKSKPGAAMVEMADGYA 54

Query: 235 ASNAM-ALDGIIFEGVAVRVR---------RPTDYNPTLAAALGPGQPSPNLNLAAVGLA 284
              A+  L+     G  + V            +      + +      S N   +    A
Sbjct: 55  VDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQA 114

Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
           +           +     P   TE    E+ +  G      +            G   + 
Sbjct: 115 AKNRIQHPSN-VLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWD 173

Query: 345 DPAVTDIACAALNGLKMGDKTLTV 368
             +        LN  +M +     
Sbjct: 174 SKSDALETLGFLNHYQMKNPNGPY 197

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 59.7 bits (144), Expect = 2e-10
 Identities = 28/222 (12%), Positives = 52/222 (23%), Gaps = 23/222 (10%)

Query: 290 GAEGPDRVFVGGL-PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           GA+ P  + V GL        ++  +   +G +     +K +      G       D   
Sbjct: 1   GADSP-VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYA 54

Query: 349 TDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTL 408
            D A   LN   M  + + V  +   +                    +    + S     
Sbjct: 55  VDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQA 114

Query: 409 GGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQN 468
                     +         +T              E+  E C + G      + +    
Sbjct: 115 AKNRIQHPSNVLHFFNAPLEVTE-------------ENFFEICDELGVKRPTSV-KVFSG 160

Query: 469 GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 510
             E    G   LE+            L+  +         Y 
Sbjct: 161 KSERSSSG--LLEWDSKSDALETLGFLNHYQMKNPNGPYPYT 200

>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 = 42.8 bits (100), Expect = 1e-04
 Identities = 14/123 (11%), Positives = 36/123 (29%), Gaps = 8/123 (6%)

Query: 127 AAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLA 186
           +  P  +PG    + + + +   F  ++   F   P Q    +    +  ++    P   
Sbjct: 77  SKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFS-TPEQAAKNRIQHPSNVLHFFNAPLEV 135

Query: 187 NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGII 245
            E+       ++          P    V    +       +E  +  +A   +  L+   
Sbjct: 136 TEENFFEICDEL------GVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQ 189

Query: 246 FEG 248
            + 
Sbjct: 190 MKN 192

>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 = 68.8 bits (169), Expect = 2e-14
 Identities = 24/103 (23%), Positives = 44/103 (42%), Gaps = 7/103 (6%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G  G   +F+  L        + +   +FG +    +V   D   SKGYGF  ++     
Sbjct: 1   GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQEAA 58

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 392
           + A   +NG+ + D+ + V R      +S+ E+E+ L    + 
Sbjct: 59  ERAIEKMNGMLLNDRKVFVGRF-----KSRKEREAELGARAKE 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 = 40.7 bits (96), Expect = 1e-04
 Identities = 21/143 (14%), Positives = 38/143 (26%), Gaps = 46/143 (32%)

Query: 177 VYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
           +++  L    + +A+   FS         V+    G+                K + FV 
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS----------------KGYGFVH 51

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGA 287
             T E A  A+  ++G++     V V R        A      +   N            
Sbjct: 52  FETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTN------------ 99

Query: 288 IGGAEGPDRVFVGGLPYYFTETQ 310
                    V++       T   
Sbjct: 100 ---------VYIKNFGPGSTRAA 113

>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 = 68.0 bits (167), Expect = 2e-14
 Identities = 18/91 (19%), Positives = 40/91 (43%)

Query: 282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
           G +  +    +G   + V  L Y  +   ++ + E +G +    + ++  T   +G+ F 
Sbjct: 1   GSSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60

Query: 342 VYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
            + D      A AA++G ++  + L V+ A 
Sbjct: 61  RFHDRRDAQDAEAAMDGAELDGRELRVQVAR 91

>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 = 46.8 bits (112), Expect = 7e-07
 Identities = 21/85 (24%), Positives = 32/85 (37%), Gaps = 19/85 (22%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEM 229
            + V  L    +  ++   F +          G    V +VYI  E        FAFV  
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEK---------YGR---VGDVYIPREPHTKAPRGFAFVRF 62

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
               +A +A  A+DG   +G  +RV
Sbjct: 63  HDRRDAQDAEAAMDGAELDGRELRV 87

>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 = 68.2 bits (167), Expect = 3e-14
 Identities = 18/98 (18%), Positives = 40/98 (40%), Gaps = 3/98 (3%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
             +++  LPY  T  ++ ++   +G +    +     T  ++G  + VY+D      A  
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVD 65

Query: 355 ALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 392
            L+G  + ++ L V    A+    K + +    Q +  
Sbjct: 66  HLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLL 103

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 46.6 bits (111), Expect = 9e-07
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 16/83 (19%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRT 231
           R +Y+  LP     + +   F +          GP   +  + + +  +    A+V    
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKY---------GP---IRQIRVGNTPETRGTAYVVYED 56

Query: 232 VEEASNAM-ALDGIIFEGVAVRV 253
           + +A NA+  L G       + V
Sbjct: 57  IFDAKNAVDHLSGFNVSNRYLVV 79

>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 = 42.4 bits (100), Expect = 3e-05
 Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 6/74 (8%)

Query: 445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 504
           E+M +  GKYG +  + +        ET G    ++ Y D      A + LSG       
Sbjct: 23  EEMYDIFGKYGPIRQIRVGNT----PETRGTA--YVVYEDIFDAKNAVDHLSGFNVSNRY 76

Query: 505 VNAFYYPEDKYFNK 518
           +   YY  ++ F K
Sbjct: 77  LVVLYYNANRAFQK 90

>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 = 17/76 (22%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+VG + Y  T   ++    S G+++   ++ D+ +G+ KGY +  + +    D A  A
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA-VA 96

Query: 356 LNGLKMGDKTLTVRRA 371
           ++      +T+ V   
Sbjct: 97  MDETVFRGRTIKVLPK 112

>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 = 58.6 bits (142), Expect = 9e-11
 Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 18/94 (19%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHE 221
           ++     R VYVG +   +  Q +   FS           G    +  + I       H 
Sbjct: 30  EKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC---------GS---INRITILCDKFSGHP 77

Query: 222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
           K +A++E         A+A+D  +F G  ++V  
Sbjct: 78  KGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLP 111

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 67.2 bits (165), Expect = 3e-14
 Identities = 27/84 (32%), Positives = 36/84 (42%), Gaps = 1/84 (1%)

Query: 290 GAEGPD-RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           G  G    VFVG L    T   I      FG +    +VKD  TG SKGYGF  + +   
Sbjct: 1   GPLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 60

Query: 349 TDIACAALNGLKMGDKTLTVRRAT 372
            + A   + G  +G + +    AT
Sbjct: 61  AENAIQQMGGQWLGGRQIRTNWAT 84

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 23/95 (24%), Positives = 32/95 (33%), Gaps = 29/95 (30%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKKFAF 226
            V+VG L P     AIA  F+         V+     G S G               + F
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKG---------------YGF 52

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRV----RRP 256
           V      +A NA+  + G    G  +R     R+P
Sbjct: 53  VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP 87

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 67.7 bits (166), Expect = 3e-14
 Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 2/96 (2%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG +     P  ++VG L    TE  I +L    G      ++ +  +     Y F  +
Sbjct: 5   SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEF 62

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK 379
            +      A AA+NG K+  K + V  AT  S Q  
Sbjct: 63  YEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKS 98

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 52.3 bits (126), Expect = 7e-09
 Identities = 23/91 (25%), Positives = 34/91 (37%), Gaps = 17/91 (18%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---- 223
            +     R +YVG L     E  I   FSQ          GP     +  +  E      
Sbjct: 9   MEDDGQPRTLYVGNLSRDVTEVLILQLFSQ---------IGP---CKSCKMITEHTSNDP 56

Query: 224 FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           + FVE     +A+ A+ A++G    G  V+V
Sbjct: 57  YCFVEFYEHRDAAAALAAMNGRKILGKEVKV 87

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 67.3 bits (165), Expect = 3e-14
 Identities = 13/88 (14%), Positives = 31/88 (35%), Gaps = 5/88 (5%)

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
                 +    L +  TE ++KE+ E        ++      G SKG  +  ++  A  +
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSEADAE 67

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQS 378
                  G ++  +++++       G  
Sbjct: 68  KNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 14/88 (15%), Positives = 28/88 (31%), Gaps = 12/88 (13%)

Query: 167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAF 226
           T +  R AR +    L     E  +   F               +  +       K  A+
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----------LEIRLVSQDGKSKGIAY 57

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           +E ++  +A   +    G   +G +V +
Sbjct: 58  IEFKSEADAEKNLEEKQGAEIDGRSVSL 85

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 67.3 bits (165), Expect = 3e-14
 Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 11/94 (11%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G +++++G L    T   +++L           L          GY F  Y D    
Sbjct: 4   GSSGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWA 57

Query: 350 DIACAALNG-LKMGDKTLTVRRATA----SSGQS 378
             A   L+G +++  K + V  + +    SSG S
Sbjct: 58  IRAIETLSGKVELHGKIMEVDYSVSKKLRSSGPS 91

>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 = 49.9 bits (120), Expect = 4e-08
 Identities = 14/82 (17%), Positives = 26/82 (31%), Gaps = 14/82 (17%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
            ++Y+G L P      +   F                  +   +  +  +AFV+      
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGD----RKL--------PLAGQVLLKSGYAFVDYPDQNW 56

Query: 235 ASNAM-ALDGII-FEGVAVRVR 254
           A  A+  L G +   G  + V 
Sbjct: 57  AIRAIETLSGKVELHGKIMEVD 78

>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 = 67.7 bits (166), Expect = 3e-14
 Identities = 23/97 (23%), Positives = 46/97 (47%), Gaps = 2/97 (2%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG       P R+ V  +P+ F +  ++++   FG +   +++ +     SKG+GF  +
Sbjct: 5   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTF 62

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKT 380
           ++ A  D A   L+G  +  + + V  ATA    +  
Sbjct: 63  ENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSG 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 = 46.1 bits (110), Expect = 1e-06
 Identities = 19/84 (22%), Positives = 31/84 (36%), Gaps = 17/84 (20%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMR 230
           +R++V  +P    +  +   F Q          G    +++V I       K F FV   
Sbjct: 16  KRLHVSNIPFRFRDPDLRQMFGQ---------FGK---ILDVEIIFNERGSKGFGFVTFE 63

Query: 231 TVEEASNAM-ALDGIIFEGVAVRV 253
              +A  A   L G + EG  + V
Sbjct: 64  NSADADRAREKLHGTVVEGRKIEV 87

>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 = 68.2 bits (167), Expect = 4e-14
 Identities = 17/81 (20%), Positives = 38/81 (46%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           +    + V GL  Y TE  ++E+   +G +    +V D+ +  S+G+ F  +++      
Sbjct: 44  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103

Query: 352 ACAALNGLKMGDKTLTVRRAT 372
           A    NG+++  + + V  + 
Sbjct: 104 AKERANGMELDGRRIRVDFSI 124

>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 = 46.3 bits (110), Expect = 2e-06
 Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 24/94 (25%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
             + V GL     E+ +   FS+          GP   + +V I ++++      FAFV 
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKY---------GP---IADVSIVYDQQSRRSRGFAFVY 94

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRV-----RRP 256
              V++A  A    +G+  +G  +RV     +RP
Sbjct: 95  FENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128

>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 = 67.8 bits (166), Expect = 4e-14
 Identities = 22/105 (20%), Positives = 40/105 (38%), Gaps = 6/105 (5%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
             G   G E   ++ V  L +  ++  I+EL   FGTL    +  DR +G S G     +
Sbjct: 25  GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHF 83

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQ 388
           +  A    A     G+ +  + + ++        S+ + E     
Sbjct: 84  ERRADALKAMKQYKGVPLDGRPMDIQLV-----ASQIDLEHHHHH 123

>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 = 40.4 bits (95), Expect = 2e-04
 Identities = 15/87 (17%), Positives = 26/87 (29%), Gaps = 24/87 (27%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++ V  L    ++  I   F++        V     G S G                A V
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG---------------TADV 81

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV 253
                 +A  AM    G+  +G  + +
Sbjct: 82  HFERRADALKAMKQYKGVPLDGRPMDI 108

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 66.9 bits (164), Expect = 5e-14
 Identities = 17/89 (19%), Positives = 32/89 (35%), Gaps = 4/89 (4%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG    +     + +  L Y  TE  ++E+ E    +     V     G SKGY F  +
Sbjct: 5   SSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEF 60

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT 372
                   A  + N  ++  + + +    
Sbjct: 61  ASFEDAKEALNSCNKREIEGRAIRLELQG 89

>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 = 46.9 bits (112), Expect = 7e-07
 Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 21/86 (24%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQ-----VMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
           ++ + +  L   A E+ +   F +     V     G S G               +AF+E
Sbjct: 15  SKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKG---------------YAFIE 59

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRV 253
             + E+A  A+ + +    EG A+R+
Sbjct: 60  FASFEDAKEALNSCNKREIEGRAIRL 85

>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 = 67.7 bits (166), Expect = 5e-14
 Identities = 30/93 (32%), Positives = 46/93 (49%), Gaps = 4/93 (4%)

Query: 284 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
            S  + G++       +FVGGLPY+ T+  +++  E FG +    ++ DR TG S+GYGF
Sbjct: 4   GSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGF 63

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATA 373
               D A  + AC   N +  G +   V  A  
Sbjct: 64  VTMADRAAAERACKDPNPIIDG-RKANVNLAYL 95

>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 = 67.3 bits (165), Expect = 5e-14
 Identities = 22/90 (24%), Positives = 39/90 (43%), Gaps = 1/90 (1%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
             G   G E   ++ V  L +  ++  I+EL   FGTL    +  DR +G S G     +
Sbjct: 19  GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHF 77

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATA 373
           +  A    A    NG+ +  + + ++  T+
Sbjct: 78  ERKADALKAMKQYNGVPLDGRPMNIQLVTS 107

>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 = 40.7 bits (96), Expect = 9e-05
 Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 24/88 (27%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++ V  L    ++  I   F++        V     G S G                A V
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG---------------TADV 75

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVR 254
                 +A  AM   +G+  +G  + ++
Sbjct: 76  HFERKADALKAMKQYNGVPLDGRPMNIQ 103

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 66.5 bits (163), Expect = 7e-14
 Identities = 23/98 (23%), Positives = 42/98 (42%), Gaps = 5/98 (5%)

Query: 284 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G      +   + V GLP+  TE  +KE   +FG +    + KD  TG+SKG+GF
Sbjct: 2   SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQS 378
             + +        +  +   +  +    +   +   Q 
Sbjct: 62  VRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQD 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 = 66.4 bits (163), Expect = 8e-14
 Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 1/84 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGG+P+   ET+++E  + FG +    ++ D +    +G+GF  ++D    D A   
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71

Query: 356 LNGLKMGDKTLTVRRATASSGQSK 379
            +   +  K + V+RA     +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 = 43.0 bits (102), Expect = 1e-05
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 18/87 (20%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKK----FAFVE 228
            +++VGG+P    E  +  +F +      G        V  V +  + EK+    F F+ 
Sbjct: 11  NKIFVGGIPHNCGETELREYFKKF-----GV-------VTEVVMIYDAEKQRPRGFGFIT 58

Query: 229 MRTVEEASNAMALDGIIFEGVAVRVRR 255
               +    A+ +      G  V V+R
Sbjct: 59  FEDEQSVDQAVNMHFHDIMGKKVEVKR 85

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 67.6 bits (165), Expect = 1e-13
 Identities = 20/82 (24%), Positives = 38/82 (46%)

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
            EG   + V  L Y  +   ++ + E +G +    + +DR T  S+G+ F  + D    +
Sbjct: 67  VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126

Query: 351 IACAALNGLKMGDKTLTVRRAT 372
            A  A++G  +  + L V+ A 
Sbjct: 127 DAMDAMDGAVLDGRELRVQMAR 148

>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 = 47.9 bits (114), Expect = 8e-07
 Identities = 24/99 (24%), Positives = 39/99 (39%), Gaps = 24/99 (24%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEM 229
            + V  L    +   +   F +          G    V +VYI  ++       FAFV  
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEK---------YGR---VGDVYIPRDRYTKESRGFAFVRF 119

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV-----RRPTDYNPT 262
               +A +AM A+DG + +G  +RV      RP D + +
Sbjct: 120 HDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHHS 158

>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 = 65.8 bits (161), Expect = 1e-13
 Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 1/85 (1%)

Query: 286 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQ 344
           G+ G +     +++G L  Y  E  I     + G T+    ++++R TG   GY F  + 
Sbjct: 1   GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60

Query: 345 DPAVTDIACAALNGLKMGDKTLTVR 369
           D A  +     +NG  +   T   R
Sbjct: 61  DLATAEKCLHKINGKPLPGATPAKR 85

>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 = 42.7 bits (101), Expect = 2e-05
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 18/88 (20%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFV 227
           A  +++G L P  +E  I+  F+ +           G+ V++V I           + FV
Sbjct: 9   AASLWMGDLEPYMDENFISRAFATM-----------GETVMSVKIIRNRLTGIPAGYCFV 57

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVR 254
           E   +  A   +  ++G    G     R
Sbjct: 58  EFADLATAEKCLHKINGKPLPGATPAKR 85

>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 = 67.5 bits (165), Expect = 1e-13
 Identities = 20/74 (27%), Positives = 34/74 (45%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
             ++VG L +Y TE QI EL    G +    +  D+    + G+ F  Y   A  + A  
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 355 ALNGLKMGDKTLTV 368
            +NG ++ D+ +  
Sbjct: 100 YINGTRLDDRIIRT 113

>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 = 46.3 bits (110), Expect = 2e-06
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 19/93 (20%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---- 223
           ++  + +  +YVG L     E+ I   FS+         +G    +  + +  +K     
Sbjct: 33  EKLLKKSCTLYVGNLSFYTTEEQIYELFSK---------SGD---IKKIIMGLDKMKKTA 80

Query: 224 --FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
             F FVE  +  +A NAM  ++G   +   +R 
Sbjct: 81  CGFCFVEYYSRADAENAMRYINGTRLDDRIIRT 113

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 64.8 bits (159), Expect = 1e-13
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL    T   +K   E FG +    L+ D+ T   +G+GF  ++   + +  C  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 356 LNGLKMGDKTLTVRRA 371
            +  ++ +K +  ++A
Sbjct: 61  -HFHEINNKMVECKKA 75

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 66.7 bits (163), Expect = 2e-13
 Identities = 20/84 (23%), Positives = 38/84 (45%)

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
              EG   + V  L Y  +   ++ + E +G +    + +DR T  S+G+ F  + D   
Sbjct: 42  PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101

Query: 349 TDIACAALNGLKMGDKTLTVRRAT 372
            + A  A++G  +  + L V+ A 
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQMAR 125

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 45.9 bits (109), Expect = 3e-06
 Identities = 24/97 (24%), Positives = 37/97 (38%), Gaps = 24/97 (24%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFV 227
              + V  L    +   +   F +          G    V +VYI  ++       FAFV
Sbjct: 47  MTSLKVDNLTYRTSPDTLRRVFEKY---------GR---VGDVYIPRDRYTKESRGFAFV 94

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV-----RRPTD 258
                 +A +AM A+DG + +G  +RV      RP D
Sbjct: 95  RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD 131

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 65.8 bits (161), Expect = 2e-13
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
               P R+ V  +P+ F +  ++++   FG +   +++ +     SKG+GF  +++ A  
Sbjct: 25  NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADA 82

Query: 350 DIACAALNGLKMGDKTLTVRRATA 373
           D A   L+G  +  + + V  ATA
Sbjct: 83  DRAREKLHGTVVEGRKIEVNNATA 106

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 20/93 (21%), Positives = 33/93 (35%), Gaps = 17/93 (18%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHE 221
           M  +     +R++V  +P    +  +   F Q          G    +++V I       
Sbjct: 21  MNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQ---------FGK---ILDVEIIFNERGS 68

Query: 222 KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           K F FV      +A  A   L G + EG  + V
Sbjct: 69  KGFGFVTFENSADADRAREKLHGTVVEGRKIEV 101

>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 = 64.9 bits (159), Expect = 2e-13
 Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 1/84 (1%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           G+ G   +F+G L     E  + +   +FG  L    +++D DTGNSKGY F  +     
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 349 TDIACAALNGLKMGDKTLTVRRAT 372
           +D A  A+NG  + ++ +TV  A 
Sbjct: 61  SDAAIEAMNGQYLCNRPITVSYAF 84

>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 = 40.6 bits (96), Expect = 7e-05
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
            +++G L P  +E+ +   FS       G        + +    + K +AF+   + + +
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAF-----GVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61

Query: 236 SNAM-ALDGIIFEGVAVRV 253
             A+ A++G       + V
Sbjct: 62  DAAIEAMNGQYLCNRPITV 80

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 67.2 bits (164), Expect = 3e-13
 Identities = 35/162 (21%), Positives = 57/162 (35%), Gaps = 18/162 (11%)

Query: 239 MALDGIIFE---------GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 289
           M+LD II           G   R  RP              +P P  +     L     G
Sbjct: 21  MSLDDIIKLNRNQRRVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCG 80

Query: 290 GAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
           G EG +   ++ V  L +  ++  I+EL   FGTL    +  DR +G S G     ++  
Sbjct: 81  GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERR 139

Query: 347 AVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQ 388
           A    A     G+ +  + + ++        S+ + E     
Sbjct: 140 ADALKAMKQYKGVPLDGRPMDIQLV-----ASQIDLEHHHHH 176

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 40.2 bits (94), Expect = 5e-04
 Identities = 12/85 (14%), Positives = 30/85 (35%), Gaps = 18/85 (21%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-----FAFVEMR 230
           ++ V  L    ++  I   F++          G    +    +++++       A V   
Sbjct: 90  KLLVSNLDFGVSDADIQELFAEF---------GT---LKKAAVDYDRSGRSLGTADVHFE 137

Query: 231 TVEEASNAMA-LDGIIFEGVAVRVR 254
              +A  AM    G+  +G  + ++
Sbjct: 138 RRADALKAMKQYKGVPLDGRPMDIQ 162

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 64.0 bits (157), Expect = 3e-13
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  T+  ++E    FG +    +++D  T  S+G+GF  + D A  D   A 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 356 LNGLKMGDKTLTVRRA 371
            +  ++  KT+  + A
Sbjct: 62  -SRHELDSKTIDPKVA 76

>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 = 68.1 bits (166), Expect = 4e-13
 Identities = 34/196 (17%), Positives = 58/196 (29%), Gaps = 25/196 (12%)

Query: 177 VYVGGLPPLA-NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 234
           + V  L P     Q++   F        G+       V  V I   KK  A V+M    +
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVY-----GD-------VQRVKILFNKKENALVQMADGNQ 84

Query: 235 ASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQP------SPNLNLAAVGLASGA 287
           A  AM  L+G    G  +R+      N  L       Q       +  L+      +   
Sbjct: 85  AQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF 144

Query: 288 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 347
                    + +  +P   +E  +K L  S G +    +   +     +           
Sbjct: 145 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVE 200

Query: 348 VTDIACAALNGLKMGD 363
               A   L+   +G+
Sbjct: 201 EAVQALIDLHNHDLGE 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 = 54.6 bits (131), Expect = 1e-08
 Identities = 29/244 (11%), Positives = 62/244 (25%), Gaps = 43/244 (17%)

Query: 272 PSPNLNLAAVGLASGAIGGAEGPDR-------VFVGGL-PYYFTETQIKELLESFGTLHG 323
              + + + +      +G    P         + V  L P   T   +  L   +G +  
Sbjct: 5   HHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQR 64

Query: 324 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQE 383
             ++ +      K        D     +A + LNG K+  K + +  +   + Q   E +
Sbjct: 65  VKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQ 119

Query: 384 SILAQAQ----QHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEE 439
                 +      +   K     +  N      +L    +   +                
Sbjct: 120 EDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVS--------------- 164

Query: 440 YEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRK 499
                ED++      G +V        ++           ++         A   L    
Sbjct: 165 ----EEDLKVLFSSNGGVVKGFK-FFQKDR------KMALIQMGSVEEAVQALIDLHNHD 213

Query: 500 FGGN 503
            G N
Sbjct: 214 LGEN 217

>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 = 47.7 bits (113), Expect = 3e-06
 Identities = 25/122 (20%), Positives = 45/122 (36%), Gaps = 13/122 (10%)

Query: 134 PGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIAT 193
             +P    E       +G + L  F   P     Q     +  +++  +PP  +E+ +  
Sbjct: 112 VQLPREGQEDQGLTKDYGNSPLHRFK-KPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKV 170

Query: 194 FFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI-IFEGVAV 251
            FS             G      +   ++K A ++M +VEEA  A+  L    + E   +
Sbjct: 171 LFSSN----------GGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHL 220

Query: 252 RV 253
           RV
Sbjct: 221 RV 222

>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 = 64.8 bits (158), Expect = 4e-13
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 4/82 (4%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIA 352
            R+F+GG+P      +I E +      +    +     D   ++G+ F  Y+      +A
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 353 CAALN--GLKMGDKTLTVRRAT 372
              L    +++    + V  A 
Sbjct: 69  RRKLMPGRIQLWGHQIAVDWAE 90

>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 = 47.9 bits (114), Expect = 3e-07
 Identities = 18/91 (19%), Positives = 35/91 (38%), Gaps = 21/91 (23%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFV 227
            R+++GG+P +   + I    ++V            + V++V +          + FAFV
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKV-----------TEGVLDVIVYASAADKMKNRGFAFV 57

Query: 228 EMRTVEEASNA---MALDGIIFEGVAVRVRR 255
           E  +   A+ A   +    I   G  + V  
Sbjct: 58  EYESHRAAAMARRKLMPGRIQLWGHQIAVDW 88

>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 = 65.0 bits (159), Expect = 4e-13
 Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VF   L        +++   + G +    ++ DR++  SKG  +  + +     +A   L
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86

Query: 357 NGLKMGDKTLTVRRATA 373
            G ++    + V+ + A
Sbjct: 87  TGQRLLGVPIIVQASQA 103

>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 = 56.9 bits (138), Expect = 2e-10
 Identities = 23/94 (24%), Positives = 33/94 (35%), Gaps = 18/94 (19%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHE 221
               R AR V+   L      + +  FFS V         G    V +V I         
Sbjct: 19  SPEERDARTVFCMQLAARIRPRDLEDFFSAV---------GK---VRDVRIISDRNSRRS 66

Query: 222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
           K  A+VE   ++    A+ L G    GV + V+ 
Sbjct: 67  KGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQA 100

>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 = 64.6 bits (158), Expect = 4e-13
 Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FV GL    TE  +KE    F       +V DR+TG+SKG+GF  +        A  A
Sbjct: 17  TLFVKGLSEDTTEETLKES---FDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73

Query: 356 LNGLKMGDKTLTVRRAT 372
           +   ++    +T+  A 
Sbjct: 74  MEDGEIDGNKVTLDWAK 90

>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 = 46.1 bits (110), Expect = 1e-06
 Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 22/93 (23%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAI------GGNSAGPGDAVVNVYINHE 221
              ++ ++ ++V GL     E+ +   F   + A        G+S G             
Sbjct: 9   NARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKG------------- 55

Query: 222 KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
             F FV+  + E+A  A  A++    +G  V +
Sbjct: 56  --FGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL 86

>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 = 64.6 bits (158), Expect = 5e-13
 Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 1/84 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  T+  ++E    FG +    +++D  T  S+G+GF  + D A  D   A 
Sbjct: 27  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86

Query: 356 LNGLKMGDKTLTVRRATASSGQSK 379
            +  ++  KT+  + A     Q K
Sbjct: 87  -SRHELDSKTIDPKVAFPRRAQPK 109

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 64.4 bits (157), Expect = 5e-13
 Identities = 17/91 (18%), Positives = 30/91 (32%), Gaps = 8/91 (8%)

Query: 290 GAEGPDR-VFVGGLPYY------FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 342
           G  G D+ + V G P          +  +  L    G +   +   D  TG +KG+ F  
Sbjct: 1   GPLGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVE 60

Query: 343 YQDPAVTDIACAALNGLKMGDK-TLTVRRAT 372
                       + +G ++  K  L +    
Sbjct: 61  CGSMNDAKKIIKSFHGKRLDLKHRLFLYTMK 91

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 14/88 (15%), Positives = 30/88 (34%), Gaps = 7/88 (7%)

Query: 435 ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA 494
               +   + + +     K G +VN+  P  D+  G+T G    F+E            +
Sbjct: 17  IPSAKVPVLKKALTSLFSKAGKVVNMEFPI-DEATGKTKGFL--FVECGSMNDAKKIIKS 73

Query: 495 LSGRKFGGN---TVNAFYYPEDKYFNKD 519
             G++        +       ++Y + D
Sbjct: 74  FHGKRLDLKHRLFLYTM-KDVERYNSDD 100

>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 = 63.3 bits (155), Expect = 5e-13
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL     E +I+E    FG +   +L  D  T   +G+ F  +++          
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 356 LNGLKMGDKTLTVRRA 371
                +G     ++ A
Sbjct: 61  -KYHNVGLSKCEIKVA 75

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

 Score = 63.9 bits (156), Expect = 6e-13
 Identities = 23/107 (21%), Positives = 41/107 (38%), Gaps = 16/107 (14%)

Query: 151 GATQLGAFPLM---PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSA 207
           G+  +G  P +    V  + + A       Y+G +P  A E  +   F            
Sbjct: 1   GSQTIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNF--------- 51

Query: 208 GPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
             G  +++     EK   F++  T E+A+  + AL    F+G  +R 
Sbjct: 52  --GF-ILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRT 95

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

 Score = 56.5 bits (137), Expect = 3e-10
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 6/73 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
             ++G +P++ TE  +  L ++FG +  F    +      KG  F  Y       +   A
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVA 82

Query: 356 LNGLKMGDKTLTV 368
           L       + L  
Sbjct: 83  LANFPFQGRNLRT 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 = 63.4 bits (155), Expect = 7e-13
 Identities = 19/88 (21%), Positives = 44/88 (50%), Gaps = 4/88 (4%)

Query: 287 AIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
            I  ++  +   ++FVGGL +  ++  +K+    FG +    +  D +TG S+G+GF ++
Sbjct: 1   GINASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILF 60

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRA 371
           +D A  +         ++  + +  ++A
Sbjct: 61  KDAASVEKVLDQKEH-RLDGRVIDPKKA 87

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative splicing, FBP interacting repressor, RRM, electron transport; 2.20A {Escherichia coli O157} Length = 222

 Score = 67.2 bits (164), Expect = 7e-13
 Identities = 30/87 (34%), Positives = 49/87 (56%), Gaps = 2/87 (2%)

Query: 438 EEYEEILE-DMREECGKYGTLVNVVIPRPDQNGGE-TPGVGKVFLEYYDAVGCATAKNAL 495
           ++ ++ LE ++ EECGK+G +  V+I +  Q   E    + K+F+E+  A     A  AL
Sbjct: 136 KDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 195

Query: 496 SGRKFGGNTVNAFYYPEDKYFNKDYSA 522
           +GR F G  V A  Y ++++ N D SA
Sbjct: 196 NGRWFAGRKVVAEVYDQERFDNSDLSA 222

>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 = 67.1 bits (163), Expect = 9e-13
 Identities = 19/138 (13%), Positives = 41/138 (29%), Gaps = 2/138 (1%)

Query: 257 TDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLE 316
               P     +    P+   ++      +           +++G L ++ T+  + E + 
Sbjct: 31  NGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVH 90

Query: 317 SFGTLHGFD--LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS 374
           S G     +    ++R  G SKG+        A +      L   ++  +   V      
Sbjct: 91  SLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ 150

Query: 375 SGQSKTEQESILAQAQQH 392
                  Q     Q+ Q 
Sbjct: 151 FLSQFEMQSRKTTQSGQM 168

>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 = 51.6 bits (123), Expect = 1e-07
 Identities = 25/180 (13%), Positives = 40/180 (22%), Gaps = 17/180 (9%)

Query: 134 PGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIAT 193
                  PE    M     T            +    T     +Y+G L     ++ +  
Sbjct: 28  SANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTE 87

Query: 194 FFSQVMTAIGGNSAGPGDAV-VNVYINHE----KKFAFVEMRTVEEASNAM-ALDGIIFE 247
                         G  D + +  + N      K FA V + +   +   M  L      
Sbjct: 88  AVHS---------LGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELH 138

Query: 248 GVAVRVR--RPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYY 305
           G    V        +     +    Q          G   G+   A        G  P  
Sbjct: 139 GQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGA 198

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 63.2 bits (154), Expect = 9e-13
 Identities = 14/86 (16%), Positives = 27/86 (31%), Gaps = 7/86 (8%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   + V  LP      ++ +LL+ +        +K      +K   F    +    
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQA 53

Query: 350 DIACAALNGLKMGDKTLTVRRATASS 375
             A    +      K L V+     +
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQPTDA 79

>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 = 51.3 bits (123), Expect = 1e-08
 Identities = 24/105 (22%), Positives = 38/105 (36%), Gaps = 21/105 (20%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           +  +  + V  LP  +N Q +                     +   Y++  K+ AFV + 
Sbjct: 2   SSGSSGILVKNLPQDSNCQEVHDLLKDY-------------DLKYCYVDRNKRTAFVTLL 48

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVRR-PTDYNPTLAAALGPGQPS 273
             E+A NA+       F G  + V+  PTD      A L  G  S
Sbjct: 49  NGEQAQNAIQMFHQYSFRGKDLIVQLQPTD------ALLCSGPSS 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 = 63.4 bits (155), Expect = 1e-12
 Identities = 22/101 (21%), Positives = 43/101 (42%), Gaps = 4/101 (3%)

Query: 282 GLASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY 338
           G +  +     G D    +FVGGL +  T+  ++     +G +    ++KD+ T  S+G+
Sbjct: 1   GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGF 60

Query: 339 GFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK 379
           GF  ++DP       A+     +  + +  +  T    Q  
Sbjct: 61  GFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGMQPS 100

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 63.1 bits (154), Expect = 1e-12
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 2/92 (2%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCV 342
           +SG +   +   ++ V  +P+   + +I+EL  +FG L    L K    TG  +G+GF  
Sbjct: 5   SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64

Query: 343 YQDPAVTDIACAAL-NGLKMGDKTLTVRRATA 373
           +        A  AL +   +  + L +  A +
Sbjct: 65  FITKQDAKKAFNALCHSTHLYGRRLVLEWADS 96

>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 = 43.4 bits (103), Expect = 1e-05
 Identities = 16/88 (18%), Positives = 29/88 (32%), Gaps = 21/88 (23%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFV 227
            ++ V  +P  AN++ I   FS           G    +  V +          + F FV
Sbjct: 16  SKILVRNIPFQANQREIRELFSTF---------GE---LKTVRLPKKMTGTGAHRGFGFV 63

Query: 228 EMRTVEEASNAMA--LDGIIFEGVAVRV 253
           +  T ++A  A           G  + +
Sbjct: 64  DFITKQDAKKAFNALCHSTHLYGRRLVL 91

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 2/81 (2%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           E P   +VG LP+   +  I  + +         LV+D+DT   KG+ +  + +      
Sbjct: 13  EPPYTAYVGNLPFNTVQGDIDAIFKDLSIR-SVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71

Query: 352 ACAALNGLKMGDKTLTVRRAT 372
           A    +G  +GD++L V  A 
Sbjct: 72  A-LTYDGALLGDRSLRVDIAE 91

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 19/85 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
              YVG LP    +  I   F  +              + +V +  +K       F +VE
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-------------IRSVRLVRDKDTDKFKGFCYVE 62

Query: 229 MRTVEEASNAMALDGIIFEGVAVRV 253
              V+    A+  DG +    ++RV
Sbjct: 63  FDEVDSLKEALTYDGALLGDRSLRV 87

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 61.2 bits (149), Expect = 5e-12
 Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 6/86 (6%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFD--LVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           D + +  +  +     I   L  + +L   +  L+KD+ T  ++G+ F            
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 353 CAALNG----LKMGDKTLTVRRATAS 374
              L      LK+  KT+ V  A ++
Sbjct: 70  LQILQSLHPPLKIDGKTIGVDFAKSA 95

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 46.2 bits (110), Expect = 8e-07
 Identities = 17/99 (17%), Positives = 32/99 (32%), Gaps = 21/99 (21%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------N 219
           M      H   + +  + P     +I T  S                V N+ +       
Sbjct: 1   MGHHHHHHMDTIILRNIAPHTVVDSIMTALSPY---------ASLA-VNNIRLIKDKQTQ 50

Query: 220 HEKKFAFVEMRTVEEASNAM-ALDG----IIFEGVAVRV 253
             + FAFV++ +  +AS  +  L      +  +G  + V
Sbjct: 51  QNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGV 89

>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 = 61.1 bits (149), Expect = 7e-12
 Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  TE  ++   E +G L    +++D  +  S+G+GF  +   A  D A AA
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88

Query: 356 LNGLKMGDKTLTVRRATA 373
                +  + +  +RA A
Sbjct: 89  -RPHSIDGRVVEPKRAVA 105

>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 = 60.7 bits (148), Expect = 9e-12
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 2/83 (2%)

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           +  P  +F+G L    +  ++K  +      +    V D  TG ++ +G+  ++     +
Sbjct: 14  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLE 72

Query: 351 IACAALNGLKMGDKTLTVRRATA 373
            A   L GLK+    + + +   
Sbjct: 73  KA-LELTGLKVFGNEIKLEKPKG 94

>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 = 55.3 bits (134), Expect = 7e-10
 Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 13/85 (15%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ---VMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTV 232
            +++G L P  +   +    S+                  VV+V     +KF +V+  + 
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLA----------VVDVRTGTNRKFGYVDFESA 68

Query: 233 EEASNAMALDGIIFEGVAVRVRRPT 257
           E+   A+ L G+   G  +++ +P 
Sbjct: 69  EDLEKALELTGLKVFGNEIKLEKPK 93

>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 = 60.7 bits (148), Expect = 1e-11
 Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 1/80 (1%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           + P  +++  LP    E +++ +L+ FG +    +++D  +G S+G GF   +     + 
Sbjct: 23  QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEA 81

Query: 352 ACAALNGLKMGDKTLTVRRA 371
                NG  +          
Sbjct: 82  VIGHFNGKFIKTPPGVSAPT 101

>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 = 41.5 bits (98), Expect = 6e-05
 Identities = 14/97 (14%), Positives = 27/97 (27%), Gaps = 24/97 (24%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVY 217
           M +Q  +    +Y+  LP   +EQ +              ++    G S G         
Sbjct: 17  MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG--------- 67

Query: 218 INHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
                   F  M + E+    +   +G   +      
Sbjct: 68  ------VGFARMESTEKCEAVIGHFNGKFIKTPPGVS 98

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 13/92 (14%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++      R++VG LPP   E+ +   F +     G            V+I+ +K F F+
Sbjct: 9   EKTFTQRSRLFVGNLPPDITEEEMRKLFEK----YG--------KAGEVFIHKDKGFGFI 56

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRRPTD 258
            + T   A  A   LD +   G  +RVR    
Sbjct: 57  RLETRTLAEIAKVELDNMPLRGKQLRVRFACH 88

>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 = 58.4 bits (142), Expect = 5e-11
 Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 9/95 (9%)

Query: 284 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ GG +      R+FVG LP   TE ++++L E +G      + KD      KG+GF
Sbjct: 2   SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGF 55

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS 375
              +   + +IA   L+ + +  K L VR A  S+
Sbjct: 56  IRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA 90

>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 = 60.0 bits (146), Expect = 2e-11
 Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 4/91 (4%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG+        ++FVG L    +E  +  L + FG +    +++  D G+SKG  F  +
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKF 63

Query: 344 QDPAVTDIACAALNG---LKMGDKTLTVRRA 371
                   A  AL+G   +     +L V+ A
Sbjct: 64  SSHTEAQAAIHALHGSQTMPGASSSLVVKFA 94

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 25/84 (29%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAF 226
           R+++VG L    +E+ +   F          V+    G+S G                AF
Sbjct: 16  RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKG---------------CAF 60

Query: 227 VEMRTVEEASNAM-ALDG-IIFEG 248
           V+  +  EA  A+ AL G     G
Sbjct: 61  VKFSSHTEAQAAIHALHGSQTMPG 84

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 59.1 bits (144), Expect = 2e-11
 Identities = 24/90 (26%), Positives = 40/90 (44%), Gaps = 8/90 (8%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G  ++F+G LP   TE +I+ L E +G +   D++        K YGF   +D    
Sbjct: 4   GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAA 55

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSK 379
           + A   L+  K+    + V  +   S  S 
Sbjct: 56  EDAIRNLHHYKLHGVNINVEASKNKSKASS 85

>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 = 49.5 bits (119), Expect = 5e-08
 Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 15/80 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
            ++++G LP  A EQ I + F Q          G    V+   I   K + FV +     
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQY---------GK---VLECDI--IKNYGFVHIEDKTA 54

Query: 235 ASNAM-ALDGIIFEGVAVRV 253
           A +A+  L      GV + V
Sbjct: 55  AEDAIRNLHHYKLHGVNINV 74

>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 = 59.7 bits (145), Expect = 3e-11
 Identities = 21/95 (22%), Positives = 42/95 (44%), Gaps = 13/95 (13%)

Query: 161 MPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH 220
           +  + +  Q++     VY GG+     +Q +   FS      G         ++ + +  
Sbjct: 12  LRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSP----FG--------QIMEIRVFP 59

Query: 221 EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR 254
           EK ++FV   T E A++A+ +++G   EG  V+  
Sbjct: 60  EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY 94

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

 Score = 51.2 bits (123), Expect = 2e-08
 Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 6/84 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+ GG+    T+  +++    FG +    +  +      KGY F  +        A  +
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS 80

Query: 356 LNGLKMGDKTLTVRRATASSGQSK 379
           +NG  +    +       S   + 
Sbjct: 81  VNGTTIEGHVVKCYWGKESPDMTS 104

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 59.0 bits (143), Expect = 3e-11
 Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 3/85 (3%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG++   +   ++ +  +P +     +  LL  +G +   + V               Y
Sbjct: 5   SSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTY 61

Query: 344 QDPAVTDIACAALNGLKMGDKTLTV 368
                   A   LNG ++ + TL V
Sbjct: 62  SSKDQARQALDKLNGFQLENFTLKV 86

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 50.9 bits (122), Expect = 2e-08
 Identities = 15/89 (16%), Positives = 33/89 (37%), Gaps = 10/89 (11%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
            +  R++ +  +PP    + + +   Q          G  ++   V  + E     V   
Sbjct: 12  RQRIRKLQIRNIPPHLQWEVLDSLLVQ---------YGVVESCEQVNTDSETAVVNVTYS 62

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVRRPTD 258
           + ++A  A+  L+G   E   ++V    D
Sbjct: 63  SKDQARQALDKLNGFQLENFTLKVAYIPD 91

>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 = 59.1 bits (144), Expect = 3e-11
 Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 10/89 (11%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++V  L     + ++++    FGT+    ++   + G SKG+GF  +  P     A   
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEEATKAVTE 74

Query: 356 LNGLKMGDKTLTV--------RRATASSG 376
           +NG  +  K L V        R++  SSG
Sbjct: 75  MNGRIVATKPLYVALAQRKEERQSGPSSG 103

>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 = 40.3 bits (95), Expect = 1e-04
 Identities = 21/87 (24%), Positives = 32/87 (36%), Gaps = 25/87 (28%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
            +YV  L    +++ +   FS         VM   GG S G               F FV
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKG---------------FGFV 60

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV 253
              + EEA+ A+  ++G I     + V
Sbjct: 61  CFSSPEEATKAVTEMNGRIVATKPLYV 87

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 59.4 bits (144), Expect = 3e-11
 Identities = 22/90 (24%), Positives = 35/90 (38%), Gaps = 10/90 (11%)

Query: 291 AEGPDR-VFVGGLPYYFTE------TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           A+G D  + V  +P    +        I ++   FG +   +     + G +KGY F  Y
Sbjct: 11  ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEY 68

Query: 344 QDPAVTDIACAALNGLKMGDK-TLTVRRAT 372
             PA    A    +G K+  + T  V   T
Sbjct: 69  ASPAHAVDAVKNADGYKLDKQHTFRVNLFT 98

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 45.9 bits (109), Expect = 2e-06
 Identities = 19/77 (24%), Positives = 27/77 (35%), Gaps = 8/77 (10%)

Query: 435 ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA 494
              +  E++   + +   K+G + N   P  D   G+T G    FLEY        A   
Sbjct: 26  VGPDRLEKLKNVIHKIFSKFGKITNDFYPEED---GKTKGYI--FLEYASPAHAVDAVKN 80

Query: 495 LSGRKFGGN---TVNAF 508
             G K        VN F
Sbjct: 81  ADGYKLDKQHTFRVNLF 97

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 24/97 (24%)

Query: 175 RRVYVGGLPPLANEQ------AIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKF 224
             + V  +P +  ++       I   FS+          G    + N +   E    K +
Sbjct: 16  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKF---------GK---ITNDFYPEEDGKTKGY 63

Query: 225 AFVEMRTVEEASNAM-ALDGIIFEG-VAVRVRRPTDY 259
            F+E  +   A +A+   DG   +     RV   TD+
Sbjct: 64  IFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDF 100

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 58.5 bits (142), Expect = 4e-11
 Identities = 21/89 (23%), Positives = 34/89 (38%), Gaps = 13/89 (14%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEK-KFAF 226
              +   R V+V G P   +   ++ +F            GP   V +V ++ +K  FA 
Sbjct: 2   SSGSSGLRSVFVSGFPRGVDSAQLSEYFLA---------FGP---VASVVMDKDKGVFAI 49

Query: 227 VEMRTVEEASNAMALDGIIFEGVAVRVRR 255
           VEM  V      ++       G  +RVR 
Sbjct: 50  VEMGDVGAREAVLSQSQHSLGGHRLRVRP 78

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 22/93 (23%), Positives = 33/93 (35%), Gaps = 6/93 (6%)

Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
              G+ G   VFV G P      Q+ E   +FG +    +V D+D G    +      D 
Sbjct: 1   GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVA--SVVMDKDKG---VFAIVEMGDV 55

Query: 347 AVTDIACAALNGLKMGDKTLTVRRATASSGQSK 379
              +    + +   +G   L VR       QS 
Sbjct: 56  GAREAVL-SQSQHSLGGHRLRVRPREQKEFQSP 87

>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 = 56.9 bits (138), Expect = 1e-10
 Identities = 17/90 (18%), Positives = 35/90 (38%), Gaps = 14/90 (15%)

Query: 167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAF 226
           +    +    +YVGGL     E  +   F Q            G+ +  + +   ++ AF
Sbjct: 5   SSGEDKTITTLYVGGLGDTITETDLRNHFYQ-----------FGE-IRTITVVQRQQCAF 52

Query: 227 VEMRTVEEASNAM--ALDGIIFEGVAVRVR 254
           ++  T + A  A   + + +I  G  + V+
Sbjct: 53  IQFATRQAAEVAAEKSFNKLIVNGRRLNVK 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 = 48.0 bits (115), Expect = 2e-07
 Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 7/74 (9%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA-CAA 355
           ++VGGL    TET ++     FG +    +V+       +   F  +      ++A   +
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68

Query: 356 LNGLKMGDKTLTVR 369
            N L +  + L V+
Sbjct: 69  FNKLIVNGRRLNVK 82

>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 = 56.9 bits (138), Expect = 2e-10
 Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTD 350
             P   F+G LPY  TE  IKE            L ++  +    KG+G+  ++D   + 
Sbjct: 13  SPPYTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYAEFEDLD-SL 70

Query: 351 IACAALNGLKMGDKTLTVRRAT 372
           ++  +LN   +G+K + V  A 
Sbjct: 71  LSALSLNEESLGNKRIRVDVAD 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 = 52.6 bits (127), Expect = 6e-09
 Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 20/87 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-------FAFV 227
              ++G LP    E++I  FF  +              +  V +  E         F + 
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGL-------------NISAVRLPREPSNPERLKGFGYA 62

Query: 228 EMRTVEEASNAMALDGIIFEGVAVRVR 254
           E   ++   +A++L+        +RV 
Sbjct: 63  EFEDLDSLLSALSLNEESLGNKRIRVD 89

>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 = 56.5 bits (137), Expect = 2e-10
 Identities = 16/90 (17%), Positives = 32/90 (35%), Gaps = 7/90 (7%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   VFVG      TE +++E    +G +    + K       + + F  + D  + 
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIA 55

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSK 379
              C     L +   ++ +  A      + 
Sbjct: 56  QSLCG--EDLIIKGISVHISNAEPKHNSNS 83

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 40.7 bits (96), Expect = 6e-05
 Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 14/89 (15%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVE 228
            +  +  V+VG       E  +  FFSQ      G+       V++V+I    + FAFV 
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQY-----GD-------VMDVFIPKPFRAFAFVT 48

Query: 229 MRTVEEASNAMALDGIIFEGVAVRVRRPT 257
               + A +    D II +G++V +    
Sbjct: 49  FADDQIAQSLCGEDLII-KGISVHISNAE 76

>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 = 56.1 bits (136), Expect = 2e-10
 Identities = 24/93 (25%), Positives = 40/93 (43%), Gaps = 8/93 (8%)

Query: 286 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           G+ G +    ++FVG +    T  +++ L E  G +   D+V        K Y F   + 
Sbjct: 1   GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEK 52

Query: 346 PAVTDIACAALNGLKMGDKTLTVRRATASSGQS 378
            A    A A LNG ++  K + V  +T    +S
Sbjct: 53  EADAKAAIAQLNGKEVKGKRINVELSTKGQKKS 85

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 51.8 bits (125), Expect = 9e-09
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 15/84 (17%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           + +  +++VG +      Q + + F +          G    V+   +   K +AFV M 
Sbjct: 6   SGNTWKIFVGNVSAACTSQELRSLFER---------RGR---VIECDV--VKDYAFVHME 51

Query: 231 TVEEASNAM-ALDGIIFEGVAVRV 253
              +A  A+  L+G   +G  + V
Sbjct: 52  KEADAKAAIAQLNGKEVKGKRINV 75

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 56.4 bits (136), Expect = 3e-10
 Identities = 21/76 (27%), Positives = 30/76 (39%), Gaps = 5/76 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+VG LP     + +K  L   G++              +   F  Y D A    A + 
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVSC 75

Query: 356 LNGLKMGDKTLTVRRA 371
           L GL++G  TL V  A
Sbjct: 76  LQGLRLGTDTLRVALA 91

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 17/87 (19%), Positives = 29/87 (33%), Gaps = 12/87 (13%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
           +    A  VYVG LP  A    +     ++           G   + +     ++ AF+ 
Sbjct: 14  EGAPLAADVYVGNLPRDARVSDLKRALREL-----------GSVPLRLTWQGPRRRAFLH 62

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRVR 254
                 A  A+  L G+      +RV 
Sbjct: 63  YPDSAAAQQAVSCLQGLRLGTDTLRVA 89

>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 = 56.6 bits (137), Expect = 3e-10
 Identities = 22/106 (20%), Positives = 38/106 (35%), Gaps = 13/106 (12%)

Query: 284 ASGAIGGAEGPD----------RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG 333
           +SG+ G + G            R++VG LP       I+++   +G +   DL   R   
Sbjct: 2   SSGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--- 58

Query: 334 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK 379
               + F  ++DP   + A    +G       L V    +  G   
Sbjct: 59  GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGS 104

>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 = 48.9 bits (117), Expect = 2e-07
 Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 10/85 (11%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           A  +  R+YVG LPP    + I   F +          G    +          FAFVE 
Sbjct: 18  AGNNDCRIYVGNLPPDIRTKDIEDVFYK---------YGAIRDIDLKNRRGGPPFAFVEF 68

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
               +A +A+   DG  ++G  +RV
Sbjct: 69  EDPRDAEDAVYGRDGYDYDGYRLRV 93

>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 = 56.1 bits (136), Expect = 3e-10
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVTD 350
             P   F+G LPY  TE  IKE            L ++  +    KG+G+  ++D   + 
Sbjct: 17  SPPYTAFLGNLPYDVTEESIKEFFRGLNIS-AVRLPREPSNPERLKGFGYAEFEDLD-SL 74

Query: 351 IACAALNGLKMGDKTLTVRRAT 372
           ++  +LN   +G++ + V  A 
Sbjct: 75  LSALSLNEESLGNRRIRVDVAD 96

>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 = 53.0 bits (128), Expect = 4e-09
 Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 20/86 (23%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-------FAFV 227
              ++G LP    E++I  FF  +              +  V +  E         F + 
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGL-------------NISAVRLPREPSNPERLKGFGYA 66

Query: 228 EMRTVEEASNAMALDGIIFEGVAVRV 253
           E   ++   +A++L+        +RV
Sbjct: 67  EFEDLDSLLSALSLNEESLGNRRIRV 92

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 56.1 bits (136), Expect = 4e-10
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 13/81 (16%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
            R++VGGL P  +  A+A  F +     G        ++  +       FA+++  +++ 
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDR----FG--------SIRTIDHVKGDSFAYIQYESLDA 65

Query: 235 ASNAM-ALDGIIFEGVAVRVR 254
           A  A   + G    G   R+R
Sbjct: 66  AQAACAKMRGFPLGGPDRRLR 86

>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 = 46.5 bits (111), Expect = 7e-07
 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 6/74 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R++VGGL    +   +    + FG++   D VK         + +  Y+       ACA 
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQAACAK 72

Query: 356 LNGLKMGDKTLTVR 369
           + G  +G     +R
Sbjct: 73  MRGFPLGGPDRRLR 86

>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 = 60.6 bits (146), Expect = 5e-10
 Identities = 17/79 (21%), Positives = 35/79 (44%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  + Y  TE++++   E +G +    +V  + +G  +GY F  Y+       A    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 357 NGLKMGDKTLTVRRATASS 375
           +G K+  + + V      +
Sbjct: 165 DGKKIDGRRVLVDVERGRT 183

>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 = 59.1 bits (142), Expect = 1e-09
 Identities = 18/89 (20%), Positives = 27/89 (30%)

Query: 23  SGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRH 82
             R R+ ++ RDR  R  +S    RR  +  +  R G  D        D   D       
Sbjct: 276 RSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGEL 335

Query: 83  RSRSHSSDRFRNRSKSLSPSRSPSKSKRR 111
                     + R +     RS    + R
Sbjct: 336 GPDGPDGPEEKGRDRDRERRRSHRSERER 364

>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 = 57.6 bits (138), Expect = 5e-09
 Identities = 14/88 (15%), Positives = 25/88 (28%)

Query: 25  RSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRS 84
           R R   R R+R  R+ +   + R    +     E            +   D       + 
Sbjct: 288 RKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKG 347

Query: 85  RSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
           R    +R R+        R   + + R 
Sbjct: 348 RDRDRERRRSHRSERERRRDRDRDRDRD 375

>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 = 57.2 bits (137), Expect = 6e-09
 Identities = 17/106 (16%), Positives = 28/106 (26%)

Query: 7   RYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRT 66
           R  +     R +S     R R+ ER +D+     +     R R +  +  +E +R     
Sbjct: 256 RSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGD 315

Query: 67  DRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
                   D                     K     R   +S R  
Sbjct: 316 MAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSE 361

>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 = 57.2 bits (137), Expect = 6e-09
 Identities = 21/114 (18%), Positives = 33/114 (28%), Gaps = 1/114 (0%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
                   A    +             G  G D      +    +RRR    + +R   R
Sbjct: 309 LRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDR 368

Query: 62  DHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFD 115
           D DR DR R++ R +    R R  +      ++       + S        G D
Sbjct: 369 DRDR-DRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGD 421

>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 = 56.8 bits (136), Expect = 9e-09
 Identities = 17/112 (15%), Positives = 30/112 (26%)

Query: 1   MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGI 60
              R  R       SR +      RSR   + +DR  +   S   +R R +  + +    
Sbjct: 252 RERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRG 311

Query: 61  RDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
              D  +     +   +            D    + +     R  S    R 
Sbjct: 312 GGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERE 363

>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 = 56.0 bits (134), Expect = 1e-08
 Identities = 21/111 (18%), Positives = 39/111 (35%), Gaps = 1/111 (0%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
             R+ + +  G G        +G +   +        D   G +++ RD++ +  R    
Sbjct: 301 RERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRS 360

Query: 62  DHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
           + +R  R RD +RD++R H+   R     R   R                S
Sbjct: 361 ERER-RRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDS 410

>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 = 56.0 bits (134), Expect = 2e-08
 Identities = 10/112 (8%), Positives = 19/112 (16%)

Query: 1   MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGI 60
                 R                      +  R R     K    DR+R  +   +R   
Sbjct: 242 RERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARR 301

Query: 61  RDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
               + +         E      +                      + + R 
Sbjct: 302 ERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRE 353

>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 = 55.6 bits (133), Expect = 2e-08
 Identities = 19/116 (16%), Positives = 34/116 (29%), Gaps = 5/116 (4%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
           S    R     E            +   E G                 D   +  R+  R
Sbjct: 293 SRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDR 352

Query: 62  DHDR-----TDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
           +  R      +R RD +RD++R   H+     S+R R+ ++     +        +
Sbjct: 353 ERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGN 408

>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 = 55.2 bits (132), Expect = 2e-08
 Identities = 16/111 (14%), Positives = 28/111 (25%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
                R        + +SS    R+R     ++          +          D     
Sbjct: 275 RRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGE 334

Query: 62  DHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
                    +       R R RS     +R R+R +     R   + +R S
Sbjct: 335 LGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGS 385

>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 = 54.5 bits (130), Expect = 4e-08
 Identities = 9/112 (8%), Positives = 23/112 (20%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
                R  +     R +S       R   R R +     +     R R++  +       
Sbjct: 249 DKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEE 308

Query: 62  DHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
                    + +   +                +  +     R   + +    
Sbjct: 309 LRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRS 360

>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 = 54.5 bits (130), Expect = 5e-08
 Identities = 13/106 (12%), Positives = 30/106 (28%)

Query: 7   RYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRT 66
           R     +    + S    + +  +R R       ++  +  R+++      +     +  
Sbjct: 264 RRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAG 323

Query: 67  DRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
           D   D     E             R R+R +  S      + + R 
Sbjct: 324 DAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRD 369

>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 = 11/113 (9%), Positives = 20/113 (17%)

Query: 1   MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGI 60
                 R          +    S       R R+R     +       R +         
Sbjct: 246 RERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERER 305

Query: 61  RDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
           ++  R          +                          R   + +RRS 
Sbjct: 306 KEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSH 358

>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 = 1e-07
 Identities = 20/112 (17%), Positives = 28/112 (25%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
             R  R  +  +    K      R R       +       G      +       +G  
Sbjct: 273 ERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPP 332

Query: 62  DHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
                D           R R R RSH S+R R R +     R     +   G
Sbjct: 333 GELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERG 384

>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 = 1e-07
 Identities = 20/119 (16%), Positives = 33/119 (27%), Gaps = 3/119 (2%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
                                        R RDR  R       +RRRD++   DR+  R
Sbjct: 319 PSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRD--R 376

Query: 62  DHDRTDRHRDYNRDKE-RRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPP 119
           +H R +R  +  RD+       +          +R   +            +G+ M   
Sbjct: 377 EHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDGYLAPENGYLMEAA 435

>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 = 52.5 bits (125), Expect = 2e-07
 Identities = 17/109 (15%), Positives = 26/109 (23%)

Query: 4   RDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDH 63
           +D   D     SR +      R R  E           S   D   D     +       
Sbjct: 282 KDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPD 341

Query: 64  DRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
              ++ RD +R++ R HR                           + R 
Sbjct: 342 GPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRD 390

>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 = 52.5 bits (125), Expect = 2e-07
 Identities = 16/112 (14%), Positives = 26/112 (23%), Gaps = 3/112 (2%)

Query: 1   MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGI 60
              RD   +               RSR+ +R R    RD +     R R K+   DR   
Sbjct: 232 DRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDR--- 288

Query: 61  RDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
           +      R R     + +          ++                      
Sbjct: 289 KRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGP 340

>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 = 52.2 bits (124), Expect = 3e-07
 Identities = 31/110 (28%), Positives = 40/110 (36%)

Query: 3   GRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRD 62
           G       V      +        R G        RD     + R R +    +RE  R 
Sbjct: 198 GTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRS 257

Query: 63  HDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
             R  R R  +RDKE R R R RS   DR R R  S S  R+  + +R+ 
Sbjct: 258 RSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKE 307

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 51.4 bits (122), Expect = 4e-07
 Identities = 19/115 (16%), Positives = 28/115 (24%), Gaps = 5/115 (4%)

Query: 4   RDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDH 63
           R  R        R +   + G         +        G              E  RD 
Sbjct: 291 RSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDR 350

Query: 64  DRTDRHRDYNRDKERRHRHRSR-----SHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
           DR  R    +  + RR R R R         +R   R +  +      +     G
Sbjct: 351 DRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEG 405

>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 = 50.6 bits (120), Expect = 6e-07
 Identities = 18/113 (15%), Positives = 32/113 (28%), Gaps = 3/113 (2%)

Query: 4   RDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDH 63
                D   +  R +      R +  ER R R     +      + ++    +R   +D 
Sbjct: 227 PLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDR 286

Query: 64  DR---TDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
           DR   + R R+  R +  R              + +    P   P       G
Sbjct: 287 DRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDG 339

>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 = 50.6 bits (120), Expect = 7e-07
 Identities = 11/112 (9%), Positives = 20/112 (17%)

Query: 1   MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGI 60
            S    +               S      ER R R     K     RR  ++ +  R   
Sbjct: 244 RSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRER 303

Query: 61  RDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
              +          +                           +   + + R 
Sbjct: 304 ERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERR 355

>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 = 50.2 bits (119), Expect = 1e-06
 Identities = 26/101 (25%), Positives = 44/101 (43%)

Query: 13  EGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDY 72
              RH     + R           HRD     +  RR+++ + D+E  R   R+   R  
Sbjct: 206 VNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRR 265

Query: 73  NRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
           +R +++  R RSR  S D+ R+R +  S SR  ++ +R   
Sbjct: 266 SRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERK 306

>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 = 49.8 bits (118), Expect = 1e-06
 Identities = 21/112 (18%), Positives = 32/112 (28%)

Query: 1   MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGI 60
            S  D R        R +        R   R RD+     +S   DRRR    +   E  
Sbjct: 216 TSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERR 275

Query: 61  RDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
           R  +R+       + +  R R R+R     +   R      +          
Sbjct: 276 RSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPP 327

>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 = 49.8 bits (118), Expect = 1e-06
 Identities = 21/115 (18%), Positives = 28/115 (24%), Gaps = 1/115 (0%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
             RD +  +     R +          G  G      +      D         D     
Sbjct: 284 KDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGP 343

Query: 62  DHDRTDRHRDYNRDKER-RHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFD 115
           +    DR R+  R     R R R R    DR R   +    S       R  G  
Sbjct: 344 EEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGG 398

>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 = 49.5 bits (117), Expect = 2e-06
 Identities = 25/103 (24%), Positives = 37/103 (35%), Gaps = 1/103 (0%)

Query: 12  GEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRD 71
               R   S +  R R  +R R+R  R  +   +  RR    +  R   R  D+ +R R 
Sbjct: 218 RYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRS 277

Query: 72  YNRDKER-RHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
             R K++ R R R  S S +R R   +     R          
Sbjct: 278 RERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPS 320

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 47.2 bits (111), Expect = 1e-05
 Identities = 20/100 (20%), Positives = 32/100 (32%)

Query: 14  GSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYN 73
           G          R R  ER      RD +      R     +  R   ++  R  R R  +
Sbjct: 224 GPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKD 283

Query: 74  RDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
           +D++R+ R       + R R R + L            +G
Sbjct: 284 KDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAG 323

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 55.5 bits (134), Expect = 6e-10
 Identities = 19/96 (19%), Positives = 32/96 (33%), Gaps = 17/96 (17%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKF-- 224
           +     R VY+ G P  A    I  +             G    V+N+ +     K F  
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDK---------GQ---VLNIQMRRTLHKAFKG 53

Query: 225 -AFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDY 259
             FV   ++E A   +   G  ++   + +    DY
Sbjct: 54  SIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDY 89

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 54.4 bits (131), Expect = 1e-09
 Identities = 18/87 (20%), Positives = 29/87 (33%), Gaps = 2/87 (2%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V++ G P   T   IKE LE  G +    + +       KG  F V+             
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAK-KFVET 71

Query: 357 NGLKMGDKTLTVRRATASSGQSKTEQE 383
            G K  +  L +        +   E++
Sbjct: 72  PGQKYKETDLLILFKDDYFAKKNEERK 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 = 55.9 bits (135), Expect = 6e-10
 Identities = 13/94 (13%), Positives = 28/94 (29%), Gaps = 1/94 (1%)

Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
           SG            +  +P+  T+  + + LE          V   + G   G     ++
Sbjct: 6   SGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFK 65

Query: 345 DPAVTDIACAALNGLKMGDKTLTVRRATASSGQS 378
           +      +   L+  K+  +   V   T    + 
Sbjct: 66  NEDDARKS-ERLHRKKLNGREAFVHVVTLEDMRE 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 = 50.5 bits (121), Expect = 4e-08
 Identities = 14/112 (12%), Positives = 33/112 (29%), Gaps = 14/112 (12%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FA 225
                    ++  +P    +  +  F   +            +  V+V +++  +    A
Sbjct: 10  DVNSAKVCAHITNIPFSITKMDVLQFLEGI---------PVDENAVHVLVDNNGQGLGQA 60

Query: 226 FVEMRTVEEASNAMALDGIIFEGVAVRVRRPT--DYNPTLAAALGPGQPSPN 275
            V+ +  ++A  +  L      G    V   T  D           G+  P+
Sbjct: 61  LVQFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPS 112

>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 = 54.9 bits (133), Expect = 6e-10
 Identities = 15/99 (15%), Positives = 32/99 (32%), Gaps = 15/99 (15%)

Query: 289 GGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           G          VFVG      T  ++++    +G +    + K       + + F  + D
Sbjct: 3   GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFAD 57

Query: 346 PAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
             V    C     L +   ++ +  A     + K  + +
Sbjct: 58  DKVAQSLCG--EDLIIKGISVHISNA-----EPKHNKLN 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 = 39.9 bits (94), Expect = 1e-04
 Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 14/89 (15%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAF 226
                H  +V+VG        + +  FF Q      G        VV+V+I    + FAF
Sbjct: 5   HHHHHHGSKVFVGRCTEDMTAEELQQFFCQY-----GE-------VVDVFIPKPFRAFAF 52

Query: 227 VEMRTVEEASNAMALDGIIFEGVAVRVRR 255
           V     + A +    D II +G++V +  
Sbjct: 53  VTFADDKVAQSLCGEDLII-KGISVHISN 80

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 54.3 bits (131), Expect = 8e-10
 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 9/79 (11%)

Query: 297 VFVGGLP------YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           + V  +P          +  I ++   FG +   +     + G +KGY F  Y  PA   
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASPAHAV 61

Query: 351 IACAALNGLKMGDK-TLTV 368
            A    +G K+  + T  V
Sbjct: 62  DAVKNADGYKLDKQHTFRV 80

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 18/75 (24%), Positives = 26/75 (34%), Gaps = 8/75 (10%)

Query: 435 ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA 494
              +  E++   + +   K+G + N   P  D   G+T G    FLEY        A   
Sbjct: 12  VGPDRLEKLKNVIHKIFSKFGKITNDFYPEED---GKTKGYI--FLEYASPAHAVDAVKN 66

Query: 495 LSGRKFGGN---TVN 506
             G K        VN
Sbjct: 67  ADGYKLDKQHTFRVN 81

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 16/83 (19%), Positives = 35/83 (42%), Gaps = 5/83 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +V+VG L     + +++     +G L    + ++       G+ F  ++DP   + A   
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 356 LNGLKMGDKTLTVRRATASSGQS 378
           L+G  +    + V  +T    +S
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRS 79

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 49.6 bits (119), Expect = 7e-08
 Identities = 26/80 (32%), Positives = 35/80 (43%), Gaps = 14/80 (17%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 234
           +VYVG L   A +  +   FS           GP   +  V+I      FAFVE     +
Sbjct: 2   KVYVGNLGTGAGKGELERAFSY---------YGP---LRTVWIARNPPGFAFVEFEDPRD 49

Query: 235 ASNAM-ALDGIIFEGVAVRV 253
           A +A+  LDG +  G  VRV
Sbjct: 50  AEDAVRGLDGKVICGSRVRV 69

>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 = 53.4 bits (129), Expect = 2e-09
 Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 15/85 (17%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           + + + +++VG + P    Q +   F +          GP   V+   I   K +AFV M
Sbjct: 6   SGKASTKLHVGNISPTCTNQELRAKFEE---------YGP---VIECDI--VKDYAFVHM 51

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
              E+A  A+  LD   F+G  + V
Sbjct: 52  ERAEDAVEAIRGLDNTEFQGKRMHV 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 = 52.2 bits (126), Expect = 5e-09
 Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           +   ++ VG +    T  +++   E +G +   D+V        K Y F   +       
Sbjct: 8   KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVE 59

Query: 352 ACAALNGLKMGDKTLTVRRAT 372
           A   L+  +   K + V+ +T
Sbjct: 60  AIRGLDNTEFQGKRMHVQLST 80

>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 = 15/93 (16%), Positives = 27/93 (29%), Gaps = 10/93 (10%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
                 R+ +  LP   + Q +     +                 +V          +E 
Sbjct: 24  LPAKRYRITMKNLPEGCSWQDLKDLARE---------NSLETTFSSVNTRDFDGTGALEF 74

Query: 230 RTVEEASNAMA-LDGIIFEGVAVRVRRPTDYNP 261
            + E    A+  L+ I F G  + V R  +  P
Sbjct: 75  PSEEILVEALERLNNIEFRGSVITVERDDNPPP 107

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 3/77 (3%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+ +  LP   +   +K+L         F      +T +  G G   +    +   A   
Sbjct: 30  RITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDGTGALEFPSEEILVEALER 86

Query: 356 LNGLKMGDKTLTVRRAT 372
           LN ++     +TV R  
Sbjct: 87  LNNIEFRGSVITVERDD 103

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 8/76 (10%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FV   P    E+++ E+   FG +    ++         G+ F  +++      A   
Sbjct: 33  RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEE 84

Query: 356 LNGLKMGDKTLTVRRA 371
           ++G    ++ L V  +
Sbjct: 85  VHGKSFANQPLEVVYS 100

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 46.9 bits (112), Expect = 7e-07
 Identities = 21/89 (23%), Positives = 30/89 (33%), Gaps = 15/89 (16%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           Q+      R++V   P    E  +   F            GP   +  V I     FAFV
Sbjct: 25  QEGELSNTRLFVRPFPLDVQESELNEIFGPF---------GP---MKEVKI--LNGFAFV 70

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRR 255
           E    E A+ A+  + G  F    + V  
Sbjct: 71  EFEEAESAAKAIEEVHGKSFANQPLEVVY 99

>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 = 53.7 bits (129), Expect = 7e-09
 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +V+VG L     +T+++     +G L    + ++       G+ F  ++DP     A   
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRE 129

Query: 356 LNGLKMGDKTLTVRRA 371
           L+G  +    + V  +
Sbjct: 130 LDGRTLCGCRVRVELS 145

>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 = 51.4 bits (123), Expect = 5e-08
 Identities = 25/101 (24%), Positives = 39/101 (38%), Gaps = 14/101 (13%)

Query: 155 LGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV 214
           +          M + +     +VYVG L    N+  +   F            GP   + 
Sbjct: 54  VTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYY---------GP---LR 101

Query: 215 NVYINHEKK-FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           +V++      FAFVE     +A++A+  LDG    G  VRV
Sbjct: 102 SVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRV 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 = 53.7 bits (129), Expect = 7e-09
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 5/85 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDL-----VKDRDTGNSKGYGFCVYQDPAVTD 350
           R++V  L  +  E  +K +   +             ++    G  KG  F    +     
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 351 IACAALNGLKMGDKTLTVRRATASS 375
            A    NG  +  K + V+ A ++ 
Sbjct: 107 KALKEANGYVLFGKPMVVQFARSAR 131

>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 = 51.9 bits (125), Expect = 9e-09
 Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 13/80 (16%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           + +YV  L    +E+ I   F+ +          PG       +   + +AFV     E+
Sbjct: 16  KILYVRNLMLSTSEEMIEKEFNNI---------KPG---AVERVKKIRDYAFVHFSNRED 63

Query: 235 ASNAM-ALDGIIFEGVAVRV 253
           A  AM AL+G + +G  + V
Sbjct: 64  AVEAMKALNGKVLDGSPIEV 83

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 13/75 (17%), Positives = 24/75 (32%), Gaps = 6/75 (8%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++V  L    +E  I++   +                  + Y F  + +      A  AL
Sbjct: 18  LYVRNLMLSTSEEMIEKEFNNIKP------GAVERVKKIRDYAFVHFSNREDAVEAMKAL 71

Query: 357 NGLKMGDKTLTVRRA 371
           NG  +    + V  A
Sbjct: 72  NGKVLDGSPIEVTLA 86

>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 = 51.4 bits (123), Expect = 2e-08
 Identities = 16/83 (19%), Positives = 27/83 (32%), Gaps = 6/83 (7%)

Query: 297 VFVGGLPYYFTETQI---KELLESFGTLHGFDLVKDRDTGNSK---GYGFCVYQDPAVTD 350
           VFV GL     + ++    E    FG +H   +        S+      +  Y       
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 351 IACAALNGLKMGDKTLTVRRATA 373
            A   +N + +  +TL     T 
Sbjct: 78  RAIQCVNNVVVDGRTLKASLGTT 100

>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 = 39.8 bits (93), Expect = 2e-04
 Identities = 13/69 (18%), Positives = 23/69 (33%)

Query: 441 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF 500
           +  +    E  GK+G +  VVI       G        ++ Y  +     A   ++    
Sbjct: 29  DPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV 88

Query: 501 GGNTVNAFY 509
            G T+ A  
Sbjct: 89  DGRTLKASL 97

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 38.7 bits (90), Expect = 6e-04
 Identities = 16/88 (18%), Positives = 33/88 (37%), Gaps = 21/88 (23%)

Query: 177 VYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---------FAF 226
           V+V GL   LA+ + +     +     G         +  V IN+             A+
Sbjct: 18  VFVVGLSQRLADPEVLKR--PEYFGKFG--------KIHKVVINNSTSYAGSQGPSASAY 67

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           V     E+A  A+  ++ ++ +G  ++ 
Sbjct: 68  VTYIRSEDALRAIQCVNNVVVDGRTLKA 95

>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 = 51.3 bits (123), Expect = 2e-08
 Identities = 14/98 (14%), Positives = 40/98 (40%), Gaps = 4/98 (4%)

Query: 284 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G +        V + GLP+  ++ +I +       +     +     G S G  F
Sbjct: 2   SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQS 378
             +    + + A    +  ++G + + + +++ +  ++
Sbjct: 62  VQFASQEIAEKAL-KKHKERIGHRYIEIFKSSRAEVRT 98

>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 = 47.0 bits (112), Expect = 6e-07
 Identities = 16/93 (17%), Positives = 35/93 (37%), Gaps = 12/93 (12%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---F 224
              T +   V + GLP   +++ I  FFS +     G         + + ++ + +    
Sbjct: 9   SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG---------MTLPVDFQGRSTGE 59

Query: 225 AFVEMRTVEEASNAMALDGIIFEGVAVRVRRPT 257
           AFV+  + E A  A+           + + + +
Sbjct: 60  AFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 92

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 50.4 bits (121), Expect = 3e-08
 Identities = 19/109 (17%), Positives = 35/109 (32%), Gaps = 13/109 (11%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
            S    G      +FV  L    TE  +++    FG L     +KD        Y F  +
Sbjct: 1   GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHF 52

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 392
            +      A   +NG  +  + + +  A     +   ++       +Q 
Sbjct: 53  DERDGAVKAMEEMNGKDLEGENIEIVFA-----KPPDQKRKERKAQRQA 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 = 45.0 bits (107), Expect = 3e-06
 Identities = 21/105 (20%), Positives = 35/105 (33%), Gaps = 19/105 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           + ++V  L     E+ +   FSQ          G    +  V     K +AF+     + 
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQF---------GK---LERVKKL--KDYAFIHFDERDG 57

Query: 235 ASNAM-ALDGIIFEGVAVRV---RRPTDYNPTLAAALGPG-QPSP 274
           A  AM  ++G   EG  + +   + P        A       PS 
Sbjct: 58  AVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSS 102

>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 = 50.2 bits (120), Expect = 6e-08
 Identities = 16/100 (16%), Positives = 28/100 (28%), Gaps = 10/100 (10%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +    LP      +I+E    FG+      +               + +P     A   L
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGS------LGRVLLPEGGITAIVEFLEPLEARKAFRHL 66

Query: 357 NGLKMGDKTLTVRRA----TASSGQSKTEQESILAQAQQH 392
              K     L +  A      ++ Q K  Q    A+  + 
Sbjct: 67  AYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAES 106

>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 = 43.3 bits (102), Expect = 1e-05
 Identities = 17/87 (19%), Positives = 24/87 (27%), Gaps = 13/87 (14%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
             + R    +    LP       I   FS+          G    +  V +      A V
Sbjct: 4   GSSGRSKTVILAKNLPAGTLAAEIQETFSR---------FGS---LGRVLLPEGGITAIV 51

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV 253
           E     EA  A   L    F  V + +
Sbjct: 52  EFLEPLEARKAFRHLAYSKFHHVPLYL 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 = 39.4 bits (92), Expect = 3e-04
 Identities = 12/71 (16%), Positives = 28/71 (39%), Gaps = 9/71 (12%)

Query: 445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 504
            +++E   ++G+L  V++P          G     +E+ + +    A   L+  KF    
Sbjct: 25  AEIQETFSRFGSLGRVLLP---------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVP 75

Query: 505 VNAFYYPEDKY 515
           +   + P   +
Sbjct: 76  LYLEWAPIGVF 86

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 49.5 bits (118), Expect = 1e-07
 Identities = 12/78 (15%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V + GLP+  T+ +I +       +     +     G   G  F  +    + + A    
Sbjct: 45  VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL-GK 103

Query: 357 NGLKMGDKTLTVRRATAS 374
           +  ++G + + V +++  
Sbjct: 104 HKERIGHRYIEVFKSSQE 121

>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 = 46.8 bits (111), Expect = 1e-06
 Identities = 16/92 (17%), Positives = 30/92 (32%), Gaps = 10/92 (10%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FA 225
              + +   V + GLP    ++ I  FFS +            + +        K    A
Sbjct: 36  SADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVP--------NGITLPVDPEGKITGEA 87

Query: 226 FVEMRTVEEASNAMALDGIIFEGVAVRVRRPT 257
           FV+  + E A  A+           + V + +
Sbjct: 88  FVQFASQELAEKALGKHKERIGHRYIEVFKSS 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 = 49.5 bits (118), Expect = 1e-07
 Identities = 16/91 (17%), Positives = 33/91 (36%), Gaps = 1/91 (1%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           E    V++ GLP+      + +  +    +     +     G + G GF  +++ A    
Sbjct: 23  EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKA 82

Query: 352 ACAALNGLKMGDKTLTVRRATASSGQSKTEQ 382
           A    +   MG++ + V   T      K + 
Sbjct: 83  AL-CRHKQYMGNRFIQVHPITKKGMLEKIDM 112

>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 = 47.5 bits (113), Expect = 5e-07
 Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 12/84 (14%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTVE 233
           VY+ GLP  A  + +  FF ++            +  + +      K     FVE R   
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKL---------DIVEDSIYIAYGPNGKATGEGFVEFRNEA 78

Query: 234 EASNAMALDGIIFEGVAVRVRRPT 257
           +   A+           ++V   T
Sbjct: 79  DYKAALCRHKQYMGNRFIQVHPIT 102

>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 = 48.9 bits (117), Expect = 1e-07
 Identities = 18/83 (21%), Positives = 31/83 (37%), Gaps = 9/83 (10%)

Query: 296 RVFVGGLPYYF-TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           RVF+G L      ++ ++ +   +G + G  +         KGY F  Y +      A  
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80

Query: 355 ALNGLKMGDKTLTVRRATASSGQ 377
             NG  +  +TL +  A      
Sbjct: 81  GENGRVLAGQTLDINMAGEPKPD 103

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 43.9 bits (104), Expect = 7e-06
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 16/82 (19%)

Query: 175 RRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
            RV++G L   L  +  + T FS+          G    V    ++  K +AFV+     
Sbjct: 28  SRVFIGNLNTALVKKSDVETIFSK---------YGR---VAGCSVH--KGYAFVQYSNER 73

Query: 234 EASNAM-ALDGIIFEGVAVRVR 254
            A  A+   +G +  G  + + 
Sbjct: 74  HARAAVLGENGRVLAGQTLDIN 95

>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 = 48.8 bits (116), Expect = 2e-07
 Identities = 19/106 (17%), Positives = 38/106 (35%), Gaps = 16/106 (15%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-----FAFVEMRT 231
           V + GLP   + + +  F S              D V  V+  + ++      AFVE+ +
Sbjct: 20  VKLRGLPWSCSIEDVQNFLS---------DCTIHDGVAGVHFIYTREGRQSGEAFVELES 70

Query: 232 VEEASNAMALDGIIFEGVAVRVRR--PTDYNPTLAAALGPGQPSPN 275
            ++   A+  D        + V +   T+ +  L  +       P+
Sbjct: 71  EDDVKLALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPS 116

>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 = 44.5 bits (105), Expect = 5e-06
 Identities = 23/119 (19%), Positives = 46/119 (38%), Gaps = 16/119 (13%)

Query: 284 ASGAIGGAEGPDR-----VFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNS 335
           +SG+ G   GP+      V + GLP+  +   ++  L        + G   +  R+ G  
Sbjct: 2   SSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQ 60

Query: 336 KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIA 394
            G  F   +      +A    +   MG + + V ++       +TE + +L  +  + A
Sbjct: 61  SGEAFVELESEDDVKLAL-KKDRESMGHRYIEVFKS------HRTEMDWVLKHSGPNSA 112

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 51.4 bits (122), Expect = 3e-07
 Identities = 15/121 (12%), Positives = 45/121 (37%), Gaps = 7/121 (5%)

Query: 296 RVFVGGLPYYFTETQIKELL----ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
            +++  L     + ++K+ L      FG +     +    +   +G  F ++++ +    
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFKEVSSATN 67

Query: 352 ACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGG 411
           A  ++ G    DK + ++ A   S      + + + + ++    +  + +T        G
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQG 127

Query: 412 M 412
            
Sbjct: 128 G 128

>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 = 47.6 bits (112), Expect = 4e-06
 Identities = 30/205 (14%), Positives = 56/205 (27%), Gaps = 15/205 (7%)

Query: 52  NYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRR 111
            Y      I    +        + ++R+ + +    +    +    +             
Sbjct: 85  QYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGM 144

Query: 112 SGFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQAT 171
                AP     +PG       PG+          + P         P            
Sbjct: 145 PPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSEN 204

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMR 230
                +++  LP   NE  ++  F+Q      G           V +   +   AFVE  
Sbjct: 205 PPNHILFLTNLPEETNELMLSMLFNQ----FPG--------FKEVRLVPGRHDIAFVEFD 252

Query: 231 TVEEASNAM-ALDGI-IFEGVAVRV 253
              +A  A  AL G  I +  A+++
Sbjct: 253 NEVQAGAARDALQGFKITQNNAMKI 277

>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 = 44.5 bits (104), Expect = 4e-05
 Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 12/92 (13%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-- 223
           M    TR    +Y+  L     +  +      + +  G         ++++ ++   K  
Sbjct: 1   MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFG--------QILDILVSRSLKMR 52

Query: 224 -FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
             AFV  + V  A+NA+ ++ G  F    +R+
Sbjct: 53  GQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 84

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 42.6 bits (99), Expect = 2e-04
 Identities = 16/75 (21%), Positives = 24/75 (32%), Gaps = 6/75 (8%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN 357
           F+  LP    E  +  L   F       LV  R         F  + +      A  AL 
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQ 265

Query: 358 GLKM-GDKTLTVRRA 371
           G K+  +  + +  A
Sbjct: 266 GFKITQNNAMKISFA 280

>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 = 48.3 bits (115), Expect = 4e-07
 Identities = 23/94 (24%), Positives = 32/94 (34%), Gaps = 18/94 (19%)

Query: 167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--- 223
               +     V++ GLP  A E  I  FFS +               V V+I        
Sbjct: 39  FTVQSTTGHCVHMRGLPYKATENDIYNFFSPL-------------NPVRVHIEIGPDGRV 85

Query: 224 --FAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
              A VE  T EEA  AM+ D    +   + +  
Sbjct: 86  TGEADVEFATHEEAVAAMSKDRANMQHRYIELFL 119

>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 = 44.8 bits (106), Expect = 6e-06
 Identities = 16/117 (13%), Positives = 32/117 (27%), Gaps = 7/117 (5%)

Query: 268 GPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLV 327
                +    +      S     +     V + GLPY  TE  I         +    + 
Sbjct: 20  HMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIE 78

Query: 328 KDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLTVRRATASSGQSKTEQ 382
              D G   G     +      + A AA+  +   M  + + +   + +   +    
Sbjct: 79  IGPD-GRVTGEADVEFATH---EEAVAAMSKDRANMQHRYIELFLNSTTGASNGAYS 131

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 47.7 bits (113), Expect = 4e-07
 Identities = 21/71 (29%), Positives = 27/71 (38%), Gaps = 5/71 (7%)

Query: 290 GAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD--TGNSKGYGFCVYQ 344
           G+ G      VFVGGLP    E +I      FG L      K         KGY F ++Q
Sbjct: 1   GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60

Query: 345 DPAVTDIACAA 355
           + +       A
Sbjct: 61  EESSVQALIDA 71

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 47.5 bits (113), Expect = 5e-07
 Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 9/86 (10%)

Query: 290 GAEGPDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP-- 346
           G+  P RV  +  LP   TE ++  L   FG +    ++K       K   F        
Sbjct: 11  GSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEA 64

Query: 347 AVTDIACAALNGLKMGDKTLTVRRAT 372
           A T +         +  + + ++ + 
Sbjct: 65  ANTMVNYYTSVTPVLRGQPIYIQFSN 90

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 15/83 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           R +++  LP    E  + +              G    V N+ +   K  AF+EM T E 
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPF---------GK---VTNLLMLKGKNQAFIEMNTEEA 64

Query: 235 ASNAMA---LDGIIFEGVAVRVR 254
           A+  +        +  G  + ++
Sbjct: 65  ANTMVNYYTSVTPVLRGQPIYIQ 87

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 47.4 bits (113), Expect = 5e-07
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 3/76 (3%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V V G+P+   E  +++       +    L+KD   G + G G   +  P  T  A    
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KR 75

Query: 357 NGLKMGDKTLTVRRAT 372
           N + M  + + V  AT
Sbjct: 76  NRMLMIQRYVEVSPAT 91

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 44.7 bits (106), Expect = 4e-06
 Identities = 20/102 (19%), Positives = 35/102 (34%), Gaps = 18/102 (17%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKK---FAFVEMRT 231
           V V G+P  A E  +  FF              G  V  V++  +H  +      V+  +
Sbjct: 19  VSVHGMPFSAMENDVRDFFH-------------GLRVDAVHLLKDHVGRNNGNGLVKFLS 65

Query: 232 VEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPS 273
            ++   A+  + ++     V V   T+     A       PS
Sbjct: 66  PQDTFEALKRNRMLMIQRYVEVSPATERQWVAAGGHITSGPS 107

>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 = 46.9 bits (112), Expect = 5e-07
 Identities = 12/81 (14%), Positives = 32/81 (39%), Gaps = 9/81 (11%)

Query: 296 RVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           R+F+G LP    ++  +  +   +G +   ++           +GF  + +P     A  
Sbjct: 24  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE 75

Query: 355 ALNGLKMGDKTLTVRRATASS 375
             +      K L +  +++++
Sbjct: 76  XESQEMNFGKKLILEVSSSNA 96

>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 = 44.6 bits (106), Expect = 3e-06
 Identities = 12/81 (14%), Positives = 30/81 (37%), Gaps = 16/81 (19%)

Query: 175 RRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
            R+++G LP    +++ +   FS           G    ++ + I     F F++    +
Sbjct: 23  SRLFIGNLPLKNVSKEDLFRIFSPY---------GH---IMQINIK--NAFGFIQFDNPQ 68

Query: 234 EASNAMA-LDGIIFEGVAVRV 253
              +A+      +  G  + +
Sbjct: 69  SVRDAIEXESQEMNFGKKLIL 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 = 46.8 bits (112), Expect = 5e-07
 Identities = 13/84 (15%), Positives = 34/84 (40%), Gaps = 7/84 (8%)

Query: 296 RVFVGGLPYYFTETQIKELL----ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
            +++  L     + ++K+ L      FG +     +    +   +G  F ++++ +    
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATN 66

Query: 352 ACAALNGLKMGDKTLTVRRATASS 375
           A  ++ G    DK + ++ A   S
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKTDS 90

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 17/95 (17%), Positives = 39/95 (41%), Gaps = 23/95 (24%)

Query: 175 RRVYVGGLPPLANE----QAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFV 227
             +Y+  L     +    +++   FS+          G    ++++ ++   K    AFV
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRF---------GQ---ILDILVSRSLKMRGQAFV 56

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV---RRPTD 258
             + V  A+NA+ ++ G  F    +R+   +  +D
Sbjct: 57  IFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD 91

>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 = 47.1 bits (112), Expect = 5e-07
 Identities = 13/83 (15%), Positives = 23/83 (27%), Gaps = 15/83 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             V+V GL     E  +     +          G    +  V +   K+ A VE   ++ 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKF---------GT---ICYVMMMPFKRQALVEFENIDS 63

Query: 235 ASNAMA---LDGIIFEGVAVRVR 254
           A   +       +   G      
Sbjct: 64  AKECVTFAADVPVYIAGQQAFFN 86

>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 = 45.9 bits (109), Expect = 1e-06
 Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 8/75 (10%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTDIACA 354
           V V GL     E  + E LE FGT      +        K      +++   A   +  A
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGT------ICYVMMMPFKRQALVEFENIDSAKECVTFA 71

Query: 355 ALNGLKMGDKTLTVR 369
           A   + +  +     
Sbjct: 72  ADVPVYIAGQQAFFN 86

>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 = 47.6 bits (113), Expect = 5e-07
 Identities = 19/109 (17%), Positives = 36/109 (33%), Gaps = 15/109 (13%)

Query: 149 PFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAG 208
                  G  P       ++ A   +R +++  LP    E  + +              G
Sbjct: 6   HHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPF---------G 56

Query: 209 PGDAVVNVYINHEKKFAFVEMRTVEEASNAM---ALDGIIFEGVAVRVR 254
               V N+ +   K  AF+EM T E A+  +        +  G  + ++
Sbjct: 57  K---VTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ 102

>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 = 47.2 bits (112), Expect = 6e-07
 Identities = 20/111 (18%), Positives = 35/111 (31%), Gaps = 11/111 (9%)

Query: 267 LGPGQP--SPNLNLAAVGLASGAIGGAEGPDRV-FVGGLPYYFTETQIKELLESFGTLHG 323
           +G        +  L   G   G    A  P RV  +  LP   TE ++  L   FG +  
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN 60

Query: 324 FDLVKDRDTGNSKGYGFCVYQDP--AVTDIACAALNGLKMGDKTLTVRRAT 372
             ++K       K   F        A T +         +  + + ++ + 
Sbjct: 61  LLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN 105

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

 Score = 46.4 bits (111), Expect = 7e-07
 Identities = 12/81 (14%), Positives = 32/81 (39%), Gaps = 9/81 (11%)

Query: 296 RVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           R+F+G LP    ++  +  +   +G +   ++           +GF  + +P     A  
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE 63

Query: 355 ALNGLKMGDKTLTVRRATASS 375
             +      K L +  +++++
Sbjct: 64  CESQEMNFGKKLILEVSSSNA 84

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

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 12/80 (15%), Positives = 30/80 (37%), Gaps = 16/80 (20%)

Query: 176 RVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           R+++G LP    +++ +   FS           G    ++ + I     F F++    + 
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSP---------YGH---IMQINIK--NAFGFIQFDNPQS 57

Query: 235 ASNAM-ALDGIIFEGVAVRV 253
             +A+      +  G  + +
Sbjct: 58  VRDAIECESQEMNFGKKLIL 77

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 46.4 bits (110), Expect = 8e-07
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 9/82 (10%)

Query: 294 PDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTD 350
           P RV  +  LP   TET++  L   FG +    ++K       K   F        A+T 
Sbjct: 14  PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITM 67

Query: 351 IACAALNGLKMGDKTLTVRRAT 372
           +   +     + ++ + ++ + 
Sbjct: 68  VNYYSAVTPHLRNQPIYIQYSN 89

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 14/83 (16%), Positives = 27/83 (32%), Gaps = 15/83 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           R +++  LP    E  +                G    V N+ +   K  AF+E+ T E 
Sbjct: 16  RVLHIRKLPGEVTETEVIALGLPF---------GK---VTNILMLKGKNQAFLELATEEA 63

Query: 235 ASNAM---ALDGIIFEGVAVRVR 254
           A   +   +          + ++
Sbjct: 64  AITMVNYYSAVTPHLRNQPIYIQ 86

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

 Score = 46.1 bits (110), Expect = 9e-07
 Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 15/87 (17%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++A R    +YV G         +   FS       GN       ++++ ++  +  AFV
Sbjct: 9   RRAPRKGNTLYVYGED--MTPTLLRGAFSPF-----GN-------IIDLSMDPPRNCAFV 54

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV 253
               +E A  A+  L+G   E V ++V
Sbjct: 55  TYEKMESADQAVAELNGTQVESVQLKV 81

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

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 22/104 (21%), Positives = 38/104 (36%), Gaps = 16/104 (15%)

Query: 284 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G    P +   ++V G     T T ++     FG       + D      +   F
Sbjct: 2   SSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGN------IIDLSMDPPRNCAF 53

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
             Y+     D A A LNG ++    L V     +  + +   +S
Sbjct: 54  VTYEKMESADQAVAELNGTQVESVQLKV-----NIARKQPMLDS 92

>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 = 46.2 bits (110), Expect = 1e-06
 Identities = 23/86 (26%), Positives = 32/86 (37%), Gaps = 18/86 (20%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-----FAFVEMRT 231
           V++ GLP  A E  I  FFS +               + V+I           A VE  T
Sbjct: 18  VHMRGLPYRATENDIYNFFSPL-------------NPMRVHIEIGPDGRVTGEADVEFAT 64

Query: 232 VEEASNAMALDGIIFEGVAVRVRRPT 257
            E+A  AMA D    +   V +   +
Sbjct: 65  HEDAVAAMAKDKANMQHRYVELFLNS 90

>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 = 45.1 bits (107), Expect = 3e-06
 Identities = 17/95 (17%), Positives = 30/95 (31%), Gaps = 7/95 (7%)

Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
           SG+   +     V + GLPY  TE  I              +    D G   G     + 
Sbjct: 6   SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFA 63

Query: 345 DPAVTDIACAAL--NGLKMGDKTLTVRRATASSGQ 377
                + A AA+  +   M  + + +   + +   
Sbjct: 64  TH---EDAVAAMAKDKANMQHRYVELFLNSTAGTS 95

>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 = 45.8 bits (109), Expect = 1e-06
 Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 9/89 (10%)

Query: 290 GAEGPDR--VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 347
           G+ G     V + G P+  TE  + E L          +V++   GN  GY F  + +  
Sbjct: 4   GSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAH-GNKTGYIFVDFSNE- 60

Query: 348 VTDIACAAL--NGLKMGDKTLTVRRATAS 374
             +    AL  N   MG + + V R  + 
Sbjct: 61  --EEVKQALKCNREYMGGRYIEVFREKSG 87

>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 = 45.4 bits (108), Expect = 2e-06
 Identities = 15/86 (17%), Positives = 25/86 (29%), Gaps = 18/86 (20%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-----FAFVEMRT 231
           V + G P    E+ +  F +                 V + I          + FV+   
Sbjct: 13  VKLRGAPFNVTEKNVMEFLA-------------PLKPVAIRIVRNAHGNKTGYIFVDFSN 59

Query: 232 VEEASNAMALDGIIFEGVAVRVRRPT 257
            EE   A+  +     G  + V R  
Sbjct: 60  EEEVKQALKCNREYMGGRYIEVFREK 85

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 20/96 (20%), Positives = 34/96 (35%), Gaps = 7/96 (7%)

Query: 164 QVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK 223
           +V    +  +   V + GLP  A  + +  FF Q          G  + ++ V     + 
Sbjct: 13  EVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQH-----CPITGGKEGILFVTYPDGRP 67

Query: 224 --FAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPT 257
              AFV     E A NA+     +     + + R T
Sbjct: 68  TGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRST 103

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 45.3 bits (107), Expect = 3e-06
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 10/84 (11%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFD----LVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           V + GLP+  T  ++         + G       V   D G   G  F ++      + A
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD-GRPTGDAFVLFACE---EYA 81

Query: 353 CAAL--NGLKMGDKTLTVRRATAS 374
             AL  +   +G + + + R+TA+
Sbjct: 82  QNALRKHKDLLGKRYIELFRSTAA 105

>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 = 46.0 bits (109), Expect = 1e-06
 Identities = 13/90 (14%), Positives = 28/90 (31%), Gaps = 8/90 (8%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FA 225
           ++       +   GLP     + +  FFS              + +  +     K+   A
Sbjct: 5   EEEVDDVFLIRAQGLPWSCTMEDVLNFFS------DCRIRNGENGIHFLLNRDGKRRGDA 58

Query: 226 FVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
            +EM + ++   A+    +      V V  
Sbjct: 59  LIEMESEQDVQKALEKHRMYMGQRYVEVYE 88

>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 = 14/98 (14%), Positives = 31/98 (31%), Gaps = 11/98 (11%)

Query: 297 VFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           +   GLP+  T   +             +G   + +RD G  +G      +       A 
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKAL 72

Query: 354 AALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQ 391
              + + MG + + V            + ++++   Q 
Sbjct: 73  -EKHRMYMGQRYVEVYEIN------NEDVDALMKSLQV 103

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 47.5 bits (112), Expect = 2e-06
 Identities = 21/123 (17%), Positives = 38/123 (30%), Gaps = 17/123 (13%)

Query: 142 EMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTA 201
           E+ +        +      +P      +     R VY+ G P  A    I  +       
Sbjct: 77  ELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDK--- 133

Query: 202 IGGNSAGPGDAVVNVYI--NHEKKF---AFVEMRTVEEASNAMALDGIIFEGVAVRVRRP 256
                 G    V+N+ +     K F    FV   ++E A   +   G  ++   + +   
Sbjct: 134 ------GQ---VLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFK 184

Query: 257 TDY 259
            DY
Sbjct: 185 DDY 187

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 19/85 (22%), Positives = 27/85 (31%), Gaps = 14/85 (16%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
           R   RV V GLPP  + Q +     +            GD V    + +      VE   
Sbjct: 13  RSENRVVVSGLPPSGSWQDLKDHMREA-----------GD-VCYADV-YRDGTGVVEFVR 59

Query: 232 VEEASNAMA-LDGIIFEGVAVRVRR 255
            E+ + A+  LD   F         
Sbjct: 60  KEDMTYAVRKLDNTKFRSHEGETAY 84

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 7/79 (8%)

Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
             +RV V GLP   +   +K+ +   G +   D+ +D       G G   +        A
Sbjct: 14  SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYA 66

Query: 353 CAALNGLKMGDKTLTVRRA 371
              L+  K           
Sbjct: 67  VRKLDNTKFRSHEGETAYI 85

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

 Score = 45.1 bits (107), Expect = 3e-06
 Identities = 15/74 (20%), Positives = 26/74 (35%), Gaps = 8/74 (10%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTDIACA 354
           V + GL     E  + E L+ FG +    ++        K      ++D   A   +  A
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYA 77

Query: 355 ALNGLKMGDKTLTV 368
           A N + +      V
Sbjct: 78  ADNQIYIAGHPAFV 91

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

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 19/82 (23%), Positives = 29/82 (35%), Gaps = 15/82 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             V++ GL     E  +     +          GP   +  V +  +K+ A VE   V  
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEF---------GP---ISYVVVMPKKRQALVEFEDVLG 69

Query: 235 ASNAM---ALDGIIFEGVAVRV 253
           A NA+   A + I   G    V
Sbjct: 70  ACNAVNYAADNQIYIAGHPAFV 91

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 296 RVFVGGLPYYFTETQIKEL-LESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
            +FVG L     +  + E  ++ + +  G  +V D+ TG SKGYGF  + D      A  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69

Query: 355 ALNG-LKMGDKTLTVRRAT 372
              G + +G K + +  A 
Sbjct: 70  ECQGAVGLGSKPVRLSVAI 88

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

 Score = 44.1 bits (104), Expect = 1e-05
 Identities = 16/101 (15%), Positives = 34/101 (33%), Gaps = 9/101 (8%)

Query: 296 RVFVGGLPYYFTETQIKELL----ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
            V +  +     + +++ LL     S G +   D+V D  + ++ G  + V+        
Sbjct: 31  VVLITNINPEVPKEKLQALLYALASSQGDI--LDIVVDL-SDDNSGKAYIVFATQESAQA 87

Query: 352 ACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 392
              A  G       L +  +      S+  ++  L     H
Sbjct: 88  FVEAFQGYPFQGNPLVITFSETPQ--SQVAEDGSLEHHHHH 126

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

 Score = 41.4 bits (97), Expect = 9e-05
 Identities = 16/108 (14%), Positives = 34/108 (31%), Gaps = 23/108 (21%)

Query: 162 PVQVMTQQATRHARRVYVGGLPPLANE----QAIATFFSQVMTAIGGNSAGPGDAVVNVY 217
           P    T   T  ++ V +  + P   +      +    S           G    ++++ 
Sbjct: 17  PDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQ---------GD---ILDIV 64

Query: 218 INHEKK---FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV---RRPTD 258
           ++        A++   T E A   + A  G  F+G  + +     P  
Sbjct: 65  VDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS 112

>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 = 43.4 bits (102), Expect = 2e-05
 Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 6/67 (8%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V  GGL    +  Q+  +LE  G +    +  +      K Y F  Y+    +  A   L
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTL 83

Query: 357 NGLKMGD 363
           NG ++ D
Sbjct: 84  NGKEVVD 90

>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 = 45.2 bits (106), Expect = 5e-05
 Identities = 65/511 (12%), Positives = 128/511 (25%), Gaps = 162/511 (31%)

Query: 50  DKNYKYDREGIR--DHDRTDRHRDYNRDKERRH--------RHRSRSHSSDRFRNRSKSL 99
             NYK+    I+      +   R Y   ++R +         + SR     + R     L
Sbjct: 88  RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLEL 147

Query: 100 SPSRSPSKSKRRSGFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFP 159
            P+                          + G               +L  G T +    
Sbjct: 148 RPA----------------------KNVLIDG---------------VLGSGKTWVALDV 170

Query: 160 LMPVQVMTQQATRHARRVY---VGG-------LPPLANEQAIATFFSQVMTAIGGNSAGP 209
            +  +V      +   +++   +         L  L           Q    I  N    
Sbjct: 171 CLSYKVQ----CKMDFKIFWLNLKNCNSPETVLEMLQK------LLYQ----IDPNWTSR 216

Query: 210 GDAVVNVYIN-HEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALG 268
            D   N+ +  H  +      R ++       L  ++   V          N     A  
Sbjct: 217 SDHSSNIKLRIHSIQAELR--RLLKSKPYENCL--LVLLNV---------QNAKAWNAFN 263

Query: 269 PGQP----SPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF 324
                   +    +            A     + +       T  ++K LL  +      
Sbjct: 264 LSCKILLTTRFKQVTDF-------LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ 316

Query: 325 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
           DL ++  T N           P    I  A             +R   A+    K     
Sbjct: 317 DLPREVLTTN-----------PRRLSI-IAES-----------IRDGLATWDNWKHVNCD 353

Query: 385 ILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETL---AKVLCLTEAITADALADDEEYE 441
            L    +  ++    L+ +    +   +S+F  +      +L L        +  D    
Sbjct: 354 KLTTIIE-SSLN--VLEPAEYRKMFDRLSVFPPSAHIPTILLSL--------IWFDVIKS 402

Query: 442 EILEDMREECGKYGTLVN-------VVIP----RPDQNGGETPGVGKVFLEYYDAVGCAT 490
           ++   +  +  KY  LV        + IP               + +  +++Y+      
Sbjct: 403 DV-MVVVNKLHKYS-LVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIP---- 456

Query: 491 AKNALSGRKFGGNTVNAFYYPEDKYFNKDYS 521
                  + F  + +       D+YF   YS
Sbjct: 457 -------KTFDSDDLIP--PYLDQYF---YS 475

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 41.9 bits (98), Expect = 7e-05
 Identities = 16/95 (16%), Positives = 31/95 (32%), Gaps = 14/95 (14%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-- 223
           M          V + GLP   + + +  F S              D    V+  + ++  
Sbjct: 36  MLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDC---------TIHDGAAGVHFIYTREGR 86

Query: 224 ---FAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
               AFVE+ + ++   A+  D        + V +
Sbjct: 87  QSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFK 121

>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 = 39.6 bits (92), Expect = 4e-04
 Identities = 17/96 (17%), Positives = 34/96 (35%), Gaps = 11/96 (11%)

Query: 297 VFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           V + GLP+  +   ++  L          G   +  R+ G   G  F          +A 
Sbjct: 47  VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMAL 105

Query: 354 AALNGLKMGDKTLTVRRATASSGQSKTEQESILAQA 389
              +   MG + + V ++       +TE + +L  +
Sbjct: 106 -KKDRESMGHRYIEVFKS------HRTEMDWVLKHS 134

>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 = 40.6 bits (95), Expect = 1e-04
 Identities = 19/85 (22%), Positives = 27/85 (31%), Gaps = 14/85 (16%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
           R   RV V GLPP  + Q +     +            GD V    + +      VE   
Sbjct: 14  RSENRVVVSGLPPSGSWQDLKDHMREA-----------GD-VCYADV-YRDGTGVVEFVR 60

Query: 232 VEEASNAMA-LDGIIFEGVAVRVRR 255
            E+ + A+  LD   F         
Sbjct: 61  KEDMTYAVRKLDNTKFRSHEGETAY 85

>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 = 39.5 bits (92), Expect = 3e-04
 Identities = 20/96 (20%), Positives = 34/96 (35%), Gaps = 16/96 (16%)

Query: 168 QQATRHARRVYVGGLP-PLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAF 226
            Q     R +++  LP    ++ A+                 P   + N  +   K  AF
Sbjct: 19  DQKQELGRVIHLSNLPHSGYSDSAVLKLAE------------PYGKIKNYILMRMKSQAF 66

Query: 227 VEMRTVEEASNAM---ALDGIIFEGVAVRVRRPTDY 259
           +EM T E+A   +       + F+G  V+V     Y
Sbjct: 67  IEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY 102

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	522
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
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.97
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.97
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.97
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.97
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.97
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.97
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.96
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.96
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.96
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	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
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.96
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.96
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.95
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.95
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.95
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.95
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.95
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.95
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.94
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.94
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.93
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.93
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.87
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.86
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.83
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.83
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.8
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.79
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.79
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.78
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.78
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.77
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.77
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.77
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.76
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.76
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.76
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.76
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.76
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.76
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.75
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.75
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.75
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.75
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.75
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.75
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.75
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.75
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.75
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.75
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.74
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.74
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.74
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.74
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.74
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.74
2div_A	99	TRNA selenocysteine associated protein; structural	99.74
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.74
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.74
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.73
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.73
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.73
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.73
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.73
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.73
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.73
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.73
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.73
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.73
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.73
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.72
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.72
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.72
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.72
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.72
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.72
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.72
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.72
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.72
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.72
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.72
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.72
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.72
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.72
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.72
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.72
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.72
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.72
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.71
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.71
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.71
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.71
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.71
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.71
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.71
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.71
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.71
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.71
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.71
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.71
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.7
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.7
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.7
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.7
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.7
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.7
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.69
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.69
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.69
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.69
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.69
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.69
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.69
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.69
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.68
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.68
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.68
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.68
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.68
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.68
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.67
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.67
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.67
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.67
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.67
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.67
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.67
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.67
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.67
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.66
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.66
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.66
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.66
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.66
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.66
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.66
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.65
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.65
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.65
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.65
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.65
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.65
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.65
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.64
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.64
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.64
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.64
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.64
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.64
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.64
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.64
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.64
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.64
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.64
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.64
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.64
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.63
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.63
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.63
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.63
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.63
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.62
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.62
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.62
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.62
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.61
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.61
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.61
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.41
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.61
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.61
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.6
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.6
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.6
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.6
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.6
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.6
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.59
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.59
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.59
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.59
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.59
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.59
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.59
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.58
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.58
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.58
1x5p_A	97	Negative elongation factor E; structure genomics,	99.58
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.57
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.57
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.56
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.56
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.56
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.56
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.56
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.55
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.55
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.55
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.55
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.55
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.55
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.54
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.54
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.54
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.54
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.54
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.53
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.53
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.53
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.53
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.53
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.53
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.52
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.52
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.52
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.52
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.52
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.51
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.51
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.51
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.51
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.51
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.51
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.51
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.51
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.5
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.5
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.5
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.5
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.5
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.5
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.5
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.5
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.5
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.5
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.5
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.5
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.5
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.5
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.49
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.49
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.49
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.49
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.49
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.49
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.49
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.49
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.49
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.49
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.49
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.48
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.48
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.48
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.48
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.48
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.48
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.48
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.48
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.48
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.48
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.47
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.47
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.47
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.47
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.47
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.47
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.47
1x5p_A	97	Negative elongation factor E; structure genomics,	99.47
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.47
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.46
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.46
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.46
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.46
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.46
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.46
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.46
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.46
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.46
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.46
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.46
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.46
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.45
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.45
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.45
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.45
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.45
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.45
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.45
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.45
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.45
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.45
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.45
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.44
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.44
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.44
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.44
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.44
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.44
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.44
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.44
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.44
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.44
2div_A	99	TRNA selenocysteine associated protein; structural	99.43
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.43
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.43
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.43
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.43
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.43
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.42
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.42
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.42
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.42
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.42
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.42
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.42
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.41
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.41
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.4
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.39
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.39
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.39
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.39
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.39
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.39
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.38
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.38
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.37
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.36
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.36
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.36
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.36
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.35
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.35
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.35
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.34
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.34
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.34
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.33
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.33
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.33
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.31
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.3
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.3
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.3
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.29
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.29
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.29
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.28
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.27
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.27
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.24
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.24
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.24
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.19
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.14
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.12
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.04
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.0
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.96
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.88
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.86
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.78
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.58
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.54
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.47
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.09
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.8
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.63
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.54
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.38
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.29
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.08
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.92
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.85
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.24
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.91
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.71
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.55
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.05
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	94.67
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	94.41
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	93.82
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	93.39
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	86.09

>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=1.6e-41  Score=326.16  Aligned_cols=247  Identities=23%  Similarity=0.305  Sum_probs=211.4

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      .....++|||+|||+++|+++|+++|..||             |..+.++.++|||||+|.+.++|..|+ .+++..|.|
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-------------i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g   84 (284)
T 3smz_A           18 QFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------------LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRE   84 (284)
T ss_dssp             HHHCCCEEEEECCCTTCCHHHHHHHTTTSC-------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHcC-------------CEEEEEecCCCEEEEEeCCHHHHHHHHHHcCCCeeCC
Confidence            345678999999999999999999999997             456667899999999999999999999 699999999


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEee
Q 009944          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (522)
Q Consensus       249 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~  328 (522)
                      +.|.|.+..                                   ...+|||+|||..+++++|.++|+.||.|..+.++.
T Consensus        85 ~~i~v~~~~-----------------------------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~  129 (284)
T 3smz_A           85 RELSVQLQP-----------------------------------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY  129 (284)
T ss_dssp             EECEEEECC-----------------------------------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEE
T ss_pred             eEEEEEecC-----------------------------------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEe
Confidence            999998732                                   225899999999999999999999999999999999


Q ss_pred             CCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccC
Q 009944          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTL  408 (522)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  408 (522)
                      ++.+|.++|||||+|.+.++|.+|+..|+|..|.|+.|.|.++.+......                             
T Consensus       130 ~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~-----------------------------  180 (284)
T 3smz_A          130 SERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPA-----------------------------  180 (284)
T ss_dssp             CTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGCCTT-----------------------------
T ss_pred             eCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCCcc-----------------------------
Confidence            988999999999999999999999999999999999999999966321110                             


Q ss_pred             CCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhH
Q 009944          409 GGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGC  488 (522)
Q Consensus       409 g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A  488 (522)
                           ........|.+|+..++.+            ++|+++|++||.|..|.|+.+. +|.+   +|+|||+|.+.++|
T Consensus       181 -----~~~~~~l~v~nlp~~~~~~------------~~l~~~f~~~G~i~~v~i~~~~-~g~~---~g~afV~f~~~~~A  239 (284)
T 3smz_A          181 -----LLHSRCLCVDRLPPGFNDV------------DALCRALSAVHSPTFCQLACGQ-DGQL---KGFAVLEYETAEMA  239 (284)
T ss_dssp             -----TTSCSEEEEECCCTTCCCH------------HHHHHHTCSSSCCSEEEEEECS-SCCE---EEEEEEECSSHHHH
T ss_pred             -----cCCccEEEEecCCcccCCH------------HHHHHHhhCCCCeEEEEEEECC-CCCc---ccEEEEEeCCHHHH
Confidence                 0111333444444443111            4999999999999999998876 4543   68999999999999


Q ss_pred             HHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          489 ATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       489 ~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      .+|+..|||..|+|++|.|.|+....
T Consensus       240 ~~A~~~l~g~~~~g~~l~v~~a~~~~  265 (284)
T 3smz_A          240 EEAQQQADGLSLGGSHLRVSFCAPGP  265 (284)
T ss_dssp             HHHHHHHTTCEETTEECEEEECCSSS
T ss_pred             HHHHHHhCCCccCCeEEEEEEecCCC
Confidence            99999999999999999999998754

>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=3.2e-41  Score=325.47  Aligned_cols=249  Identities=16%  Similarity=0.241  Sum_probs=199.8

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC----CCcEEEEEEeCHHHHHHHHHhcCc
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH----EKKFAFVEMRTVEEASNAMALDGI  244 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~----~~g~afV~f~~~~~a~~a~~~~~~  244 (522)
                      ......++|||+|||+.+|+++|+++|..||.            |..+.+..    ++|||||+|.+.++|.+|+++++.
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~~~~~  103 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGP------------IIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK  103 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSC------------EEEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEECCCCCcEEEEEEECCHHHHHHHHHhCCc
Confidence            34566889999999999999999999999997            45554433    589999999999999999999999


Q ss_pred             eecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcC-CceE
Q 009944          245 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-TLHG  323 (522)
Q Consensus       245 ~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G-~i~~  323 (522)
                      .|.|+.|.|.++                                    ..++|||+|||..+++++|.++|+.|| .|..
T Consensus       104 ~~~g~~i~v~~~------------------------------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~  147 (292)
T 2ghp_A          104 VVGQNEIIVSHL------------------------------------TECTLWMTNFPPSYTQRNIRDLLQDINVVALS  147 (292)
T ss_dssp             EETTEECEEEEC------------------------------------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCE
T ss_pred             EeCCcEEEEEEC------------------------------------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEE
Confidence            999999999863                                    236899999999999999999999999 9999


Q ss_pred             EEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhcc
Q 009944          324 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTS  403 (522)
Q Consensus       324 v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  403 (522)
                      |.++.+.. |.++|||||+|.+.++|.+|+..|+|..|.|+.|.|.++.+.......                       
T Consensus       148 v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~-----------------------  203 (292)
T 2ghp_A          148 IRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRT-----------------------  203 (292)
T ss_dssp             EECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC-----------------------------
T ss_pred             EEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccc-----------------------
Confidence            99998864 889999999999999999999999999999999999999764322111                       


Q ss_pred             CCccCCCCcCCCCCCcceEEEeeCC-CCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCC-CCCCCCCccEEEEE
Q 009944          404 GMNTLGGGMSLFGETLAKVLCLTEA-ITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQ-NGGETPGVGKVFLE  481 (522)
Q Consensus       404 ~~~~~g~~~~~~~~~~~~v~~l~~~-~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~-~g~~~~g~G~afV~  481 (522)
                             .........+.|.+|+.. ++.+             +|+++|++||.|..|.|+.+.. +|.+   +|+|||+
T Consensus       204 -------~~~~~~~~~l~v~nlp~~~~t~~-------------~l~~~F~~~G~v~~v~i~~~~~~tg~~---~g~afV~  260 (292)
T 2ghp_A          204 -------DSATLEGREIMIRNLSTELLDEN-------------LLRESFEGFGSIEKINIPAGQKEHSFN---NCCAFMV  260 (292)
T ss_dssp             ----------CCTTTEEEEEEECTTTCCHH-------------HHHHHHGGGSCEEEEECCSCCC---CC---CEEEEEE
T ss_pred             -------cccCCCCceEEEECCCcccCCHH-------------HHHHHHhccCCeeEEEEEecCCcCCCC---ceEEEEE
Confidence                   000111245556666655 5544             9999999999999999999765 3544   6899999


Q ss_pred             ecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          482 YYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       482 F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      |.+.++|.+|+ .|||..|+|++|.|.|+..+
T Consensus       261 F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          261 FENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             ESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             eCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            99999999999 99999999999999998764

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=100.00  E-value=1.4e-31  Score=242.66  Aligned_cols=193  Identities=46%  Similarity=0.798  Sum_probs=160.4

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~  252 (522)
                      ..++|||+|||+.+|+++|+++|..||.|.+... .+...|.++.++.++|||||+|.+.++|.+|+.+++..|.|+.|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~-~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al~l~g~~~~g~~i~   81 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQ-APGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLK   81 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCS-SSSCSEEEEEEETTTTEEEEEESCSHHHHHHGGGTTEEETTEEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhccccc-CCCCceEEeEecCCCCEEEEEeCCHHHHHHHHHhcCCEEcCceEE
Confidence            4689999999999999999999999998876432 223468999999999999999999999999999999999999999


Q ss_pred             EecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCC
Q 009944          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (522)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~  332 (522)
                      |.++..+.........+....+         ...........++|||+|||..+++++|+++|++||.|..|.++.++.+
T Consensus        82 v~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~  152 (198)
T 2yh0_A           82 IRRPHDYQPLPGMSENPSVYVP---------GVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSAT  152 (198)
T ss_dssp             EECCCCCCCCCCSSSCSSCCCT---------TSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTT
T ss_pred             EeCCCCCCCCCCCcCCCcCCCC---------CCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCC
Confidence            9998766433211111000000         0011122355689999999999999999999999999999999999889


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCC
Q 009944          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (522)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (522)
                      |.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.++.
T Consensus       153 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          153 GLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             CSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            9999999999999999999999999999999999999998754

>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=100.00  E-value=6.9e-32  Score=238.91  Aligned_cols=170  Identities=52%  Similarity=0.917  Sum_probs=152.6

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~  252 (522)
                      +.++|||+|||+++|+++|+++|.+||.+.+... .++..|.++.++.++|||||+|.+.++|.+|+.+++..+.|++|.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~-~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~   81 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQ-APGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLK   81 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCS-SSSCSEEEEEEETTTTEEEEEESSHHHHHHHGGGTTCEETTEECE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhccccc-CCCCceeeeEecCCCCEEEEEeCCHHHHHHHHHhCCcEecCceee
Confidence            5689999999999999999999999988765321 223368999999999999999999999999999999999999999


Q ss_pred             EecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCC
Q 009944          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (522)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~  332 (522)
                      |.++..+..                             .....+|||+|||..+++++|+++|++||.|..|.++.++.+
T Consensus        82 v~~~~~~~~-----------------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~  132 (172)
T 2g4b_A           82 IRRPHDYQP-----------------------------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSAT  132 (172)
T ss_dssp             EECCSSCCC-----------------------------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTT
T ss_pred             ecCCcccCC-----------------------------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCC
Confidence            998654432                             122468999999999999999999999999999999999889


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      |.++|||||+|.+.++|.+|+..|||..|+|+.|.|.||.
T Consensus       133 g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          133 GLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             CSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            9999999999999999999999999999999999999973

>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=9.3e-31  Score=230.16  Aligned_cols=159  Identities=23%  Similarity=0.427  Sum_probs=142.2

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      ++|||+|||+++|+++|+++|..||.            |..+.+     +.++|||||+|.+.++|.+|+ .+++..+.|
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~------------i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g   68 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGP------------IANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIEN   68 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSC------------EEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCC------------eEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCC
Confidence            58999999999999999999999997            444544     456799999999999999999 799999999


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEee
Q 009944          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (522)
Q Consensus       249 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~  328 (522)
                      +.|.|.++......                           ......+|||+|||..+++++|+++|+.||.|..+.++.
T Consensus        69 ~~i~v~~~~~~~~~---------------------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~  121 (166)
T 3md3_A           69 NIVKINWAFQSQQS---------------------------SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW  121 (166)
T ss_dssp             EECEEEECCCCCCC---------------------------CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEE
T ss_pred             CeeEEEEcCCCCCC---------------------------CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEe
Confidence            99999986543211                           123446899999999999999999999999999999999


Q ss_pred             CCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.|+.
T Consensus       122 ~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             CTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             cCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            98899999999999999999999999999999999999999985

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.97  E-value=6.2e-31  Score=240.66  Aligned_cols=167  Identities=20%  Similarity=0.360  Sum_probs=139.7

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      .+.++|||+|||+++|+++|+++|.+||.|..+.      ++.+..++.++|||||+|.+.++|.+|+ .+++..+.|+.
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~------i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~   86 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIR------VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP   86 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEE------EecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcc
Confidence            4467999999999999999999999999843210      0111123556899999999999999999 79999999999


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCC
Q 009944          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (522)
Q Consensus       251 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~  330 (522)
                      |++.++.......                           .....+|||+|||..+++++|+++|+.||.|..|.|+.+.
T Consensus        87 i~~~~~~~~~~~~---------------------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~  139 (213)
T 4f02_A           87 VRIMWSQRDPSLR---------------------------KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE  139 (213)
T ss_dssp             CEEEECCCCTHHH---------------------------HHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET
T ss_pred             ccccccccccccc---------------------------ccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC
Confidence            9998765433211                           1123589999999999999999999999999999999884


Q ss_pred             CCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                        +.++|||||+|.+.++|.+||+.|||..|+|+.|.|.++.+
T Consensus       140 --~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          140 --NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             --TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             --CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence              55799999999999999999999999999999999999965

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.97  E-value=1.8e-30  Score=230.41  Aligned_cols=165  Identities=18%  Similarity=0.361  Sum_probs=146.3

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCce
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~  250 (522)
                      ....++|||+|||+.+|+++|+++|..||.+.+       ..+.+..++.++|||||+|.+.++|.+|+++++..|.|++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-------~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~   82 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-------LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNE   82 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-------CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-------EEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeE
Confidence            445789999999999999999999999999875       1377888999999999999999999999999999999999


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCC
Q 009944          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (522)
Q Consensus       251 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~  330 (522)
                      |.|.++......                           ......+|||+|||..+++++|+++|+.||.|..+     .
T Consensus        83 l~v~~~~~~~~~---------------------------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~  130 (175)
T 1fje_B           83 IKLEKPKGRDSK---------------------------KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----S  130 (175)
T ss_dssp             EEEECCCCSSCS---------------------------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----C
T ss_pred             EEEecCCCcccc---------------------------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----c
Confidence            999987643211                           11234689999999999999999999999988665     4


Q ss_pred             CCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      .+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+.++
T Consensus       131 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          131 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             SSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             CCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            58899999999999999999999999999999999999999764

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.97  E-value=5.2e-31  Score=241.21  Aligned_cols=169  Identities=17%  Similarity=0.234  Sum_probs=142.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      .+.++|||+|||+.+|+++|+++|++||.|..|.|++++.+|.++|||||+|.+.++|.+||..+++..+.|+.|.+.++
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            34578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHh
Q 009944          372 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  451 (522)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f  451 (522)
                      .....   .  .             . .                ....+.|.+|+..+++             ++|+++|
T Consensus        93 ~~~~~---~--~-------------~-~----------------~~~~l~v~nl~~~~t~-------------~~l~~~F  124 (213)
T 4f02_A           93 QRDPS---L--R-------------K-S----------------GVGNIFIKNLDKSIDN-------------KALYDTF  124 (213)
T ss_dssp             CCCTH---H--H-------------H-H----------------CTTEEEEESCCTTCCH-------------HHHHHHH
T ss_pred             ccccc---c--c-------------c-c----------------ccccceECCcccccHH-------------HHHHHHH
Confidence            65210   0  0             0 0                0133445555555444             4999999


Q ss_pred             hccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          452 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       452 ~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++||.|..|.|+.+...     .+|+|||+|.+.++|.+||+.|||..|+|++|.|.|+...
T Consensus       125 ~~~G~i~~~~i~~d~~~-----~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          125 SAFGNILSCKVVCDENG-----SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             GGGSCEEEEEEEEETTE-----EEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             hhcCCeEEEEeeccCCC-----CceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            99999999999887522     3689999999999999999999999999999999998753

>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=1.6e-30  Score=229.20  Aligned_cols=164  Identities=20%  Similarity=0.325  Sum_probs=140.8

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~  251 (522)
                      ..++|||+|||+++|+++|+++|..||.|....      .+.+...+.++|||||+|.+.++|..|+ .+++..+.|++|
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l   75 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCR------IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL   75 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEE------CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE------EEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEE
Confidence            357899999999999999999999999743211      0111123446799999999999999999 599999999999


Q ss_pred             EEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCC
Q 009944          252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD  331 (522)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~  331 (522)
                      .|.++.....                             .....+|||+|||..+++++|+++|++||.|..+.++.++.
T Consensus        76 ~v~~~~~~~~-----------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~  126 (168)
T 1b7f_A           76 KVSYARPGGE-----------------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL  126 (168)
T ss_dssp             EEEECCCCSS-----------------------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTT
T ss_pred             EEEecCCCcc-----------------------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCC
Confidence            9998654321                             12346899999999999999999999999999999999988


Q ss_pred             CCCcceEEEEEEcChHHHHHHHHHHcCCccCC--eEEEEEEc
Q 009944          332 TGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  371 (522)
Q Consensus       332 ~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~  371 (522)
                      +|.++|||||+|.+.++|.+|+..|||..|.|  ++|.|.||
T Consensus       127 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          127 TGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            99999999999999999999999999999977  99999986

>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=4e-30  Score=232.68  Aligned_cols=171  Identities=22%  Similarity=0.422  Sum_probs=142.1

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEEeCHHHHHHHHHhcC
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDG  243 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~a~~~~~  243 (522)
                      .....++|||+|||+++|+++|+++|..||.|            ..+.+      +.++|||||+|.+.++|.+|+++++
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i------------~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~   76 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTL------------TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP   76 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCE------------EEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCE------------EEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCC
Confidence            34567899999999999999999999999984            33332      4468999999999999999998899


Q ss_pred             ceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceE
Q 009944          244 IIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG  323 (522)
Q Consensus       244 ~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~  323 (522)
                      ..|.|+.|.|.++........                       .......++|||+|||..+++++|+++|+.||.|..
T Consensus        77 ~~~~g~~l~v~~~~~~~~~~~-----------------------~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~  133 (196)
T 1l3k_A           77 HKVDGRVVEPKRAVSREDSQR-----------------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV  133 (196)
T ss_dssp             CEETTEECEEEECCC----------------------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEE
T ss_pred             CEECCEEeeeecccCcccccc-----------------------cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEE
Confidence            999999999998654432110                       011234479999999999999999999999999999


Q ss_pred             EEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCC
Q 009944          324 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  376 (522)
Q Consensus       324 v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~  376 (522)
                      |.++.++.+|.++|||||+|.+.++|.+||.. +|..|.|+.|.|.++.++..
T Consensus       134 v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~  185 (196)
T 1l3k_A          134 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQE  185 (196)
T ss_dssp             EEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC----
T ss_pred             EEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhH
Confidence            99999988999999999999999999999986 89999999999999977543

>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=4.3e-30  Score=226.43  Aligned_cols=164  Identities=25%  Similarity=0.365  Sum_probs=141.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+
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            46999999999999999999999999999999999988999999999999999999999999999999999999999876


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhc
Q 009944          374 SSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGK  453 (522)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~  453 (522)
                      ....                                     .......|.+|+..++.             ++|+++|++
T Consensus        83 ~~~~-------------------------------------~~~~~l~v~nl~~~~t~-------------~~l~~~f~~  112 (168)
T 1b7f_A           83 GGES-------------------------------------IKDTNLYVTNLPRTITD-------------DQLDTIFGK  112 (168)
T ss_dssp             CSST-------------------------------------TTTCEEEEESCCTTCCH-------------HHHHHHHTS
T ss_pred             Cccc-------------------------------------CCCCCEEEeCCCCCCCH-------------HHHHHhhhc
Confidence            3211                                     00123333344443333             499999999


Q ss_pred             cCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCC--eEEEEEEe
Q 009944          454 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYY  510 (522)
Q Consensus       454 ~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~G--r~l~v~~~  510 (522)
                      ||.|..|.++.+..++.+   +|+|||+|.+.++|.+|++.|||..|.|  ++|.|.|+
T Consensus       113 ~G~i~~~~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          113 YGSIVQKNILRDKLTGRP---RGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             SSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCcEEEEEEEEcCCCCCc---ceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            999999999998766654   6899999999999999999999999988  99999985

>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=7.5e-30  Score=224.57  Aligned_cols=164  Identities=28%  Similarity=0.455  Sum_probs=141.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||+.+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+
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            36899999999999999999999999999999999988999999999999999999999999999999999999999865


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhc
Q 009944          374 SSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGK  453 (522)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~  453 (522)
                      ....                                     .......|.+|+..++.             ++|+++|++
T Consensus        82 ~~~~-------------------------------------~~~~~l~v~nl~~~~t~-------------~~l~~~f~~  111 (167)
T 1fxl_A           82 SSAS-------------------------------------IRDANLYVSGLPKTMTQ-------------KELEQLFSQ  111 (167)
T ss_dssp             CCGG-------------------------------------GTTCEEEEESCCTTCCH-------------HHHHHHHGG
T ss_pred             Cccc-------------------------------------CCCCcEEECCCCCcCCH-------------HHHHHHHHh
Confidence            3210                                     00133344444444433             499999999


Q ss_pred             cCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeE--EEEEEe
Q 009944          454 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT--VNAFYY  510 (522)
Q Consensus       454 ~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~--l~v~~~  510 (522)
                      ||.|..|.++.+..+|.+   .|+|||+|.+.++|.+|++.|||..|+|+.  |.|.|+
T Consensus       112 ~G~i~~~~i~~~~~~g~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          112 YGRIITSRILVDQVTGVS---RGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             GSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             cCCEeEEEEEecCCCCCc---cceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            999999999988766654   689999999999999999999999999975  888885

>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=1.5e-29  Score=222.68  Aligned_cols=157  Identities=22%  Similarity=0.387  Sum_probs=138.9

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEEeCHHHHHHHH-HhcCcee
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~a~-~~~~~~~  246 (522)
                      .++|||+|||+.+|+++|+++|..||.|            ..+.+      +.++|||||+|.+.++|..|+ .+++..+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i------------~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~   69 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEI------------ESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL   69 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCE------------EEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCe------------EEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            4789999999999999999999999974            44443      344699999999999999999 5999999


Q ss_pred             cCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEE
Q 009944          247 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (522)
Q Consensus       247 ~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~  326 (522)
                      .|+.|.|.++......                             ....+|||+|||..+++++|+++|++||.|..+.+
T Consensus        70 ~g~~l~v~~~~~~~~~-----------------------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i  120 (167)
T 1fxl_A           70 QTKTIKVSYARPSSAS-----------------------------IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI  120 (167)
T ss_dssp             TTEECEEEECCCCCGG-----------------------------GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEE
T ss_pred             CCceEEEEecCCCccc-----------------------------CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEE
Confidence            9999999986543211                             22368999999999999999999999999999999


Q ss_pred             eeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeE--EEEEEc
Q 009944          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT--LTVRRA  371 (522)
Q Consensus       327 ~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~--l~v~~~  371 (522)
                      +.+..+|.++|||||+|.+.++|.+|+..|||..|.|+.  |.|.||
T Consensus       121 ~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            999889999999999999999999999999999999964  888875

>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=6.7e-30  Score=224.65  Aligned_cols=166  Identities=18%  Similarity=0.286  Sum_probs=139.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      ++|||+|||..+++++|+++|+.||.|..|.++.++ ++.++|||||+|.+.++|.+|+..|+|..+.|+.|.|.++.+.
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            489999999999999999999999999999999986 5789999999999999999999999999999999999998664


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhcc
Q 009944          375 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  454 (522)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~  454 (522)
                      .....                                   .......|.+|+..++.             ++|+++|++|
T Consensus        80 ~~~~~-----------------------------------~~~~~l~v~nl~~~~t~-------------~~l~~~f~~~  111 (166)
T 3md3_A           80 QQSSS-----------------------------------DDTFNLFVGDLNVNVDD-------------ETLRNAFKDF  111 (166)
T ss_dssp             CCCCC-----------------------------------TTCEEEEEESCCTTCCH-------------HHHHHHHTTS
T ss_pred             CCCCC-----------------------------------CCCceEEECCCCCCCCH-------------HHHHHHHhcc
Confidence            32110                                   00122333334333333             4999999999


Q ss_pred             CCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          455 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       455 G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      |.|..|.++.+..+|.+   +|+|||+|.+.++|.+|+..|||..|+|++|.|.|+.+
T Consensus       112 G~i~~~~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          112 PSYLSGHVMWDMQTGSS---RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             TTEEEEEEEECTTTCCE---EEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             CCeeEEEEEecCCCCCc---ceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            99999999988767654   78999999999999999999999999999999999864

>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=1e-29  Score=233.75  Aligned_cols=177  Identities=26%  Similarity=0.424  Sum_probs=148.2

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE------ecCCCcEEEEEEeCHHHHHHHH-Hh
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY------INHEKKFAFVEMRTVEEASNAM-AL  241 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~------~~~~~g~afV~f~~~~~a~~a~-~~  241 (522)
                      ......++|||+|||+++|+++|+++|..||.|            ..+.      .+.++|||||+|.+.++|.+|+ .+
T Consensus        23 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i------------~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l   90 (216)
T 2qfj_A           23 GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPI------------KSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM   90 (216)
T ss_dssp             HHHHHHTEEEEECCCTTCCHHHHHHHHGGGSCE------------EEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHH
T ss_pred             cccCcCCEEEEECCCCCCCHHHHHHHHHhCCCE------------EEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHc
Confidence            455678899999999999999999999999974            4443      3557899999999999999999 59


Q ss_pred             cCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCc
Q 009944          242 DGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL  321 (522)
Q Consensus       242 ~~~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i  321 (522)
                      ++..|.|+.|.|.++...........          .        ........++|||+|||..+++++|+++|++||.|
T Consensus        91 ~~~~~~g~~l~v~~~~~~~~~~~~~~----------~--------~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v  152 (216)
T 2qfj_A           91 NSVMLGGRNIKVGRPSNIGQAQPIID----------Q--------LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKI  152 (216)
T ss_dssp             SSCCCC-CCCEEECCSCCGGGHHHHH----------H--------HHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCE
T ss_pred             cCCeeCCeeEEEecCCCccccchhhh----------h--------hhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCe
Confidence            99999999999988665432110000          0        00011334799999999999999999999999999


Q ss_pred             eEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCC
Q 009944          322 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (522)
Q Consensus       322 ~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (522)
                      ..|.++.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.|+.++.
T Consensus       153 ~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          153 KSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             EEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             eEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            999999998899999999999999999999999999999999999999998753

>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=6.8e-31  Score=231.29  Aligned_cols=159  Identities=22%  Similarity=0.496  Sum_probs=139.7

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEEeCHHHHHHHHHhcCcee
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDGIIF  246 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~a~~~~~~~~  246 (522)
                      +.++|||+|||+++|+++|+++|..||.            |..+.+      +.++|||||+|.+.++|.+|++ ++..+
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~   68 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGT------------VTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-TQHIL   68 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCC------------EEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH-SCCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEEECCCCCCccceEEEEEccHHHHHHHHh-ccccc
Confidence            4689999999999999999999999997            444443      5568999999999999999996 46789


Q ss_pred             cCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEE
Q 009944          247 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (522)
Q Consensus       247 ~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~  326 (522)
                      .|+.|.|.++......                             ....+|||+|||..+++++|+++|++||.|..|.+
T Consensus        69 ~g~~i~v~~~~~~~~~-----------------------------~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i  119 (167)
T 2cjk_A           69 DGKVIDPKRAIPRDEQ-----------------------------DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQL  119 (167)
T ss_dssp             TTEECCCEECCCHHHH-----------------------------HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEEC
T ss_pred             CCeEcccccccchhhc-----------------------------cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEE
Confidence            9999998875432111                             12358999999999999999999999999999999


Q ss_pred             eeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       327 ~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      +.++.+|.++|||||+|.+.++|.+|++ ++|..|.|+.|.|.|+.++
T Consensus       120 ~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          120 MLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             CCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             EEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            9998899999999999999999999998 8999999999999999764

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

Probab=99.96  E-value=3.7e-29  Score=229.98  Aligned_cols=179  Identities=21%  Similarity=0.372  Sum_probs=142.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|+|..|.|+.|.|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            36899999999999999999999999999999999988999999999999999999999999999999999999998765


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhc
Q 009944          374 SSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGK  453 (522)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~  453 (522)
                      .....     ....      ......               .....+.|.+|+..++.             ++|+++|++
T Consensus       108 ~~~~~-----~~~~------~~~~~~---------------~~~~~l~v~nlp~~~t~-------------~~l~~~f~~  148 (216)
T 2qfj_A          108 IGQAQ-----PIID------QLAEEA---------------RAFNRIYVASVHQDLSD-------------DDIKSVFEA  148 (216)
T ss_dssp             CGGGH-----HHHH------HHHHHH---------------TTSCEEEEECCCTTCCH-------------HHHHHHHTT
T ss_pred             ccccc-----hhhh------hhhccc---------------CCCcEEEEeCCCCcCCH-------------HHHHHHHhc
Confidence            32110     0000      000000               00133334444444333             499999999


Q ss_pred             cCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          454 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       454 ~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ||.|..|.|+.+..+|..   +|+|||+|.+.++|.+|+..|||..|+|++|.|.|+....
T Consensus       149 ~G~v~~v~i~~~~~~g~~---~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          149 FGKIKSATLARDPTTGKH---KGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             SSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             cCCeeEEEEEecCCCCCc---CceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            999999999998777654   7899999999999999999999999999999999987643

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.96  E-value=2.6e-29  Score=227.28  Aligned_cols=174  Identities=20%  Similarity=0.317  Sum_probs=140.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+|+++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+||+. ++..|.|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecc
Confidence            3457999999999999999999999999999999999998999999999999999999999985 899999999999998


Q ss_pred             cCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHh
Q 009944          372 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  451 (522)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f  451 (522)
                      ........+.                               .......+.|.+|+..++.             ++|+++|
T Consensus        90 ~~~~~~~~~~-------------------------------~~~~~~~l~V~nLp~~~t~-------------~~l~~~F  125 (196)
T 1l3k_A           90 VSREDSQRPG-------------------------------AHLTVKKIFVGGIKEDTEE-------------HHLRDYF  125 (196)
T ss_dssp             CC------------------------------------------CCSEEEEECCTTTCCH-------------HHHHHHH
T ss_pred             cCcccccccc-------------------------------cCCCcceEEEeCCCCCCCH-------------HHHHHHH
Confidence            6532211000                               0000123334444444333             4999999


Q ss_pred             hccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          452 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       452 ~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++||.|..|.|+.+..+|.+   +|+|||+|.+.++|.+|+.. +|..|+|++|.|.|+....
T Consensus       126 ~~~G~i~~v~i~~~~~~g~~---~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~  184 (196)
T 1l3k_A          126 EQYGKIEVIEIMTDRGSGKK---RGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQ  184 (196)
T ss_dssp             TTTSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC---
T ss_pred             hcCCCeEEEEEeecCCCCCc---cceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChh
Confidence            99999999999998767654   78999999999999999986 8999999999999987654

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.96  E-value=7.2e-29  Score=220.09  Aligned_cols=165  Identities=21%  Similarity=0.324  Sum_probs=134.7

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec--CCCcEEEEEEeCHHHHHHHH-HhcCceec--
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--HEKKFAFVEMRTVEEASNAM-ALDGIIFE--  247 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~--~~~g~afV~f~~~~~a~~a~-~~~~~~~~--  247 (522)
                      +.++|||+|||+++|+++|+++|.+||.|....      .+.+...+  .++|||||+|.+.++|.+|+ .+++..+.  
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~------i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~   75 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEIN------VLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPG   75 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEE------EEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTT
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE------EEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccC
Confidence            357999999999999999999999999853210      01111111  57899999999999999999 69998776  


Q ss_pred             -CceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEE
Q 009944          248 -GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (522)
Q Consensus       248 -g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~  326 (522)
                       ++.+.+.++.....                            ......+|||+|||..+++++|+++|++||.|..|.+
T Consensus        76 ~~~~~~~~~~~~~~~----------------------------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~  127 (175)
T 3nmr_A           76 MHHPIQMKPADSEKN----------------------------NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRI  127 (175)
T ss_dssp             CSSCCEEEECGGGCC----------------------------SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEE
T ss_pred             CccceEEcccccccc----------------------------ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEE
Confidence             57777776432211                            0123468999999999999999999999999999999


Q ss_pred             eeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC---CeEEEEEEcc
Q 009944          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG---DKTLTVRRAT  372 (522)
Q Consensus       327 ~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~---g~~l~v~~~~  372 (522)
                      +.++ +|.++|||||+|.+.++|.+|+..|||..+.   |++|.|.||.
T Consensus       128 ~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          128 LRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             EECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             EECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            9985 6999999999999999999999999998775   4999999973

>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=1.8e-28  Score=221.63  Aligned_cols=185  Identities=15%  Similarity=0.112  Sum_probs=138.1

Q ss_pred             ccceeEEeCCC-ccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          173 HARRVYVGGLP-PLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       173 ~~~~v~v~nlp-~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~-~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ..++|||+||| ..+|+++|+++|..||.            |.++.+.. .+|||||+|.+.++|..|+ .|||..|.|+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~------------v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~   70 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGN------------VEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQ   70 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSC------------EEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCC------------eEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            35689999999 79999999999999997            66666554 5799999999999999999 6999999999


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCC-cccccccCCC-------CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCc
Q 009944          250 AVRVRRPTDYNPTLAAALGPGQPSPN-LNLAAVGLAS-------GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL  321 (522)
Q Consensus       250 ~~~v~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~-------~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i  321 (522)
                      +|.|.+++.................. ..........       .......+..+|||+|||+.+++++|+++|++||.|
T Consensus        71 ~l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v  150 (205)
T 3tyt_A           71 KMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVK  150 (205)
T ss_dssp             ECEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCC
T ss_pred             eEEEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCc
Confidence            99999876432110000000000000 0000000000       001112345789999999999999999999999998


Q ss_pred             --eEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCe----EEEEEEc
Q 009944          322 --HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK----TLTVRRA  371 (522)
Q Consensus       322 --~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~----~l~v~~~  371 (522)
                        ..|+++.+.  +..+|||||+|.+.++|.+||..|||..|.|.    ++.|.++
T Consensus       151 ~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          151 RPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             ceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence              889988774  56679999999999999999999999999876    6777765

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.96  E-value=2.4e-28  Score=216.76  Aligned_cols=165  Identities=19%  Similarity=0.322  Sum_probs=137.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCC--CcceEEEEEEcChHHHHHHHHHHcCCccC---CeEEEE
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG--NSKGYGFCVYQDPAVTDIACAALNGLKMG---DKTLTV  368 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g--~~~g~afV~f~~~~~A~~Al~~l~g~~~~---g~~l~v  368 (522)
                      .++|||+|||+.+++++|+++|++||.|..|.++.++.+|  .++|||||+|.+.++|.+|++.|+|..+.   ++.+.+
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            3689999999999999999999999999999999998776  89999999999999999999999998775   688888


Q ss_pred             EEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHH
Q 009944          369 RRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMR  448 (522)
Q Consensus       369 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~  448 (522)
                      .++........                                    ......|.+|+..++.             ++|+
T Consensus        83 ~~~~~~~~~~~------------------------------------~~~~l~v~nl~~~~t~-------------~~l~  113 (175)
T 3nmr_A           83 KPADSEKNNAV------------------------------------EDRKLFIGMISKKCTE-------------NDIR  113 (175)
T ss_dssp             EECGGGCCSCG------------------------------------GGSEEEEESCCTTCCH-------------HHHH
T ss_pred             ccccccccccC------------------------------------CCCeEEEcCCCCcCCH-------------HHHH
Confidence            88755322110                                    0133444445444444             4999


Q ss_pred             HHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccC---CeEEEEEEeC
Q 009944          449 EECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG---GNTVNAFYYP  511 (522)
Q Consensus       449 ~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~---Gr~l~v~~~~  511 (522)
                      ++|++||.|..|.++.+. +|.+   +|+|||+|.+.++|.+|++.|||..+.   |++|.|.|++
T Consensus       114 ~~F~~~G~i~~v~~~~~~-~g~~---~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          114 VMFSSFGQIEECRILRGP-DGLS---RGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HHHGGGSCEEEEEEEECT-TSCE---EEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             HHHHhCCCEEEEEEEECC-CCCE---EEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            999999999999999886 4543   689999999999999999999998776   4999999985

>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=3.2e-29  Score=220.53  Aligned_cols=164  Identities=20%  Similarity=0.337  Sum_probs=142.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+|+++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|+..  +..+.|+.|.|.++.+
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            36899999999999999999999999999999999988999999999999999999999984  6789999999999854


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhc
Q 009944          374 SSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGK  453 (522)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~  453 (522)
                      .     ..               .. .                .....|.+|+..++.+             +|+++|++
T Consensus        81 ~-----~~---------------~~-~----------------~~~l~V~nlp~~~t~~-------------~l~~~F~~  110 (167)
T 2cjk_A           81 R-----DE---------------QD-K----------------TGKIFVGGIGPDVRPK-------------EFEEFFSQ  110 (167)
T ss_dssp             H-----HH---------------HH-H----------------CEEEEEEEECTTCCHH-------------HHHHHHHT
T ss_pred             h-----hh---------------cc-C----------------CCeEEECCCCCCCCHH-------------HHHHHHHh
Confidence            1     00               00 0                1456666676665554             99999999


Q ss_pred             cCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          454 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       454 ~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ||.|..|.|+.+..+|.+   +|+|||+|.+.++|.+|++ |+|..|+|++|.|.|+...
T Consensus       111 ~G~i~~~~i~~~~~~g~~---~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          111 WGTIIDAQLMLDKDTGQS---RGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             TSCCSEEECCCSSSSSTT---SEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             CccEEEEEEEEcCCCCcc---ceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            999999999998777665   7899999999999999998 8999999999999998754

>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=1.2e-27  Score=221.33  Aligned_cols=187  Identities=19%  Similarity=0.203  Sum_probs=142.8

Q ss_pred             hcccceeEEeCCCc-cCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC-CcEEEEEEeCHHHHHHHH-HhcCceec
Q 009944          171 TRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-KKFAFVEMRTVEEASNAM-ALDGIIFE  247 (522)
Q Consensus       171 ~~~~~~v~v~nlp~-~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~-~g~afV~f~~~~~a~~a~-~~~~~~~~  247 (522)
                      ....++|||+|||+ .+|+++|+++|..||.            |..+.+... +|||||+|.+.++|.+|+ .+++..|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~------------i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~   98 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGD------------VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLH   98 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTC------------EEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCS
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCC------------eEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeEC
Confidence            34578999999999 9999999999999997            666666544 699999999999999999 59999999


Q ss_pred             CceEEEecCCCCCccccccCCCCCCCC------CcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcC-C
Q 009944          248 GVAVRVRRPTDYNPTLAAALGPGQPSP------NLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-T  320 (522)
Q Consensus       248 g~~~~v~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G-~  320 (522)
                      |+.|.|.++..................      ..................+.++|||+|||..+++++|+++|+.|| .
T Consensus        99 g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~  178 (229)
T 2adc_A           99 GKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGV  178 (229)
T ss_dssp             SSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCC
T ss_pred             CeEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCC
Confidence            999999987654322111000000000      000000000000011234468999999999999999999999999 9


Q ss_pred             ceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC-CeEEEEEEccCC
Q 009944          321 LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRATAS  374 (522)
Q Consensus       321 i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~~~~~  374 (522)
                      |..|.++..     .+|||||+|.+.++|.+|+..|+|..|. |+.|.|.|+.++
T Consensus       179 i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          179 VKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             EEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             eeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            999998653     3689999999999999999999999999 999999999763

>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=1.3e-27  Score=228.98  Aligned_cols=188  Identities=21%  Similarity=0.328  Sum_probs=140.8

Q ss_pred             hcccceeEEeCCCccCcHHHHH----HHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCce
Q 009944          171 TRHARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII  245 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~----~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~  245 (522)
                      ....++|||+|||+.+|+++|+    ++|..||.|..         |.....+.++|||||+|.+.++|.+|+ .|++..
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~---------v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   76 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILD---------ILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFP   76 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEE---------EEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCe
Confidence            4557899999999999999966    89999997432         222235678999999999999999999 799999


Q ss_pred             ecCceEEEecCCCCCccccccCCCCC-----------------------------------CCC----------------
Q 009944          246 FEGVAVRVRRPTDYNPTLAAALGPGQ-----------------------------------PSP----------------  274 (522)
Q Consensus       246 ~~g~~~~v~~~~~~~~~~~~~~~~~~-----------------------------------~~~----------------  274 (522)
                      |.|+.|+|.+++..........+...                                   +..                
T Consensus        77 ~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (282)
T 3pgw_A           77 FYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHH  156 (282)
T ss_pred             eCCcEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCccccccccccc
Confidence            99999999987654321100000000                                   000                


Q ss_pred             ----------CcccccccCCCC---------------------CCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceE
Q 009944          275 ----------NLNLAAVGLASG---------------------AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG  323 (522)
Q Consensus       275 ----------~~~~~~~~~~~~---------------------~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~  323 (522)
                                .......+....                     ........++|||+|||..+++++|+++|++||.|..
T Consensus       157 ~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~  236 (282)
T 3pgw_A          157 MPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKE  236 (282)
T ss_pred             CCCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEE
Confidence                      000000000000                     0012234578999999999999999999999999999


Q ss_pred             EEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC-CeEEEEEEcc
Q 009944          324 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRAT  372 (522)
Q Consensus       324 v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~~~  372 (522)
                      |.++.+.     +|||||+|.+.++|.+|+..|||..|. |+.|.|.|+.
T Consensus       237 v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          237 VRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            9998653     589999999999999999999999999 9999999984

>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=4.9e-28  Score=228.58  Aligned_cols=156  Identities=22%  Similarity=0.358  Sum_probs=141.5

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++|||+|||+++|+++|+++|..||.            |..+.+..++|||||+|.+.++|..|+ .+++..|.|+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~   86 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGE------------PSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSR   86 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCC------------CSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCC------------EEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcEECCc
Confidence            445679999999999999999999999997            667778889999999999999999999 5999999999


Q ss_pred             eEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeC
Q 009944          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (522)
Q Consensus       250 ~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~  329 (522)
                      .|.|.++..                                   ..+|||+|||..+|+++|+++|+.||.|..|.++.+
T Consensus        87 ~l~v~~a~~-----------------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~  131 (261)
T 3sde_A           87 PLRIRFATH-----------------------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD  131 (261)
T ss_dssp             ECEEEECCC-----------------------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE
T ss_pred             eeEeeeccc-----------------------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC
Confidence            999998532                                   358999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEEcChHHHHHHHHHHc-CCccC---CeEEEEEEccCC
Q 009944          330 RDTGNSKGYGFCVYQDPAVTDIACAALN-GLKMG---DKTLTVRRATAS  374 (522)
Q Consensus       330 ~~~g~~~g~afV~f~~~~~A~~Al~~l~-g~~~~---g~~l~v~~~~~~  374 (522)
                       .+|.++|||||+|.+.++|.+|+..|| |..+.   +++|.|.++...
T Consensus       132 -~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          132 -DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             -TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             -CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeecccc
Confidence             589999999999999999999999995 44544   999999998764

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.95  E-value=6.1e-27  Score=224.27  Aligned_cols=199  Identities=16%  Similarity=0.229  Sum_probs=138.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~----~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      ...++|||+|||..+++++|+    ++|+.||.|..|.+++   +|.++|||||+|.+.++|.+|++.|||..|.|+.|.
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   83 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   83 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            456799999999999999966    9999999999998885   688999999999999999999999999999999999


Q ss_pred             EEEccCCCCCCch--------HHHHHHH--HHHHHHHHHHHHhhccCC--------------------------------
Q 009944          368 VRRATASSGQSKT--------EQESILA--QAQQHIAIQKMALQTSGM--------------------------------  405 (522)
Q Consensus       368 v~~~~~~~~~~~~--------~~~~~~~--~~~~~~~~~~~~~~~~~~--------------------------------  405 (522)
                      |.|+.........        .......  ..................                                
T Consensus        84 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  163 (282)
T 3pgw_A           84 IQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPY  163 (282)
T ss_pred             EEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCC
Confidence            9999765421100        0000000  000000000000000000                                


Q ss_pred             -ccCC------CCc----------------------CCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCC
Q 009944          406 -NTLG------GGM----------------------SLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGT  456 (522)
Q Consensus       406 -~~~g------~~~----------------------~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~  456 (522)
                       ..++      ...                      ......+.+++.+.|+..          ..++++|+++|++||.
T Consensus       164 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~----------~~~~~~l~~~F~~~G~  233 (282)
T 3pgw_A          164 MPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPE----------ETNELMLSMLFNQFPG  233 (282)
T ss_pred             CCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCC----------cCCHHHHHHHHHhcCC
Confidence             0000      000                      001112233444444421          2233599999999999


Q ss_pred             eEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccC-CeEEEEEEeC
Q 009944          457 LVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG-GNTVNAFYYP  511 (522)
Q Consensus       457 I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~-Gr~l~v~~~~  511 (522)
                      |..|.|+.+.        .|+|||+|.+.++|.+|++.|||..|+ |+.|+|.|+.
T Consensus       234 i~~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          234 FKEVRLVPGR--------HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             eEEEEEecCC--------CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            9999998653        378999999999999999999999999 9999999985

>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=99.95  E-value=2.6e-27  Score=209.40  Aligned_cols=158  Identities=20%  Similarity=0.342  Sum_probs=133.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhc----C-------CceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESF----G-------TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~----G-------~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  362 (522)
                      .++|||+|||..+|+++|+++|+.|    |       .|..+.+.      .++|||||+|.+.++|.+|+ .|+|..|.
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~~   76 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEec
Confidence            4689999999999999999999999    6       56666554      34799999999999999999 89999999


Q ss_pred             CeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHH
Q 009944          363 DKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEE  442 (522)
Q Consensus       363 g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~  442 (522)
                      |+.|.|.++.......                                     ......|.+|+..++.           
T Consensus        77 g~~i~v~~~~~~~~~~-------------------------------------~~~~l~v~nlp~~~t~-----------  108 (172)
T 2g4b_A           77 GQSLKIRRPHDYQPLP-------------------------------------GAHKLFIGGLPNYLND-----------  108 (172)
T ss_dssp             TEECEEECCSSCCCCT-------------------------------------TTTCEEEECCCTTCCH-----------
T ss_pred             CceeeecCCcccCCCC-------------------------------------CCCEEEEEcCCCcCCH-----------
Confidence            9999999876532111                                     0144555566655554           


Q ss_pred             HHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          443 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       443 ~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                        ++|+++|++||.|..|.|+.+..+|.+   +|+|||+|.+.++|.+|++.|||..|+|++|.|.|+.
T Consensus       109 --~~l~~~f~~~G~v~~v~i~~~~~~g~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          109 --DQVKELLTSFGPLKAFNLVKDSATGLS---KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             --HHHHHHHHTTSCEEEEEEEECTTTCSE---EEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             --HHHHHHHHhcCCceEEEEEecCCCCCc---ceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence              399999999999999999998767654   7899999999999999999999999999999999974

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

Probab=99.95  E-value=1.8e-27  Score=229.19  Aligned_cols=172  Identities=15%  Similarity=0.333  Sum_probs=139.2

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHH-HhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVM-TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g-~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ..++|||+|||+.+|+++|+++|..|| .|..+.+      + ....+.++|||||+|.+.++|.+|+ .|++..|.|+.
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i------~-~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~  188 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRL------P-SLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYT  188 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEEC------C--------CCEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEE------E-eCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            578999999999999999999999999 7533211      1 1112557899999999999999999 59999999999


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCceEEEEeeC
Q 009944          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKD  329 (522)
Q Consensus       251 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~-~t~~~l~~~F~~~G~i~~v~~~~~  329 (522)
                      |.|.++.........                      ........+|||+|||.. +++++|+++|+.||.|..|.++.+
T Consensus       189 l~v~~a~~~~~~~~~----------------------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~  246 (292)
T 2ghp_A          189 LVTKVSNPLEKSKRT----------------------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAG  246 (292)
T ss_dssp             CEEEECCCC-------------------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSC
T ss_pred             EEEEECCCCcccccc----------------------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEec
Confidence            999986543321100                      012334579999999999 999999999999999999999998


Q ss_pred             CC-CCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          330 RD-TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       330 ~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      .. ||.++|||||+|.+.++|.+|+ .|||..|+|+.|.|.|+.++
T Consensus       247 ~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          247 QKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             CC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             CCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            65 5999999999999999999999 99999999999999999774

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

Probab=99.95  E-value=2.3e-27  Score=214.77  Aligned_cols=183  Identities=19%  Similarity=0.215  Sum_probs=140.1

Q ss_pred             cceeEEeCCCc-cCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC-CcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          174 ARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-KKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       174 ~~~v~v~nlp~-~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~-~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      .++|||+|||+ .+|+++|+++|..||.            |..+.+... +|||||+|.+.++|.+|+ .+++..|.|+.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~------------i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~   70 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGD------------VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKP   70 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCC------------CSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCC------------EEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeE
Confidence            47899999999 9999999999999997            555555444 699999999999999999 59999999999


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccc-------cccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcC-Cce
Q 009944          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLA-------AVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-TLH  322 (522)
Q Consensus       251 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G-~i~  322 (522)
                      |.|.++................ ......       .............+.++|||+|||..+++++|+++|+.|| .|.
T Consensus        71 l~v~~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~  149 (198)
T 1qm9_A           71 IRITLSKHQNVQLPREGQEDQG-LTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK  149 (198)
T ss_dssp             CEEEECCCCSCCCSSSSSSSSS-CEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCC
T ss_pred             EEEEEecCCCcCCCCcCCcccc-ccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCce
Confidence            9999876543211110000000 000000       0000000111234468899999999999999999999999 999


Q ss_pred             EEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC-CeEEEEEEccCC
Q 009944          323 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRATAS  374 (522)
Q Consensus       323 ~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~~~~~  374 (522)
                      .|.++.+     .+|+|||+|.+.++|.+|+..|||..|+ |+.|.|.|+.++
T Consensus       150 ~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          150 GFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             EEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             EEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            9998764     2689999999999999999999999999 999999999763

>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=99.95  E-value=1e-27  Score=212.67  Aligned_cols=165  Identities=18%  Similarity=0.289  Sum_probs=131.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|..||.|.. .++.+..+|.++|||||+|.+.++|.+|++ |+|..|.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~   87 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEec
Confidence            345679999999999999999999999998766 333444578899999999999999999995 999999999999999


Q ss_pred             ccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHH
Q 009944          371 ATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREE  450 (522)
Q Consensus       371 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~  450 (522)
                      +.........                                   ......|.+|+..++.             ++|+++
T Consensus        88 ~~~~~~~~~~-----------------------------------~~~~l~v~nlp~~~t~-------------~~l~~~  119 (175)
T 1fje_B           88 PKGRDSKKVR-----------------------------------AARTLLAKNLSFNITE-------------DELKEV  119 (175)
T ss_dssp             CCCSSCSTTG-----------------------------------GGGEEEEESCCSSCCH-------------HHHHHH
T ss_pred             CCCccccccc-----------------------------------cCCEEEEeCCCCCCCH-------------HHHHHH
Confidence            8764221100                                   0123334444444333             499999


Q ss_pred             hhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          451 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       451 f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      |++||.|..+     ..++.   .+|+|||+|.+.++|.+|+..|||..|+|++|.|.|+.+.
T Consensus       120 F~~~g~v~~~-----~~~~~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          120 FEDALEIRLV-----SQDGK---SKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             CTTCSEEEEE-----CSSSS---CCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHhcCeEEEe-----cCCCC---CceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            9999999877     22333   3689999999999999999999999999999999998764

>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=1.1e-27  Score=217.03  Aligned_cols=177  Identities=19%  Similarity=0.302  Sum_probs=134.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcC-----------CceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFG-----------TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G-----------~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  362 (522)
                      .++|||+|||..+++++|+++|+.||           .|..+.+      +.++|||||+|.+.++|.+|| .|||..|.
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            47999999999999999999999994           4444443      456899999999999999999 79999999


Q ss_pred             CeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEE---eeCCCCcCcCCChHH
Q 009944          363 DKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLC---LTEAITADALADDEE  439 (522)
Q Consensus       363 g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~---l~~~~~~~~l~~~~~  439 (522)
                      |+.|.|.++..........                   .......++. .......+...+.   |+..++.        
T Consensus        77 g~~i~v~~~~~~~~~~~~~-------------------~~~~~~~~~~-~~~~~~~~~~~l~v~nl~~~~~~--------  128 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGMS-------------------ENPSVYVPGV-VSTVVPDSAHKLFIGGLPNYLND--------  128 (198)
T ss_dssp             TEEEEEECCCCCCCCCCSS-------------------SCSSCCCTTS-SCCCSSCCCCEEEEECCCTTCCH--------
T ss_pred             CceEEEeCCCCCCCCCCCc-------------------CCCcCCCCCC-ccCCCCCCCCEEEEeCCCCCCCH--------
Confidence            9999999987653222110                   0000011111 1111112233333   4333333        


Q ss_pred             HHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          440 YEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       440 ~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                           ++|+++|++||.|..|.++.+..+|.+   +|+|||+|.+.++|.+|++.|||..|+|++|.|.|+...
T Consensus       129 -----~~l~~~f~~~G~v~~~~~~~~~~~~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  194 (198)
T 2yh0_A          129 -----DQVKELLTSFGPLKAFNLVKDSATGLS---KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG  194 (198)
T ss_dssp             -----HHHHHHHHTBSCEEEEEEEECTTTCSE---EEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             -----HHHHHHHHHcCCccEEEEeecCCCCCc---ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence                 499999999999999999998766654   789999999999999999999999999999999998764

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.95  E-value=2.1e-27  Score=227.78  Aligned_cols=171  Identities=18%  Similarity=0.185  Sum_probs=143.6

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||+|||+.+|+++|+++|..||.|....      .+.+..++.++|||||+|.+.++|..|+ .+++..+.|+.
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~  166 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCF------LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRT  166 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEE------EEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            4567899999999999999999999999743210      0111113446799999999999999999 79999999999


Q ss_pred             EEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCC-CHHHHHHHHHhcCCceEEEEeeC
Q 009944          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYF-TETQIKELLESFGTLHGFDLVKD  329 (522)
Q Consensus       251 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~-t~~~l~~~F~~~G~i~~v~~~~~  329 (522)
                      |.|.++......                          .......+|||+|||..+ ++++|+++|+.||.|..|.|+.+
T Consensus       167 i~v~~a~~~~~~--------------------------~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~  220 (284)
T 3smz_A          167 LYVHWTDAGQLT--------------------------PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG  220 (284)
T ss_dssp             CEEEECCGGGCC--------------------------TTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEEC
T ss_pred             EEEEECCCCCCC--------------------------cccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEEC
Confidence            999986532210                          012345789999999995 99999999999999999999998


Q ss_pred             CCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCC
Q 009944          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (522)
Q Consensus       330 ~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (522)
                      . +|.++|+|||+|.+.++|.+|+..|||..|+|+.|.|.|+.++.
T Consensus       221 ~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~  265 (284)
T 3smz_A          221 Q-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGP  265 (284)
T ss_dssp             S-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSS
T ss_pred             C-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCC
Confidence            6 89999999999999999999999999999999999999997753

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.94  E-value=1.5e-26  Score=208.96  Aligned_cols=183  Identities=13%  Similarity=0.125  Sum_probs=129.5

Q ss_pred             CCeEEEcCCC-CCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          294 PDRVFVGGLP-YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       294 ~~~l~v~nLp-~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      .++|||+||| ..+++++|+++|++||.|..|+++.+     .+|||||+|.+.++|++||+.|||..|.|+.|.|.++.
T Consensus         4 ~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~   78 (205)
T 3tyt_A            4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK   78 (205)
T ss_dssp             CSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            4689999999 89999999999999999999999865     37999999999999999999999999999999999987


Q ss_pred             CCCCCCchHHHHHHHHHHHHHHHHHHHhh-ccCCccC---CCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHH
Q 009944          373 ASSGQSKTEQESILAQAQQHIAIQKMALQ-TSGMNTL---GGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMR  448 (522)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~---g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~  448 (522)
                      .+...+.....  ....  .......... ......+   +......+...+.|.+|+..++++             +|+
T Consensus        79 ~~~~~p~~~~~--~~~~--~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~-------------~L~  141 (205)
T 3tyt_A           79 QPAIMPGQSYG--LEDG--SCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEE-------------NFF  141 (205)
T ss_dssp             CSCCCCCSCCB--CTTS--CBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHH-------------HHH
T ss_pred             CCccCCCcccc--cccC--CccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHH-------------HHH
Confidence            54321110000  0000  0000000000 0000000   000000112345566676665554             999


Q ss_pred             HHhhccCCe--EEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCe
Q 009944          449 EECGKYGTL--VNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGN  503 (522)
Q Consensus       449 ~~f~~~G~I--~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr  503 (522)
                      ++|++||.|  ..|++..+.  +.   ..|+|||+|.+.++|.+||..|||..|+|.
T Consensus       142 ~~F~~~G~v~~~~v~~~~~~--~~---~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~  193 (205)
T 3tyt_A          142 EICDELGVKRPTSVKVFSGK--SE---RSSSGLLEWDSKSDALETLGFLNHYQMKNP  193 (205)
T ss_dssp             HHHHHHTCCCCSEEEECSCC--SS---SSEEEEEECSSHHHHHHHHHHHTTCEECCS
T ss_pred             HHHHhcCCcceEEEEEEcCC--CC---CceEEEEEeCCHHHHHHHHHHhCCCCccCC
Confidence            999999999  899998765  22   148899999999999999999999999987

>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=99.94  E-value=3.2e-26  Score=211.77  Aligned_cols=193  Identities=13%  Similarity=0.127  Sum_probs=136.9

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          292 EGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       292 ~~~~~l~v~nLp~-~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      .+.++|||+|||. .+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|.+|++.|+|..|.|+.|.|.+
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4567999999999 99999999999999999999999874     78999999999999999999999999999999999


Q ss_pred             ccCCCCCCchHHHHHHHHHHHHHHHHHHHhh-ccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHH
Q 009944          371 ATASSGQSKTEQESILAQAQQHIAIQKMALQ-TSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMRE  449 (522)
Q Consensus       371 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~  449 (522)
                      +................      ........ ......++.........+..++.+.|+....          +.++|++
T Consensus       107 a~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~----------t~~~l~~  170 (229)
T 2adc_A          107 SKHQNVQLPREGQEDQG------LTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSV----------SEEDLKV  170 (229)
T ss_dssp             CSCCCCCCCCSSSSTTT------TEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTC----------CHHHHHH
T ss_pred             ecCccccCccccccccc------cccccccCcccccCCccccccccCCCCCCEEEEeCCCccC----------CHHHHHH
Confidence            97653221110000000      00000000 0000000100001111223444444442211          1149999


Q ss_pred             HhhccC-CeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccC-CeEEEEEEeCCc
Q 009944          450 ECGKYG-TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG-GNTVNAFYYPED  513 (522)
Q Consensus       450 ~f~~~G-~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~-Gr~l~v~~~~~~  513 (522)
                      +|++|| .|..|.|....        .|+|||+|.+.++|.+|+..|||..|+ |++|.|.|+...
T Consensus       171 ~f~~~G~~i~~v~i~~~~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          171 LFSSNGGVVKGFKFFQKD--------RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             HHHTTSCCEEEEEECSSS--------TTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             HHHHcCCCeeEEEEEECC--------CcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            999999 99999996532        478899999999999999999999999 999999998753

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

Probab=99.93  E-value=3.4e-26  Score=207.06  Aligned_cols=191  Identities=13%  Similarity=0.116  Sum_probs=136.3

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          294 PDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       294 ~~~l~v~nLp~-~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      .++|||+|||. .+++++|+++|+.||.|..|.++.++     +|||||+|.+.++|.+|+..|+|..|.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            36899999999 99999999999999999999998764     7899999999999999999999999999999999997


Q ss_pred             CCCCCCchHHHHHHHHHHHHHHHHHHHh-hccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHh
Q 009944          373 ASSGQSKTEQESILAQAQQHIAIQKMAL-QTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  451 (522)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f  451 (522)
                      ...............      ....... .......++.........+..++.+.++....          +.++|+++|
T Consensus        78 ~~~~~~~~~~~~~~~------~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~----------~~~~l~~~f  141 (198)
T 1qm9_A           78 HQNVQLPREGQEDQG------LTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSV----------SEEDLKVLF  141 (198)
T ss_dssp             CCSCCCSSSSSSSSS------CEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTC----------CHHHHHHHH
T ss_pred             CCCcCCCCcCCcccc------ccccccCCchhhccCccccccccCCCCccEEEEeCCCCCC----------CHHHHHHHH
Confidence            653221110000000      0000000 00000001110011111234445554442211          125999999


Q ss_pred             hccC-CeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccC-CeEEEEEEeCCc
Q 009944          452 GKYG-TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG-GNTVNAFYYPED  513 (522)
Q Consensus       452 ~~~G-~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~-Gr~l~v~~~~~~  513 (522)
                      ++|| .|..|.|..+.        .|+|||+|.+.++|.+|+..|||..|+ |++|.|.|+...
T Consensus       142 ~~~G~~v~~v~i~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          142 SSNGGVVKGFKFFQKD--------RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             HHTTSCCCEEEESSTT--------SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             HHcCCCceEEEEEeCC--------CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            9999 99999996642        478899999999999999999999999 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=99.93  E-value=2e-25  Score=210.60  Aligned_cols=156  Identities=25%  Similarity=0.360  Sum_probs=133.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||+.+|+++|+++|+.||.|..|.+.++      +|||||+|.+.++|.+|+..|+|..|.|+.|.|.++
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            34468999999999999999999999999999998643      689999999999999999999999999999999998


Q ss_pred             cCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHh
Q 009944          372 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  451 (522)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f  451 (522)
                      .+                                           ...+.|.+|+..++.             ++|+++|
T Consensus        94 ~~-------------------------------------------~~~l~v~nl~~~~t~-------------~~l~~~F  117 (261)
T 3sde_A           94 TH-------------------------------------------GAALTVKNLSPVVSN-------------ELLEQAF  117 (261)
T ss_dssp             CC-------------------------------------------SSEEEEESCCTTCCH-------------HHHHHHH
T ss_pred             cc-------------------------------------------CCcccccCCCCCCCH-------------HHHHHHH
Confidence            53                                           134445555544444             4999999


Q ss_pred             hccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHH-hCCccC---CeEEEEEEeCCc
Q 009944          452 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL-SGRKFG---GNTVNAFYYPED  513 (522)
Q Consensus       452 ~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~l-ng~~~~---Gr~l~v~~~~~~  513 (522)
                      +.||.|..|.|+.+. +|.+   +|+|||+|.+.++|.+|+..| +|..+.   |++|.|.++...
T Consensus       118 ~~~G~i~~v~i~~~~-~g~~---~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          118 SQFGPVEKAVVVVDD-RGRA---TGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             GGGSCEEEEEEEEET-TSCE---EEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             HhcCCeEEEEeeeCC-CCCc---CcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeecccc
Confidence            999999999999884 5544   789999999999999999999 555555   999999998754

>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=99.87  E-value=1.2e-21  Score=170.11  Aligned_cols=141  Identities=18%  Similarity=0.185  Sum_probs=106.4

Q ss_pred             cCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeE
Q 009944          219 NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRV  297 (522)
Q Consensus       219 ~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  297 (522)
                      ...+|||||+|.+.++|++|+ .+++....+..+.+..........   ..             ..............+|
T Consensus        10 ~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~---~~-------------~~~~~~~~~~~~~~~l   73 (158)
T 2kn4_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVT---EG-------------SHHHHHHMDVEGMTSL   73 (158)
T ss_dssp             SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEE---CC-------------CCCSSCCCCCCBCCEE
T ss_pred             ccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCcccccccc---cc-------------ccccccccCCCCCCEE
Confidence            357899999999999999999 565533222222222111000000   00             0000011122345799


Q ss_pred             EEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCC
Q 009944          298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (522)
Q Consensus       298 ~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (522)
                      ||+|||+.+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.++.++.
T Consensus        74 ~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           74 KVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             EEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             EEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            999999999999999999999999999999998899999999999999999999999999999999999999998753

>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=99.86  E-value=9.6e-22  Score=156.52  Aligned_cols=102  Identities=42%  Similarity=0.821  Sum_probs=95.1

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhC
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  497 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng  497 (522)
                      .+++|++|.|++++.++.++++|+++.++|+++|++||.|.+|.|+++..++. .+++|+|||+|.+.++|.+|++.|||
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~-~~~~G~~fV~f~~~~~A~~Ai~~lnG   81 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVE-VPGCGKIFVEFTSVFDCQKAMQGLTG   81 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBC-CTTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCC-cCCcEEEEEEECCHHHHHHHHHHhCC
Confidence            78999999999999999999999999999999999999999999998875432 24579999999999999999999999


Q ss_pred             CccCCeEEEEEEeCCcccccccC
Q 009944          498 RKFGGNTVNAFYYPEDKYFNKDY  520 (522)
Q Consensus       498 ~~~~Gr~l~v~~~~~~~~~~~~~  520 (522)
                      +.|+||+|.|.|+++++|..++|
T Consensus        82 ~~f~GR~i~v~~~~~~~f~~~~~  104 (105)
T 3v4m_A           82 RKFANRVVVTKYCDPDSYHRRDF  104 (105)
T ss_dssp             CEETTEECEEEEECHHHHHTTCC
T ss_pred             CEeCCCEEEEEEeCHHHHhhccC
Confidence            99999999999999999999987

>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=99.83  E-value=3.1e-20  Score=146.62  Aligned_cols=80  Identities=31%  Similarity=0.542  Sum_probs=77.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+|+++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.||.|
T Consensus        19 gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           19 GTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999965

>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=99.83  E-value=2.9e-20  Score=159.63  Aligned_cols=136  Identities=15%  Similarity=0.159  Sum_probs=109.7

Q ss_pred             CCCcEEEEEEeCHHHHHHHH-Hh-cCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeE
Q 009944          220 HEKKFAFVEMRTVEEASNAM-AL-DGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRV  297 (522)
Q Consensus       220 ~~~g~afV~f~~~~~a~~a~-~~-~~~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  297 (522)
                      .-+|+++|+|.+.++|++|+ ++ ++..+.| .+.+.++.............             ............++|
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~l   76 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHH-------------HHHMHRDSCPLDCKV   76 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSC-------------CCCSCSSSSTTSCEE
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccc-------------cccccccCCCCCCEE
Confidence            45799999999999999999 78 9999999 99998765322111000000             000111223456799


Q ss_pred             EEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       298 ~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      ||+|||+.+++++|+++|+.||.|..|.++.+     ++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+.++
T Consensus        77 ~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           77 YVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             EEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             EEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            99999999999999999999999999999876     5899999999999999999999999999999999999764

>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=99.80  E-value=6.6e-20  Score=148.51  Aligned_cols=100  Identities=31%  Similarity=0.505  Sum_probs=87.7

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCC-CCCCCccEEEEEecChHhHHHHHHHHh
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG-GETPGVGKVFLEYYDAVGCATAKNALS  496 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g-~~~~g~G~afV~F~~~~~A~~Ai~~ln  496 (522)
                      .+++|++|.|++++++|.++     ++++|+++|++||.|.+|.|+++..+. ...+++|+|||+|.+.++|.+|++.||
T Consensus        18 ~ps~vl~L~Nm~~~~el~dd-----leedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~Ln   92 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDD-----LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN   92 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTT-----HHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCHHHHHHH-----HHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHC
Confidence            67899999999999887654     568999999999999999999876421 012456899999999999999999999


Q ss_pred             CCccCCeEEEEEEeCCcccccccCCC
Q 009944          497 GRKFGGNTVNAFYYPEDKYFNKDYSA  522 (522)
Q Consensus       497 g~~~~Gr~l~v~~~~~~~~~~~~~~~  522 (522)
                      |+.|+||+|.|.|+++++|.+++|+.
T Consensus        93 Gr~f~GR~i~v~~~~~~~f~~~~~~~  118 (118)
T 3ue2_A           93 GRWFAGRKVVAEVYDQERFDNSDLSA  118 (118)
T ss_dssp             TCEETTEECEEEEECHHHHHTTCCCC
T ss_pred             CCEECCcEEEEEEcChHhccccccCC
Confidence            99999999999999999999999973

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.79  E-value=8.4e-20  Score=141.85  Aligned_cols=82  Identities=20%  Similarity=0.328  Sum_probs=76.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcC-CceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHH-cCCccCCeEEEEEEcc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVRRAT  372 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G-~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v~~~~  372 (522)
                      ++|||+|||+.+|+++|+++|++|| .|..|.|++++.+|.++|||||+|.+.++|.+||+.+ ++..|.|+.|.|.|+.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            5899999999999999999999999 7999999999999999999999999999999999987 4578999999999998


Q ss_pred             CCCC
Q 009944          373 ASSG  376 (522)
Q Consensus       373 ~~~~  376 (522)
                      ++..
T Consensus        82 ~~~~   85 (91)
T 2lxi_A           82 PKPK   85 (91)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7644

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

Probab=99.79  E-value=5.4e-19  Score=142.19  Aligned_cols=82  Identities=11%  Similarity=0.123  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.++
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            34579999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 009944          372 TA  373 (522)
Q Consensus       372 ~~  373 (522)
                      ..
T Consensus        84 ~~   85 (110)
T 3s8s_A           84 IK   85 (110)
T ss_dssp             ST
T ss_pred             CC
Confidence            54

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.78  E-value=4.3e-19  Score=138.21  Aligned_cols=81  Identities=20%  Similarity=0.322  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCC--ceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCC----ccCCeEE
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGT--LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL----KMGDKTL  366 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~--i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~----~~~g~~l  366 (522)
                      .-.+|||+|||+.+|+++|+++|++||.  |..|.+++++.+|.++|||||+|.+.++|.+|++.|||.    .|.|++|
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            3469999999999999999999999995  679999999999999999999999999999999999996    5899999


Q ss_pred             EEEEccC
Q 009944          367 TVRRATA  373 (522)
Q Consensus       367 ~v~~~~~  373 (522)
                      .|.||..
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999864

>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=99.78  E-value=5.1e-19  Score=142.22  Aligned_cols=94  Identities=26%  Similarity=0.430  Sum_probs=87.0

Q ss_pred             CCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHh
Q 009944          417 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  496 (522)
Q Consensus       417 ~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~ln  496 (522)
                      +.+++|++|.|+++++++.++++|++++++|+++|++||.|.+|.|+++.       ++|+|||+|.+.++|.+|++.||
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~-------~~G~~fV~f~~~e~A~~Ai~~ln   76 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS-------AQGNVYVKCPSIAAAIAAVNALH   76 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC-------TTCCEEEECSSHHHHHHHHHHHT
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC-------CcEEEEEEECCHHHHHHHHHHhC
Confidence            46899999999999999999999999999999999999999999998763       25788999999999999999999


Q ss_pred             CCccCCeEEEEEEeCCccccc
Q 009944          497 GRKFGGNTVNAFYYPEDKYFN  517 (522)
Q Consensus       497 g~~~~Gr~l~v~~~~~~~~~~  517 (522)
                      |+.|+|++|.|.|+++..|..
T Consensus        77 G~~f~GR~i~v~~~~~~~y~~   97 (114)
T 3s6e_A           77 GRWFAGKMITAAYVPLPTYHN   97 (114)
T ss_dssp             TCEETTEECEEEEECHHHHHH
T ss_pred             CCEECCEEEEEEEEcHHHHHH
Confidence            999999999999999988754

>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=99.77  E-value=1.8e-18  Score=133.67  Aligned_cols=82  Identities=30%  Similarity=0.455  Sum_probs=76.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||..+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.
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            44689999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             CC
Q 009944          373 AS  374 (522)
Q Consensus       373 ~~  374 (522)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            64

>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=99.77  E-value=2.6e-18  Score=148.91  Aligned_cols=150  Identities=22%  Similarity=0.217  Sum_probs=102.5

Q ss_pred             EEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhc
Q 009944          323 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQT  402 (522)
Q Consensus       323 ~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  402 (522)
                      .+.|+.+.  ..++|||||+|.+.++|++|+..+++....+..+.+.........                        .
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~------------------------~   55 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTV------------------------T   55 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEE------------------------E
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccc------------------------c
Confidence            35666663  468999999999999999999998875443333333321110000                        0


Q ss_pred             cCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEe
Q 009944          403 SGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEY  482 (522)
Q Consensus       403 ~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F  482 (522)
                      .................++|-+|+..+++             ++|+++|++||.|..|.|+.+..+|..   +|+|||+|
T Consensus        56 ~~~~~~~~~~~~~~~~~l~v~nl~~~~~~-------------~~l~~~F~~~G~v~~~~i~~~~~~g~~---~g~afV~f  119 (158)
T 2kn4_A           56 EGSHHHHHHMDVEGMTSLKVDNLTYRTSP-------------DTLRRVFEKYGRVGDVYIPRDRYTKES---RGFAFVRF  119 (158)
T ss_dssp             CCCCCSSCCCCCCBCCEEEEESCCTTCCH-------------HHHHHHHHHHSCEEEEECCCCSSCTTS---CCEEEEEE
T ss_pred             ccccccccccCCCCCCEEEEeCCCCCCCH-------------HHHHHHHHhcCCeEEEEEeecCCCCcc---ceEEEEEE
Confidence            00000000001111123333334444343             499999999999999999998877765   78999999


Q ss_pred             cChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          483 YDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       483 ~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      .+.++|.+||+.|||..|+|++|.|.|+....
T Consensus       120 ~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A          120 HDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             SBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             CCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            99999999999999999999999999998754

>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=99.77  E-value=1.7e-18  Score=140.97  Aligned_cols=81  Identities=23%  Similarity=0.494  Sum_probs=74.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ...+|||+|||+.+++++|+++|+.||.|..|+|+.+.  +.++|||||+|.+.++|++||+.|+|..|.|+.|.|.++.
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            34689999999999999999999999999999999984  5589999999999999999999999999999999999997


Q ss_pred             CCC
Q 009944          373 ASS  375 (522)
Q Consensus       373 ~~~  375 (522)
                      ++.
T Consensus        82 ~~~   84 (115)
T 4f25_A           82 SRK   84 (115)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            643

>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=99.77  E-value=3e-18  Score=131.04  Aligned_cols=80  Identities=21%  Similarity=0.408  Sum_probs=77.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      .+|||+|||..+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.++
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            48999999999999999999999999999999999889999999999999999999999999999999999999999775

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=4.3e-18  Score=135.77  Aligned_cols=86  Identities=29%  Similarity=0.560  Sum_probs=80.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.+
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            45568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009944          371 ATASSG  376 (522)
Q Consensus       371 ~~~~~~  376 (522)
                      +.++..
T Consensus        89 a~~~~~   94 (102)
T 1x5s_A           89 AGKSSD   94 (102)
T ss_dssp             EECCCC
T ss_pred             CCCCCC
Confidence            987543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=5.2e-18  Score=133.37  Aligned_cols=83  Identities=20%  Similarity=0.418  Sum_probs=78.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34457899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccC
Q 009944          371 ATA  373 (522)
Q Consensus       371 ~~~  373 (522)
                      +..
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            854

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=4.6e-18  Score=133.67  Aligned_cols=84  Identities=33%  Similarity=0.651  Sum_probs=79.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ..+++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.++
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            34579999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      .++.
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            7754

>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=99.76  E-value=7.8e-19  Score=136.40  Aligned_cols=81  Identities=17%  Similarity=0.339  Sum_probs=72.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcC--CceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFG--TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G--~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      .+|||+|||..+++++|+++|+.||  .|..|.++.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            3799999999999999999999999  99999999999999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 009944          373 ASS  375 (522)
Q Consensus       373 ~~~  375 (522)
                      ++.
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            743

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=3.9e-18  Score=136.03  Aligned_cols=86  Identities=19%  Similarity=0.303  Sum_probs=80.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.+
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            44567999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009944          371 ATASSG  376 (522)
Q Consensus       371 ~~~~~~  376 (522)
                      +.++..
T Consensus        89 a~~~~~   94 (102)
T 2cqb_A           89 AKPMRI   94 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987643

>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=99.76  E-value=3.8e-18  Score=131.15  Aligned_cols=81  Identities=19%  Similarity=0.336  Sum_probs=77.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++
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            34579999999999999999999999999999999999889999999999999999999999999999999999999997


Q ss_pred             c
Q 009944          372 T  372 (522)
Q Consensus       372 ~  372 (522)
                      .
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.75  E-value=9.2e-18  Score=136.98  Aligned_cols=87  Identities=30%  Similarity=0.442  Sum_probs=81.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|++||+.|+|..|.|+.|.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 009944          371 ATASSGQ  377 (522)
Q Consensus       371 ~~~~~~~  377 (522)
                      +.++...
T Consensus        92 a~~~~~~   98 (115)
T 2dgo_A           92 ATRKPPA   98 (115)
T ss_dssp             SSCCCCC
T ss_pred             ccCCCCC
Confidence            9876443

>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=99.75  E-value=5.9e-18  Score=134.14  Aligned_cols=85  Identities=26%  Similarity=0.431  Sum_probs=80.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            44578999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009944          372 TASSG  376 (522)
Q Consensus       372 ~~~~~  376 (522)
                      .++..
T Consensus        86 ~~~~~   90 (99)
T 1whw_A           86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCcc
Confidence            87643

>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=4.5e-18  Score=135.85  Aligned_cols=85  Identities=20%  Similarity=0.382  Sum_probs=80.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34567999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      +....
T Consensus        90 a~~~~   94 (103)
T 2dnm_A           90 ARYGR   94 (103)
T ss_dssp             CSSCC
T ss_pred             CCcCC
Confidence            98653

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=5.4e-18  Score=135.40  Aligned_cols=86  Identities=29%  Similarity=0.436  Sum_probs=80.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            34567899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009944          371 ATASSG  376 (522)
Q Consensus       371 ~~~~~~  376 (522)
                      +.++..
T Consensus        92 a~~~~~   97 (103)
T 2cq0_A           92 AKPSTN   97 (103)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987543

>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=99.75  E-value=5.8e-18  Score=133.25  Aligned_cols=82  Identities=32%  Similarity=0.551  Sum_probs=78.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|+|..|.|+.|.|.++.+
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            46899999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CC
Q 009944          374 SS  375 (522)
Q Consensus       374 ~~  375 (522)
                      +.
T Consensus        82 ~~   83 (96)
T 2x1f_A           82 SD   83 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=7.8e-18  Score=133.38  Aligned_cols=84  Identities=25%  Similarity=0.538  Sum_probs=79.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||+ |+|..|.|+.|.|.++
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEEC
Confidence            455799999999999999999999999999999999998899999999999999999999998 9999999999999999


Q ss_pred             cCCCC
Q 009944          372 TASSG  376 (522)
Q Consensus       372 ~~~~~  376 (522)
                      .++..
T Consensus        87 ~~~~~   91 (99)
T 2dgs_A           87 EPRDS   91 (99)
T ss_dssp             CCCCC
T ss_pred             CCCcc
Confidence            87644

>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=99.75  E-value=1.1e-17  Score=136.57  Aligned_cols=85  Identities=25%  Similarity=0.480  Sum_probs=80.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||+.|||..|.|+.|.|.|+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  102 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK  102 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            44578999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009944          372 TASSG  376 (522)
Q Consensus       372 ~~~~~  376 (522)
                      .++..
T Consensus       103 ~~~~~  107 (115)
T 2cpz_A          103 RSKND  107 (115)
T ss_dssp             CCSCC
T ss_pred             CCCCc
Confidence            87643

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=6.2e-18  Score=132.62  Aligned_cols=82  Identities=23%  Similarity=0.448  Sum_probs=77.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|
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            34567899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cc
Q 009944          371 AT  372 (522)
Q Consensus       371 ~~  372 (522)
                      +.
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            73

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.75  E-value=3.8e-18  Score=135.52  Aligned_cols=99  Identities=28%  Similarity=0.446  Sum_probs=85.0

Q ss_pred             CCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHh
Q 009944          417 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  496 (522)
Q Consensus       417 ~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~ln  496 (522)
                      +.++++++|.|+++++++.+     ++.++|+++|++||.|.+|.|+++..++.  ..+|+|||+|.+.++|.+|++.||
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~d-----d~~~dl~~~f~~~G~V~~v~i~~~~~~~~--~~~G~~FV~f~~~~~A~~Ai~~ln   77 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDE-----DLEVETKEECEKYGKVGKCVIFEIPGAPD--DEAVRIFLEFERVESAIKAVVDLN   77 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC--------CHHHHHHHGGGGSCEEEEEEEECSSCCT--TTSEEEEEEESSHHHHHHHHHHHT
T ss_pred             CCCCCEEEEEcCCChHHhhH-----HHHHHHHHHHHhcCCEEEEEEecCCCCCC--CCcEEEEEEECCHHHHHHHHHHHC
Confidence            37789999999998877643     35679999999999999999998764321  236899999999999999999999


Q ss_pred             CCccCCeEEEEEEeCCcccccccCCC
Q 009944          497 GRKFGGNTVNAFYYPEDKYFNKDYSA  522 (522)
Q Consensus       497 g~~~~Gr~l~v~~~~~~~~~~~~~~~  522 (522)
                      |+.|+|++|.|.|+++.+|..++|+.
T Consensus        78 G~~~~Gr~i~v~~a~~~~f~~~~~~~  103 (105)
T 2pe8_A           78 GRYFGGRVVKACFYNLDKFRVLDLAE  103 (105)
T ss_dssp             TCEETTEECEEEECCHHHHHTTCCCC
T ss_pred             CCEECCcEEEEEEcCHHHhhhhhccc
Confidence            99999999999999999999999863

>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=99.75  E-value=7.3e-18  Score=135.19  Aligned_cols=86  Identities=29%  Similarity=0.436  Sum_probs=80.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            34567999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009944          371 ATASSG  376 (522)
Q Consensus       371 ~~~~~~  376 (522)
                      +.++..
T Consensus        92 a~~~~~   97 (105)
T 1x5u_A           92 ASAHNK   97 (105)
T ss_dssp             TTTTSC
T ss_pred             CCCCCc
Confidence            977543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.74  E-value=8.6e-19  Score=146.87  Aligned_cols=122  Identities=19%  Similarity=0.285  Sum_probs=80.4

Q ss_pred             EEEEEEeCHHHHHHHH-HhcCceecCceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCC
Q 009944          224 FAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGL  302 (522)
Q Consensus       224 ~afV~f~~~~~a~~a~-~~~~~~~~g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL  302 (522)
                      ++|++|.+...+..|| .+++....|+.- +.+..                             ........++|||+||
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~~-----------------------------~~~~~~~~~~l~V~nL   55 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYGR-----------------------------PPPDVEGMTSLKVDNL   55 (135)
T ss_dssp             ------------------------------CCSCC-----------------------------SCSSGGGCCCEEEECC
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCC-CCcCC-----------------------------CCCCCCCCCEEEEeCC
Confidence            6788888888888888 577766555431 11100                             0111234578999999


Q ss_pred             CCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCC
Q 009944          303 PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (522)
Q Consensus       303 p~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (522)
                      |..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|++||..|||..|.|+.|.|.++.+..
T Consensus        56 p~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A           56 TYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  128 (135)
T ss_dssp             CSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCC
T ss_pred             CCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            9999999999999999999999999998899999999999999999999999999999999999999998754

>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=99.74  E-value=6.8e-18  Score=147.08  Aligned_cols=141  Identities=20%  Similarity=0.177  Sum_probs=79.8

Q ss_pred             EEEeCHHHHHHHH-HhcCceec--CceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCC
Q 009944          227 VEMRTVEEASNAM-ALDGIIFE--GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLP  303 (522)
Q Consensus       227 V~f~~~~~a~~a~-~~~~~~~~--g~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp  303 (522)
                      .+|.+.++|..|+ .+++....  |+.+...+..............+.+         .............++|||+|||
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~---------~~~~~~~~~~~~~~~l~V~nLp   81 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDD---------DELEPGPQRSVEGWILFVTSIH   81 (165)
T ss_dssp             ----------------------------------------------------------------CCCCC-CEEEEEESCC
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCC---------CCCCCCCCCCCCCCEEEEeCCC
Confidence            7899999999999 67775554  4444444321110000000000000         0000001112345689999999


Q ss_pred             CCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCC
Q 009944          304 YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  376 (522)
Q Consensus       304 ~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~  376 (522)
                      ..+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.|+.++..
T Consensus        82 ~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A           82 EEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             TTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-
T ss_pred             CCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            9999999999999999999999999988999999999999999999999999999999999999999987543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.9e-17  Score=131.48  Aligned_cols=83  Identities=22%  Similarity=0.542  Sum_probs=78.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|+.||.|..|.++.++ +|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.++
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            445789999999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      .++.
T Consensus        94 ~~~~   97 (100)
T 2do4_A           94 NSGP   97 (100)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7754

>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=99.74  E-value=7.3e-18  Score=135.43  Aligned_cols=84  Identities=33%  Similarity=0.693  Sum_probs=79.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|+|..|.|+.|.|.+
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            44567999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 009944          371 ATAS  374 (522)
Q Consensus       371 ~~~~  374 (522)
                      +.++
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            9764

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=5.4e-18  Score=133.53  Aligned_cols=84  Identities=30%  Similarity=0.518  Sum_probs=79.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEE-EEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGF-DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v-~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      +.++|||+|||..+++++|+++|+.||.|..| .|+.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA   83 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45799999999999999999999999999999 99999889999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009944          372 TASSG  376 (522)
Q Consensus       372 ~~~~~  376 (522)
                      .++..
T Consensus        84 ~~~~~   88 (96)
T 1x5t_A           84 FKKDS   88 (96)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            87543

>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=99.74  E-value=8.8e-18  Score=134.96  Aligned_cols=85  Identities=29%  Similarity=0.472  Sum_probs=79.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc---CCeEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM---GDKTLT  367 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~---~g~~l~  367 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..+   .|+.|.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            34557899999999999999999999999999999999988999999999999999999999999999887   899999


Q ss_pred             EEEccCCC
Q 009944          368 VRRATASS  375 (522)
Q Consensus       368 v~~~~~~~  375 (522)
                      |.++.++.
T Consensus        90 v~~a~~~~   97 (106)
T 2dgp_A           90 VKPADSES   97 (106)
T ss_dssp             EEECCCCS
T ss_pred             EEECCccc
Confidence            99998754

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=6.5e-18  Score=133.89  Aligned_cols=84  Identities=24%  Similarity=0.396  Sum_probs=79.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCce-EEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeE----
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLH-GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT----  365 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~-~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~----  365 (522)
                      ....++|||+|||..+++++|+++|++||.|. .|.++.++.+|.++|||||+|.+.++|++|+..|||..|.|+.    
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            34567999999999999999999999999999 9999999989999999999999999999999999999999999    


Q ss_pred             EEEEEccCC
Q 009944          366 LTVRRATAS  374 (522)
Q Consensus       366 l~v~~~~~~  374 (522)
                      |.|.|+.+.
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999999764

>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=1.5e-17  Score=134.84  Aligned_cols=87  Identities=28%  Similarity=0.410  Sum_probs=81.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHc------CCccCCe
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN------GLKMGDK  364 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~------g~~~~g~  364 (522)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||..||      |..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            3456789999999999999999999999999999999999899999999999999999999999999      9999999


Q ss_pred             EEEEEEccCCCCC
Q 009944          365 TLTVRRATASSGQ  377 (522)
Q Consensus       365 ~l~v~~~~~~~~~  377 (522)
                      .|.|.++.++...
T Consensus        92 ~l~v~~a~~~~~~  104 (111)
T 1x4h_A           92 QLKVDLAVTRDEA  104 (111)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEEEEECCCCccC
Confidence            9999999876543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.74  E-value=1.2e-17  Score=132.21  Aligned_cols=82  Identities=24%  Similarity=0.418  Sum_probs=77.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceE--------EEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHG--------FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~--------v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  362 (522)
                      ....++|||+|||..+++++|+++|++||.|..        |.++.++.+|.++|||||+|.+.++|.+|++.|||..|.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            344579999999999999999999999999999        999999889999999999999999999999999999999


Q ss_pred             CeEEEEEEcc
Q 009944          363 DKTLTVRRAT  372 (522)
Q Consensus       363 g~~l~v~~~~  372 (522)
                      |+.|.|.+|+
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999973

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.2e-17  Score=134.22  Aligned_cols=82  Identities=26%  Similarity=0.359  Sum_probs=78.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||..+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.
T Consensus        22 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  101 (106)
T 1p27_B           22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF  101 (106)
T ss_dssp             TBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeec
Confidence            34689999999999999999999999999999999999899999999999999999999999999999999999999997


Q ss_pred             CC
Q 009944          373 AS  374 (522)
Q Consensus       373 ~~  374 (522)
                      ++
T Consensus       102 ~~  103 (106)
T 1p27_B          102 VR  103 (106)
T ss_dssp             ES
T ss_pred             CC
Confidence            64

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.73  E-value=2.1e-18  Score=136.67  Aligned_cols=80  Identities=16%  Similarity=0.268  Sum_probs=76.8

Q ss_pred             CCeEEEcCCCC------CCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC-eEE
Q 009944          294 PDRVFVGGLPY------YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD-KTL  366 (522)
Q Consensus       294 ~~~l~v~nLp~------~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g-~~l  366 (522)
                      .++|||+|||.      .+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|.| +.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            36899999999      99999999999999999999999999899999999999999999999999999999999 999


Q ss_pred             EEEEccC
Q 009944          367 TVRRATA  373 (522)
Q Consensus       367 ~v~~~~~  373 (522)
                      .|.++.+
T Consensus        86 ~V~~a~~   92 (100)
T 3ns6_A           86 FLYTMKD   92 (100)
T ss_dssp             EEEESHH
T ss_pred             EEEECch
Confidence            9999854

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=9.8e-18  Score=132.58  Aligned_cols=84  Identities=24%  Similarity=0.457  Sum_probs=77.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCC---CCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~---~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (522)
                      .+.++|||+|||..+++++|+++|++||.|..|.|+.++.   ++.++|||||+|.+.++|.+|+..|||..|.|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3457899999999999999999999999999999998876   5689999999999999999999999999999999999


Q ss_pred             EEccCCC
Q 009944          369 RRATASS  375 (522)
Q Consensus       369 ~~~~~~~  375 (522)
                      .++.++.
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9997754

>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=99.73  E-value=3.9e-18  Score=138.86  Aligned_cols=104  Identities=19%  Similarity=0.250  Sum_probs=64.8

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~----~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      ..+|||+|||+.+|+++|+++|..||.|            .++.+    +.++|||||+|.+.++|++|+ .|++..|.|
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v------------~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g   72 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNI------------LSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLND   72 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCE------------EEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCE------------EEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECC
Confidence            4579999999999999999999999984            33333    335799999999999999999 699999999


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHH
Q 009944          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQ  310 (522)
Q Consensus       249 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~  310 (522)
                      ++|.|.++..........                     .......++|||+|||+.+|++.
T Consensus        73 ~~i~V~~a~~~~~~~~~~---------------------~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           73 RKVFVGRFKSRKEREAEL---------------------GARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             EECEEEESSCCCC-------------------------------------------------
T ss_pred             EEEEEEECCCcccccccc---------------------ccccCCCCceEeCCCCCCccccc
Confidence            999999866443211000                     00122335799999999999863

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=2.1e-17  Score=132.99  Aligned_cols=86  Identities=23%  Similarity=0.449  Sum_probs=80.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeC-CCCCCcceEEEEEEcChHHHHHHHHHH-cCCccCCeEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTV  368 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~-~~~g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v  368 (522)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.+ +.++.++|||||+|.+.++|.+||..| ||..|.|+.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            345578999999999999999999999999999999998 789999999999999999999999999 999999999999


Q ss_pred             EEccCCCC
Q 009944          369 RRATASSG  376 (522)
Q Consensus       369 ~~~~~~~~  376 (522)
                      .|+.++..
T Consensus        92 ~~a~~~~~   99 (107)
T 2cph_A           92 EWADSEVT   99 (107)
T ss_dssp             EECCCCCC
T ss_pred             EeCCCCCC
Confidence            99987643

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.73  E-value=1.7e-17  Score=130.45  Aligned_cols=81  Identities=31%  Similarity=0.550  Sum_probs=76.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++. |.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus        14 ~~~~~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           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            4457999999999999999999999999999999999974 999999999999999999999999999999999999998


Q ss_pred             cC
Q 009944          372 TA  373 (522)
Q Consensus       372 ~~  373 (522)
                      ..
T Consensus        93 ~~   94 (95)
T 2ywk_A           93 SS   94 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.73  E-value=2.5e-17  Score=132.58  Aligned_cols=81  Identities=25%  Similarity=0.393  Sum_probs=77.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|.++|++||.|..|.|+.++ +|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.+
T Consensus        26 ~~~~~~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           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3456789999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             cc
Q 009944          371 AT  372 (522)
Q Consensus       371 ~~  372 (522)
                      ++
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.73  E-value=1.8e-17  Score=123.53  Aligned_cols=73  Identities=18%  Similarity=0.301  Sum_probs=69.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..-|||+||++.+|+++|+++|.+||+|..+.+..      ++|||||+|.+.++|.+|++.|||..+.|++|.|.+|+
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            45799999999999999999999999999999865      58999999999999999999999999999999999983

>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=2.6e-17  Score=129.38  Aligned_cols=81  Identities=20%  Similarity=0.256  Sum_probs=74.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~----~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      ...++|||+|||..+++++|+    ++|++||.|..|.|+.++.+   +|||||+|.+.++|.+|++.|||..|.|+.|.
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            345789999999999999999    99999999999999988654   88999999999999999999999999999999


Q ss_pred             EEEccCCC
Q 009944          368 VRRATASS  375 (522)
Q Consensus       368 v~~~~~~~  375 (522)
                      |.++.+..
T Consensus        84 V~~a~~~~   91 (96)
T 2dgx_A           84 VSLATGAS   91 (96)
T ss_dssp             EEECCCSS
T ss_pred             EEEcCCCC
Confidence            99997653

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.73  E-value=2.5e-17  Score=131.48  Aligned_cols=84  Identities=25%  Similarity=0.504  Sum_probs=78.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.|| |..|.|+.++.+|.++|||||+|.+.++|.+|| .|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            34557899999999999999999999997 999999999989999999999999999999999 8999999999999999


Q ss_pred             ccCCCC
Q 009944          371 ATASSG  376 (522)
Q Consensus       371 ~~~~~~  376 (522)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2dng_A           90 AEGRKQ   95 (103)
T ss_dssp             CCCCCC
T ss_pred             ecCCCC
Confidence            987543

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.73  E-value=1.6e-17  Score=135.32  Aligned_cols=83  Identities=30%  Similarity=0.572  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|.++|++||.|..|.|+.+. +|.++|||||+|.+.++|++|++.|||..|.|+.|.|.++
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   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            445799999999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      .++.
T Consensus        84 ~~~~   87 (116)
T 2fy1_A           84 KKPS   87 (116)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7653

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.72  E-value=2.1e-17  Score=133.72  Aligned_cols=83  Identities=28%  Similarity=0.340  Sum_probs=78.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||..+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+.
T Consensus        25 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  104 (110)
T 1oo0_B           25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF  104 (110)
T ss_dssp             TBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcc
Confidence            44689999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             CCC
Q 009944          373 ASS  375 (522)
Q Consensus       373 ~~~  375 (522)
                      ++.
T Consensus       105 ~~~  107 (110)
T 1oo0_B          105 VKG  107 (110)
T ss_dssp             ESS
T ss_pred             cCC
Confidence            653

>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=99.72  E-value=4.3e-17  Score=130.64  Aligned_cols=84  Identities=24%  Similarity=0.388  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC---eEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD---KTLTV  368 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g---~~l~v  368 (522)
                      ...++|||+|||..+++++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|.+||+.|||..|.|   +.|.|
T Consensus        13 ~~~~~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           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            346799999999999999999999999999999999997 79999999999999999999999999999988   99999


Q ss_pred             EEccCCCC
Q 009944          369 RRATASSG  376 (522)
Q Consensus       369 ~~~~~~~~  376 (522)
                      .++.++..
T Consensus        92 ~~a~~~~~   99 (105)
T 2dnh_A           92 KFADTDKE   99 (105)
T ss_dssp             EESCSSCC
T ss_pred             EECccCcc
Confidence            99987543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.7e-17  Score=131.33  Aligned_cols=84  Identities=23%  Similarity=0.399  Sum_probs=78.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.+  +|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            345679999999999999999999999999999999998  899999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009944          371 ATASSG  376 (522)
Q Consensus       371 ~~~~~~  376 (522)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2d9p_A           90 AQRKEE   95 (103)
T ss_dssp             CSSCCC
T ss_pred             eccccc
Confidence            987643

>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=99.72  E-value=2.6e-17  Score=141.08  Aligned_cols=139  Identities=20%  Similarity=0.138  Sum_probs=101.2

Q ss_pred             CCCcceEEEEEEcChHHHHHHHHHH-cCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCC
Q 009944          332 TGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG  410 (522)
Q Consensus       332 ~g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~  410 (522)
                      ...-+|+++|+|.+.++|++|++.+ ||..+.| .|.+.++..........                     ........
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~---------------------~~~~~~~~   66 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGS---------------------HHHHHHMH   66 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSS---------------------SSCCCCSC
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccccc---------------------cccccccc
Confidence            3456899999999999999999999 9999999 99999875421000000                     00000000


Q ss_pred             CcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHH
Q 009944          411 GMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCAT  490 (522)
Q Consensus       411 ~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~  490 (522)
                      .........+.|-+|+..+++             ++|+++|++||.|..|.|+.+.        +|+|||+|.+.++|.+
T Consensus        67 ~~~~~~~~~l~V~nl~~~~t~-------------~~l~~~F~~~G~i~~v~i~~~~--------~g~afV~f~~~~~a~~  125 (150)
T 2i2y_A           67 RDSCPLDCKVYVGNLGNNGNK-------------TELERAFGYYGPLRSVWVARNP--------PGFAFVEFEDPRDAAD  125 (150)
T ss_dssp             SSSSTTSCEEEEESCCSCCSC-------------HHHHHHHHHHSCEEEEEECSSS--------CSEEEEEESSHHHHHH
T ss_pred             ccCCCCCCEEEEeCCCCCCCH-------------HHHHHHHHhhCCEEEEEEeeCC--------CcEEEEEECCHHHHHH
Confidence            011111233334445444444             3999999999999999998862        4899999999999999


Q ss_pred             HHHHHhCCccCCeEEEEEEeCCc
Q 009944          491 AKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       491 Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      |+..|||..|+|++|+|.|+...
T Consensus       126 A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A          126 AVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             HHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHcCCCEECCeEEEEEEcCCC
Confidence            99999999999999999998764

>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=99.72  E-value=1.2e-17  Score=138.66  Aligned_cols=84  Identities=20%  Similarity=0.397  Sum_probs=79.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ..+.++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++||+.|+|..|.|+.|.|.|
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45567899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 009944          371 ATAS  374 (522)
Q Consensus       371 ~~~~  374 (522)
                      +.++
T Consensus       123 a~~~  126 (129)
T 2kxn_B          123 SITK  126 (129)
T ss_dssp             CSSS
T ss_pred             ecCC
Confidence            9764

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.8e-17  Score=133.65  Aligned_cols=86  Identities=21%  Similarity=0.363  Sum_probs=80.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCce--------EEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~--------~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  362 (522)
                      ....++|||+|||..+++++|+++|+.||.|.        .|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            34567999999999999999999999999999        6999999889999999999999999999999999999999


Q ss_pred             CeEEEEEEccCCCC
Q 009944          363 DKTLTVRRATASSG  376 (522)
Q Consensus       363 g~~l~v~~~~~~~~  376 (522)
                      |+.|.|.++.++..
T Consensus        92 g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           92 GSKLKVSLARKKPP  105 (113)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CCEEEEEECCCCCC
Confidence            99999999987543

>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=99.72  E-value=7.2e-17  Score=128.80  Aligned_cols=84  Identities=26%  Similarity=0.391  Sum_probs=76.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++  +.++|||||+|.+.++|.+|+..|+|..|.|+.|.|.|
T Consensus        12 ~~~~~~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           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC--CSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC--CCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            3456799999999999999999999999999999999985  33689999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009944          371 ATASSG  376 (522)
Q Consensus       371 ~~~~~~  376 (522)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2cqi_A           90 ATTPSS   95 (103)
T ss_dssp             CCCTTC
T ss_pred             CCCCcc
Confidence            987543

>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=99.72  E-value=1.8e-17  Score=128.20  Aligned_cols=81  Identities=23%  Similarity=0.491  Sum_probs=76.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCC-cceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN-SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~-~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      +++|||+|||..+++++|.++|++||.|..|.++.+..++. ++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   83 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVL   83 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECC
Confidence            46899999999999999999999999999999999877666 89999999999999999999999999999999999997


Q ss_pred             CC
Q 009944          373 AS  374 (522)
Q Consensus       373 ~~  374 (522)
                      ++
T Consensus        84 ~~   85 (88)
T 4a8x_A           84 AP   85 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.1e-17  Score=132.50  Aligned_cols=86  Identities=23%  Similarity=0.501  Sum_probs=80.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||.. +|..|.|+.|.|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            45568999999999999999999999999999999999988999999999999999999999998 99999999999999


Q ss_pred             ccCCCCC
Q 009944          371 ATASSGQ  377 (522)
Q Consensus       371 ~~~~~~~  377 (522)
                      +.++...
T Consensus        92 a~~~~~~   98 (105)
T 2dh8_A           92 CTPRGMQ   98 (105)
T ss_dssp             SCCSSCC
T ss_pred             ccCCCCC
Confidence            9876543

>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=99.72  E-value=2.7e-17  Score=127.51  Aligned_cols=79  Identities=16%  Similarity=0.377  Sum_probs=76.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      ++|||+|||..+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.++.+.
T Consensus         7 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A            7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCC
Confidence            68999999999999999999999999999999999889999999999999999999999 89999999999999998763

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.72  E-value=2.4e-17  Score=135.17  Aligned_cols=81  Identities=28%  Similarity=0.507  Sum_probs=77.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            44567899999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             c
Q 009944          371 A  371 (522)
Q Consensus       371 ~  371 (522)
                      +
T Consensus       117 a  117 (118)
T 2khc_A          117 K  117 (118)
T ss_dssp             C
T ss_pred             c
Confidence            7

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.8e-17  Score=130.10  Aligned_cols=81  Identities=12%  Similarity=0.168  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcC--CccCCeEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTV  368 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v  368 (522)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|++.|++  ..|.|++|.|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345679999999999999999999999999999999864      69999999999999999998864  7899999999


Q ss_pred             EEccCCCCC
Q 009944          369 RRATASSGQ  377 (522)
Q Consensus       369 ~~~~~~~~~  377 (522)
                      .|+..+...
T Consensus        87 ~~A~~~~~~   95 (105)
T 1sjq_A           87 QFSNHKELK   95 (105)
T ss_dssp             CCCSSSSCC
T ss_pred             EEcCCCCCC
Confidence            999876443

>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=1.5e-17  Score=131.46  Aligned_cols=84  Identities=15%  Similarity=0.322  Sum_probs=78.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..|.|+.|.|.+
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            34457899999999999999999999999999888888888999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 009944          371 ATAS  374 (522)
Q Consensus       371 ~~~~  374 (522)
                      +..+
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8653

>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=99.72  E-value=3.7e-17  Score=126.11  Aligned_cols=79  Identities=24%  Similarity=0.566  Sum_probs=74.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||+.+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|++ +++..|.|+.|.|.+|
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            456799999999999999999999999999999999998899999999999999999999996 5888999999999875

>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=7.7e-18  Score=132.38  Aligned_cols=82  Identities=16%  Similarity=0.345  Sum_probs=75.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++||+.|||..|.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            34578999999999999999999999999998988888889999999999999999999999999999999999999988


Q ss_pred             cC
Q 009944          372 TA  373 (522)
Q Consensus       372 ~~  373 (522)
                      ..
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            53

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=2e-17  Score=132.37  Aligned_cols=84  Identities=26%  Similarity=0.394  Sum_probs=78.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHh-cCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCc-cCCeEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLES-FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK-MGDKTLTVR  369 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~-~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~-~~g~~l~v~  369 (522)
                      ...++|||+|||..+++++|+++|+. ||.|..|.|+.++ +|.++|||||+|.+.++|.+||..|+|.. |.|+.|.|.
T Consensus         7 ~~~~~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            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            34578999999999999999999999 9999999999998 99999999999999999999999999999 999999999


Q ss_pred             EccCCCC
Q 009944          370 RATASSG  376 (522)
Q Consensus       370 ~~~~~~~  376 (522)
                      ++.++..
T Consensus        86 ~a~~~~~   92 (104)
T 2dhg_A           86 VAIPKAS   92 (104)
T ss_dssp             BCCCCCS
T ss_pred             EccCCCc
Confidence            9976543

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.7e-17  Score=131.55  Aligned_cols=83  Identities=28%  Similarity=0.492  Sum_probs=77.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCC-CCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT-GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ...++|||+|||..+++++|+++|+.|| |..|.|+.++.+ |.++|||||+|.+.++|.+|| .|||..|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            4457999999999999999999999999 999999999887 999999999999999999999 8999999999999999


Q ss_pred             ccCCCC
Q 009944          371 ATASSG  376 (522)
Q Consensus       371 ~~~~~~  376 (522)
                      +.++..
T Consensus        91 a~~~~~   96 (104)
T 1wi8_A           91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            987643

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

Probab=99.72  E-value=4e-17  Score=127.40  Aligned_cols=82  Identities=30%  Similarity=0.589  Sum_probs=76.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|++||.|..|.++.+  +|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus         6 ~~~~~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            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45579999999999999999999999999999999984  8899999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      .+..
T Consensus        84 ~~~~   87 (92)
T 2dgv_A           84 RNAS   87 (92)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            7753

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=8.6e-17  Score=128.37  Aligned_cols=84  Identities=25%  Similarity=0.556  Sum_probs=77.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.+..  .++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~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           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            44568999999999999999999999999999999998853  3899999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009944          371 ATASSG  376 (522)
Q Consensus       371 ~~~~~~  376 (522)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2cq3_A           90 ATARVM   95 (103)
T ss_dssp             CCSSCC
T ss_pred             cccCCC
Confidence            987654

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.71  E-value=2.5e-17  Score=141.21  Aligned_cols=81  Identities=25%  Similarity=0.430  Sum_probs=76.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcC--CceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFG--TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G--~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ..++|||+|||+.+++++|+++|+.||  .|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            457999999999999999999999999  899999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 009944          371 ATA  373 (522)
Q Consensus       371 ~~~  373 (522)
                      +.+
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            964

>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=99.71  E-value=1e-16  Score=127.88  Aligned_cols=85  Identities=24%  Similarity=0.393  Sum_probs=78.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||.  ++..|.|+.|.|.+
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            4456789999999999999999999999999999999998899999999999999999999998  57899999999999


Q ss_pred             ccCCCCC
Q 009944          371 ATASSGQ  377 (522)
Q Consensus       371 ~~~~~~~  377 (522)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cqg_A           90 PNSKQSQ   96 (103)
T ss_dssp             CCTTCCC
T ss_pred             cCCCCcC
Confidence            9876543

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

Probab=99.71  E-value=5.1e-17  Score=126.17  Aligned_cols=77  Identities=17%  Similarity=0.160  Sum_probs=70.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCc--cCCeEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK--MGDKTLTVR  369 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~--~~g~~l~v~  369 (522)
                      .+.++|||+|||..+|+++|.++|++||.|..|.+++      .+|||||+|.+.++|.+|++.|+|..  |.|++|.|.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            4457899999999999999999999999999999885      36899999999999999999999865  789999999


Q ss_pred             EccCC
Q 009944          370 RATAS  374 (522)
Q Consensus       370 ~~~~~  374 (522)
                      |++.+
T Consensus        93 ~S~~k   97 (100)
T 3r27_A           93 YSTSQ   97 (100)
T ss_dssp             ECSCS
T ss_pred             ecccc
Confidence            99764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.71  E-value=1.2e-16  Score=135.22  Aligned_cols=85  Identities=31%  Similarity=0.531  Sum_probs=80.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.+
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      +.++.
T Consensus       119 a~~~~  123 (139)
T 1u6f_A          119 AASGH  123 (139)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            98754

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=1.2e-16  Score=130.18  Aligned_cols=83  Identities=23%  Similarity=0.372  Sum_probs=77.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            3456799999999999999999999999999999999997 699999999999999999999999999999999999999


Q ss_pred             ccCC
Q 009944          371 ATAS  374 (522)
Q Consensus       371 ~~~~  374 (522)
                      +...
T Consensus        91 a~~~   94 (114)
T 2do0_A           91 DERA   94 (114)
T ss_dssp             CSCC
T ss_pred             cccC
Confidence            8653

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=8.1e-17  Score=125.31  Aligned_cols=81  Identities=23%  Similarity=0.365  Sum_probs=76.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ....+|||+|||..+++++|+++|+.| .|..|.|+.+ .+|.++|||||+|.+.++|.+||. |||..|.|+.|.|.++
T Consensus         8 ~~~~~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            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            445799999999999999999999999 9999999999 689999999999999999999999 9999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      .++.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7753

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.71  E-value=1.3e-16  Score=131.85  Aligned_cols=85  Identities=21%  Similarity=0.345  Sum_probs=79.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            4556789999999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009944          371 ATASSG  376 (522)
Q Consensus       371 ~~~~~~  376 (522)
                      +.....
T Consensus       111 a~~~~~  116 (124)
T 2kt5_A          111 VASQID  116 (124)
T ss_dssp             ECCTTC
T ss_pred             eCCCCC
Confidence            987543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.71  E-value=1.1e-17  Score=125.04  Aligned_cols=75  Identities=25%  Similarity=0.585  Sum_probs=72.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      +|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|++|++ |+|..|.|+.|.|.+|
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            58999999999999999999999999999999998899999999999999999999998 9999999999999875

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=5.9e-17  Score=132.36  Aligned_cols=83  Identities=33%  Similarity=0.605  Sum_probs=78.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||..|++ .|.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            34567999999999999999999999999999999999988999999999999999999999999998 89999999999


Q ss_pred             ccCC
Q 009944          371 ATAS  374 (522)
Q Consensus       371 ~~~~  374 (522)
                      +...
T Consensus        93 a~~~   96 (116)
T 2cqd_A           93 AYLG   96 (116)
T ss_dssp             STTT
T ss_pred             cccC
Confidence            9664

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.7e-17  Score=131.59  Aligned_cols=77  Identities=22%  Similarity=0.266  Sum_probs=73.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      .++|||+|||+.+|+++|.++|++||.|..|.|+.++. |.++|||||+|.+.++|.+||. ++|..|.|+.|.|.++.
T Consensus        11 ~~~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           11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             GGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            46899999999999999999999999999999999986 9999999999999999999999 99999999999999874

>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=99.71  E-value=3.3e-17  Score=136.06  Aligned_cols=84  Identities=25%  Similarity=0.345  Sum_probs=79.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||..+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.|+.
T Consensus        21 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  100 (126)
T 3ex7_B           21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF  100 (126)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEec
Confidence            45689999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 009944          373 ASSG  376 (522)
Q Consensus       373 ~~~~  376 (522)
                      ++..
T Consensus       101 ~~~~  104 (126)
T 3ex7_B          101 VRGP  104 (126)
T ss_dssp             ESSS
T ss_pred             CCCC
Confidence            7543

>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=99.70  E-value=2.5e-17  Score=131.81  Aligned_cols=81  Identities=42%  Similarity=0.727  Sum_probs=77.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.++.+
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   87 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCC
Confidence            36899999999999999999999999999999999988999999999999999999999999999999999999999976


Q ss_pred             C
Q 009944          374 S  374 (522)
Q Consensus       374 ~  374 (522)
                      .
T Consensus        88 ~   88 (104)
T 1p1t_A           88 E   88 (104)
T ss_dssp             T
T ss_pred             c
Confidence            3

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.70  E-value=3.8e-17  Score=131.55  Aligned_cols=86  Identities=26%  Similarity=0.434  Sum_probs=77.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||..+ +..|.|+.|.|.+
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            345579999999999999999999999999999999999889999999999999999999999976 5999999999999


Q ss_pred             ccCCCCC
Q 009944          371 ATASSGQ  377 (522)
Q Consensus       371 ~~~~~~~  377 (522)
                      +.++...
T Consensus       101 a~~~~~~  107 (109)
T 2rs2_A          101 AFPRRAQ  107 (109)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9876544

>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=99.70  E-value=4.6e-18  Score=170.55  Aligned_cols=83  Identities=20%  Similarity=0.425  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||+.||+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.|+
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            34579999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCC
Q 009944          372 TAS  374 (522)
Q Consensus       372 ~~~  374 (522)
                      ...
T Consensus       180 ~~~  182 (437)
T 3pgw_S          180 RGR  182 (437)
T ss_pred             CCC
Confidence            764

>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=99.70  E-value=4.3e-17  Score=132.97  Aligned_cols=79  Identities=20%  Similarity=0.408  Sum_probs=73.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|.++|+.||.|..|.++.+   +.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+
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 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            34579999999999999999999999999999999865   556999999999999999999999999999999999999


Q ss_pred             cC
Q 009944          372 TA  373 (522)
Q Consensus       372 ~~  373 (522)
                      .+
T Consensus        83 ~~   84 (115)
T 3lqv_A           83 NA   84 (115)
T ss_dssp             CH
T ss_pred             cC
Confidence            65

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=8.4e-18  Score=129.15  Aligned_cols=81  Identities=21%  Similarity=0.420  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      .+.++|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|+|.++
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            34579999999999999999999999999999999999889999999999999999999999999999999999988775


Q ss_pred             c
Q 009944          372 T  372 (522)
Q Consensus       372 ~  372 (522)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=1.2e-16  Score=137.87  Aligned_cols=85  Identities=24%  Similarity=0.372  Sum_probs=80.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.|||..|.|+.|.|.|+
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            45679999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009944          372 TASSG  376 (522)
Q Consensus       372 ~~~~~  376 (522)
                      .+...
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            87543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=6.6e-17  Score=130.19  Aligned_cols=82  Identities=26%  Similarity=0.585  Sum_probs=76.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.++.+.  +.++|||||+|.+.++|.+|+..|+|..|.|+.|.|.+
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            4456899999999999999999999999999999999884  45899999999999999999999999999999999999


Q ss_pred             ccCC
Q 009944          371 ATAS  374 (522)
Q Consensus       371 ~~~~  374 (522)
                      +.++
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9764

>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=99.69  E-value=4.6e-17  Score=132.57  Aligned_cols=79  Identities=18%  Similarity=0.365  Sum_probs=75.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|| .|||..|.|+.|.|.++.+
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            468999999999999999999999999999999999989999999999999999999999 9999999999999999854

>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=99.69  E-value=5.7e-17  Score=131.12  Aligned_cols=84  Identities=18%  Similarity=0.270  Sum_probs=76.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH---HHHHhcCCceEEEEeeCCCCC---CcceEEEEEEcChHHHHHHHHHHcCCccCCeE
Q 009944          292 EGPDRVFVGGLPYYFTETQIK---ELLESFGTLHGFDLVKDRDTG---NSKGYGFCVYQDPAVTDIACAALNGLKMGDKT  365 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~---~~F~~~G~i~~v~~~~~~~~g---~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~  365 (522)
                      ...++|||+|||+.+++++|.   ++|++||.|..|.|+.+..++   .++|||||+|.+.++|++||+.|||..|.|+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            345789999999999999999   999999999999999887644   55699999999999999999999999999999


Q ss_pred             EEEEEccCCC
Q 009944          366 LTVRRATASS  375 (522)
Q Consensus       366 l~v~~~~~~~  375 (522)
                      |.|.++.++.
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999998764

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.69  E-value=1e-16  Score=135.83  Aligned_cols=82  Identities=20%  Similarity=0.343  Sum_probs=77.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEE
Q 009944          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (522)
Q Consensus       290 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (522)
                      .....++|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.
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            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             Ec
Q 009944          370 RA  371 (522)
Q Consensus       370 ~~  371 (522)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            85

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.69  E-value=2.7e-17  Score=137.34  Aligned_cols=82  Identities=22%  Similarity=0.295  Sum_probs=77.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceE--EEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCC----ccCCeE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHG--FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL----KMGDKT  365 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~--v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~----~~~g~~  365 (522)
                      ...++|||+|||+.+++++|+++|++||.|..  |.|+.++.+|.++|||||+|.+. +|.+|+..|||.    .|.|+.
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            45679999999999999999999999999976  99999999999999999999999 999999999999    999999


Q ss_pred             EEEEEccCC
Q 009944          366 LTVRRATAS  374 (522)
Q Consensus       366 l~v~~~~~~  374 (522)
                      |.|.++.+.
T Consensus       100 l~V~~a~~~  108 (131)
T 2m2b_A          100 INVEFAKGS  108 (131)
T ss_dssp             CCCEECCCS
T ss_pred             EEEEECCCC
Confidence            999999764

>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=99.69  E-value=1.1e-17  Score=129.96  Aligned_cols=80  Identities=33%  Similarity=0.561  Sum_probs=74.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      ++|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.+ |.+|+..|||..|.|+.|.|.++.+.
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            48999999999999999999999999999999999889999999999999999 99999999999999999999999764


Q ss_pred             C
Q 009944          375 S  375 (522)
Q Consensus       375 ~  375 (522)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.69  E-value=1e-16  Score=128.15  Aligned_cols=80  Identities=24%  Similarity=0.320  Sum_probs=74.3

Q ss_pred             CCCeEEEcCCCCCC------CHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCe-E
Q 009944          293 GPDRVFVGGLPYYF------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK-T  365 (522)
Q Consensus       293 ~~~~l~v~nLp~~~------t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~-~  365 (522)
                      ..++|||+|||..+      ++++|+++|++||.|..|.|+  ..+|.++|||||+|.+.++|.+|+..|||..|.|+ .
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            35789999999999      789999999999999999988  35899999999999999999999999999999998 9


Q ss_pred             EEEEEccCC
Q 009944          366 LTVRRATAS  374 (522)
Q Consensus       366 l~v~~~~~~  374 (522)
                      |.|.++...
T Consensus        92 l~V~~a~~~  100 (105)
T 2nlw_A           92 FRVNLFTDF  100 (105)
T ss_dssp             EEEECSCCC
T ss_pred             EEEEEcchH
Confidence            999999764

>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=6.6e-17  Score=132.07  Aligned_cols=82  Identities=27%  Similarity=0.502  Sum_probs=77.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||.. +|..|.|+.|.|.++.+
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCC
Confidence            47999999999999999999999999999999999988999999999999999999999997 99999999999999987


Q ss_pred             CCC
Q 009944          374 SSG  376 (522)
Q Consensus       374 ~~~  376 (522)
                      +..
T Consensus       106 ~~~  108 (116)
T 1x4b_A          106 REE  108 (116)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            654

>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=99.68  E-value=5.6e-17  Score=128.60  Aligned_cols=81  Identities=16%  Similarity=0.207  Sum_probs=74.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      .....+|||+|||+.+++++|+++|+.||.| .|.|+.++ +|.++|||||+|.+.++|++||+ +|+..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3455799999999999999999999999955 99999997 89999999999999999999995 799999999999999


Q ss_pred             ccCC
Q 009944          371 ATAS  374 (522)
Q Consensus       371 ~~~~  374 (522)
                      +...
T Consensus        89 ~~~~   92 (102)
T 1wez_A           89 NSTA   92 (102)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8764

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=2.6e-17  Score=123.80  Aligned_cols=76  Identities=28%  Similarity=0.494  Sum_probs=73.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ++|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|+..++ ..|.|+.|.|.+|
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            379999999999999999999999999999999998899999999999999999999999999 9999999999987

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=3.3e-16  Score=126.33  Aligned_cols=82  Identities=20%  Similarity=0.395  Sum_probs=74.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.|..   ++.++|||||+|.+.++|++||+.|||..|.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34567999999999999999999999999999999865   456899999999999999999999999999999999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      +.+..
T Consensus        96 a~~~~  100 (109)
T 1x4a_A           96 PRSGR  100 (109)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            97754

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.68  E-value=9.7e-17  Score=131.09  Aligned_cols=80  Identities=18%  Similarity=0.308  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCC---ceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGT---LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~---i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (522)
                      ...++|||+|||+.+|+++|+++|+.||.   |..|.|+.++. |.++|||||+|.+.++|.+||+ |||..|+|+.|.|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            45578999999999999999999999999   89999999975 9999999999999999999999 9999999999999


Q ss_pred             EEccC
Q 009944          369 RRATA  373 (522)
Q Consensus       369 ~~~~~  373 (522)
                      .++..
T Consensus        93 ~~a~~   97 (118)
T 2db1_A           93 FKSHR   97 (118)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            99853

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=2e-16  Score=124.46  Aligned_cols=79  Identities=14%  Similarity=0.153  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHc--CCccCCeEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTVR  369 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~v~  369 (522)
                      .+.++|||+|||..+++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|++.|+  +..|.|++|.|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   86 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   86 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEE
Confidence            45579999999999999999999999999999988764      7999999999999999999875  678999999999


Q ss_pred             EccCCCC
Q 009944          370 RATASSG  376 (522)
Q Consensus       370 ~~~~~~~  376 (522)
                      |+..+..
T Consensus        87 ~a~~~~~   93 (101)
T 2cq1_A           87 YSNHKEL   93 (101)
T ss_dssp             ECSCSSC
T ss_pred             EcCcccC
Confidence            9987543

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=6.1e-17  Score=131.59  Aligned_cols=81  Identities=12%  Similarity=0.215  Sum_probs=75.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCc-eEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTL-HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i-~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (522)
                      ....++|||+|||+.+++++|+++|+.||.| ..|.|+.++ +|.++|||||+|.+.++|.+||.. ||..|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            3456799999999999999999999999999 899999998 999999999999999999999986 9999999999999


Q ss_pred             EccC
Q 009944          370 RATA  373 (522)
Q Consensus       370 ~~~~  373 (522)
                      ++.+
T Consensus        90 ~a~~   93 (114)
T 2cpy_A           90 VVTL   93 (114)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            9854

>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=99.68  E-value=1.7e-16  Score=127.89  Aligned_cols=80  Identities=13%  Similarity=0.168  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcC--CccCCeEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVR  369 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v~  369 (522)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|++.|++  ..|.|++|.|.
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            34578999999999999999999999999999999875      69999999999999999999874  68999999999


Q ss_pred             EccCCCCC
Q 009944          370 RATASSGQ  377 (522)
Q Consensus       370 ~~~~~~~~  377 (522)
                      |+..+...
T Consensus       103 ~a~~k~~~  110 (119)
T 2ad9_A          103 FSNHKELK  110 (119)
T ss_dssp             ECSSSSCC
T ss_pred             EccCCCCC
Confidence            99876443

>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=99.67  E-value=1.2e-16  Score=129.02  Aligned_cols=83  Identities=19%  Similarity=0.338  Sum_probs=77.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCC-ceEEEEe-eCCCCCCcceEEEEEEcChHHHHHHHHHHc--CCccCCeEEEE
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLV-KDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTV  368 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~-i~~v~~~-~~~~~g~~~g~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~v  368 (522)
                      ..++|||+|||..+++++|+++|+.||. |..|.++ .+..+|.++|||||+|.+.++|.+|+..|+  +..|.|+.|.|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V   86 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   86 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEE
Confidence            3468999999999999999999999998 9999998 787889999999999999999999999996  59999999999


Q ss_pred             EEccCCC
Q 009944          369 RRATASS  375 (522)
Q Consensus       369 ~~~~~~~  375 (522)
                      .|+.++.
T Consensus        87 ~~a~~~~   93 (109)
T 2dis_A           87 DWAEPEI   93 (109)
T ss_dssp             EESCSSC
T ss_pred             EEcCCCC
Confidence            9998754

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=2.1e-16  Score=128.61  Aligned_cols=82  Identities=21%  Similarity=0.484  Sum_probs=77.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc--------CC
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--------GD  363 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--------~g  363 (522)
                      ...++|||+|||..+++++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|.+|+..|||..|        .+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            455799999999999999999999999999999999997 999999999999999999999999999999        68


Q ss_pred             eEEEEEEccCC
Q 009944          364 KTLTVRRATAS  374 (522)
Q Consensus       364 ~~l~v~~~~~~  374 (522)
                      ++|.|.|+.++
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            88999999764

>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=99.67  E-value=1.3e-16  Score=127.32  Aligned_cols=82  Identities=16%  Similarity=0.329  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceE-EEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~-v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....+|||+|||+.+++++|+++|+.||.|.. |.|+.+ .+|.++|||||+|.+.++|.+||.. ++..|+|+.|.|.+
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            44579999999999999999999999999987 888888 6999999999999999999999997 99999999999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      +....
T Consensus        91 ~~~~~   95 (104)
T 1wg5_A           91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            87643

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=1e-16  Score=125.89  Aligned_cols=77  Identities=14%  Similarity=0.102  Sum_probs=70.1

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCC--ccCCeEEEE
Q 009944          292 EGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL--KMGDKTLTV  368 (522)
Q Consensus       292 ~~~~~l~v~nLp~-~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~--~~~g~~l~v  368 (522)
                      .+.++|||+|||+ .+++++|+++|++||.|..|.|+++      +|||||+|.+.++|.+|++.|++.  .|.|++|.|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            3567899999999 9999999999999999999999865      479999999999999999999864  599999999


Q ss_pred             EEccCC
Q 009944          369 RRATAS  374 (522)
Q Consensus       369 ~~~~~~  374 (522)
                      .|+...
T Consensus        87 ~~a~~~   92 (102)
T 1x4d_A           87 HLSQKY   92 (102)
T ss_dssp             EEECCC
T ss_pred             EECCCC
Confidence            999854

>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=99.67  E-value=2.7e-17  Score=130.36  Aligned_cols=81  Identities=27%  Similarity=0.506  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCC-CCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~-~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ...++|||+|||..+++++|+++|+.|| |..|.|+.++ .+|.++|||||+|.+.++|.+|+ .|+|..|.|+.|.|.+
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            4457999999999999999999999999 9999999987 58999999999999999999999 8999999999999999


Q ss_pred             ccCC
Q 009944          371 ATAS  374 (522)
Q Consensus       371 ~~~~  374 (522)
                      +.++
T Consensus        95 a~~~   98 (100)
T 2j76_E           95 ADQA   98 (100)
T ss_dssp             CCCS
T ss_pred             ccCC
Confidence            9764

>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=99.67  E-value=2.8e-16  Score=124.51  Aligned_cols=78  Identities=17%  Similarity=0.155  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCC--ccCCeEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL--KMGDKTLTVR  369 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~--~~~g~~l~v~  369 (522)
                      .+.++|||+|||..+++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|++.|++.  .|.|++|.|.
T Consensus        13 ~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           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            44579999999999999999999999999999998753      689999999999999999998764  5999999999


Q ss_pred             EccCCC
Q 009944          370 RATASS  375 (522)
Q Consensus       370 ~~~~~~  375 (522)
                      |+..+.
T Consensus        87 ~a~~~~   92 (104)
T 1wex_A           87 YSTSKR   92 (104)
T ss_dssp             ECSSSS
T ss_pred             EccCcc
Confidence            997754

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.67  E-value=1.6e-16  Score=131.47  Aligned_cols=80  Identities=21%  Similarity=0.422  Sum_probs=76.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.++..
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            479999999999999999999999999999999999889999999999999999999999 7999999999999999876


Q ss_pred             C
Q 009944          374 S  374 (522)
Q Consensus       374 ~  374 (522)
                      .
T Consensus       115 ~  115 (124)
T 2jwn_A          115 N  115 (124)
T ss_dssp             C
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=99.67  E-value=9.2e-17  Score=133.66  Aligned_cols=80  Identities=18%  Similarity=0.279  Sum_probs=75.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCC---ceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGT---LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~---i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (522)
                      ...++|||+|||+.+|+++|+++|+.||.   |..|.|+.++. |.++|||||+|.+.++|++||+ |||..|+|+.|.|
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  119 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            44578999999999999999999999999   89999999976 9999999999999999999999 9999999999999


Q ss_pred             EEccC
Q 009944          369 RRATA  373 (522)
Q Consensus       369 ~~~~~  373 (522)
                      .++..
T Consensus       120 ~~a~~  124 (136)
T 2hgl_A          120 FKSHR  124 (136)
T ss_dssp             EECCH
T ss_pred             EECCh
Confidence            99853

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=4.8e-16  Score=125.00  Aligned_cols=77  Identities=22%  Similarity=0.289  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC-----eEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD-----KTL  366 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g-----~~l  366 (522)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.+       |||||+|.+.++|++||+.|||..|.|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            44579999999999999999999999999999999875       799999999999999999999999999     999


Q ss_pred             EEEEccCCC
Q 009944          367 TVRRATASS  375 (522)
Q Consensus       367 ~v~~~~~~~  375 (522)
                      .|.++.++.
T Consensus        86 ~V~~a~~~~   94 (108)
T 1x4c_A           86 RVKVDGPRS   94 (108)
T ss_dssp             EEEESSCCS
T ss_pred             EEEeCCCCC
Confidence            999998754

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

Probab=99.66  E-value=2.3e-16  Score=129.69  Aligned_cols=80  Identities=13%  Similarity=0.231  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~----~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      .+.++|||+|||+.+++++|+    ++|++||.|..|.+..   ++.++|||||+|.+.++|.+|+..|||..|.|++|.
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            345789999999999999866    7999999999887753   688999999999999999999999999999999999


Q ss_pred             EEEccCC
Q 009944          368 VRRATAS  374 (522)
Q Consensus       368 v~~~~~~  374 (522)
                      |.|+..+
T Consensus       104 V~~a~~~  110 (127)
T 2a3j_A          104 ITFSETP  110 (127)
T ss_dssp             EEECCCC
T ss_pred             EEEccCc
Confidence            9999764

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.66  E-value=2e-16  Score=126.66  Aligned_cols=79  Identities=16%  Similarity=0.155  Sum_probs=71.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcC-CceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G-~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....+|||+|||+.+++++|+++|+.|| .|..+.+..    +.++|||||+|.+.++|++||+.|||..|.|+.|.|.+
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3456899999999999999999999999 899998863    24789999999999999999999999999999999999


Q ss_pred             ccCC
Q 009944          371 ATAS  374 (522)
Q Consensus       371 ~~~~  374 (522)
                      +..+
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            8653

>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=99.66  E-value=5.3e-17  Score=121.40  Aligned_cols=75  Identities=23%  Similarity=0.432  Sum_probs=71.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      +|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|++ +++..|.|+.|.|.+|
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            58999999999999999999999999999999998899999999999999999999999 5899999999999875

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=4e-16  Score=121.02  Aligned_cols=77  Identities=29%  Similarity=0.510  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|++||.|..|.++        +|||||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus         6 ~~~~~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            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            455799999999999999999999999999999987        579999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009944          372 TASSG  376 (522)
Q Consensus       372 ~~~~~  376 (522)
                      .++..
T Consensus        78 ~~~~~   82 (90)
T 2dnq_A           78 KNKSK   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87543

>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=99.66  E-value=5.2e-17  Score=134.24  Aligned_cols=82  Identities=18%  Similarity=0.309  Sum_probs=75.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      .....+|||+|||+.+++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+||. |||..|.|+.|.|.+
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            3455799999999999999999999999999886666666799999999999999999999999 999999999999999


Q ss_pred             ccC
Q 009944          371 ATA  373 (522)
Q Consensus       371 ~~~  373 (522)
                      +..
T Consensus       101 a~~  103 (124)
T 1wel_A          101 ITK  103 (124)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            854

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=3.7e-16  Score=124.17  Aligned_cols=81  Identities=17%  Similarity=0.308  Sum_probs=73.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|   .++.+ .++.++|||||+|.+.++|++||..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            3456899999999999999999999999977   55665 5899999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      +.++.
T Consensus        88 a~~~~   92 (101)
T 2fc9_A           88 QGPRG   92 (101)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            98754

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=1.8e-16  Score=126.70  Aligned_cols=76  Identities=25%  Similarity=0.373  Sum_probs=71.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..+|||+|||+.+++++|+++|+.| .|..|.|+.++. |.++|||||+|.+.++|.+|| .+||..|+|+.|.|..+.
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            3589999999999999999999999 899999999974 999999999999999999999 699999999999999874

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.65  E-value=6e-17  Score=122.96  Aligned_cols=72  Identities=25%  Similarity=0.401  Sum_probs=67.4

Q ss_pred             CeEEEcCCCCCC------CHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCe-EEE
Q 009944          295 DRVFVGGLPYYF------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK-TLT  367 (522)
Q Consensus       295 ~~l~v~nLp~~~------t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~-~l~  367 (522)
                      ++|||+|||..+      ++++|+++|++||.|..|.++  +.+|.++|||||+|.+.++|.+|+..|||..|.|+ +|.
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            589999999999      779999999999999999988  35899999999999999999999999999999999 887


Q ss_pred             E
Q 009944          368 V  368 (522)
Q Consensus       368 v  368 (522)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=5.5e-16  Score=123.42  Aligned_cols=82  Identities=27%  Similarity=0.401  Sum_probs=74.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.|+   .|.++.++.++.++|||||+|.+.++|.+||..|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            34567899999999999999999999773   677888888999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      +.++.
T Consensus        89 a~~~~   93 (102)
T 2fc8_A           89 AKPKG   93 (102)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            98754

>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=99.65  E-value=7.4e-16  Score=122.81  Aligned_cols=78  Identities=19%  Similarity=0.305  Sum_probs=71.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.++        +|||||+|.+.++|.+|++.|||..|.|+.|.|.+
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            3456789999999999999999999999999999887        35999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009944          371 ATASSG  376 (522)
Q Consensus       371 ~~~~~~  376 (522)
                      +.++..
T Consensus        80 a~~~~~   85 (103)
T 2dgu_A           80 AKPPDQ   85 (103)
T ss_dssp             CCCCCC
T ss_pred             cCCCcc
Confidence            987654

>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=4.8e-17  Score=129.33  Aligned_cols=82  Identities=18%  Similarity=0.308  Sum_probs=74.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ....+|||+|||..+++++|+++|+.||.|.. .++.+..+|.++|||||+|.+.++|.+||+ |||..|.|+.|.|.++
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            34578999999999999999999999999887 666666689999999999999999999998 9999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      .++.
T Consensus        93 ~~~~   96 (101)
T 1fj7_A           93 KGRD   96 (101)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7754

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.65  E-value=5.4e-16  Score=115.60  Aligned_cols=72  Identities=18%  Similarity=0.233  Sum_probs=67.5

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~  252 (522)
                      +..|||+||++.+|+++|+++|.+||+            |.++.+..++|||||+|.++++|.+|+ .||+..+.|++|+
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~------------V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~   74 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGP------------LVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTIF   74 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCC------------EEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEE
Confidence            457999999999999999999999997            788888889999999999999999999 7999999999999


Q ss_pred             EecCC
Q 009944          253 VRRPT  257 (522)
Q Consensus       253 v~~~~  257 (522)
                      |..+.
T Consensus        75 V~~A~   79 (89)
T 2wbr_A           75 AESPS   79 (89)
T ss_dssp             EECCC
T ss_pred             EEECC
Confidence            99863

>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=99.65  E-value=5.6e-16  Score=122.06  Aligned_cols=78  Identities=26%  Similarity=0.523  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC--CeEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG--DKTLTVR  369 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~--g~~l~v~  369 (522)
                      ...++|||+|||..+++++|+++|++||.|..|.++.+      +|||||+|.+.++|++|++.|||..|.  |+.|.|.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            34578999999999999999999999999999988754      689999999999999999999999999  9999999


Q ss_pred             EccCCC
Q 009944          370 RATASS  375 (522)
Q Consensus       370 ~~~~~~  375 (522)
                      |+.++.
T Consensus        89 ~a~~~~   94 (97)
T 1why_A           89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            997753

>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=99.65  E-value=2.3e-16  Score=144.52  Aligned_cols=81  Identities=17%  Similarity=0.334  Sum_probs=76.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcC--CceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFG--TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G--~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ..++|||+|||+.+|+++|+++|+.||  .|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.+
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  999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 009944          371 ATA  373 (522)
Q Consensus       371 ~~~  373 (522)
                      +.+
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=7.1e-16  Score=121.99  Aligned_cols=79  Identities=33%  Similarity=0.532  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|++.|+|..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            345579999999999999999999999999999998854      68999999999999999999999999999999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      +.++.
T Consensus        86 a~~~~   90 (99)
T 2cpj_A           86 ACHSA   90 (99)
T ss_dssp             SSCCS
T ss_pred             cCCCC
Confidence            97754

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.64  E-value=8.4e-17  Score=129.15  Aligned_cols=81  Identities=16%  Similarity=0.265  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCC---ceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGT---LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~---i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      .....+|||+|||+.+|+++|+++|+.||.   |..|.|+.++. |.++|||||+|.+.++|.+||. ++|..|+|+.|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            345678999999999999999999999998   89999999976 9999999999999999999999 999999999999


Q ss_pred             EEEccC
Q 009944          368 VRRATA  373 (522)
Q Consensus       368 v~~~~~  373 (522)
                      |.++.+
T Consensus        86 V~~a~~   91 (107)
T 2lmi_A           86 VYEINN   91 (107)
T ss_dssp             CEECCH
T ss_pred             EEECCH
Confidence            999854

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=1e-15  Score=118.77  Aligned_cols=77  Identities=27%  Similarity=0.397  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|++||.|..|.+++        +||||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            4557899999999999999999999999999999874        38999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009944          372 TASSG  376 (522)
Q Consensus       372 ~~~~~  376 (522)
                      .+...
T Consensus        79 ~~~~~   83 (90)
T 2dnp_A           79 TKGQK   83 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.64  E-value=3.5e-16  Score=124.56  Aligned_cols=79  Identities=13%  Similarity=0.092  Sum_probs=72.1

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcC----hHH----HHHHHH--HHcCCc
Q 009944          295 DRVFVGGL----PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD----PAV----TDIACA--ALNGLK  360 (522)
Q Consensus       295 ~~l~v~nL----p~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~----~~~----A~~Al~--~l~g~~  360 (522)
                      +.|||+||    |+.+++++|+++|+.||.|..+.++.|+.||.++|||||+|.+    +++    |.+|+.  .|+|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            58999999    9999999999999999999999999999999999999999996    333    788888  789999


Q ss_pred             cCCeEEEEEEccC
Q 009944          361 MGDKTLTVRRATA  373 (522)
Q Consensus       361 ~~g~~l~v~~~~~  373 (522)
                      |+|+.|.|.+...
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999998754

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

Probab=99.64  E-value=2.9e-16  Score=124.81  Aligned_cols=75  Identities=20%  Similarity=0.403  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||..+++++|+++|+.||.|..|.+..      ++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+.
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 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            457999999999999999999999999999999873      57999999999999999999999999999999999986


Q ss_pred             C
Q 009944          373 A  373 (522)
Q Consensus       373 ~  373 (522)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.64  E-value=2.6e-16  Score=124.05  Aligned_cols=80  Identities=14%  Similarity=0.360  Sum_probs=74.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~----~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      .+.++|||+|||..+++++|+    ++|++||.|..|.++.   +|.++|||||+|.+.++|.+|+..|||..|.|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            345799999999999999999    9999999999998873   577889999999999999999999999999999999


Q ss_pred             EEEccCC
Q 009944          368 VRRATAS  374 (522)
Q Consensus       368 v~~~~~~  374 (522)
                      |.|+.++
T Consensus        83 v~~a~~~   89 (97)
T 1nu4_A           83 IQYAKTD   89 (97)
T ss_dssp             EEECSSC
T ss_pred             EEEccCC
Confidence            9999774

>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=99.64  E-value=5.9e-17  Score=135.25  Aligned_cols=81  Identities=16%  Similarity=0.197  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ....+|||+|||+++|+++|+++|++|| |..|.|+.++. |.++|||||+|.+.++|++|| .+|+..|.|+.|.|.++
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  120 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            3457899999999999999999999999 66999999975 999999999999999999999 68999999999999998


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      ....
T Consensus       121 ~~~~  124 (139)
T 2hgn_A          121 STTG  124 (139)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7643

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=9.7e-16  Score=120.65  Aligned_cols=79  Identities=28%  Similarity=0.426  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|+.||.|. +.++.    +.++|||||+|.+.++|++|+..|||..|.|+.|.|.++
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            4457999999999999999999999999997 66664    357899999999999999999999999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      .++.
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7753

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=1.8e-15  Score=117.84  Aligned_cols=76  Identities=20%  Similarity=0.346  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|++||.|..|.+++        +||||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            4457899999999999999999999999999999874        39999999999999999999999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      .++.
T Consensus        80 ~~~~   83 (92)
T 2dgt_A           80 TSRL   83 (92)
T ss_dssp             SCCC
T ss_pred             cCCC
Confidence            7754

>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=99.64  E-value=1e-15  Score=123.34  Aligned_cols=79  Identities=18%  Similarity=0.372  Sum_probs=73.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|+.||.|..|.|+.+      +|||||+|.+.++|.+|+..|+|..|.|+.|.|.|+
T Consensus        23 ~~~~~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           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            34579999999999999999999999999999999875      689999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009944          372 TASSG  376 (522)
Q Consensus       372 ~~~~~  376 (522)
                      .+...
T Consensus        97 ~~~~~  101 (109)
T 1x4g_A           97 KESPD  101 (109)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            87543

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=7.5e-16  Score=118.17  Aligned_cols=75  Identities=21%  Similarity=0.403  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHH-cCCccCCeEEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVRR  370 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v~~  370 (522)
                      ...++|||+|||..+++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|+..| +|..|.|+.|.|.|
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            44578999999999999999999999999999999863      689999999999999999998 99999999999999


Q ss_pred             cc
Q 009944          371 AT  372 (522)
Q Consensus       371 ~~  372 (522)
                      +.
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            73

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.64  E-value=4.9e-16  Score=123.44  Aligned_cols=76  Identities=20%  Similarity=0.375  Sum_probs=71.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      ++|||+|||..+++++|+++|++||.|..|.++.+     ++|||||+|.+.++|.+|++.|+|..|.|+.|.|.++.++
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            47999999999999999999999999999999876     6899999999999999999999999999999999999775


Q ss_pred             C
Q 009944          375 S  375 (522)
Q Consensus       375 ~  375 (522)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.64  E-value=8.5e-16  Score=123.25  Aligned_cols=77  Identities=18%  Similarity=0.446  Sum_probs=71.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|++||.|..|.++        +|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3456799999999999999999999999999999987        68999999999999999999999999999999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      +.++.
T Consensus       100 a~~~~  104 (108)
T 2jvo_A          100 SKLPA  104 (108)
T ss_dssp             CSCCC
T ss_pred             ecCCC
Confidence            97753

>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=99.63  E-value=1.7e-16  Score=129.46  Aligned_cols=85  Identities=20%  Similarity=0.258  Sum_probs=73.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|+.||.|..+.+..+..+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            34579999999999999999999999999844322222227889999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009944          372 TASSG  376 (522)
Q Consensus       372 ~~~~~  376 (522)
                      .++..
T Consensus       103 ~~~~~  107 (115)
T 2cpx_A          103 KNKKQ  107 (115)
T ss_dssp             CCCSC
T ss_pred             cCCCC
Confidence            87543

>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=99.63  E-value=1.9e-15  Score=118.73  Aligned_cols=75  Identities=16%  Similarity=0.363  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          292 EGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       292 ~~~~~l~v~nLp~-~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ...++|||+|||. .+++++|+++|+.||.|..|.+.        +|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus        20 ~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   91 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEV   91 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4457999999998 99999999999999999999883        68999999999999999999999999999999999


Q ss_pred             ccCC
Q 009944          371 ATAS  374 (522)
Q Consensus       371 ~~~~  374 (522)
                      +..+
T Consensus        92 a~~~   95 (97)
T 2xnq_A           92 SSSN   95 (97)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8764

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=3.3e-16  Score=127.89  Aligned_cols=79  Identities=19%  Similarity=0.282  Sum_probs=72.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCc----eEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEE
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTL----HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i----~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (522)
                      ...+|||+|||+.+|+++|+++|++||.|    ..|.|+.+ .+|.++|||||+|.+.++|.+||+. |+..|+|+.|.|
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            45799999999999999999999999975    68999998 4899999999999999999999995 999999999999


Q ss_pred             EEccC
Q 009944          369 RRATA  373 (522)
Q Consensus       369 ~~~~~  373 (522)
                      ..+..
T Consensus       100 ~~a~~  104 (123)
T 2dha_A          100 FRSTA  104 (123)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            98843

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.63  E-value=4.6e-16  Score=122.35  Aligned_cols=79  Identities=15%  Similarity=0.304  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|+..|+|..|.|+.|.|.++
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            345799999999999999999999999988766     247889999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      .++.
T Consensus        89 ~~~~   92 (96)
T 1fjc_A           89 GEKG   92 (96)
T ss_dssp             SSSC
T ss_pred             CCCC
Confidence            7653

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.63  E-value=7.5e-16  Score=135.09  Aligned_cols=82  Identities=22%  Similarity=0.364  Sum_probs=77.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|+.||.|..|.|+.+. +|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            345799999999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             cCC
Q 009944          372 TAS  374 (522)
Q Consensus       372 ~~~  374 (522)
                      ...
T Consensus       165 ~~~  167 (177)
T 2f3j_A          165 ASQ  167 (177)
T ss_dssp             SSG
T ss_pred             cCC
Confidence            763

>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=99.62  E-value=3.6e-16  Score=124.56  Aligned_cols=79  Identities=14%  Similarity=0.213  Sum_probs=70.6

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcC--CccCCeEEE
Q 009944          291 AEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLT  367 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~-~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~  367 (522)
                      ..+.++|||+|||+. +++++|+++|++||.|..|.|++      ++|||||+|.+.++|.+|++.|++  ..|.|++|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            345679999999998 99999999999999999999874      378999999999999999999864  569999999


Q ss_pred             EEEccCCC
Q 009944          368 VRRATASS  375 (522)
Q Consensus       368 v~~~~~~~  375 (522)
                      |.|+..+.
T Consensus        96 V~~a~~~~  103 (112)
T 1x4f_A           96 VDLSEKYK  103 (112)
T ss_dssp             EEEECSCS
T ss_pred             EEECcccc
Confidence            99997654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.62  E-value=6.9e-16  Score=122.59  Aligned_cols=74  Identities=34%  Similarity=0.468  Sum_probs=65.2

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCcEEEEEEeCHHHHHHHH-HhcCceecCceEE
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~-~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~  252 (522)
                      ++|||+|||+.+|+++|+++|.+||.            |..+.+.. ++|||||+|.+.++|.+|+ .|++..|.|+.|.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   68 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGP------------LRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVR   68 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCC------------CSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEE
Confidence            47999999999999999999999997            44555544 5999999999999999999 5999999999999


Q ss_pred             EecCCCCC
Q 009944          253 VRRPTDYN  260 (522)
Q Consensus       253 v~~~~~~~  260 (522)
                      |.+++...
T Consensus        69 V~~a~~~~   76 (101)
T 2hvz_A           69 VELSTGMP   76 (101)
T ss_dssp             EEESSSCC
T ss_pred             EEEccCCC
Confidence            99876554

>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=99.62  E-value=1.1e-15  Score=119.28  Aligned_cols=78  Identities=23%  Similarity=0.393  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCC-ceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcC-CccCCeEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG-LKMGDKTLTVR  369 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~-i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g-~~~~g~~l~v~  369 (522)
                      ...++|||+|||..+++++|+++|++||. |..+.+.       ++|||||+|.+.++|.+|++.||| ..|.|+.|.|.
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            44578999999999999999999999999 6666553       478999999999999999999999 99999999999


Q ss_pred             EccCCCC
Q 009944          370 RATASSG  376 (522)
Q Consensus       370 ~~~~~~~  376 (522)
                      ++.++..
T Consensus        79 ~a~~~~~   85 (93)
T 2cqh_A           79 YSVSKKL   85 (93)
T ss_dssp             ECCCCCC
T ss_pred             EccCccc
Confidence            9987543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.62  E-value=5.6e-16  Score=123.34  Aligned_cols=79  Identities=29%  Similarity=0.586  Sum_probs=74.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+++++|+++|+.||.|..|.++.++ +|.++|||||+|.+.++|.+|+.  +|..|.|+.|.|.++.+
T Consensus         9 ~~~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            9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             EEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCc
Confidence            4689999999999999999999999999999999998 99999999999999999999999  99999999999999976


Q ss_pred             CC
Q 009944          374 SS  375 (522)
Q Consensus       374 ~~  375 (522)
                      +.
T Consensus        86 ~~   87 (102)
T 2xs2_A           86 KQ   87 (102)
T ss_dssp             CC
T ss_pred             Cc
Confidence            53

>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=99.61  E-value=9.8e-16  Score=123.61  Aligned_cols=77  Identities=18%  Similarity=0.141  Sum_probs=71.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+++++|+++|++||.|..|.|+.      ++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+..
T Consensus        10 ~~~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           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            46899999999999999999999999999998874      468999999999999999999999999999999999976


Q ss_pred             CCC
Q 009944          374 SSG  376 (522)
Q Consensus       374 ~~~  376 (522)
                      ...
T Consensus        84 ~~~   86 (111)
T 1whx_A           84 GVF   86 (111)
T ss_dssp             TTT
T ss_pred             Ccc
Confidence            543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.61  E-value=6.3e-16  Score=119.86  Aligned_cols=80  Identities=21%  Similarity=0.196  Sum_probs=66.7

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHH-HhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHH-h-cCceecCce
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVM-TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-L-DGIIFEGVA  250 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g-~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~-~-~~~~~~g~~  250 (522)
                      +++|||+|||+++|+++|+++|.+|| .|...      .++.+..++.++|||||+|.+.++|.+|++ + ++..|.|++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v------~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~   74 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREV------RLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQK   74 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBC------CSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEE------EEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEE
Confidence            36899999999999999999999999 55432      234455567889999999999999999994 5 467799999


Q ss_pred             EEEecCCCC
Q 009944          251 VRVRRPTDY  259 (522)
Q Consensus       251 ~~v~~~~~~  259 (522)
                      |.|.++.+.
T Consensus        75 i~V~~a~~~   83 (91)
T 2lxi_A           75 VSMHYSDPK   83 (91)
T ss_dssp             EEEECCCSC
T ss_pred             EEEEEcCCC
Confidence            999987644

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=1.5e-15  Score=119.23  Aligned_cols=76  Identities=20%  Similarity=0.238  Sum_probs=67.9

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHH-hc--CceecC
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LD--GIIFEG  248 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~-~~--~~~~~g  248 (522)
                      ...++|||+|||+.+|+++|+++|.+||.            |.++.+...+|||||+|.+.++|+.|++ ++  +..|.|
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~------------V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~G   81 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGK------------VTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRG   81 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            45679999999999999999999999997            7778887889999999999999999994 65  478999


Q ss_pred             ceEEEecCCCC
Q 009944          249 VAVRVRRPTDY  259 (522)
Q Consensus       249 ~~~~v~~~~~~  259 (522)
                      ++|.|.+++..
T Consensus        82 r~l~V~~A~~~   92 (105)
T 1sjq_A           82 QPIYIQFSNHK   92 (105)
T ss_dssp             EECCBCCCSSS
T ss_pred             EEEEEEEcCCC
Confidence            99999987654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.41  E-value=4.2e-17  Score=133.21  Aligned_cols=82  Identities=24%  Similarity=0.417  Sum_probs=77.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceE--------EEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCe
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHG--------FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK  364 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~--------v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~  364 (522)
                      ..++|||+|||..+++++|+++|++||.|..        |.|+.++.+|.++|||||+|.+.++|.+|+..|||..|.|+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   85 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN   85 (116)
Confidence            4468999999999999999999999999998        89999988999999999999999999999999999999999


Q ss_pred             EEEEEEccCC
Q 009944          365 TLTVRRATAS  374 (522)
Q Consensus       365 ~l~v~~~~~~  374 (522)
                      .|.|.++.++
T Consensus        86 ~l~V~~a~~~   95 (116)
T 2lcw_A           86 PIKVSFATRR   95 (116)
Confidence            9999999764

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=6.1e-15  Score=116.57  Aligned_cols=76  Identities=18%  Similarity=0.285  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhc--CCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESF--GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~--G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (522)
                      ...++|||+|||..+++++|+++|++|  |.|..|.++        +|||||+|.+.++|.+|+..|||..|.|+.|.|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT   84 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            455799999999999999999999999  889988765        5699999999999999999999999999999999


Q ss_pred             EccCCC
Q 009944          370 RATASS  375 (522)
Q Consensus       370 ~~~~~~  375 (522)
                      ++.++.
T Consensus        85 ~a~~~~   90 (99)
T 2cpd_A           85 LAKPVD   90 (99)
T ss_dssp             CCCCCC
T ss_pred             ECCCCC
Confidence            998754

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=2e-15  Score=113.50  Aligned_cols=73  Identities=12%  Similarity=0.161  Sum_probs=65.2

Q ss_pred             CCe-EEEcCCCCCCCHHH----HHHHHHhcC-CceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          294 PDR-VFVGGLPYYFTETQ----IKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       294 ~~~-l~v~nLp~~~t~~~----l~~~F~~~G-~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      ..+ |||+|||..+++++    |+++|++|| .|.+|       +|   |+|||+|.+.++|.+|++.|+|..|.|++|+
T Consensus         8 ~~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            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            445 99999999999987    568999995 99887       33   8999999999999999999999999999999


Q ss_pred             EEEccCCCC
Q 009944          368 VRRATASSG  376 (522)
Q Consensus       368 v~~~~~~~~  376 (522)
                      |.||.....
T Consensus        78 v~~A~~~sd   86 (96)
T 2diu_A           78 VSFTPKNRE   86 (96)
T ss_dssp             EESSCCSCC
T ss_pred             EEecCCCcc
Confidence            999987643

>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=99.60  E-value=6.7e-16  Score=126.25  Aligned_cols=79  Identities=19%  Similarity=0.376  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCce--EEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLH--GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~--~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (522)
                      ....+|||+|||+.+|+++|+++|+.| .|.  .|.|+.++. |.++|||||+|.+.++|.+||+ +++..|+|+.|.|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~  116 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVF  116 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEE
Confidence            445789999999999999999999999 566  899999976 9999999999999999999998 57899999999999


Q ss_pred             EccC
Q 009944          370 RATA  373 (522)
Q Consensus       370 ~~~~  373 (522)
                      ++..
T Consensus       117 ~a~~  120 (126)
T 2hgm_A          117 KSSQ  120 (126)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8854

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=3.1e-15  Score=117.55  Aligned_cols=78  Identities=18%  Similarity=0.252  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEE-EEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGF-DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v-~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ..++|||+|||+.+++++|+++|+.||.|..| .++.++.+    |.|||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~----~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45789999999999999999999999999999 47777543    44999999999999999999999999999999999


Q ss_pred             cCC
Q 009944          372 TAS  374 (522)
Q Consensus       372 ~~~  374 (522)
                      .++
T Consensus        90 ~~~   92 (96)
T 2e44_A           90 PDE   92 (96)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            875

>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=99.60  E-value=7.7e-15  Score=118.42  Aligned_cols=74  Identities=24%  Similarity=0.466  Sum_probs=69.2

Q ss_pred             CCCeEEEcCCCCC-CCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          293 GPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       293 ~~~~l~v~nLp~~-~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ..++|||+|||.. +++++|+++|++||.|..|.+        ++|||||+|.+.++|++|+..|+|..|.|+.|.|.++
T Consensus        26 ~~~~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           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            3479999999999 999999999999999999988        4689999999999999999999999999999999999


Q ss_pred             cCC
Q 009944          372 TAS  374 (522)
Q Consensus       372 ~~~  374 (522)
                      ..+
T Consensus        98 ~~~  100 (110)
T 1wf1_A           98 GEP  100 (110)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

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

Probab=99.60  E-value=2.1e-15  Score=117.02  Aligned_cols=76  Identities=21%  Similarity=0.155  Sum_probs=67.6

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCc--eecC
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI--IFEG  248 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~--~~~g  248 (522)
                      .++++|||+|||+.+|+++|+++|.+||.            |.++.+.+.+|||||+|.+.++|..|+ .+++.  .|.|
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~------------V~~v~i~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~G   86 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGP------------ISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAG   86 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCEEETT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCC------------EEEEEEEcCCCEEEEEECCHHHHHHHHHHhcCCCceeCC
Confidence            45679999999999999999999999997            777887789999999999999999999 57775  4889


Q ss_pred             ceEEEecCCCC
Q 009944          249 VAVRVRRPTDY  259 (522)
Q Consensus       249 ~~~~v~~~~~~  259 (522)
                      ++|.|.+++..
T Consensus        87 r~i~V~~S~~k   97 (100)
T 3r27_A           87 HPAFVNYSTSQ   97 (100)
T ss_dssp             EEEEEEECSCS
T ss_pred             cEEEEEecccc
Confidence            99999987643

>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=99.60  E-value=9.2e-16  Score=130.24  Aligned_cols=81  Identities=21%  Similarity=0.269  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEE--------EEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGF--------DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v--------~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  363 (522)
                      ...++|||+|||+.+++++|+++|+.||.|..+        .+.   .+|.++|||||+|.+.++|.+||..|||..|.|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~---~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g  119 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM---KEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG  119 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE---EETTTEEEEEEECSSHHHHHHHHHHHTTBEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec---cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            345789999999999999999999999998764        333   378899999999999999999999999999999


Q ss_pred             eEEEEEEccCCC
Q 009944          364 KTLTVRRATASS  375 (522)
Q Consensus       364 ~~l~v~~~~~~~  375 (522)
                      +.|.|.++.+..
T Consensus       120 ~~l~V~~a~~~~  131 (143)
T 3egn_A          120 KPMVVQFARSAR  131 (143)
T ss_dssp             EECEEEECCCSC
T ss_pred             cEEEEEECCCCC
Confidence            999999997643

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

Probab=99.60  E-value=1.9e-15  Score=118.68  Aligned_cols=76  Identities=16%  Similarity=0.372  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          292 EGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       292 ~~~~~l~v~nLp~-~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      .+.++|||+|||. .+++++|+++|++||.|..|.+.        +|||||+|.+.++|.+|+..|+|..|.|+.|.|.+
T Consensus         8 ~~~~~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            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            3457899999998 99999999999999999999984        68999999999999999999999999999999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      +.+..
T Consensus        80 a~~~~   84 (96)
T 2kvi_A           80 SSSNA   84 (96)
T ss_dssp             EECCC
T ss_pred             cCcCC
Confidence            97653

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.59  E-value=4.9e-15  Score=120.83  Aligned_cols=77  Identities=22%  Similarity=0.320  Sum_probs=69.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceE-EEEEEcChHHHHHHHHHHcCCccCC--eEEEEEE
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY-GFCVYQDPAVTDIACAALNGLKMGD--KTLTVRR  370 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~-afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~  370 (522)
                      ...|||+||++.+|+++|+++|++||.|..|.++..     .+|| |||+|.+.++|.+|++.|||..|.|  +.|+|.|
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 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  102 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEe
Confidence            346889999999999999999999999999988764     2677 9999999999999999999999988  9999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      +.+..
T Consensus       103 ak~~~  107 (130)
T 3zzy_A          103 SKLTS  107 (130)
T ss_dssp             CSCSS
T ss_pred             cCCCc
Confidence            98753

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=2.8e-15  Score=119.45  Aligned_cols=77  Identities=23%  Similarity=0.327  Sum_probs=69.1

Q ss_pred             CCCCeEEE--cCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc-----CCe
Q 009944          292 EGPDRVFV--GGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-----GDK  364 (522)
Q Consensus       292 ~~~~~l~v--~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~-----~g~  364 (522)
                      .+..+|||  +||+..+++++|+++|++||.|..|.|+.      .+|||||+|.+.++|++|++.|||..|     .|+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            34578999  77999999999999999999999988763      268999999999999999999999988     789


Q ss_pred             EEEEEEccCC
Q 009944          365 TLTVRRATAS  374 (522)
Q Consensus       365 ~l~v~~~~~~  374 (522)
                      +|.|.|+...
T Consensus        97 ~l~v~~a~~~  106 (114)
T 2cq2_A           97 TLYLNFVEKV  106 (114)
T ss_dssp             ECEEEEESCC
T ss_pred             EEEEEecccC
Confidence            9999998754

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.59  E-value=7e-15  Score=116.63  Aligned_cols=82  Identities=15%  Similarity=0.080  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCC-----CCCHHHHHHHHHhcCCceEEEEeeCCCC-CCcceEEEEEEcChHHHHHHHHHHcCCccCCeE
Q 009944          292 EGPDRVFVGGLPY-----YFTETQIKELLESFGTLHGFDLVKDRDT-GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT  365 (522)
Q Consensus       292 ~~~~~l~v~nLp~-----~~t~~~l~~~F~~~G~i~~v~~~~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~  365 (522)
                      .+.++|+|.||..     +.++++|+++|++||.|..|.|+.++.+ +.++|||||+|.+.++|.+|+..|||..|.|+.
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            3457899999963     2378999999999999999999998654 688999999999999999999999999999999


Q ss_pred             EEEEEccC
Q 009944          366 LTVRRATA  373 (522)
Q Consensus       366 l~v~~~~~  373 (522)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999853

>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=99.59  E-value=8.5e-16  Score=125.23  Aligned_cols=99  Identities=19%  Similarity=0.242  Sum_probs=84.1

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe---cCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~---~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      ..++|||+|||+.+|+++|+++|..||.            |..+.+   +.++|||||+|.+.++|..|+ .|+|..|.|
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   74 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGP------------IRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSN   74 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            4579999999999999999999999997            444544   566899999999999999999 599999999


Q ss_pred             ceEEEecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCC
Q 009944          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT  320 (522)
Q Consensus       249 ~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~  320 (522)
                      +.|.|.++.....                                     ..+++...++++|.++|++||.
T Consensus        75 ~~l~v~~a~~~~~-------------------------------------~~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           75 RYLVVLYYNANRA-------------------------------------FQKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             CBCEEEECCHHHH-------------------------------------TTTSCHHHHHHHHHHHHHHHCC
T ss_pred             eEEEEEEecCChh-------------------------------------hhhhhHhHhHHHHHHHHHHhCC
Confidence            9999998543211                                     0467788899999999999985

>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=99.59  E-value=5.2e-15  Score=125.36  Aligned_cols=78  Identities=23%  Similarity=0.288  Sum_probs=70.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC--eEEEEEEc
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  371 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~  371 (522)
                      ..+|||+||++.+++++|+++|++||.|..|.|...    .++|||||+|.+.++|++|++.|||..|.|  +.|+|.|+
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 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            356999999999999999999999999999998754    257999999999999999999999999955  99999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      .++.
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            8753

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.59  E-value=3e-15  Score=115.43  Aligned_cols=76  Identities=17%  Similarity=0.242  Sum_probs=69.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||..+++++|+++|++| .|..|.+.      .++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            34689999999999999999999999 99999884      468999999999999999999999999999999999986


Q ss_pred             CCC
Q 009944          373 ASS  375 (522)
Q Consensus       373 ~~~  375 (522)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            643

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=3.7e-15  Score=116.56  Aligned_cols=78  Identities=24%  Similarity=0.420  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+++++|+++|+.||.|..|  +.++.+|.   ||||+|.+.++|.+||. |+|..|.|+.|.|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            345799999999999999999999999999987  55555665   99999999999999999 9999999999999998


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      ..+.
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            7654

>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=99.58  E-value=2.8e-15  Score=118.05  Aligned_cols=79  Identities=24%  Similarity=0.335  Sum_probs=68.3

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhC
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  497 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng  497 (522)
                      ..+.|-+|+..++++             +|+++|++||.|..|.|+++..+|..   +|+|||+|.+.++|.+|++.|||
T Consensus        20 t~lfV~nLp~~~te~-------------~L~~~F~~~G~I~~v~i~~d~~tg~~---kG~afV~f~~~~~A~~Ai~~lng   83 (99)
T 4fxv_A           20 TNLIVNYLPQNMTQD-------------ELRSLFSSIGEVESAKLIRDKVAGHS---LGYGFVNYVTAKDAERAINTLNG   83 (99)
T ss_dssp             SEEEEESCCTTCCHH-------------HHHHHHHTTSCEEEEEEEECSSSCCE---EEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CEEEEeCCCCCCCHH-------------HHHHHHHhcCCEEEeEeeecCCCCcc---cccEEEEECCHHHHHHHHHHhCC
Confidence            445555566555554             99999999999999999998877765   78999999999999999999999


Q ss_pred             CccCCeEEEEEEeCC
Q 009944          498 RKFGGNTVNAFYYPE  512 (522)
Q Consensus       498 ~~~~Gr~l~v~~~~~  512 (522)
                      ..|+|++|+|.|+.+
T Consensus        84 ~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           84 LRLQSKTIKVSYARP   98 (99)
T ss_dssp             CEETTEECEEEECCB
T ss_pred             CEECCEEEEEEEeeC
Confidence            999999999999854

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.58  E-value=1e-14  Score=115.76  Aligned_cols=81  Identities=21%  Similarity=0.431  Sum_probs=73.2

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceE
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~  251 (522)
                      ...++|||+|||+.+|+++|+++|..||.|.. .      .+.+..++.++|||||+|.+.++|.+|++|++..|.|+.|
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~------~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l   87 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-L------AVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEI   87 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-C------CCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-E------EEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEE
Confidence            34679999999999999999999999999875 2      3777788999999999999999999999999999999999


Q ss_pred             EEecCCCC
Q 009944          252 RVRRPTDY  259 (522)
Q Consensus       252 ~v~~~~~~  259 (522)
                      .|.++...
T Consensus        88 ~V~~a~~~   95 (101)
T 1fj7_A           88 KLEKPKGR   95 (101)
T ss_dssp             EEECCSCC
T ss_pred             EEEEcCCC
Confidence            99987654

>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=99.58  E-value=5.4e-15  Score=117.25  Aligned_cols=87  Identities=22%  Similarity=0.359  Sum_probs=69.6

Q ss_pred             eEEEeeCCCC-cCcCCC--------------hHHHHHHHHHHHHHh-hccCCeEEEEecCCCCCCCCCCCccEEEEEecC
Q 009944          421 KVLCLTEAIT-ADALAD--------------DEEYEEILEDMREEC-GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYD  484 (522)
Q Consensus       421 ~v~~l~~~~~-~~~l~~--------------~~~~~~~~~~l~~~f-~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~  484 (522)
                      .+++|.|+++ +.....              ...|.++.++|+++| ++||.|.+|.|+++.. +.   .+|+|||+|.+
T Consensus         2 ~~~~l~nm~~~p~~~~~~~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~---~~G~~fV~f~~   77 (104)
T 1jmt_A            2 QTIALLNIYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DH---LVGNVYVKFRR   77 (104)
T ss_dssp             CEEEEEEEEECCC------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SS---SEEEEEEEESC
T ss_pred             cEEEEeeccCCccccccccCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CC---ccEEEEEEECC
Confidence            4677777773 432221              234667788899999 9999999999998763 33   37899999999


Q ss_pred             hHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          485 AVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       485 ~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                      .++|.+|+..|||+.|+|++|.|.|+|
T Consensus        78 ~~~A~~A~~~lng~~~~Gr~i~v~~sp  104 (104)
T 1jmt_A           78 EEDAEKAVIDLNNRWFNGQPIHAELSP  104 (104)
T ss_dssp             HHHHHHHHHHHTTCEETTEECCEEECC
T ss_pred             HHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            999999999999999999999999975

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

Probab=99.58  E-value=1.5e-14  Score=113.84  Aligned_cols=77  Identities=22%  Similarity=0.338  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+||  .+++++|+++|++||.|..|.|.      .++|||||+|.+.++|.+||..|+|..|.|+.|.|.|+
T Consensus        13 ~~~~~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           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   84 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            34579999996  89999999999999999999884      45789999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009944          372 TASSG  376 (522)
Q Consensus       372 ~~~~~  376 (522)
                      .++..
T Consensus        85 ~~~~~   89 (97)
T 1x5p_A           85 RKQPM   89 (97)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            87543

>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=99.57  E-value=1.4e-14  Score=117.07  Aligned_cols=97  Identities=22%  Similarity=0.346  Sum_probs=81.4

Q ss_pred             CCCCcceEEEeeCCCCcCcCC-ChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHH
Q 009944          415 FGETLAKVLCLTEAITADALA-DDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKN  493 (522)
Q Consensus       415 ~~~~~~~v~~l~~~~~~~~l~-~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~  493 (522)
                      ..+.++++++|.|++...++. ++.+|++++++|+++|++||.|..|.|+...       .+|+|||+|.+.++|.+|+.
T Consensus        10 ~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~-------~~G~afV~f~~~~~A~~Ai~   82 (112)
T 2dit_A           10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH-------PDGVASVSFRDPEEADYCIQ   82 (112)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC-------TTCEEEEECSCHHHHHHHHH
T ss_pred             CCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCC-------CCEEEEEEECCHHHHHHHHH
Confidence            345788999999998887653 4567899999999999999999999774321       25889999999999999999


Q ss_pred             HHhCCccCCeEEEEEEeCC-cccccc
Q 009944          494 ALSGRKFGGNTVNAFYYPE-DKYFNK  518 (522)
Q Consensus       494 ~lng~~~~Gr~l~v~~~~~-~~~~~~  518 (522)
                      .|||..|+|++|.|.|+.. .+|..+
T Consensus        83 ~lng~~~~gr~l~v~~a~~~~~~~~~  108 (112)
T 2dit_A           83 TLDGRWFGGRQITAQAWDGTTDYQSG  108 (112)
T ss_dssp             HSTTCEETTEECEEEECCSCCCSSCC
T ss_pred             HcCCCEECCcEEEEEEeCCCCCcccC
Confidence            9999999999999999876 455443

>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=99.57  E-value=3.5e-15  Score=149.62  Aligned_cols=66  Identities=21%  Similarity=0.318  Sum_probs=60.9

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++|.++|++||.|+.|.|+.+..++..   +|||||+|.+.++|.+||+.|||..|+|++|.|.|+...
T Consensus       117 ~~L~~~F~~~G~I~~v~i~~d~~tg~~---kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~  182 (437)
T 3pgw_S          117 SKLRREFEVYGPIKRIHMVYSKRSGKP---RGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGR  182 (437)
T ss_pred             HHHHHHHHHcCCeeEEEeeccCCCCCc---cceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            499999999999999999998777765   689999999999999999999999999999999998753

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.56  E-value=1.7e-14  Score=117.34  Aligned_cols=74  Identities=19%  Similarity=0.230  Sum_probs=67.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceE-EEEEEcChHHHHHHHHHHcCCccCC--eEEEEEEcc
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY-GFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRAT  372 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~-afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~~  372 (522)
                      .|||+||++.+++++|+++|++||.|..|.|+..      .|| |||+|.+.++|..|++.|||..|.|  +.|.|.|+.
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            4789999999999999999999999999998752      276 9999999999999999999999977  699999998


Q ss_pred             CCC
Q 009944          373 ASS  375 (522)
Q Consensus       373 ~~~  375 (522)
                      ++.
T Consensus       101 ~~~  103 (124)
T 2e5i_A          101 PTR  103 (124)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            754

>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=99.56  E-value=3.6e-15  Score=121.15  Aligned_cols=74  Identities=22%  Similarity=0.302  Sum_probs=66.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeE-----EE
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT-----LT  367 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~-----l~  367 (522)
                      ..++|||+|||+.+++++|+++|++||.|..|.|+.+       |||||+|.+.++|++||+.|||..|.|+.     |.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            4578999999999999999999999999999998765       89999999999999999999999999988     77


Q ss_pred             EEEccC
Q 009944          368 VRRATA  373 (522)
Q Consensus       368 v~~~~~  373 (522)
                      |..+.+
T Consensus        88 v~~~~~   93 (115)
T 3beg_B           88 VKVDGP   93 (115)
T ss_dssp             EEECC-
T ss_pred             eccCCC
Confidence            776654

>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=99.56  E-value=1.3e-14  Score=111.63  Aligned_cols=84  Identities=46%  Similarity=0.825  Sum_probs=71.8

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceE
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~  251 (522)
                      ...++|||+|||+.+|+++|+++|.+||.+.+... .++..|..+.+..++|||||+|.+.++|.+|+.+++..|.|+.|
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~-~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~~l~g~~~~g~~l   82 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQ-APGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSL   82 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCS-SSSCSEEEEEECSSSSEEEEEESSHHHHHHHGGGTTCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhccccc-CCCCcceEEEecCCCcEEEEEcCCHHHHHHHHhcCCCEECCeEE
Confidence            45689999999999999999999999965443211 12335889999999999999999999999999999999999999


Q ss_pred             EEecC
Q 009944          252 RVRRP  256 (522)
Q Consensus       252 ~v~~~  256 (522)
                      +|++|
T Consensus        83 ~V~rp   87 (87)
T 2hzc_A           83 KIRRP   87 (87)
T ss_dssp             EEECC
T ss_pred             EEeCC
Confidence            99863

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=7.8e-15  Score=115.38  Aligned_cols=76  Identities=17%  Similarity=0.161  Sum_probs=67.6

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-Hh--cCceecC
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-AL--DGIIFEG  248 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~--~~~~~~g  248 (522)
                      .+.++|||+|||+.+|+++|+++|.+||.            |.++.+...+|||||+|.+.++|..|+ .+  ++..|.|
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~------------v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G   80 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGK------------VTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRN   80 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            45679999999999999999999999997            677777778999999999999999999 44  5788999


Q ss_pred             ceEEEecCCCC
Q 009944          249 VAVRVRRPTDY  259 (522)
Q Consensus       249 ~~~~v~~~~~~  259 (522)
                      ++|.|.+++..
T Consensus        81 r~l~V~~a~~~   91 (101)
T 2cq1_A           81 QPIYIQYSNHK   91 (101)
T ss_dssp             EECEEEECSCS
T ss_pred             cEEEEEEcCcc
Confidence            99999997654

>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=99.56  E-value=1.2e-14  Score=112.00  Aligned_cols=74  Identities=18%  Similarity=0.344  Sum_probs=63.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCc--cCCeEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK--MGDKTLTVR  369 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~--~~g~~l~v~  369 (522)
                      ...++|||+|||+.+|+++|+++|++||.|..|.|+.+     ++|||||+|.+.++|.+    ++|..  +.|+.|.|.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            45579999999999999999999999999999999874     68999999999999983    56654  569999999


Q ss_pred             EccCC
Q 009944          370 RATAS  374 (522)
Q Consensus       370 ~~~~~  374 (522)
                      ++.++
T Consensus        80 ~a~~k   84 (89)
T 3d2w_A           80 NAEPK   84 (89)
T ss_dssp             ECC--
T ss_pred             EcCCC
Confidence            99764

>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=99.55  E-value=9e-15  Score=115.79  Aligned_cols=77  Identities=18%  Similarity=0.172  Sum_probs=67.2

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcC--ceecC
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG--IIFEG  248 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~--~~~~g  248 (522)
                      .+.++|||+|||+.+|+++|+++|.+||.            |..+.+...+|||||+|.+.++|.+|+ .|++  ..|.|
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~------------V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~G   80 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGT------------ICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAG   80 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            34679999999999999999999999997            677777778999999999999999999 4654  56999


Q ss_pred             ceEEEecCCCCC
Q 009944          249 VAVRVRRPTDYN  260 (522)
Q Consensus       249 ~~~~v~~~~~~~  260 (522)
                      ++|.|.+++...
T Consensus        81 r~l~V~~a~~~~   92 (104)
T 1wex_A           81 QQAFFNYSTSKR   92 (104)
T ss_dssp             SBCEEEECSSSS
T ss_pred             EEEEEEEccCcc
Confidence            999999976543

>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=99.55  E-value=3.8e-15  Score=116.99  Aligned_cols=77  Identities=22%  Similarity=0.235  Sum_probs=68.4

Q ss_pred             cccceeEEeCCCc-cCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcC--ceec
Q 009944          172 RHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG--IIFE  247 (522)
Q Consensus       172 ~~~~~v~v~nlp~-~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~--~~~~  247 (522)
                      .+.++|||+|||+ .+|+++|+++|.+||.            |.++.+...+|||||+|.+.++|..|+ .|++  ..|.
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~------------V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~   80 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGV------------ISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVF   80 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSC------------EEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEET
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCC------------EEEEEEEcCCCEEEEEECCHHHHHHHHHHHcCCCceEC
Confidence            3578999999999 9999999999999997            788888888999999999999999999 5765  5699


Q ss_pred             CceEEEecCCCCC
Q 009944          248 GVAVRVRRPTDYN  260 (522)
Q Consensus       248 g~~~~v~~~~~~~  260 (522)
                      |++|.|.++..+.
T Consensus        81 Gr~l~V~~a~~~~   93 (102)
T 1x4d_A           81 GKPVRVHLSQKYK   93 (102)
T ss_dssp             TEECEEEEECCCT
T ss_pred             CcEEEEEECCCCC
Confidence            9999999876543

>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=99.55  E-value=4.3e-15  Score=121.02  Aligned_cols=85  Identities=16%  Similarity=0.261  Sum_probs=68.4

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      .....++|||+|||+.+|+++|+++|..||.|..+.      ++.+...+.++|||||+|.+.++|++|+ .|++..|.|
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   94 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAK------VFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM   94 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEE------EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECC
Confidence            344568999999999999999999999999854210      0111123456799999999999999999 799999999


Q ss_pred             ceEEEecCCCCC
Q 009944          249 VAVRVRRPTDYN  260 (522)
Q Consensus       249 ~~~~v~~~~~~~  260 (522)
                      +.|+|.++....
T Consensus        95 ~~l~V~~a~~~~  106 (115)
T 2cpz_A           95 KRLKVQLKRSKN  106 (115)
T ss_dssp             EECEEECCCCSC
T ss_pred             EEEEEEEcCCCC
Confidence            999999876553

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=1.4e-14  Score=113.99  Aligned_cols=78  Identities=21%  Similarity=0.277  Sum_probs=68.2

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++|||+|||+.+|+++|+++|.+||.|           ...+.++.++|||||+|.+.++|++|+ .|++..|.|+
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v-----------~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   84 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSV-----------PLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTD   84 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCC-----------CSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCE-----------EEEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            3446799999999999999999999999975           134456789999999999999999999 7999999999


Q ss_pred             eEEEecCCCC
Q 009944          250 AVRVRRPTDY  259 (522)
Q Consensus       250 ~~~v~~~~~~  259 (522)
                      .|.|.++...
T Consensus        85 ~l~V~~a~~~   94 (97)
T 2e5j_A           85 TLRVALARQQ   94 (97)
T ss_dssp             CCEEEECCCC
T ss_pred             EEEEEEcCCC
Confidence            9999986543

>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=99.55  E-value=3.7e-14  Score=112.96  Aligned_cols=78  Identities=27%  Similarity=0.381  Sum_probs=67.5

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec----CCCcEEEEEEeCHHHHHHHH-HhcCc
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAM-ALDGI  244 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~----~~~g~afV~f~~~~~a~~a~-~~~~~  244 (522)
                      .....++|||+|||+.+|+++|+++|..||.            |..+.+.    .++|||||+|.+.++|.+|+ .|++.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   78 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGP------------CKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGR   78 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSC------------EEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCC------------EeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCC
Confidence            3455789999999999999999999999997            4444443    36799999999999999999 59999


Q ss_pred             eecCceEEEecCCCC
Q 009944          245 IFEGVAVRVRRPTDY  259 (522)
Q Consensus       245 ~~~g~~~~v~~~~~~  259 (522)
                      .|.|+.|+|.++...
T Consensus        79 ~~~g~~l~V~~a~~~   93 (103)
T 2cqi_A           79 KILGKEVKVNWATTP   93 (103)
T ss_dssp             EETTEEEEEEECCCT
T ss_pred             CcCCCeEEEEECCCC
Confidence            999999999987654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=7.8e-15  Score=119.07  Aligned_cols=76  Identities=28%  Similarity=0.433  Sum_probs=64.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCC---CCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT---GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~---g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (522)
                      ...++|||+|||+.+++++|+++|++||.|. +.++.+..+   |.++|||||+|.+.++|++||+.|+  .+.|+.|.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            3457899999999999999999999999999 888887766   7999999999999999999999983  245555544


Q ss_pred             EE
Q 009944          369 RR  370 (522)
Q Consensus       369 ~~  370 (522)
                      ..
T Consensus        83 ~~   84 (114)
T 2dnl_A           83 VS   84 (114)
T ss_dssp             EC
T ss_pred             cc
Confidence            43

>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=99.54  E-value=3.7e-14  Score=114.18  Aligned_cols=80  Identities=25%  Similarity=0.415  Sum_probs=72.0

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceec
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~  247 (522)
                      ......++|||+|||..+|+++|+++|..||.            |..+.+...+|||||+|.+.++|.+|+ .|++..|.
T Consensus        20 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~------------i~~v~i~~~~g~afV~f~~~~~a~~A~~~l~g~~~~   87 (109)
T 1x4g_A           20 QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQ------------IMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIE   87 (109)
T ss_dssp             HSCSSCCEEEEECCSSCCCHHHHHHHHHHHSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEeCCCCEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            34456789999999999999999999999997            778888878999999999999999999 79999999


Q ss_pred             CceEEEecCCCCC
Q 009944          248 GVAVRVRRPTDYN  260 (522)
Q Consensus       248 g~~~~v~~~~~~~  260 (522)
                      |+.|+|.+++...
T Consensus        88 g~~l~v~~a~~~~  100 (109)
T 1x4g_A           88 GHVVKCYWGKESP  100 (109)
T ss_dssp             TEECEEECCCCCC
T ss_pred             CcEEEEEecCCCC
Confidence            9999999976543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.54  E-value=1.2e-14  Score=116.19  Aligned_cols=74  Identities=18%  Similarity=0.191  Sum_probs=64.9

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHH-HhhcCCCCCCCCceEEEEe--cCCCcEEEEEEeCHHHHHHHH-HhcCceec
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVM-TAIGGNSAGPGDAVVNVYI--NHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g-~~~~~~~~~~~~~v~~~~~--~~~~g~afV~f~~~~~a~~a~-~~~~~~~~  247 (522)
                      ....+|||+|||+.+|+++|+++|.+|| .|            ..+.+  ..++|||||+|.+.++|++|+ .|||..|.
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v------------~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~   93 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLET------------TFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFR   93 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCC------------SEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEET
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCee------------EEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            3457999999999999999999999999 63            33333  468999999999999999999 69999999


Q ss_pred             CceEEEecCC
Q 009944          248 GVAVRVRRPT  257 (522)
Q Consensus       248 g~~~~v~~~~  257 (522)
                      |+.|+|.++.
T Consensus        94 Gr~i~V~~a~  103 (111)
T 2jvr_A           94 GSVITVERDD  103 (111)
T ss_dssp             TEEEEEEESC
T ss_pred             CeEEEEEECC
Confidence            9999999754

>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=99.54  E-value=1.1e-14  Score=111.62  Aligned_cols=74  Identities=22%  Similarity=0.364  Sum_probs=67.5

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHH-h-cCceecC
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-L-DGIIFEG  248 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~-~-~~~~~~g  248 (522)
                      ....++|||+|||..+|+++|+++|.+||.            |..+.+..++|||||+|.+.++|.+|+. | ++..+.|
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~------------i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g   76 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGE------------IRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNG   76 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSC------------EEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETT
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCC------------EeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECC
Confidence            345689999999999999999999999987            7778887889999999999999999994 8 9999999


Q ss_pred             ceEEEecC
Q 009944          249 VAVRVRRP  256 (522)
Q Consensus       249 ~~~~v~~~  256 (522)
                      ++|+|.|+
T Consensus        77 ~~l~v~~a   84 (85)
T 2ytc_A           77 RRLNVKWG   84 (85)
T ss_dssp             EECCEEEC
T ss_pred             CEEEEEec
Confidence            99999885

>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=99.54  E-value=2.1e-14  Score=115.61  Aligned_cols=78  Identities=28%  Similarity=0.489  Sum_probs=67.3

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe---cCCCcEEEEEEeCHHHHHHHH-HhcCcee
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~---~~~~g~afV~f~~~~~a~~a~-~~~~~~~  246 (522)
                      ....++|||+|||+.+|+++|+++|.+||.            |..+.+   ..++|||||+|.+.++|++|+ .|++..|
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   86 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGA------------IRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDY   86 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEE
Confidence            345689999999999999999999999997            444443   345889999999999999999 7999999


Q ss_pred             cCceEEEecCCCCC
Q 009944          247 EGVAVRVRRPTDYN  260 (522)
Q Consensus       247 ~g~~~~v~~~~~~~  260 (522)
                      .|+.|+|.+++...
T Consensus        87 ~g~~l~V~~a~~~~  100 (109)
T 1x4a_A           87 DGYRLRVEFPRSGR  100 (109)
T ss_dssp             TTEECEEECCCCCC
T ss_pred             CCeEEEEEEcccCC
Confidence            99999999876543

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

Probab=99.54  E-value=1.1e-14  Score=115.57  Aligned_cols=75  Identities=23%  Similarity=0.405  Sum_probs=68.2

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||+|||..+|+++|+++|..||.            |..+.+..++|||||+|.+.++|..|+ .|++..|.|+.
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~------------i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   92 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGF------------ILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRN   92 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSC------------CSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCC------------EEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            34689999999999999999999999997            566777789999999999999999999 79999999999


Q ss_pred             EEEecCCC
Q 009944          251 VRVRRPTD  258 (522)
Q Consensus       251 ~~v~~~~~  258 (522)
                      |+|.|++.
T Consensus        93 l~V~~a~~  100 (101)
T 2la4_A           93 LRTGWGKE  100 (101)
T ss_dssp             CCCCBCCC
T ss_pred             EEEEeccC
Confidence            99998653

>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=99.53  E-value=1.4e-14  Score=111.48  Aligned_cols=71  Identities=24%  Similarity=0.541  Sum_probs=65.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhc----C-------CceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESF----G-------TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM  361 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~----G-------~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~  361 (522)
                      ..++|||+|||..+++++|+++|++|    |       .|..+.+..+      +|||||+|.+.++|.+|+ .|||..|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            34799999999999999999999999    8       8999888754      799999999999999999 9999999


Q ss_pred             CCeEEEEEE
Q 009944          362 GDKTLTVRR  370 (522)
Q Consensus       362 ~g~~l~v~~  370 (522)
                      .|+.|.|..
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999974

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

Probab=99.53  E-value=1.4e-14  Score=116.30  Aligned_cols=67  Identities=18%  Similarity=0.239  Sum_probs=61.9

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|.+|.|+.+..++.+   +|+|||+|.+.++|.+||+.|||..|+|++|.|.++....
T Consensus        21 ~~L~~~F~~~G~i~~v~i~~d~~tg~~---rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~~~   87 (110)
T 3s8s_A           21 TFLKDMCRKYGEVEEVEILLHPRTRKH---LGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQ   87 (110)
T ss_dssp             HHHHHHHTTTSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSTTH
T ss_pred             HHHHHHHHhcCCeeEEEEEECCCCCce---eeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            499999999999999999999877765   7899999999999999999999999999999999987643

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.53  E-value=2.9e-15  Score=125.29  Aligned_cols=123  Identities=19%  Similarity=0.195  Sum_probs=68.9

Q ss_pred             EEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCC
Q 009944          338 YGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGE  417 (522)
Q Consensus       338 ~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~  417 (522)
                      ++|++|.+...+..|+..++|-...|+. .+.+..+                                     ..+....
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~~~-------------------------------------~~~~~~~   47 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYGRP-------------------------------------PPDVEGM   47 (135)
T ss_dssp             ------------------------------CCSCCS-------------------------------------CSSGGGC
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCC-CCCcCCC-------------------------------------CCCCCCC
Confidence            5788888888899999888875554432 1111111                                     0001111


Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhC
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  497 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng  497 (522)
                      ..+.|-+|+..+++             ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|.+||+.|||
T Consensus        48 ~~l~V~nLp~~~te-------------~~L~~~F~~~G~i~~v~i~~~~~~g~~---~G~afV~F~~~~~A~~Ai~~l~g  111 (135)
T 2lea_A           48 TSLKVDNLTYRTSP-------------DTLRRVFEKYGRVGDVYIPRDRYTKES---RGFAFVRFHDKRDAEDAMDAMDG  111 (135)
T ss_dssp             CCEEEECCCSSCHH-------------HHHHHHHGGGSCCSEEECCCCSSSSSC---CSCCEEECSCHHHHHHHHTTTTT
T ss_pred             CEEEEeCCCCCCCH-------------HHHHHHHHhcCCEEEEEEEecCCCCcc---ceEEEEEECCHHHHHHHHHHcCC
Confidence            33444445444333             499999999999999999998766654   67889999999999999999999


Q ss_pred             CccCCeEEEEEEeCCcc
Q 009944          498 RKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       498 ~~~~Gr~l~v~~~~~~~  514 (522)
                      ..|.|++|+|.|+....
T Consensus       112 ~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A          112 AVLDGRELRVQMARYGR  128 (135)
T ss_dssp             CCSSSSCCEEEECCCCC
T ss_pred             CEECCEEEEEEECCCCC
Confidence            99999999999988654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=2.4e-14  Score=112.18  Aligned_cols=75  Identities=27%  Similarity=0.402  Sum_probs=65.4

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEEeCHHHHHHHH-HhcC
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG  243 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~a~-~~~~  243 (522)
                      ....++|||+|||+.+|+++|+++|..||.|            ..+.+      +.++|||||+|.+.++|.+|+ .|++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v------------~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g   79 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPI------------ADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG   79 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCE------------EEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCe------------eEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCC
Confidence            3456799999999999999999999999974            44443      456799999999999999999 5999


Q ss_pred             ceecCceEEEecCC
Q 009944          244 IIFEGVAVRVRRPT  257 (522)
Q Consensus       244 ~~~~g~~~~v~~~~  257 (522)
                      ..|.|++|+|.+++
T Consensus        80 ~~~~g~~l~v~~a~   93 (95)
T 2cqc_A           80 MELDGRRIRVSGPS   93 (95)
T ss_dssp             EEETTEEEEEECCS
T ss_pred             CEECCEEEEEEecC
Confidence            99999999999865

>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=99.53  E-value=7.6e-15  Score=118.27  Aligned_cols=77  Identities=19%  Similarity=0.231  Sum_probs=66.9

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-Hhc--CceecC
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD--GIIFEG  248 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~--~~~~~g  248 (522)
                      .+.++|||+|||+.+|+++|+++|.+||.            |.++.+...+|||||+|.+.++|.+|+ .++  +..|.|
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~------------V~~v~i~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~G   96 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGK------------VTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRG   96 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSC------------CCEEEEEGGGTEEEEECSCHHHHHHHHHHHHHHCCCBTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEeCCCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            44679999999999999999999999997            566666667999999999999999999 466  468999


Q ss_pred             ceEEEecCCCCC
Q 009944          249 VAVRVRRPTDYN  260 (522)
Q Consensus       249 ~~~~v~~~~~~~  260 (522)
                      ++|.|.+++...
T Consensus        97 r~l~V~~a~~k~  108 (119)
T 2ad9_A           97 QPIYIQFSNHKE  108 (119)
T ss_dssp             BCCEEEECSSSS
T ss_pred             eEEEEEEccCCC
Confidence            999999876543

>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=99.53  E-value=3e-14  Score=111.86  Aligned_cols=75  Identities=15%  Similarity=0.330  Sum_probs=66.2

Q ss_pred             hhcccceeEEeCCCc-cCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceec
Q 009944          170 ATRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~-~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~  247 (522)
                      .....++|||+|||+ .+++++|+++|..||.            |..+.+  .+|||||+|.+.++|.+|+ .+++..+.
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~------------v~~v~i--~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGH------------IMQINI--KNAFGFIQFDNPQSVRDAIEXESQEMNF   83 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSC------------EEEEEE--CSSEEEEEESSHHHHHHHHHHHTTSEET
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCC------------EEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            344578999999998 9999999999999997            566666  4899999999999999999 59999999


Q ss_pred             CceEEEecCCC
Q 009944          248 GVAVRVRRPTD  258 (522)
Q Consensus       248 g~~~~v~~~~~  258 (522)
                      |+.|.|.+++.
T Consensus        84 g~~l~V~~a~~   94 (97)
T 2xnq_A           84 GKKLILEVSSS   94 (97)
T ss_dssp             TEECEEEECCC
T ss_pred             CEEEEEEecCC
Confidence            99999998654

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

Probab=99.52  E-value=1.2e-14  Score=119.52  Aligned_cols=78  Identities=14%  Similarity=0.228  Sum_probs=66.8

Q ss_pred             cccceeEEeCCCccCcHHHHH----HHHHHHHHhhcCCCCCCCCceEEEE---ecCCCcEEEEEEeCHHHHHHHH-HhcC
Q 009944          172 RHARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-ALDG  243 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~----~~f~~~g~~~~~~~~~~~~~v~~~~---~~~~~g~afV~f~~~~~a~~a~-~~~~  243 (522)
                      .+.++|||+|||+.+++++|+    ++|.+||.|            .++.   .+.++|||||+|.+.++|..|+ .|||
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I------------~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng   94 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDI------------LDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQG   94 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCE------------EEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCe------------EEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCC
Confidence            346789999999999999876    699999984            4443   3578999999999999999999 7999


Q ss_pred             ceecCceEEEecCCCCCc
Q 009944          244 IIFEGVAVRVRRPTDYNP  261 (522)
Q Consensus       244 ~~~~g~~~~v~~~~~~~~  261 (522)
                      ..|.|++|+|.|++....
T Consensus        95 ~~l~gr~l~V~~a~~~~~  112 (127)
T 2a3j_A           95 YPFQGNPLVITFSETPQS  112 (127)
T ss_dssp             CCCTTSCCEEEECCCCCH
T ss_pred             CEeCCCEEEEEEccCcch
Confidence            999999999999876543

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.52  E-value=3.5e-14  Score=111.67  Aligned_cols=76  Identities=21%  Similarity=0.349  Sum_probs=68.7

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceec--C
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE--G  248 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~--g  248 (522)
                      ...++|||+|||+.+|+++|+++|.+||.            |..+.+...+|||||+|.+.++|++|+ .|++..|.  |
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g   82 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGS------------IRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPD   82 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSC------------EEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCCC
Confidence            34579999999999999999999999997            777777777999999999999999999 59999999  9


Q ss_pred             ceEEEecCCCC
Q 009944          249 VAVRVRRPTDY  259 (522)
Q Consensus       249 ~~~~v~~~~~~  259 (522)
                      +.|.|.++...
T Consensus        83 ~~l~V~~a~~~   93 (97)
T 1why_A           83 RRLRVDFAKSG   93 (97)
T ss_dssp             CBCEEEECCCC
T ss_pred             cEEEEEECCCC
Confidence            99999987654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.52  E-value=3.8e-14  Score=115.97  Aligned_cols=75  Identities=19%  Similarity=0.300  Sum_probs=65.5

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEEeCHHHHHHHH-Hhc
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALD  242 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~a~-~~~  242 (522)
                      .....++|||+|||+++|+++|+++|..||.            |..+.+      +.++|||||+|.+.++|++|+ .|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~  103 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGN------------VISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMN  103 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCE------------EEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcC
Confidence            3456789999999999999999999999997            444443      456899999999999999999 699


Q ss_pred             CceecCceEEEecC
Q 009944          243 GIIFEGVAVRVRRP  256 (522)
Q Consensus       243 ~~~~~g~~~~v~~~  256 (522)
                      +..|.|+.|+|.++
T Consensus       104 g~~~~g~~l~V~~a  117 (118)
T 2khc_A          104 GFQVGTKRLKVQLK  117 (118)
T ss_dssp             CCEETTEECCEEEC
T ss_pred             CCEECCEEEEEEec
Confidence            99999999999875

>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=99.52  E-value=1e-14  Score=115.24  Aligned_cols=77  Identities=29%  Similarity=0.480  Sum_probs=69.6

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++|||+|||+.+|+++|+++|.+||.            |..+.+..++|||||+|.+.++|.+|+ .|++..|.|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~   79 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGK------------AGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGK   79 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCC------------CSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCC------------eEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            345679999999999999999999999987            667777788999999999999999999 7999999999


Q ss_pred             eEEEecCCCC
Q 009944          250 AVRVRRPTDY  259 (522)
Q Consensus       250 ~~~v~~~~~~  259 (522)
                      +|+|.++...
T Consensus        80 ~l~v~~a~~~   89 (99)
T 2cpj_A           80 QLRVRFACHS   89 (99)
T ss_dssp             CCEEEESSCC
T ss_pred             eEEEEEcCCC
Confidence            9999987654

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=5.4e-14  Score=110.28  Aligned_cols=75  Identities=17%  Similarity=0.174  Sum_probs=66.0

Q ss_pred             ccceeEEeCCCccCcHHHHH----HHHHHHHHhhcCCCCCCCCceEEEEecCC---CcEEEEEEeCHHHHHHHH-HhcCc
Q 009944          173 HARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVYINHE---KKFAFVEMRTVEEASNAM-ALDGI  244 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~----~~f~~~g~~~~~~~~~~~~~v~~~~~~~~---~g~afV~f~~~~~a~~a~-~~~~~  244 (522)
                      ..++|||+|||+.+++++|+    ++|.+||.            |..+.+...   +|||||+|.+.++|.+|+ .||+.
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~------------v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~   75 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGK------------VKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRY   75 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSC------------EEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCc------------EEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCC
Confidence            45689999999999999999    99999997            566665433   899999999999999999 59999


Q ss_pred             eecCceEEEecCCCC
Q 009944          245 IFEGVAVRVRRPTDY  259 (522)
Q Consensus       245 ~~~g~~~~v~~~~~~  259 (522)
                      .|.|++|+|.+++..
T Consensus        76 ~~~gr~l~V~~a~~~   90 (96)
T 2dgx_A           76 KIGSKKILVSLATGA   90 (96)
T ss_dssp             EETTEEEEEEECCCS
T ss_pred             EECCeEEEEEEcCCC
Confidence            999999999987543

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=4.7e-14  Score=114.82  Aligned_cols=83  Identities=16%  Similarity=0.268  Sum_probs=71.3

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||+|||+.+|+++|+++|..||.|....      ...+...+.++|||||+|.+.++|..|+ .|++..|.|+.
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~------~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   96 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPP------IQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKI   96 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSC------CEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceE------EEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            3468999999999999999999999999974321      2455557888999999999999999999 69999999999


Q ss_pred             EEEecCCCCC
Q 009944          251 VRVRRPTDYN  260 (522)
Q Consensus       251 ~~v~~~~~~~  260 (522)
                      |.|.++....
T Consensus        97 l~v~~a~~~~  106 (115)
T 2cpx_A           97 LVIEFGKNKK  106 (115)
T ss_dssp             CEEEECCCCS
T ss_pred             EEEEEccCCC
Confidence            9999976543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.51  E-value=2.7e-13  Score=114.36  Aligned_cols=79  Identities=18%  Similarity=0.298  Sum_probs=67.8

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEEeCHHHHHHHH-Hhc
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALD  242 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~a~-~~~  242 (522)
                      .....++|||+|||..+|+++|+++|..||.|            ..+.+      +.++|||||+|.+.++|.+|+ .|+
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i------------~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~  105 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI------------ESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLN  105 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCE------------EEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhC
Confidence            34567899999999999999999999999984            33333      345899999999999999999 599


Q ss_pred             CceecCceEEEecCCCCC
Q 009944          243 GIIFEGVAVRVRRPTDYN  260 (522)
Q Consensus       243 ~~~~~g~~~~v~~~~~~~  260 (522)
                      +..|.|+.|+|.++....
T Consensus       106 g~~~~g~~l~v~~a~~~~  123 (139)
T 1u6f_A          106 GFNILNKRLKVALAASGH  123 (139)
T ss_dssp             TEECSSCEEEEEESSCCC
T ss_pred             CCEECCeEEEEEECCCCC
Confidence            999999999999876543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=1.9e-14  Score=114.00  Aligned_cols=76  Identities=21%  Similarity=0.326  Sum_probs=66.4

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCcEEEEEEeCHHHHHHHHHhcCcee
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDGIIF  246 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~a~~~~~~~~  246 (522)
                      ...++|||+|||+++|+++|+++|.+||.|            .++.+     +.++|||||+|.+.++|..|+.+++..|
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v------------~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~~~~~~~   76 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQV------------LNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKY   76 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCE------------EEEEEECCCTTSCCCEEEEEESSHHHHHHHHTSSCCCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCE------------EEEEEEECCCCCCccEEEEEECCHHHHHHHHHcCCCEE
Confidence            346799999999999999999999999974            44443     5578999999999999999999999999


Q ss_pred             cCceEEEecCCCC
Q 009944          247 EGVAVRVRRPTDY  259 (522)
Q Consensus       247 ~g~~~~v~~~~~~  259 (522)
                      .|+.|.|.+...+
T Consensus        77 ~gr~l~V~~~~~~   89 (103)
T 1s79_A           77 KETDLLILFKDDY   89 (103)
T ss_dssp             TTTTCEEEEHHHH
T ss_pred             CCEEEEEEEchHH
Confidence            9999999876543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=8e-14  Score=110.06  Aligned_cols=77  Identities=26%  Similarity=0.399  Sum_probs=66.9

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHH--HHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCcee
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQV--MTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~--g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~  246 (522)
                      .....++|||+|||+.+|+++|+++|.+|  |.            |..+.+  .+|||||+|.+.++|.+|+ .|++..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~------------v~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~   76 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGA------------VERVKK--IRDYAFVHFSNREDAVEAMKALNGKVL   76 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTC------------EEEEEE--CSSEEEEEESSHHHHHHHHHHHSSEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcc------------eEEEEE--eCCeEEEEeCCHHHHHHHHHHhCCCEe
Confidence            34557899999999999999999999999  65            555554  4789999999999999999 5999999


Q ss_pred             cCceEEEecCCCCC
Q 009944          247 EGVAVRVRRPTDYN  260 (522)
Q Consensus       247 ~g~~~~v~~~~~~~  260 (522)
                      .|+.|+|.+++...
T Consensus        77 ~g~~l~v~~a~~~~   90 (99)
T 2cpd_A           77 DGSPIEVTLAKPVD   90 (99)
T ss_dssp             TTEEEEEECCCCCC
T ss_pred             CCcEEEEEECCCCC
Confidence            99999999876543

>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=99.51  E-value=5.7e-14  Score=111.83  Aligned_cols=79  Identities=24%  Similarity=0.382  Sum_probs=68.1

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec----CCCcEEEEEEeCHHHHHHHH-HhcCc
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAM-ALDGI  244 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~----~~~g~afV~f~~~~~a~~a~-~~~~~  244 (522)
                      .....++|||+|||+.+|+++|+++|..||.            |..+.+.    .++|||||+|.+.++|.+|+ .|++.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~------------v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   78 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGK------------ILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGT   78 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSC------------EEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            3455789999999999999999999999997            5555543    34899999999999999999 69999


Q ss_pred             eecCceEEEecCCCCC
Q 009944          245 IFEGVAVRVRRPTDYN  260 (522)
Q Consensus       245 ~~~g~~~~v~~~~~~~  260 (522)
                      .|.|+.|.|.++....
T Consensus        79 ~~~g~~l~v~~a~~~~   94 (103)
T 2cq3_A           79 VVEGRKIEVNNATARV   94 (103)
T ss_dssp             EETTEECEEEECCSSC
T ss_pred             EECCEEEEEEEcccCC
Confidence            9999999999876543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.51  E-value=6.3e-15  Score=109.94  Aligned_cols=75  Identities=15%  Similarity=0.280  Sum_probs=63.0

Q ss_pred             eeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEEEec
Q 009944          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (522)
Q Consensus       176 ~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~v~~  255 (522)
                      +|||+|||+.+|+++|+++|.+||.|....+      +.+...+.++|||||+|.+.++|++|+++++..|.|++|.|++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   74 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAML------MFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECC------CBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEEC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEE------EecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEe
Confidence            5899999999999999999999998543221      2222245678999999999999999999999999999999986


Q ss_pred             C
Q 009944          256 P  256 (522)
Q Consensus       256 ~  256 (522)
                      +
T Consensus        75 A   75 (75)
T 2mss_A           75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=7.8e-14  Score=108.00  Aligned_cols=75  Identities=23%  Similarity=0.418  Sum_probs=66.4

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++|||+|||+.+|+++|+++|.+||.            |..+.+.  ++||||+|.+.++|++|+ .|++..|.|+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~~~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~   71 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGR------------VIECDVV--KDYAFVHMEKEADAKAAIAQLNGKEVKGK   71 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSC------------EEEEEEC--SSCEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCC------------EEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            345679999999999999999999999997            6666665  569999999999999999 5999999999


Q ss_pred             eEEEecCCCC
Q 009944          250 AVRVRRPTDY  259 (522)
Q Consensus       250 ~~~v~~~~~~  259 (522)
                      .|+|.++...
T Consensus        72 ~l~v~~a~~~   81 (90)
T 2dnp_A           72 RINVELSTKG   81 (90)
T ss_dssp             ECEEEESCCC
T ss_pred             EEEEEECCCC
Confidence            9999987654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=5.1e-14  Score=109.04  Aligned_cols=75  Identities=27%  Similarity=0.448  Sum_probs=66.7

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||+|||..+|+++|+++|.+||.            |..+.+.  +|||||+|.+.++|++|+ .|++..|.|++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   71 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGK------------VLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLHGVN   71 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSC------------EEEEEEE--TTEEEEEESSHHHHHHHHHHHTTCBCSSCB
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEE--CCEEEEEECCHHHHHHHHHHhcCCccCCcE
Confidence            34679999999999999999999999997            5556555  899999999999999999 79999999999


Q ss_pred             EEEecCCCCC
Q 009944          251 VRVRRPTDYN  260 (522)
Q Consensus       251 ~~v~~~~~~~  260 (522)
                      |+|.++....
T Consensus        72 l~v~~a~~~~   81 (90)
T 2dnq_A           72 INVEASKNKS   81 (90)
T ss_dssp             CEEECSSCCC
T ss_pred             EEEEECCCCC
Confidence            9999876554

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=1.1e-14  Score=118.07  Aligned_cols=91  Identities=21%  Similarity=0.208  Sum_probs=69.2

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCC--CCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCcee
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAG--PGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~--~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~  246 (522)
                      .....++|||+|||+.+|+++|+++|..||.|.......  .+.++.+..++.++|||||+|.+.++|++|+ .|++..|
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            445678999999999999999999999999864100000  0001111123556899999999999999999 5999999


Q ss_pred             cCceEEEecCCCCC
Q 009944          247 EGVAVRVRRPTDYN  260 (522)
Q Consensus       247 ~g~~~~v~~~~~~~  260 (522)
                      .|+.|+|.+++...
T Consensus        91 ~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           91 QGSKLKVSLARKKP  104 (113)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCCEEEEEECCCCC
Confidence            99999999876554

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.50  E-value=2.8e-14  Score=114.29  Aligned_cols=76  Identities=24%  Similarity=0.310  Sum_probs=66.0

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      .....++|||+|||..+|+++|+++|.+||.|            ..+.+.  +|||||+|.+.++|++|+ .|+|..|.|
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i------------~~v~i~--kg~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPM------------KEVKIL--NGFAFVEFEEAESAAKAIEEVHGKSFAN   92 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCC------------CEEEEE--TTEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCE------------EEEEEE--CCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            44567899999999999999999999999974            444444  899999999999999999 699999999


Q ss_pred             ceEEEecCCCC
Q 009944          249 VAVRVRRPTDY  259 (522)
Q Consensus       249 ~~~~v~~~~~~  259 (522)
                      +.|.|.++...
T Consensus        93 ~~l~V~~a~~~  103 (108)
T 2jvo_A           93 QPLEVVYSKLP  103 (108)
T ss_dssp             EECEEESCSCC
T ss_pred             eEEEEEEecCC
Confidence            99999986543

>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=99.50  E-value=7.6e-14  Score=112.03  Aligned_cols=76  Identities=25%  Similarity=0.339  Sum_probs=67.4

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC--
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--  248 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g--  248 (522)
                      ...++|||+|||+++|+++|+++|.+||.            |..+.+... |||||+|.+.++|++|| .||+..|.|  
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   79 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGD------------VCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHE   79 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSC------------EEEEEEETT-TEEEEEESSHHHHHHHHHHSSSEEEECTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EeEEEEecC-CEEEEEECCHHHHHHHHHHHCcCCccCCc
Confidence            34679999999999999999999999997            666666655 99999999999999999 599999999  


Q ss_pred             ---ceEEEecCCCCC
Q 009944          249 ---VAVRVRRPTDYN  260 (522)
Q Consensus       249 ---~~~~v~~~~~~~  260 (522)
                         +.|+|.++....
T Consensus        80 ~~~~~i~V~~a~~~~   94 (108)
T 1x4c_A           80 GETAYIRVKVDGPRS   94 (108)
T ss_dssp             SCEEEEEEEESSCCS
T ss_pred             CcceEEEEEeCCCCC
Confidence               999999876643

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.50  E-value=1.6e-14  Score=119.32  Aligned_cols=85  Identities=21%  Similarity=0.350  Sum_probs=68.8

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecC
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g  248 (522)
                      ......++|||+|||..+|+++|+++|..||.|..+.      ++.+...+.++|||||+|.+.++|.+|+++++..|.|
T Consensus        31 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g  104 (124)
T 2jwn_A           31 KKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRIT------ILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRG  104 (124)
T ss_dssp             HHHHHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEE------EEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETT
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE------EEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECC
Confidence            3445678999999999999999999999999853210      0111123566899999999999999999999999999


Q ss_pred             ceEEEecCCCC
Q 009944          249 VAVRVRRPTDY  259 (522)
Q Consensus       249 ~~~~v~~~~~~  259 (522)
                      +.|.|.+++..
T Consensus       105 ~~l~V~~a~~~  115 (124)
T 2jwn_A          105 RTIKVLPKRTN  115 (124)
T ss_dssp             EECEEEESSCC
T ss_pred             eEEEEEECCCC
Confidence            99999987644

>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=99.50  E-value=2.1e-14  Score=115.76  Aligned_cols=76  Identities=21%  Similarity=0.153  Sum_probs=69.3

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++|||+|||+.+|+++|+++|.+||.            |..+.+..++|||||+|.+.++|+.|+ .||+..|.|+
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~------------i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   74 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGS------------LGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHV   74 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCe
Confidence            345679999999999999999999999997            777888889999999999999999999 6999999999


Q ss_pred             eEEEecCCC
Q 009944          250 AVRVRRPTD  258 (522)
Q Consensus       250 ~~~v~~~~~  258 (522)
                      .|.|.|+..
T Consensus        75 ~l~V~~a~~   83 (111)
T 1whx_A           75 PLYLEWAPI   83 (111)
T ss_dssp             BCEEEEEET
T ss_pred             EEEEEECCC
Confidence            999998654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.50  E-value=8.6e-14  Score=113.24  Aligned_cols=80  Identities=24%  Similarity=0.367  Sum_probs=68.1

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEEeCHHHHHHHH-Hhc
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALD  242 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~a~-~~~  242 (522)
                      .....++|||+|||..+|+++|+++|..||.|            ..+.+      +.++|||||+|.+.++|++|+ .|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i------------~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~   78 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRI------------SDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMG   78 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCE------------EEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTT
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhC
Confidence            34457899999999999999999999999974            44433      344799999999999999999 699


Q ss_pred             CceecCceEEEecCCCCCc
Q 009944          243 GIIFEGVAVRVRRPTDYNP  261 (522)
Q Consensus       243 ~~~~~g~~~~v~~~~~~~~  261 (522)
                      +..|.|+.|.|.++.....
T Consensus        79 g~~~~g~~l~V~~a~~~~~   97 (115)
T 2dgo_A           79 GQWLGGRQIRTNWATRKPP   97 (115)
T ss_dssp             TCEETTEECEEEESSCCCC
T ss_pred             CCEECCEEEEEEEccCCCC
Confidence            9999999999999776543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=1.6e-14  Score=116.13  Aligned_cols=82  Identities=21%  Similarity=0.340  Sum_probs=67.1

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceec
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~  247 (522)
                      ......++|||+|||..+|+++|+++|.+||.|....        +....+.++|||||+|.+.++|++|+ .|++..|.
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~--------i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~   95 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE--------IIFNERGSKGFGFVTFENSADADRAREKLHGTVVE   95 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEE--------ECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEET
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEE--------EEECCCCCceEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            4455678999999999999999999999999854211        10112346899999999999999999 59999999


Q ss_pred             CceEEEecCCC
Q 009944          248 GVAVRVRRPTD  258 (522)
Q Consensus       248 g~~~~v~~~~~  258 (522)
                      |+.|.|.+++.
T Consensus        96 g~~l~V~~a~~  106 (109)
T 2err_A           96 GRKIEVNNATA  106 (109)
T ss_dssp             TEECEEEECCC
T ss_pred             CEEEEEEECCC
Confidence            99999998654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.50  E-value=5.1e-14  Score=111.02  Aligned_cols=82  Identities=21%  Similarity=0.280  Sum_probs=66.0

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE---ecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~---~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      +.++|||+|||+.+|+++|+++|..||.|..+.      ++.+..   ++.++|||||+|.+.++|++|+ .|++..|.|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   77 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCT------ISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDG   77 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEE------EEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            467999999999999999999999999853210      011111   2256799999999999999999 599999999


Q ss_pred             ceEEEecCCCCC
Q 009944          249 VAVRVRRPTDYN  260 (522)
Q Consensus       249 ~~~~v~~~~~~~  260 (522)
                      +.|.|.++....
T Consensus        78 ~~l~V~~a~~~~   89 (98)
T 2cpf_A           78 HKLEVRISERAT   89 (98)
T ss_dssp             EECEEECSSCSS
T ss_pred             eEEEEEEccCCC
Confidence            999999876543

>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=6.2e-14  Score=111.25  Aligned_cols=81  Identities=11%  Similarity=0.205  Sum_probs=70.4

Q ss_pred             CCCeEEEcCC--CCCCC--------HHHHHHHHHhcCCceEEEEeeCCCC--CCcceEEEEEEcChHHHHHHHHHHcCCc
Q 009944          293 GPDRVFVGGL--PYYFT--------ETQIKELLESFGTLHGFDLVKDRDT--GNSKGYGFCVYQDPAVTDIACAALNGLK  360 (522)
Q Consensus       293 ~~~~l~v~nL--p~~~t--------~~~l~~~F~~~G~i~~v~~~~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~g~~  360 (522)
                      ++++|.|.|+  |..+.        +++|+++|++||.|..|.|+++..+  +.++|+|||+|.+.++|.+|+..|||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4578999998  33333        3799999999999999999988654  3679999999999999999999999999


Q ss_pred             cCCeEEEEEEccC
Q 009944          361 MGDKTLTVRRATA  373 (522)
Q Consensus       361 ~~g~~l~v~~~~~  373 (522)
                      |+|+.|.|.|+..
T Consensus        84 f~GR~i~v~~~~~   96 (105)
T 3v4m_A           84 FANRVVVTKYCDP   96 (105)
T ss_dssp             ETTEECEEEEECH
T ss_pred             eCCCEEEEEEeCH
Confidence            9999999999853

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.50  E-value=5.4e-14  Score=112.98  Aligned_cols=79  Identities=13%  Similarity=0.275  Sum_probs=64.1

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEEeCHHHHHHHHHhc
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALD  242 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~a~~~~  242 (522)
                      ......++|||+|||..+|+++|+++|..||.            |..+.+      +.++|||||+|.+.++|.+|++..
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~------------i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~   87 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGE------------VKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS   87 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSC------------EEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCC------------eEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC
Confidence            44556789999999999999999999999997            444443      556899999999999999999766


Q ss_pred             CceecCceEEEecCCCC
Q 009944          243 GIIFEGVAVRVRRPTDY  259 (522)
Q Consensus       243 ~~~~~g~~~~v~~~~~~  259 (522)
                      +..|.|+.|.|.++...
T Consensus        88 ~~~l~g~~l~V~~a~~~  104 (109)
T 2rs2_A           88 RHELDSKTIDPKVAFPR  104 (109)
T ss_dssp             CEEETTEEEEEEECCCC
T ss_pred             CCcCCCEEEEEEEccCC
Confidence            79999999999986544

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.50  E-value=1.6e-13  Score=110.73  Aligned_cols=86  Identities=19%  Similarity=0.278  Sum_probs=73.6

Q ss_pred             CCCcceEEEeeCCCCcCcCCChHHHHHHHHHHH---HHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHH
Q 009944          416 GETLAKVLCLTEAITADALADDEEYEEILEDMR---EECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAK  492 (522)
Q Consensus       416 ~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~---~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai  492 (522)
                      ....+.|.+|+..++++             +|.   ++|++||.|..|.|+++..++.....+|+|||+|.+.++|.+||
T Consensus        14 ~~~~l~V~nLp~~~~~~-------------~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai   80 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADP-------------EVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAI   80 (111)
T ss_dssp             CSSCEEEEEECTTTCCH-------------HHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHH-------------HHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHH
Confidence            34566777788777765             888   99999999999999998766544445689999999999999999


Q ss_pred             HHHhCCccCCeEEEEEEeCCcc
Q 009944          493 NALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       493 ~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      +.|||..|+|++|+|.|+....
T Consensus        81 ~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           81 QCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             HHHTTEEETTEEEEEESCCCCS
T ss_pred             HHhCCCEECCEEEEEEeccccc
Confidence            9999999999999999988754

>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=99.50  E-value=1.8e-14  Score=111.15  Aligned_cols=77  Identities=19%  Similarity=0.424  Sum_probs=65.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||..+++++|+++|++||.|..|.++.+     ++|||||+|.+.++|++|+..  ...+.|+.|.|.++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecC
Confidence            4579999999999999999999999999999999864     689999999999999864321  345699999999998


Q ss_pred             CCCC
Q 009944          373 ASSG  376 (522)
Q Consensus       373 ~~~~  376 (522)
                      ++..
T Consensus        77 ~~~~   80 (88)
T 1wf0_A           77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>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=99.50  E-value=3.5e-14  Score=109.23  Aligned_cols=75  Identities=15%  Similarity=0.376  Sum_probs=64.7

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEEeCHHHHHHHHHhcC
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDG  243 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~a~~~~~  243 (522)
                      .....++|||+|||+.+|+++|+++|.+||.|            ..+.+      +.++|||||+|.+.++|.+|+++++
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i------------~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~   74 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEV------------VDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKE   74 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCE------------EEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCE------------EEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCC
Confidence            34567899999999999999999999999974            33333      4558999999999999999998899


Q ss_pred             ceecCceEEEecC
Q 009944          244 IIFEGVAVRVRRP  256 (522)
Q Consensus       244 ~~~~g~~~~v~~~  256 (522)
                      ..|.|+.|.|+++
T Consensus        75 ~~~~g~~i~v~~A   87 (87)
T 3s7r_A           75 HRLDGRVIDPKKA   87 (87)
T ss_dssp             EEETTEEEEEEEC
T ss_pred             CEECCEEEEEEeC
Confidence            9999999999863

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.49  E-value=3.6e-14  Score=110.30  Aligned_cols=79  Identities=14%  Similarity=0.211  Sum_probs=66.1

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCC--eEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHH
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGT--LVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL  495 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~--I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~l  495 (522)
                      ..+.|-+|+..++++             +|+++|++||.  |.+|.|++++.+|.+   +|+|||+|.+.++|.+|++.|
T Consensus        10 ~tlfV~nL~~~~tee-------------~L~~~F~~~G~i~v~~v~i~~d~~tg~s---rG~aFV~f~~~~~A~~Ai~~l   73 (95)
T 2lkz_A           10 DTIILRNIAPHTVVD-------------SIMTALSPYASLAVNNIRLIKDKQTQQN---RGFAFVQLSSAMDASQLLQIL   73 (95)
T ss_dssp             CEEEEESCCTTCCHH-------------HHHHHSTTTCCCCGGGEECCCCSSSSSC---SSEEEEECSSSHHHHHHHHHH
T ss_pred             CEEEEeCCCCcCCHH-------------HHHHHHHhhCCccEEEEEEEecCCCCCC---ceEeEEEECCHHHHHHHHHHh
Confidence            344555566555554             99999999995  678999999888765   789999999999999999999


Q ss_pred             hCC----ccCCeEEEEEEeCC
Q 009944          496 SGR----KFGGNTVNAFYYPE  512 (522)
Q Consensus       496 ng~----~~~Gr~l~v~~~~~  512 (522)
                      ||.    .|+|++|.|.|+..
T Consensus        74 ng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           74 QSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             HSSSSCEEETTEEEEEEECCC
T ss_pred             cCCCCCceECCEEEEEEEccC
Confidence            997    48999999999863

>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=99.49  E-value=1.2e-14  Score=115.69  Aligned_cols=78  Identities=23%  Similarity=0.312  Sum_probs=67.9

Q ss_pred             hcccceeEEeCCCcc-CcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-Hhc--Ccee
Q 009944          171 TRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD--GIIF  246 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~-~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~--~~~~  246 (522)
                      ..+.++|||+|||++ +|+++|+++|.+||.            |.++.+..++|||||+|.+.++|..|+ .|+  +..|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~------------V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l   89 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGK------------IKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWF   89 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSC------------CSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCC------------EEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCceE
Confidence            445789999999998 999999999999997            666777788999999999999999999 564  5679


Q ss_pred             cCceEEEecCCCCC
Q 009944          247 EGVAVRVRRPTDYN  260 (522)
Q Consensus       247 ~g~~~~v~~~~~~~  260 (522)
                      .|++|.|.++..+.
T Consensus        90 ~Gr~l~V~~a~~~~  103 (112)
T 1x4f_A           90 QGRCVKVDLSEKYK  103 (112)
T ss_dssp             SSSCCEEEEECSCS
T ss_pred             CCEEEEEEECcccc
Confidence            99999999876543

>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=99.49  E-value=2e-14  Score=113.36  Aligned_cols=81  Identities=16%  Similarity=0.117  Sum_probs=68.6

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||+|||+.+|+++|+++|..||.|...      ..+.+...+.++|||||+|.+.++|++|+ .|++..|.|+.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~------~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   86 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGS------VCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRK   86 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTT------CEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccce------EEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeE
Confidence            345789999999999999999999999987532      23444455677899999999999999999 79999999999


Q ss_pred             EEEecCCC
Q 009944          251 VRVRRPTD  258 (522)
Q Consensus       251 ~~v~~~~~  258 (522)
                      |+|.++..
T Consensus        87 l~V~~a~~   94 (98)
T 2cqp_A           87 VKLVLGSG   94 (98)
T ss_dssp             CEEEESSC
T ss_pred             EEEEEcCC
Confidence            99998653

>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=99.49  E-value=2e-13  Score=108.65  Aligned_cols=75  Identities=21%  Similarity=0.317  Sum_probs=66.4

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||+|||+.+|+++|+++|.+||.            |..+.+.  ++||||+|.+.++|++|+ .|++..|.|+.
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~------------i~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~   74 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGK------------LERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEGEN   74 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSC------------EEEEEEC--SSCEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEE--CCEEEEEeCCHHHHHHHHHHHCCCccCCCE
Confidence            34679999999999999999999999997            5566554  679999999999999999 59999999999


Q ss_pred             EEEecCCCCC
Q 009944          251 VRVRRPTDYN  260 (522)
Q Consensus       251 ~~v~~~~~~~  260 (522)
                      |.|.++....
T Consensus        75 l~v~~a~~~~   84 (103)
T 2dgu_A           75 IEIVFAKPPD   84 (103)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEEcCCCc
Confidence            9999976554

>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=99.49  E-value=4.3e-14  Score=108.75  Aligned_cols=66  Identities=12%  Similarity=0.342  Sum_probs=59.6

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|+|++|.|.|+..+
T Consensus        21 ~~l~~~F~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A           21 AAIAAAFAPFGRISDARVVKDMATGKS---KGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             HHHHHHHHhcCCEeEEEEEecCCCCcc---ceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            499999999999999999998766654   789999999999999999999999999999999998753

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=8e-14  Score=109.21  Aligned_cols=67  Identities=19%  Similarity=0.312  Sum_probs=61.7

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|+|++|+|.|+.+..
T Consensus        20 ~~l~~~f~~~G~v~~v~i~~~~~~~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   86 (95)
T 2dnz_A           20 DMLRGIFEPFGKIDNIVLMKDSDTGRS---KGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERL   86 (95)
T ss_dssp             HHHHHHHTTTSCEEEEEEECCSSSCCC---CSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCC
T ss_pred             HHHHHHHHhcCCEeEEEEeecCCCCce---eeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccccc
Confidence            499999999999999999998877654   7899999999999999999999999999999999998754

>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=99.49  E-value=1.2e-13  Score=111.55  Aligned_cols=78  Identities=22%  Similarity=0.359  Sum_probs=67.7

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEEeCHHHHHHHH-Hhc-
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALD-  242 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~a~-~~~-  242 (522)
                      ....++|||+|||+.+|+++|+++|..||.            |..+.+      +.++|||||+|.+.++|.+|+ .++ 
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~   79 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGD------------LKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASL   79 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhcc
Confidence            345689999999999999999999999997            455544      456899999999999999999 698 


Q ss_pred             -----CceecCceEEEecCCCCC
Q 009944          243 -----GIIFEGVAVRVRRPTDYN  260 (522)
Q Consensus       243 -----~~~~~g~~~~v~~~~~~~  260 (522)
                           +..|.|+.|.|.++....
T Consensus        80 ~~~~~~~~~~g~~l~v~~a~~~~  102 (111)
T 1x4h_A           80 EAEGGGLKLDGRQLKVDLAVTRD  102 (111)
T ss_dssp             TTTTCCEESSSCEEEEECCCCCC
T ss_pred             ccccCCcEEcCEEEEEEECCCCc
Confidence                 999999999999876543

>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=99.49  E-value=5e-14  Score=110.36  Aligned_cols=76  Identities=30%  Similarity=0.468  Sum_probs=65.7

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCcEEEEEEeCHHHHHHHH-HhcC
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDG  243 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~a~-~~~~  243 (522)
                      .....++|||+|||+.+++++|+++|..||.            |..+.+     +.++|||||+|.+.++|.+|+ .|++
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~------------i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g   79 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGP------------LTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNG   79 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSC------------EEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCC------------EEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCC
Confidence            3455689999999999999999999999997            444444     345799999999999999999 5999


Q ss_pred             ceecCceEEEecCC
Q 009944          244 IIFEGVAVRVRRPT  257 (522)
Q Consensus       244 ~~~~g~~~~v~~~~  257 (522)
                      ..|.|+.|.|.+++
T Consensus        80 ~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           80 IRLYGRPINVSGPS   93 (95)
T ss_dssp             CEETTEECEEECCC
T ss_pred             CEECCCEEEEEEcC
Confidence            99999999999864

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=9.7e-14  Score=109.81  Aligned_cols=77  Identities=18%  Similarity=0.344  Sum_probs=66.5

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCcEEEEEEeCHHHHHHHH-HhcCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDGI  244 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~a~-~~~~~  244 (522)
                      ....++|||+|||+.+|+++|+++|..||.|            ..+.+     +.++|||||+|.+.++|.+|+ .|++.
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i------------~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   81 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTV------------KDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGM   81 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCE------------EEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCe------------EEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCC
Confidence            3456899999999999999999999999974            44443     345699999999999999999 79999


Q ss_pred             eecCceEEEecCCCC
Q 009944          245 IFEGVAVRVRRPTDY  259 (522)
Q Consensus       245 ~~~g~~~~v~~~~~~  259 (522)
                      .|.|+.|+|.++...
T Consensus        82 ~~~g~~l~v~~a~~~   96 (100)
T 2do4_A           82 TIKENIIKVAISNSG   96 (100)
T ss_dssp             ESSSCEEEEEECCCC
T ss_pred             EECCEEEEEEECCCC
Confidence            999999999986644

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=2.1e-14  Score=113.95  Aligned_cols=79  Identities=20%  Similarity=0.298  Sum_probs=67.8

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++|||+|||+.+|+++|+++|.+||.|.          +.....+..+|||||+|.+.++|++|+ .|++..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~----------~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   81 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFIK----------VPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGR   81 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEEE----------CCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEE----------EEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCe
Confidence            44578999999999999999999999998752          222245678999999999999999999 5999999999


Q ss_pred             eEEEecCCCC
Q 009944          250 AVRVRRPTDY  259 (522)
Q Consensus       250 ~~~v~~~~~~  259 (522)
                      .|+|.++...
T Consensus        82 ~l~v~~a~~~   91 (101)
T 2fc9_A           82 AIRLELQGPR   91 (101)
T ss_dssp             EEEEEECSSC
T ss_pred             EEEEEEcCCC
Confidence            9999987654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=1.3e-13  Score=107.74  Aligned_cols=64  Identities=20%  Similarity=0.345  Sum_probs=59.0

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|+|++|+|.|+.
T Consensus        31 ~~l~~~f~~~G~v~~v~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           31 NDLYRIFSKYGKVVKVTIMKDKDTRKS---KGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             HHHHHHTTTTSCEEEEEECCCSSSCCC---TTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhcCCeEEEEEEeCCCCCCc---ccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            499999999999999999998876654   6889999999999999999999999999999999873

>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=99.48  E-value=1.1e-13  Score=109.28  Aligned_cols=68  Identities=19%  Similarity=0.275  Sum_probs=62.1

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|.|++|.|.|+....-
T Consensus        23 ~~l~~~F~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   90 (99)
T 1whw_A           23 EDLEKLFSAYGPLSELHYPIDSLTKKP---KGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE   90 (99)
T ss_dssp             HHHHHHHHTTSCEEEEECCCCTTTCCC---CSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCST
T ss_pred             HHHHHHHHhcCCEeEEEEEecCCCCCc---CeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCcc
Confidence            499999999999999999998877655   68999999999999999999999999999999999887543

>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=99.48  E-value=5.8e-14  Score=107.50  Aligned_cols=63  Identities=17%  Similarity=0.253  Sum_probs=58.3

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEe
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  510 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~  510 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|+|++|+|.|+
T Consensus        22 ~~l~~~f~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A           22 KVLHAAFIPFGDITDIQIPLDYETEKH---RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             HHHHHHHGGGSCEEEEECCEETTTTEE---CSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             HHHHHHHhccCCEEEEEEEECCCCCcc---ccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            499999999999999999988766654   689999999999999999999999999999999986

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.48  E-value=2.2e-13  Score=119.30  Aligned_cols=75  Identities=16%  Similarity=0.215  Sum_probs=65.2

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCcEEEEEEeCHHHHHHHH-HhcCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDGII  245 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~a~-~~~~~~  245 (522)
                      ...++|||+|||+.+++++|+++|..||.|.            .+.+     +.++|||||+|.+.++|.+|+ .|++..
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~------------~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~  153 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLK------------KAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVP  153 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCS------------EEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE------------EEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCE
Confidence            3457999999999999999999999999753            3333     567899999999999999999 599999


Q ss_pred             ecCceEEEecCCC
Q 009944          246 FEGVAVRVRRPTD  258 (522)
Q Consensus       246 ~~g~~~~v~~~~~  258 (522)
                      |.|++|+|.++..
T Consensus       154 l~Gr~l~V~~a~~  166 (177)
T 2f3j_A          154 LDGRPMDIQLVAS  166 (177)
T ss_dssp             CSSSBCEEEEESS
T ss_pred             ECCEEEEEEEecC
Confidence            9999999998653

>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=99.48  E-value=6.1e-14  Score=112.11  Aligned_cols=78  Identities=22%  Similarity=0.273  Sum_probs=66.5

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCcEEEEEEeCHHHHHHHH-HhcCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDGI  244 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~a~-~~~~~  244 (522)
                      ....++|||+|||+.+|+++|+++|..||.|            ..+.+     +.++|||||+|.+.++|.+|+ .|++.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i------------~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   79 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVI------------DECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGS   79 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCE------------EEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCC
Confidence            3457899999999999999999999999974            44433     344899999999999999999 69999


Q ss_pred             eecC---ceEEEecCCCCC
Q 009944          245 IFEG---VAVRVRRPTDYN  260 (522)
Q Consensus       245 ~~~g---~~~~v~~~~~~~  260 (522)
                      .|.|   +.|.|.++....
T Consensus        80 ~~~gg~~~~l~V~~a~~~~   98 (105)
T 2dnh_A           80 QTMPGASSSLVVKFADTDK   98 (105)
T ss_dssp             CCCTTCSSCCEEEESCSSC
T ss_pred             ccCCCCCccEEEEECccCc
Confidence            9998   999999876543

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.48  E-value=2.1e-14  Score=112.60  Aligned_cols=79  Identities=18%  Similarity=0.176  Sum_probs=66.5

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~  251 (522)
                      ..++|||+|||+.+|+++|+++|.+||.|...      ..+.+...+.++|||||+|.+.++|++|+ .|++..|.|+.|
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~------~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l   87 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGS------VCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKV   87 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTC------CEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccce------EEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEE
Confidence            35799999999999999999999999986432      22334345567899999999999999999 599999999999


Q ss_pred             EEecCC
Q 009944          252 RVRRPT  257 (522)
Q Consensus       252 ~v~~~~  257 (522)
                      +|.++.
T Consensus        88 ~v~~a~   93 (95)
T 2ek1_A           88 KLSGPS   93 (95)
T ss_dssp             EEECCC
T ss_pred             EEEecc
Confidence            998754

>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=99.48  E-value=1.2e-14  Score=119.93  Aligned_cols=82  Identities=18%  Similarity=0.182  Sum_probs=69.5

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCce
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~  250 (522)
                      ....++|||+|||+.+|+++|+++|..||.|...      ..+.+..++.++|||||+|.+.++|.+||++++..|.|+.
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~------~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~   95 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDS------IYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRF   95 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTT------CEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccce------EEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcE
Confidence            3456899999999999999999999999986431      2244445677899999999999999999999999999999


Q ss_pred             EEEecCCC
Q 009944          251 VRVRRPTD  258 (522)
Q Consensus       251 ~~v~~~~~  258 (522)
                      |.|.++..
T Consensus        96 i~V~~a~~  103 (124)
T 1wel_A           96 IQVHPITK  103 (124)
T ss_dssp             BEEEEECH
T ss_pred             EEEEECCH
Confidence            99987653

>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=99.48  E-value=7.5e-14  Score=111.15  Aligned_cols=77  Identities=18%  Similarity=0.279  Sum_probs=67.4

Q ss_pred             cccceeEE--eCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCcee--
Q 009944          172 RHARRVYV--GGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF--  246 (522)
Q Consensus       172 ~~~~~v~v--~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~--  246 (522)
                      .+.++|||  +||++.+|+++|+++|.+||.            |..+.+..++|||||+|.+.++|++|+ .|||..|  
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~------------v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~   90 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGL------------VDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVD   90 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSC------------EEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCC------------eEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEcc
Confidence            34678999  779999999999999999997            677777778999999999999999999 6999988  


Q ss_pred             ---cCceEEEecCCCCC
Q 009944          247 ---EGVAVRVRRPTDYN  260 (522)
Q Consensus       247 ---~g~~~~v~~~~~~~  260 (522)
                         .|++|.|.++....
T Consensus        91 ~lg~g~~l~v~~a~~~p  107 (114)
T 2cq2_A           91 DLGQKITLYLNFVEKVQ  107 (114)
T ss_dssp             TTSCEEECEEEEESCCC
T ss_pred             ccCCCcEEEEEecccCc
Confidence               68899998865443

>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=99.48  E-value=6.8e-14  Score=113.63  Aligned_cols=76  Identities=29%  Similarity=0.412  Sum_probs=67.1

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEEeCHHHHHHHHHhcC
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDG  243 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~a~~~~~  243 (522)
                      .....++|||+|||..+|+++|+++|..||.            |..+.+      +.++|||||+|.+.++|++|+.|++
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g   88 (114)
T 2cq4_A           21 EERDARTVFCMQLAARIRPRDLEDFFSAVGK------------VRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTG   88 (114)
T ss_dssp             THHHHTEEEEESCCTTCCHHHHHHHHTTTSC------------EEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTT
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhCCC------------EeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCC
Confidence            3456789999999999999999999999997            445544      5678999999999999999999999


Q ss_pred             ceecCceEEEecCC
Q 009944          244 IIFEGVAVRVRRPT  257 (522)
Q Consensus       244 ~~~~g~~~~v~~~~  257 (522)
                      ..|.|+.|.|.++.
T Consensus        89 ~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           89 QRLLGVPIIVQASQ  102 (114)
T ss_dssp             EEETTEEEEEEEHH
T ss_pred             CEeCCeEEEEEecC
Confidence            99999999998754

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=1.3e-13  Score=107.18  Aligned_cols=76  Identities=28%  Similarity=0.447  Sum_probs=66.1

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++|||+|||+.+|+++|+++|.+||.            |..+.+.  ++||||+|.+.++|.+|+ .|++..|.|+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~   72 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGP------------VIECDIV--KDYAFVHMERAEDAVEAIRGLDNTEFQGK   72 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSC------------CCEEEEC--SSEEEEEESCHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCeeCCc
Confidence            345689999999999999999999999997            4455554  569999999999999999 6999999999


Q ss_pred             eEEEecCCCCC
Q 009944          250 AVRVRRPTDYN  260 (522)
Q Consensus       250 ~~~v~~~~~~~  260 (522)
                      .|+|.++....
T Consensus        73 ~l~V~~a~~~~   83 (92)
T 2dgt_A           73 RMHVQLSTSRL   83 (92)
T ss_dssp             EEEEEESSCCC
T ss_pred             EEEEEEccCCC
Confidence            99999876543

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.48  E-value=9.8e-14  Score=112.76  Aligned_cols=80  Identities=23%  Similarity=0.442  Sum_probs=66.8

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE--ecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY--INHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~--~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      ...++|||+|||..+|+++|+++|.+||.|..         |.-+.  .+.++|||||+|.+.++|++|+ .|++..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~---------v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g   75 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISE---------VLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHG   75 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSE---------EEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEE---------EEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            34679999999999999999999999998532         11111  3456799999999999999999 699999999


Q ss_pred             ceEEEecCCCCC
Q 009944          249 VAVRVRRPTDYN  260 (522)
Q Consensus       249 ~~~~v~~~~~~~  260 (522)
                      +.|+|.+++...
T Consensus        76 ~~l~V~~a~~~~   87 (116)
T 2fy1_A           76 KAIKVEQAKKPS   87 (116)
T ss_dssp             SBCEEEECCCSS
T ss_pred             EEEEEEECCCCC
Confidence            999999876544

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.47  E-value=4.2e-14  Score=111.02  Aligned_cols=79  Identities=18%  Similarity=0.278  Sum_probs=68.5

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      .....++|||+|||+.+|+++|+++|..||.|.          ++ ...+.++|||||+|.+.++|.+|+ .|++..|.|
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~----------~~-~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   80 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIR----------LV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG   80 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEEC----------CE-EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEE----------Ee-CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            344678999999999999999999999999753          22 456678999999999999999999 599999999


Q ss_pred             ceEEEecCCCC
Q 009944          249 VAVRVRRPTDY  259 (522)
Q Consensus       249 ~~~~v~~~~~~  259 (522)
                      +.|.|.++...
T Consensus        81 ~~l~v~~a~~~   91 (96)
T 1fjc_A           81 RSVSLYYTGEK   91 (96)
T ss_dssp             EEEEEEECSSS
T ss_pred             eEEEEEEcCCC
Confidence            99999986554

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=8.9e-14  Score=110.51  Aligned_cols=67  Identities=16%  Similarity=0.299  Sum_probs=61.4

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|+|++|+|.|+....
T Consensus        27 ~~l~~~f~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   93 (102)
T 1x5s_A           27 QSLEQVFSKYGQISEVVVVKDRETQRS---RGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSS   93 (102)
T ss_dssp             HHHHHHHHHHSCCCEEEECCCSSSCSC---CSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCC
T ss_pred             HHHHHHHHhcCCeEEEEEEeCCCCCCc---ccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            499999999999999999998776654   6899999999999999999999999999999999987654

>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=99.47  E-value=1.2e-13  Score=122.83  Aligned_cols=78  Identities=22%  Similarity=0.256  Sum_probs=72.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      ++|||+|||..+++++|.++|++||.|..|.|+.+. +|.++|||||+|.+.++|.+|+..+ +..|.|+.|.|.++...
T Consensus       110 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDY  187 (193)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC
T ss_pred             CEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHH
Confidence            689999999999999999999999999999999986 5999999999999999999999865 46999999999997653

>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=99.47  E-value=9.3e-14  Score=107.12  Aligned_cols=73  Identities=23%  Similarity=0.383  Sum_probs=63.8

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cC-CCcEEEEEEeCHHHHHHHH-HhcCc
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NH-EKKFAFVEMRTVEEASNAM-ALDGI  244 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~-~~g~afV~f~~~~~a~~a~-~~~~~  244 (522)
                      ..++|||+|||+.+|+++|+++|.+||.            |..+.+      +. .+|||||+|.+.++|.+|+ .|++.
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   70 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGK------------IKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGG   70 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSC------------EEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCC
Confidence            3578999999999999999999999997            444443      22 7899999999999999999 59999


Q ss_pred             eecCceEEEecCC
Q 009944          245 IFEGVAVRVRRPT  257 (522)
Q Consensus       245 ~~~g~~~~v~~~~  257 (522)
                      .|.|+.|.|.++.
T Consensus        71 ~~~g~~l~v~~a~   83 (88)
T 4a8x_A           71 QIDGQEITATAVL   83 (88)
T ss_dssp             EETTEECEEEEEC
T ss_pred             eECCeEEEEEECC
Confidence            9999999999754

>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=99.47  E-value=1.4e-13  Score=107.95  Aligned_cols=68  Identities=24%  Similarity=0.424  Sum_probs=62.1

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      ++|+++|+.||.|..|.|+.+..+|..   +|+|||+|.+.++|.+|++.|||..|+|++|.|.|+.....
T Consensus        17 ~~l~~~F~~~G~i~~v~i~~~~~~g~~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   84 (96)
T 2x1f_A           17 EQILDLCSNVGPVINLKMMFDPQTGRS---KGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDI   84 (96)
T ss_dssp             HHHHHHHHTTSCEEEEECCBCTTTCCB---CSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSSG
T ss_pred             HHHHHHHHhcCCEEEEEEEeCCCCCcc---ceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCCC
Confidence            499999999999999999998766654   68999999999999999999999999999999999987653

>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=99.47  E-value=7.1e-14  Score=108.06  Aligned_cols=81  Identities=23%  Similarity=0.400  Sum_probs=66.0

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceE
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~  251 (522)
                      ...++|||+|||+.+|+++|+++|..||.|....      .+.+...+.++|||||+|.+.++|.+|+.+++..|.|+.|
T Consensus         4 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l   77 (89)
T 3ucg_A            4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVT------ILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQI   77 (89)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEE------EEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEEC
T ss_pred             CcCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE------EEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEE
Confidence            3467999999999999999999999999743210      0111123456899999999999999999999999999999


Q ss_pred             EEecCCC
Q 009944          252 RVRRPTD  258 (522)
Q Consensus       252 ~v~~~~~  258 (522)
                      +|.+++.
T Consensus        78 ~V~~a~~   84 (89)
T 3ucg_A           78 KVIPKRT   84 (89)
T ss_dssp             EEEETTT
T ss_pred             EEEEccC
Confidence            9998654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=1.2e-13  Score=109.84  Aligned_cols=68  Identities=16%  Similarity=0.224  Sum_probs=62.0

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|+|++|.|.|+....-
T Consensus        27 ~~l~~~f~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2cqb_A           27 KVLHAAFIPFGDITDIQIPLDYETEKH---RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI   94 (102)
T ss_dssp             HHHHHHHTTTSCCCCEECCCCSSSCCC---SSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             HHHHHHhhccCCEEEEEEEecCCCCCc---ceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCC
Confidence            499999999999999999998777654   78999999999999999999999999999999999886543

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

Probab=99.47  E-value=2.2e-13  Score=107.00  Aligned_cols=74  Identities=23%  Similarity=0.362  Sum_probs=67.5

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||+||  .+|+++|+++|.+||.            |..+.+..++|||||+|.+.++|.+|+ .|++..|.|+.
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~------------i~~v~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   78 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGN------------IIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQ   78 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEETTEE
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCC------------EEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            45679999996  8999999999999997            778888899999999999999999999 79999999999


Q ss_pred             EEEecCCCC
Q 009944          251 VRVRRPTDY  259 (522)
Q Consensus       251 ~~v~~~~~~  259 (522)
                      |+|.++...
T Consensus        79 l~v~~a~~~   87 (97)
T 1x5p_A           79 LKVNIARKQ   87 (97)
T ss_dssp             EEEECCSSC
T ss_pred             EEEEECCCC
Confidence            999987654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=2.1e-13  Score=107.66  Aligned_cols=66  Identities=20%  Similarity=0.246  Sum_probs=60.4

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+||+ |||..|+|++|.|.|+....
T Consensus        25 ~~l~~~F~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~   90 (99)
T 2dgs_A           25 TELREYFKKFGVVTEVVMIYDAEKQRP---RGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPRD   90 (99)
T ss_dssp             HHHHHHHSSSSCEEEEEECCCTTTCSC---CSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECCCCC
T ss_pred             HHHHHHHHhcCCeEEEEEEeCCCCCCC---CceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECCCCc
Confidence            499999999999999999998777654   6899999999999999999 99999999999999988654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=1.2e-13  Score=110.01  Aligned_cols=67  Identities=22%  Similarity=0.401  Sum_probs=61.5

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|+|++|.|.|+....
T Consensus        28 ~~l~~~f~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2dnm_A           28 DSLRRVFEKYGRVGDVYIPREPHTKAP---RGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGR   94 (103)
T ss_dssp             HHHHHHHTTTSCEEEEECCBCSSSCSB---CSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSCC
T ss_pred             HHHHHHHHhcCCEEEEEEEeCCCCCCC---CeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcCC
Confidence            499999999999999999998876654   6889999999999999999999999999999999998654

>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=99.46  E-value=3.8e-14  Score=110.54  Aligned_cols=75  Identities=21%  Similarity=0.418  Sum_probs=64.0

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcC-ceecCce
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG-IIFEGVA  250 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~-~~~~g~~  250 (522)
                      ..++|||+|||+.+|+++|+++|.+||.++..        +. +   .++|||||+|.+.++|++|+ .|++ ..|.|+.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~--------~~-~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~   74 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAG--------QV-L---LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKI   74 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSS--------CE-E---EETTEEEECCSCHHHHHHHHHHHTTTCEETTEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEE--------EE-E---cCCCEEEEEECCHHHHHHHHHHccCCeeECCEE
Confidence            45799999999999999999999999973211        11 1   36899999999999999999 6999 9999999


Q ss_pred             EEEecCCCC
Q 009944          251 VRVRRPTDY  259 (522)
Q Consensus       251 ~~v~~~~~~  259 (522)
                      |+|.++...
T Consensus        75 l~v~~a~~~   83 (93)
T 2cqh_A           75 MEVDYSVSK   83 (93)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEEccCc
Confidence            999987654

>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=99.46  E-value=1.8e-14  Score=107.47  Aligned_cols=74  Identities=18%  Similarity=0.279  Sum_probs=62.1

Q ss_pred             eeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEEEec
Q 009944          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (522)
Q Consensus       176 ~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~v~~  255 (522)
                      +|||+|||+.+|+++|+++|.+||.|....+      +.+..++.++|||||+|.+.++|.+|+++++..+.|+.|.|++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~v~~   74 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIEL------PMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKV   74 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECC------CCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE------EecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEE
Confidence            5899999999999999999999998543211      2222346678999999999999999998899999999999875

>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=99.46  E-value=1.7e-13  Score=109.56  Aligned_cols=67  Identities=18%  Similarity=0.203  Sum_probs=61.4

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|+|++|+|.|+....
T Consensus        30 ~~l~~~F~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   96 (105)
T 1x5u_A           30 PLLWELFLQAGPVVNTHMPKDRVTGQH---QGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN   96 (105)
T ss_dssp             HHHHHHHHTTSCEEEEECCBCSSSCSB---CSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             HHHHHHHHhcCCeEEEEEEecCCCCcC---CcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCC
Confidence            499999999999999999998877654   6889999999999999999999999999999999987654

>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=99.46  E-value=1.2e-13  Score=105.15  Aligned_cols=66  Identities=14%  Similarity=0.261  Sum_probs=60.8

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|+|++|.|.|+...
T Consensus        16 ~~l~~~f~~~G~i~~~~i~~~~~~~~~---~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A           16 ETLRNAFKDFPSYLSGHVMWDMQTGSS---RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             HHHHHHHTTSTTEEEEEEEECTTTCCE---EEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             HHHHHHHHhcCCeeEEEEEEcCCCCCc---cceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            499999999999999999988767654   789999999999999999999999999999999998764

>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=99.46  E-value=1.7e-14  Score=117.08  Aligned_cols=82  Identities=12%  Similarity=0.094  Sum_probs=67.0

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHh-hcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTA-IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~-~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~  249 (522)
                      ....++|||+|||+.+|+++|+++|..||.| ..+.      ++.+ .++.++|||||+|.+.++|++||++++..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~------i~~d-~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr   84 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVH------VLVD-NNGQGLGQALVQFKNEDDARKSERLHRKKLNGR   84 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEE------ECCC-TTSSCSSCEEEECSSHHHHHHHGGGCSEEETTE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEE------EEEC-CCCCcceEEEEEECCHHHHHHHHHhCCCccCCe
Confidence            3456899999999999999999999999875 2211      1111 246689999999999999999997799999999


Q ss_pred             eEEEecCCCC
Q 009944          250 AVRVRRPTDY  259 (522)
Q Consensus       250 ~~~v~~~~~~  259 (522)
                      .|.|.++...
T Consensus        85 ~i~v~~a~~~   94 (114)
T 2cpy_A           85 EAFVHVVTLE   94 (114)
T ss_dssp             EEEEEEECHH
T ss_pred             EEEEEECCHH
Confidence            9999986543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.46  E-value=3.9e-13  Score=107.79  Aligned_cols=70  Identities=20%  Similarity=0.329  Sum_probs=62.5

Q ss_pred             HHHHHHhhccCCeEEEEecCC-CCCCCCCCCccEEEEEecChHhHHHHHHHH-hCCccCCeEEEEEEeCCccccc
Q 009944          445 EDMREECGKYGTLVNVVIPRP-DQNGGETPGVGKVFLEYYDAVGCATAKNAL-SGRKFGGNTVNAFYYPEDKYFN  517 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~-~~~g~~~~g~G~afV~F~~~~~A~~Ai~~l-ng~~~~Gr~l~v~~~~~~~~~~  517 (522)
                      ++|+++|++||.|..|.|+.+ ..++..   +|+|||+|.+.++|.+||..| ||..|+|++|.|.|+....-..
T Consensus        30 ~~l~~~F~~~G~i~~v~i~~~~~~~~~~---~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~~~~  101 (107)
T 2cph_A           30 REIRELFSTFGELKTVRLPKKMTGTGAH---RGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ  101 (107)
T ss_dssp             HHHHHHHHTTSCEEEEECCCCCSSSCSS---CSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCCCC
T ss_pred             HHHHHHHHccCCeEEEEEecCCCCCCCc---CceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCCCCC
Confidence            499999999999999999988 556654   689999999999999999999 9999999999999998765443

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.46  E-value=1e-13  Score=109.47  Aligned_cols=72  Identities=14%  Similarity=0.245  Sum_probs=65.7

Q ss_pred             HHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCC-eEEEEEEeCC
Q 009944          438 EEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG-NTVNAFYYPE  512 (522)
Q Consensus       438 ~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~G-r~l~v~~~~~  512 (522)
                      +.+..++++|+++|++||.|..|.|+.+..+|.+   +|+|||+|.+.++|.+||+.|||..|+| ++|.|.++..
T Consensus        20 ~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~---kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~   92 (100)
T 3ns6_A           20 AKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKT---KGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKD   92 (100)
T ss_dssp             GGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEE---CSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHH
T ss_pred             HHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCcc---ceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECch
Confidence            4457788899999999999999999999877765   6899999999999999999999999999 9999999865

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.46  E-value=1.1e-13  Score=110.35  Aligned_cols=77  Identities=22%  Similarity=0.335  Sum_probs=66.4

Q ss_pred             cccceeEEeCCCccC------cHHHHHHHHHHHHHhhcCCCCCCCCceEEEE----ecCCCcEEEEEEeCHHHHHHHH-H
Q 009944          172 RHARRVYVGGLPPLA------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVY----INHEKKFAFVEMRTVEEASNAM-A  240 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~------t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~----~~~~~g~afV~f~~~~~a~~a~-~  240 (522)
                      ...++|||+|||+.+      |+++|+++|.+||.|            ..+.    ++.++|||||+|.+.++|.+|+ .
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v------------~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~   80 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKI------------TNDFYPEEDGKTKGYIFLEYASPAHAVDAVKN   80 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCE------------EEEECCCBTTBSCCEEEEEECSSSHHHHHHHH
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCE------------EEEEeeCCCCCeeeEEEEEECCHHHHHHHHHH
Confidence            346799999999999      889999999999984            4443    3467899999999999999999 5


Q ss_pred             hcCceecCc-eEEEecCCCCC
Q 009944          241 LDGIIFEGV-AVRVRRPTDYN  260 (522)
Q Consensus       241 ~~~~~~~g~-~~~v~~~~~~~  260 (522)
                      |||..|.|+ +|.|.++....
T Consensus        81 l~g~~~~g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           81 ADGYKLDKQHTFRVNLFTDFD  101 (105)
T ss_dssp             CSSEECSTTCEEEEECSCCCC
T ss_pred             hCCcccCCCceEEEEEcchHh
Confidence            999999999 99999876543

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

Probab=99.46  E-value=6.2e-14  Score=109.12  Aligned_cols=80  Identities=18%  Similarity=0.219  Sum_probs=65.8

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||+|||..+|+++|+++|.+||.|...        .+....+.++|||||+|.+.++|.+|+ .|++..|.|+.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~--------~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~   77 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYA--------DIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGRE   77 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEE--------EEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEE--------EEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            346799999999999999999999999985321        111123446899999999999999999 59999999999


Q ss_pred             EEEecCCCC
Q 009944          251 VRVRRPTDY  259 (522)
Q Consensus       251 ~~v~~~~~~  259 (522)
                      |+|.++...
T Consensus        78 l~v~~a~~~   86 (92)
T 2dgv_A           78 IDVRIDRNA   86 (92)
T ss_dssp             CCCEECSCC
T ss_pred             EEEEEcCCC
Confidence            999986654

>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=99.46  E-value=4e-13  Score=108.48  Aligned_cols=82  Identities=17%  Similarity=0.296  Sum_probs=69.7

Q ss_pred             CCCCCeEEEcCCCCCCC-----------HHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCC
Q 009944          291 AEGPDRVFVGGLPYYFT-----------ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL  359 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t-----------~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~  359 (522)
                      ....++|+|.||....+           +++|+++|++||.|..|.| .++   .++|||||+|.+.++|.+|+..|||.
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            34567899999944332           5899999999999999965 443   37999999999999999999999999


Q ss_pred             ccCCeEEEEEEccCCCC
Q 009944          360 KMGDKTLTVRRATASSG  376 (522)
Q Consensus       360 ~~~g~~l~v~~~~~~~~  376 (522)
                      .|.|+.|.|.++.++..
T Consensus        88 ~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           88 WFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             EETTEECEEEECCSCCC
T ss_pred             EECCcEEEEEEeCCCCC
Confidence            99999999999977543

>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=99.46  E-value=1.6e-13  Score=110.85  Aligned_cols=80  Identities=14%  Similarity=0.144  Sum_probs=69.9

Q ss_pred             CCCeEEEcCCC--CCC---CHHHHHHHHHhcCCceEEEEeeCCC----CCCcceEEEEEEcChHHHHHHHHHHcCCccCC
Q 009944          293 GPDRVFVGGLP--YYF---TETQIKELLESFGTLHGFDLVKDRD----TGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (522)
Q Consensus       293 ~~~~l~v~nLp--~~~---t~~~l~~~F~~~G~i~~v~~~~~~~----~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  363 (522)
                      ++++|+|.||-  .++   .+++|+++|++||.|..|.|+.+..    ++.++|+|||+|.+.++|.+|+..|||.+|+|
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            34689999993  222   3689999999999999999998754    45678999999999999999999999999999


Q ss_pred             eEEEEEEcc
Q 009944          364 KTLTVRRAT  372 (522)
Q Consensus       364 ~~l~v~~~~  372 (522)
                      +.|.|.|+.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999984

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=1.3e-13  Score=109.82  Aligned_cols=67  Identities=16%  Similarity=0.306  Sum_probs=61.6

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+||+.|||..|+|++|+|.|+....
T Consensus        30 ~~l~~~f~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   96 (103)
T 2cq0_A           30 TDLQELFRPFGSISRIYLAKDKTTGQS---KGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPST   96 (103)
T ss_dssp             HHHHTTSTTTCCEEEEEEEECSSSCSE---EEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             HHHHHHHHhCCCeEEEEEeecCCCCce---eeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCC
Confidence            499999999999999999998767654   7899999999999999999999999999999999987654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=1.7e-13  Score=111.60  Aligned_cols=85  Identities=19%  Similarity=0.329  Sum_probs=68.0

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCc
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~  249 (522)
                      .....++|||+|||+.+|+++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|.+|++.++..|.|+
T Consensus        23 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~   96 (116)
T 1x4b_A           23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCV------VMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGR   96 (116)
T ss_dssp             HHHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEE------EECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE------EEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCE
Confidence            345578999999999999999999999999853210      01111225568999999999999999996699999999


Q ss_pred             eEEEecCCCCC
Q 009944          250 AVRVRRPTDYN  260 (522)
Q Consensus       250 ~~~v~~~~~~~  260 (522)
                      .|.|.++....
T Consensus        97 ~l~V~~a~~~~  107 (116)
T 1x4b_A           97 VVEPKRAVARE  107 (116)
T ss_dssp             EEEEECCSSCC
T ss_pred             EEEEEECCCCc
Confidence            99999876553

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.45  E-value=4.5e-14  Score=115.16  Aligned_cols=80  Identities=18%  Similarity=0.191  Sum_probs=66.0

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHH---hhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceec
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMT---AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFE  247 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~---~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~  247 (522)
                      ....++|||+|||+++|+++|+++|..||.   |....      ++.+ ..++++|||||+|.+.++|++|+++++..|.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~------i~~~-~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~   86 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVH------FIYT-REGRQSGEAFVELESEDDVKLALKKDRESMG   86 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEE------EEEC-SSSCEEEEEEEEBSSHHHHHHHGGGTTEEET
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEE------EEEC-CCCCCCeEEEEEECCHHHHHHHHhcCCCeEC
Confidence            345688999999999999999999999987   43211      1111 2256789999999999999999999999999


Q ss_pred             CceEEEecCC
Q 009944          248 GVAVRVRRPT  257 (522)
Q Consensus       248 g~~~~v~~~~  257 (522)
                      |+.|+|.++.
T Consensus        87 gr~i~V~~a~   96 (118)
T 2db1_A           87 HRYIEVFKSH   96 (118)
T ss_dssp             TEEEEEEEEC
T ss_pred             CeEEEEEECC
Confidence            9999998764

>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=99.45  E-value=1.5e-13  Score=113.81  Aligned_cols=67  Identities=22%  Similarity=0.370  Sum_probs=61.5

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+||+.|||..|+|++|.|.|+..++
T Consensus        61 ~~L~~~F~~~G~I~~v~i~~d~~tg~~---~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~~  127 (129)
T 2kxn_B           61 RDLREVFSKYGPIADVSIVYDQQSRRS---RGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR  127 (129)
T ss_dssp             HHHHHHHTTTSCEEEEEEECCSSSSCC---CCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSSS
T ss_pred             HHHHHHHHhcCCeEEEEEEecCCCCcc---ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            399999999999999999998877654   7899999999999999999999999999999999987654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.45  E-value=3.3e-14  Score=118.47  Aligned_cols=86  Identities=15%  Similarity=0.271  Sum_probs=70.0

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCc----e
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI----I  245 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~----~  245 (522)
                      ....++|||+|||+.+|+++|+++|.+||.|...+    +.++.+..++.++|||||+|.+. +|.+|+ .|++.    .
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~----v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~   94 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSN----VRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT   94 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTT----EECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceee----EEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc
Confidence            35568999999999999999999999999863200    11233344677899999999999 999999 79999    9


Q ss_pred             ecCceEEEecCCCCCc
Q 009944          246 FEGVAVRVRRPTDYNP  261 (522)
Q Consensus       246 ~~g~~~~v~~~~~~~~  261 (522)
                      |.|+.|.|.++.....
T Consensus        95 ~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           95 IDGKTINVEFAKGSKR  110 (131)
T ss_dssp             GGGCCCCCEECCCSCC
T ss_pred             CCCEEEEEEECCCCCC
Confidence            9999999998776543

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=2e-13  Score=102.70  Aligned_cols=70  Identities=14%  Similarity=0.146  Sum_probs=60.7

Q ss_pred             eeEEeCCCccCcHHH----HHHHHHHHH-HhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          176 RVYVGGLPPLANEQA----IATFFSQVM-TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       176 ~v~v~nlp~~~t~~~----l~~~f~~~g-~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      .|||+|||+.+++++    |+++|.+|| .            |+++ +   .|+|||+|.+.++|+.|+ .|+|..|.|+
T Consensus        11 ~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~------------Vl~V-t---gG~AfV~F~~~esA~~A~~~l~G~~l~gr   74 (96)
T 2diu_A           11 LLYVYNLPANKDGKSVSNRLRRLSDNCGGK------------VLSI-T---GCSAILRFINQDSAERAQKRMENEDVFGN   74 (96)
T ss_dssp             EEEEESCCTTSCHHHHHHHHHHHHHTTTCC------------EEEC-C---TTCEEEEESSHHHHHHHHHHHTTCCSSSS
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHHHHHcCCe------------eEEE-e---cCEEEEEECCHHHHHHHHHHhcCCccCCc
Confidence            399999999999988    558999995 7            5555 2   299999999999999999 7999999999


Q ss_pred             eEEEecCCCCCc
Q 009944          250 AVRVRRPTDYNP  261 (522)
Q Consensus       250 ~~~v~~~~~~~~  261 (522)
                      +|+|.+++....
T Consensus        75 ~i~v~~A~~~sd   86 (96)
T 2diu_A           75 RIIVSFTPKNRE   86 (96)
T ss_dssp             CCEEESSCCSCC
T ss_pred             eEEEEecCCCcc
Confidence            999999876543

>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=99.45  E-value=9.1e-14  Score=120.81  Aligned_cols=66  Identities=23%  Similarity=0.367  Sum_probs=60.7

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++|+++|++||.|..|.|+.+..+|..   +|+|||+|.+.++|.+||..|||..|.|++|.|.|+...
T Consensus        87 ~~L~~~F~~~G~i~~v~i~~~~~~g~~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  152 (165)
T 1rk8_A           87 DEIQEKFCDYGEIKNIHLNLDRRTGFS---KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK  152 (165)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTSSE---EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             HHHHHHhhcCCCEEEEEEEecCCCCcE---eeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            499999999999999999998777654   789999999999999999999999999999999998654

>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=99.45  E-value=1.3e-13  Score=108.54  Aligned_cols=77  Identities=19%  Similarity=0.398  Sum_probs=67.1

Q ss_pred             cccceeEEeCCCccCcHHHHH----HHHHHHHHhhcCCCCCCCCceEEEEe---cCCCcEEEEEEeCHHHHHHHH-HhcC
Q 009944          172 RHARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDG  243 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~----~~f~~~g~~~~~~~~~~~~~v~~~~~---~~~~g~afV~f~~~~~a~~a~-~~~~  243 (522)
                      .+.++|||+|||..+++++|+    ++|.+||.            |..+.+   +.++|||||+|.+.++|..|+ .|+|
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~------------i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g   73 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQ------------ILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQG   73 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSC------------EEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCC------------EEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCC
Confidence            456799999999999999999    99999997            455544   467899999999999999999 6999


Q ss_pred             ceecCceEEEecCCCCC
Q 009944          244 IIFEGVAVRVRRPTDYN  260 (522)
Q Consensus       244 ~~~~g~~~~v~~~~~~~  260 (522)
                      ..|.|+.|.|.++....
T Consensus        74 ~~~~g~~l~v~~a~~~~   90 (97)
T 1nu4_A           74 FPFYDKPMRIQYAKTDS   90 (97)
T ss_dssp             CEETTEECEEEECSSCC
T ss_pred             CEECCcEEEEEEccCCC
Confidence            99999999999876543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=2e-13  Score=108.82  Aligned_cols=77  Identities=18%  Similarity=0.288  Sum_probs=66.3

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHH-HHHhhcCCCCCCCCceEEEE-----ecCCCcEEEEEEeCHHHHHHHH-HhcCc
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQ-VMTAIGGNSAGPGDAVVNVY-----INHEKKFAFVEMRTVEEASNAM-ALDGI  244 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~-~g~~~~~~~~~~~~~v~~~~-----~~~~~g~afV~f~~~~~a~~a~-~~~~~  244 (522)
                      ...++|||+|||+.+|+++|+++|.. ||.|            ..+.     ++.++|||||+|.+.++|.+|+ .|++.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v------------~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   74 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSC------------RGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGA   74 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTE------------EEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCe------------EEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCC
Confidence            34679999999999999999999999 9984            3333     3456899999999999999999 59999


Q ss_pred             e-ecCceEEEecCCCCC
Q 009944          245 I-FEGVAVRVRRPTDYN  260 (522)
Q Consensus       245 ~-~~g~~~~v~~~~~~~  260 (522)
                      . |.|+.|.|.++....
T Consensus        75 ~~~~g~~l~v~~a~~~~   91 (104)
T 2dhg_A           75 VGLGSKPVRLSVAIPKA   91 (104)
T ss_dssp             CSSSSSCCCCCBCCCCC
T ss_pred             cccCCEeEEEEEccCCC
Confidence            9 999999999876543

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.45  E-value=1.7e-13  Score=110.51  Aligned_cols=74  Identities=22%  Similarity=0.388  Sum_probs=65.5

Q ss_pred             cccceeEEeCCCcc-CcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          172 RHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       172 ~~~~~v~v~nlp~~-~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ...++|||+|||+. +|+++|+++|.+||.            |..+.+  .+|||||+|.+.++|++|+ .|++..|.|+
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~------------v~~v~i--~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   90 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGR------------VAGCSV--HKGYAFVQYSNERHARAAVLGENGRVLAGQ   90 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSC------------CSEEEE--ETTEEEEECSSSHHHHHHHHHHTTCEETTE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCC------------eEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            34579999999999 999999999999997            444555  7899999999999999999 7999999999


Q ss_pred             eEEEecCCCC
Q 009944          250 AVRVRRPTDY  259 (522)
Q Consensus       250 ~~~v~~~~~~  259 (522)
                      .|+|.++...
T Consensus        91 ~l~V~~a~~~  100 (110)
T 1wf1_A           91 TLDINMAGEP  100 (110)
T ss_dssp             ECCEEESCCC
T ss_pred             EEEEEECCCC
Confidence            9999987643

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.45  E-value=2e-13  Score=107.76  Aligned_cols=64  Identities=16%  Similarity=0.327  Sum_probs=58.9

Q ss_pred             HHHHHHhhccCCeEE--------EEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          445 EDMREECGKYGTLVN--------VVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~--------v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                      ++|+++|++||.|..        |.|+.+..+|..   +|+|||+|.+.++|.+|++.|||..|+|++|+|.|+.
T Consensus        28 ~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~---~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           28 ESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL---KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             HHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSE---EEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHhCCEeeccccccccEEEEecCCCCCe---eeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEecC
Confidence            499999999999999        999988767654   7899999999999999999999999999999999874

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=2e-14  Score=114.95  Aligned_cols=78  Identities=21%  Similarity=0.368  Sum_probs=66.6

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEEeCHHHHHHHHHhcCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDGI  244 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~a~~~~~~  244 (522)
                      ....++|||+|||+.+|+++|+++|..||.|            ..+.+      +.++|||||+|.+.++|.+|++.++.
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v------------~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~   80 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEV------------VDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPH   80 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCE------------EEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCC
Confidence            4557899999999999999999999999974            33333      34579999999999999999966999


Q ss_pred             eecCceEEEecCCCCC
Q 009944          245 IFEGVAVRVRRPTDYN  260 (522)
Q Consensus       245 ~~~g~~~~v~~~~~~~  260 (522)
                      .|.|+.|.|.++....
T Consensus        81 ~~~g~~l~V~~a~~~~   96 (105)
T 2dh8_A           81 TLDGRNIDPKPCTPRG   96 (105)
T ss_dssp             EETTEEEBCCCSCCSS
T ss_pred             eECCEEEEEEEccCCC
Confidence            9999999999876543

>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=99.44  E-value=3.9e-13  Score=106.94  Aligned_cols=84  Identities=21%  Similarity=0.315  Sum_probs=66.0

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCc
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~  249 (522)
                      .....++|||+|||+.+|+++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|++|+. ++..|.|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~   83 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQ------VKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGR   83 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEE------EEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEE------EEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCe
Confidence            345578999999999999999999999999843210      01111124567999999999999999996 57899999


Q ss_pred             eEEEecCCCCC
Q 009944          250 AVRVRRPTDYN  260 (522)
Q Consensus       250 ~~~v~~~~~~~  260 (522)
                      .|.|.++....
T Consensus        84 ~l~v~~a~~~~   94 (103)
T 2cqg_A           84 WCDCKLPNSKQ   94 (103)
T ss_dssp             EEEEECCCTTC
T ss_pred             EEEEEecCCCC
Confidence            99999876553

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

Probab=99.44  E-value=1.2e-13  Score=125.43  Aligned_cols=77  Identities=22%  Similarity=0.396  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCCC---------CHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc-
Q 009944          292 EGPDRVFVGGLPYYF---------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-  361 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~---------t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~-  361 (522)
                      ...++|||+||+..+         ++++|+++|++||.|..|.|+.      ++|||||+|.+.++|+.|+++|+|..| 
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            345799999999998         7999999999999999999985      379999999999999999999999999 


Q ss_pred             -----------CCeEEEEEEccCC
Q 009944          362 -----------GDKTLTVRRATAS  374 (522)
Q Consensus       362 -----------~g~~l~v~~~~~~  374 (522)
                                 .|+.|.|.||...
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC--
T ss_pred             ccccccccccCCCCEEEEEEccCC
Confidence                       8999999999764

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=3.9e-14  Score=112.58  Aligned_cols=81  Identities=21%  Similarity=0.322  Sum_probs=66.0

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++|||+|||+.+|+++|+++|..|+.+.         .+.+...+.++|||||+|.+.++|++|+ .|++..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~---------~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   82 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSVRAR---------IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGN   82 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCSEEE---------EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCeEEE---------EEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            44568999999999999999999999774321         1222234556899999999999999999 5999999999


Q ss_pred             eEEEecCCCCC
Q 009944          250 AVRVRRPTDYN  260 (522)
Q Consensus       250 ~~~v~~~~~~~  260 (522)
                      .|.|.+++...
T Consensus        83 ~l~V~~a~~~~   93 (102)
T 2fc8_A           83 KVTLDWAKPKG   93 (102)
T ss_dssp             ECEEEECCCCC
T ss_pred             EEEEEEecCCC
Confidence            99999976554

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.44  E-value=6.6e-14  Score=107.85  Aligned_cols=73  Identities=23%  Similarity=0.361  Sum_probs=64.3

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~  251 (522)
                      ..++|||+|||+.+++++|+++|.+| .            |..+.+..++|||||+|.+.++|.+|+ .|++..+.|++|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~------------v~~~~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   70 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-D------------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDL   70 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-C------------CCCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-C------------eEEEEEeCCCcEEEEEECCHHHHHHHHHHhCCCeECCcEE
Confidence            45789999999999999999999999 6            344444588999999999999999999 699999999999


Q ss_pred             EEecCCC
Q 009944          252 RVRRPTD  258 (522)
Q Consensus       252 ~v~~~~~  258 (522)
                      +|.++..
T Consensus        71 ~V~~a~~   77 (88)
T 1wg1_A           71 IVQLQPT   77 (88)
T ss_dssp             EEEECCC
T ss_pred             EEEEcCC
Confidence            9998643

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=1.3e-13  Score=109.99  Aligned_cols=73  Identities=19%  Similarity=0.252  Sum_probs=63.1

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCcEEEEEEeCHHHHHHHHHhcCceec
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDGIIFE  247 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~a~~~~~~~~~  247 (522)
                      ...+|||+|||+.+|+++|+++|..| .|            .++.+     ++++|||||+|.+.++|++||++++..|.
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v------------~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~   81 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RV------------DAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRMLMI   81 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CC------------CEEEECCCTTCCCCSEEEEECSSHHHHHHHHHTTTEEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-Ce------------eEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeEC
Confidence            35789999999999999999999998 43            33332     56789999999999999999999999999


Q ss_pred             CceEEEecCCC
Q 009944          248 GVAVRVRRPTD  258 (522)
Q Consensus       248 g~~~~v~~~~~  258 (522)
                      |+.|.|..+..
T Consensus        82 gr~i~V~~a~~   92 (109)
T 2dnn_A           82 QRYVEVSPATE   92 (109)
T ss_dssp             TEEEEEEECCH
T ss_pred             CeEEEEEECCc
Confidence            99999987543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=2e-13  Score=106.63  Aligned_cols=76  Identities=25%  Similarity=0.402  Sum_probs=64.4

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCc-EEEEEEeCHHHHHHHHHhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEEASNAMALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g-~afV~f~~~~~a~~a~~~~~~~~~g~~  250 (522)
                      ...++|||+|||+.+|+++|+++|..||.            |..+......| ||||+|.+.++|.+|++|++..|.|+.
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~------------v~~v~~~~~~g~~afV~f~~~~~a~~ai~l~g~~~~g~~   73 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGP------------VASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHSLGGHR   73 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSC------------EEEEEECSSSCCEEEEEESSHHHHHHHHTCSCCEETTEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCC------------eEEEEEcCCCCcEEEEEECCHHHHHHHHhcCCeEECCEE
Confidence            34579999999999999999999999997            44454433322 999999999999999999999999999


Q ss_pred             EEEecCCCC
Q 009944          251 VRVRRPTDY  259 (522)
Q Consensus       251 ~~v~~~~~~  259 (522)
                      |.|.++...
T Consensus        74 l~V~~a~~~   82 (94)
T 2e5g_A           74 LRVRPREQK   82 (94)
T ss_dssp             CCCBCSCCS
T ss_pred             EEEEECCcC
Confidence            999976544

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=3.1e-13  Score=109.72  Aligned_cols=77  Identities=18%  Similarity=0.207  Sum_probs=65.9

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCcEEEEEEeCHHHHHHHH-HhcCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDGI  244 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~a~-~~~~~  244 (522)
                      ....++|||+|||+.+|+++|+++|..||.|            ..+.+     +.++|||||+|.+.++|++|+ .|++.
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i------------~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   79 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVV------------VRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQ   79 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCE------------EEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            3456899999999999999999999999974            44433     334799999999999999999 59999


Q ss_pred             eecCceEEEecCCCC
Q 009944          245 IFEGVAVRVRRPTDY  259 (522)
Q Consensus       245 ~~~g~~~~v~~~~~~  259 (522)
                      .|.|+.|.|.++...
T Consensus        80 ~~~g~~l~v~~a~~~   94 (114)
T 2do0_A           80 LLFDRPMHVKMDERA   94 (114)
T ss_dssp             EETTEECEEEECSCC
T ss_pred             EeCCCEEEEEEcccC
Confidence            999999999986543

>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=99.44  E-value=1.9e-13  Score=109.63  Aligned_cols=63  Identities=17%  Similarity=0.308  Sum_probs=58.5

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                      ++|+++|++||.|..|.|+.+. +|..   +|+|||+|.+.++|.+|++.|||..|+|++|.|.|++
T Consensus        44 ~~l~~~F~~~G~i~~v~i~~~~-~g~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           44 ADIQELFAEFGTLKKAAVHYDR-SGRS---LGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             HHHHHHHHTTSCEEEEEEEECT-TSCE---EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHHHhcCCeEEEEEEECC-CCCc---ceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            4999999999999999999887 6554   7899999999999999999999999999999999986

>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=99.44  E-value=1.9e-13  Score=109.49  Aligned_cols=66  Identities=17%  Similarity=0.278  Sum_probs=60.5

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++|+++|++||.|..|.|+.+..+|..   +|+|||+|.+.++|.+|++.|||..|+|++|.|.|+.+.
T Consensus        41 ~~l~~~F~~~G~i~~v~i~~~~~~g~~---~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k  106 (108)
T 2jrs_A           41 DMLRGIFEPFGRIESIQLMMDSETGRS---KGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER  106 (108)
T ss_dssp             HHHHHHHTTTSCEEEEEEEEETTTTEE---EEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSS
T ss_pred             HHHHHHHHhcCCeEEEEEEEcCCCCcc---ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccC
Confidence            499999999999999999988766654   789999999999999999999999999999999998754

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=8e-14  Score=110.12  Aligned_cols=69  Identities=20%  Similarity=0.254  Sum_probs=62.4

Q ss_pred             HHHHHHhhccCCeE-EEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeE----EEEEEeCCcccc
Q 009944          445 EDMREECGKYGTLV-NVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT----VNAFYYPEDKYF  516 (522)
Q Consensus       445 ~~l~~~f~~~G~I~-~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~----l~v~~~~~~~~~  516 (522)
                      ++|+++|++||.|. .|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|.|+.    |+|.|+......
T Consensus        24 ~~l~~~F~~~G~i~~~v~i~~~~~~g~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~~~~   97 (99)
T 2div_A           24 NFISRAFATMGETVMSVKIIRNRLTGIP---AGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPS   97 (99)
T ss_dssp             HHHHHHHHHTTCCCCEEEEEECSSSCCE---EEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTCCSSS
T ss_pred             HHHHHHHHHhCCcceEEEEeecCCCCCc---CCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCCCCCC
Confidence            49999999999999 9999998877655   789999999999999999999999999999    999999876543

>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=99.43  E-value=6.3e-13  Score=106.96  Aligned_cols=77  Identities=25%  Similarity=0.377  Sum_probs=65.4

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-------CCCcEEEEEEeCHHHHHHHH-Hhc--
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-------HEKKFAFVEMRTVEEASNAM-ALD--  242 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~-------~~~g~afV~f~~~~~a~~a~-~~~--  242 (522)
                      ..++|||+|||+.+|+++|+++|..||..           |..+.+.       .++|||||+|.+.++|..|+ .|+  
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~-----------v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g   75 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEG-----------VLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPG   75 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTT-----------EEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCC-----------ceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCC
Confidence            46799999999999999999999999861           3444443       67899999999999999999 585  


Q ss_pred             CceecCceEEEecCCCCC
Q 009944          243 GIIFEGVAVRVRRPTDYN  260 (522)
Q Consensus       243 ~~~~~g~~~~v~~~~~~~  260 (522)
                      +..|.|+.|+|.++....
T Consensus        76 ~~~~~g~~l~V~~a~~~~   93 (109)
T 2dis_A           76 RIQLWGHQIAVDWAEPEI   93 (109)
T ss_dssp             CSCBTTBCCEEEESCSSC
T ss_pred             CceecCCeEEEEEcCCCC
Confidence            589999999999976543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=1.5e-13  Score=107.92  Aligned_cols=68  Identities=15%  Similarity=0.289  Sum_probs=61.8

Q ss_pred             HHHHHHhhccCCeEEE-EecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          445 EDMREECGKYGTLVNV-VIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v-~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      ++|+++|++||.|..| .|+.+..++..   +|+|||+|.+.++|.+|++.|||..|+|++|.|.|+....-
T Consensus        20 ~~l~~~F~~~G~i~~~~~i~~~~~~g~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   88 (96)
T 1x5t_A           20 KLLYDTFSAFGVILQTPKIMRDPDTGNS---KGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDS   88 (96)
T ss_dssp             HHHHHHHHTTSCBSSCCEECCCTTTCSC---CSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCC
T ss_pred             HHHHHHHHhcCCeeEEEEEEEcCCCCCc---CeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccCC
Confidence            4999999999999999 99998767654   68999999999999999999999999999999999876543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=3.8e-13  Score=107.02  Aligned_cols=65  Identities=15%  Similarity=0.264  Sum_probs=58.9

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+.+  ++.   .+|+|||+|.+.++|.+|++.|||..|+|++|.|.|+....
T Consensus        30 ~~l~~~F~~~G~i~~v~i~~~--~g~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2d9p_A           30 ERLRKAFSPFGTITSAKVMME--GGR---SKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKE   94 (103)
T ss_dssp             HHHHHTTTTTSCEEEEEEEEC--SSS---EEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCC
T ss_pred             HHHHHHHHhcCCEEEEEEEcC--CCC---cCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecccc
Confidence            399999999999999999987  443   37899999999999999999999999999999999987654

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.43  E-value=1.1e-13  Score=104.71  Aligned_cols=67  Identities=22%  Similarity=0.359  Sum_probs=59.1

Q ss_pred             ceeEEeCCCccC------cHHHHHHHHHHHHHhhcCCCCCCCCceEEEE----ecCCCcEEEEEEeCHHHHHHHH-HhcC
Q 009944          175 RRVYVGGLPPLA------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVY----INHEKKFAFVEMRTVEEASNAM-ALDG  243 (522)
Q Consensus       175 ~~v~v~nlp~~~------t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~----~~~~~g~afV~f~~~~~a~~a~-~~~~  243 (522)
                      ++|||+|||..+      |+++|+++|.+||.|            ..+.    ++.++|||||+|.+.++|.+|+ .|||
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i------------~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng   69 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKI------------TNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADG   69 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCE------------EEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSS
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCe------------EEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcC
Confidence            689999999999      789999999999984            4443    3467899999999999999999 6999


Q ss_pred             ceecCc-eEEE
Q 009944          244 IIFEGV-AVRV  253 (522)
Q Consensus       244 ~~~~g~-~~~v  253 (522)
                      ..|.|+ +|+|
T Consensus        70 ~~~~g~~~l~V   80 (81)
T 2krb_A           70 YKLDKQHTFRV   80 (81)
T ss_dssp             CCCSSSSCCCC
T ss_pred             cccCCceeEEe
Confidence            999999 8876

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

Probab=99.43  E-value=9.1e-14  Score=109.00  Aligned_cols=75  Identities=15%  Similarity=0.312  Sum_probs=64.5

Q ss_pred             hcccceeEEeCCCc-cCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          171 TRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       171 ~~~~~~v~v~nlp~-~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      ..+.++|||+|||+ .+|+++|+++|.+||.            |..+.+  .+|||||+|.+.++|..|+ .|++..+.|
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~------------v~~v~i--~~g~afV~f~~~~~A~~A~~~l~g~~~~g   72 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGH------------IMQINI--KNAFGFIQFDNPQSVRDAIECESQEMNFG   72 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCC------------CCEEEE--ETTEEEEEESCHHHHHHHHHHHTCSSCBT
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCC------------EEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCeeCC
Confidence            44578999999998 9999999999999997            444544  3899999999999999999 599999999


Q ss_pred             ceEEEecCCCC
Q 009944          249 VAVRVRRPTDY  259 (522)
Q Consensus       249 ~~~~v~~~~~~  259 (522)
                      ++|.|.+++..
T Consensus        73 ~~l~V~~a~~~   83 (96)
T 2kvi_A           73 KKLILEVSSSN   83 (96)
T ss_dssp             TTBCEEEEECC
T ss_pred             cEEEEEEcCcC
Confidence            99999986543

>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=99.42  E-value=3.1e-13  Score=108.21  Aligned_cols=67  Identities=16%  Similarity=0.279  Sum_probs=61.1

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCcc---CCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF---GGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~---~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..+   .|++|.|.|+....
T Consensus        28 ~~l~~~F~~~G~i~~v~i~~~~~~g~~---~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~   97 (106)
T 2dgp_A           28 KDLKPLFEEFGKIYELTVLKDRFTGMH---KGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSES   97 (106)
T ss_dssp             HHHHHHHHHHSCCCEEECCCCSSSCSC---CSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCS
T ss_pred             HHHHHHHHhcCCeeEEEEEecCCCCCc---ceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCccc
Confidence            499999999999999999998877654   68999999999999999999999998   89999999987654

>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=99.42  E-value=3.4e-14  Score=118.15  Aligned_cols=80  Identities=19%  Similarity=0.191  Sum_probs=66.3

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHH---hhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceec
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMT---AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFE  247 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~---~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~  247 (522)
                      ....++|||+|||+++|+++|+++|..||.   |...      .++.+. .++++|||||+|.+.++|++|+++++..|.
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v------~i~~d~-~g~srG~aFV~F~~~e~a~~Al~~~g~~l~  113 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGV------HFIYTR-EGRQSGEAFVELGSEDDVKMALKKDRESMG  113 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTE------EEEECS-SSCEEEEEEEECSSHHHHHHHHTTTEEESS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEE------EEEECC-CCCCCeEEEEEECCHHHHHHHHhcCCCEEC
Confidence            345689999999999999999999999997   3321      112222 266789999999999999999999999999


Q ss_pred             CceEEEecCC
Q 009944          248 GVAVRVRRPT  257 (522)
Q Consensus       248 g~~~~v~~~~  257 (522)
                      |+.|.|.++.
T Consensus       114 gr~i~V~~a~  123 (136)
T 2hgl_A          114 HRYIEVFKSH  123 (136)
T ss_dssp             SSEEEEEECC
T ss_pred             CEEEEEEECC
Confidence            9999998764

>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=99.42  E-value=8.3e-14  Score=110.37  Aligned_cols=72  Identities=13%  Similarity=0.259  Sum_probs=63.3

Q ss_pred             EcCCCCCCCHHHHHHHH------------HhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEE
Q 009944          299 VGGLPYYFTETQIKELL------------ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (522)
Q Consensus       299 v~nLp~~~t~~~l~~~F------------~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (522)
                      +.||+..+++++|+++|            ++||.|..|.|+.+. ++.++|||||+|.+.++|.+|+..|||..|.|+.|
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            45677777777666655            999999999999885 58899999999999999999999999999999999


Q ss_pred             EEEEc
Q 009944          367 TVRRA  371 (522)
Q Consensus       367 ~v~~~  371 (522)
                      .|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>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=99.42  E-value=6.3e-14  Score=108.47  Aligned_cols=66  Identities=15%  Similarity=0.174  Sum_probs=58.2

Q ss_pred             HHHHHHhhccC--CeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYG--TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G--~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++|+++|++||  .|.+|.|+.+..+|..   +|+|||+|.+.++|.+|++.|||..|+|++|.|.++...
T Consensus        16 ~~l~~~F~~~G~~~v~~v~i~~~~~~g~~---kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~   83 (90)
T 3p5t_L           16 EDLTEAVHSLGVNDILEIKFFENRANGQS---KGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKL   83 (90)
T ss_dssp             HHHHHHHHTTTCCCCCCEEEEECTTTCCE---EEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC---
T ss_pred             HHHHHHHHHhCCCceEEEEEEecCCCCcc---CcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCC
Confidence            49999999999  9999999998877765   789999999999999999999999999999999998754

>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=99.42  E-value=1.1e-13  Score=110.49  Aligned_cols=85  Identities=31%  Similarity=0.434  Sum_probs=68.0

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++|||+|||+.+|+++|+++|..||.|..+.      .+.+...+.++|||||+|.+.++|.+|+ .|++..|.|+
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   78 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFR------LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGR   78 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEE------EEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSS
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEE------EEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCc
Confidence            44568999999999999999999999999853210      0111113455899999999999999999 6999999999


Q ss_pred             eEEEecCCCCCc
Q 009944          250 AVRVRRPTDYNP  261 (522)
Q Consensus       250 ~~~v~~~~~~~~  261 (522)
                      .|.|.++.....
T Consensus        79 ~l~v~~a~~~~~   90 (104)
T 1p1t_A           79 ALRVDNAASEKN   90 (104)
T ss_dssp             CBEEEETTCTTH
T ss_pred             EEEEEeCCCccc
Confidence            999998776543

>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=99.42  E-value=2.4e-13  Score=115.24  Aligned_cols=88  Identities=16%  Similarity=0.181  Sum_probs=70.1

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||+|||+.+|+++|+++|..||.|..+.. .....+....++.++|||||+|.+.++|.+|+ .||+..|.|+.
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~-~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQ-RIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHH-HHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccc-cceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            44678999999999999999999999998642100 00000333467889999999999999999999 59999999999


Q ss_pred             EEEecCCCCC
Q 009944          251 VRVRRPTDYN  260 (522)
Q Consensus       251 ~~v~~~~~~~  260 (522)
                      |.|.+++...
T Consensus       122 l~V~~a~~~~  131 (143)
T 3egn_A          122 MVVQFARSAR  131 (143)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999876543

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.42  E-value=3.6e-13  Score=123.36  Aligned_cols=100  Identities=32%  Similarity=0.506  Sum_probs=85.8

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCC-CCCccEEEEEecChHhHHHHHHHHh
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGE-TPGVGKVFLEYYDAVGCATAKNALS  496 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~-~~g~G~afV~F~~~~~A~~Ai~~ln  496 (522)
                      ....++.|.+.++..++..+     +.++|.+.|++||.|.+|.|+++..++.. .+++|++||+|.+.++|.+|++.||
T Consensus       122 ~~s~v~~l~n~v~~~e~~~e-----~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~  196 (222)
T 3dxb_A          122 MESTVMVLRNMVDPKDIDDD-----LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN  196 (222)
T ss_dssp             CBCSEEEEESSCCGGGCCTT-----HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             cccccchhhcCCCHHHHHHH-----HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhc
Confidence            55678999999999877654     44699999999999999999866544321 1457899999999999999999999


Q ss_pred             CCccCCeEEEEEEeCCcccccccCCC
Q 009944          497 GRKFGGNTVNAFYYPEDKYFNKDYSA  522 (522)
Q Consensus       497 g~~~~Gr~l~v~~~~~~~~~~~~~~~  522 (522)
                      |+.|+||+|.+.|+++++|..++|++
T Consensus       197 gr~~~gr~i~~~~~~~~~f~~~~~~~  222 (222)
T 3dxb_A          197 GRWFAGRKVVAEVYDQERFDNSDLSA  222 (222)
T ss_dssp             TCBSSSSBCEEEECCHHHHHTTCCCC
T ss_pred             CceECCeEEEEEEcCHHHhhhcccCC
Confidence            99999999999999999999999985

>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=99.41  E-value=4.3e-13  Score=108.10  Aligned_cols=66  Identities=23%  Similarity=0.367  Sum_probs=60.5

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++|+++|+.||.|..|.|+.+..+|..   +|+|||+|.+.++|.+|+..|||..|+|++|.|.|+...
T Consensus        41 ~~l~~~F~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  106 (110)
T 1oo0_B           41 DEIQEKFCDYGEIKNIHLNLDRRTGFS---KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK  106 (110)
T ss_dssp             HHHHHHHGGGSCEEEEECCBCTTTSSB---CSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEES
T ss_pred             HHHHHHHHhcCCEEEEEEEecCCCCCc---ceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccC
Confidence            499999999999999999988777654   689999999999999999999999999999999998653

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=3.1e-13  Score=108.14  Aligned_cols=66  Identities=20%  Similarity=0.342  Sum_probs=60.6

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++|+++|+.||.|..|.|+.+..+|..   +|+|||+|.+.++|.+|++.|||..|+|++|.|.|+...
T Consensus        38 ~~l~~~f~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~  103 (106)
T 1p27_B           38 EDIHDKFAEYGEIKNIHLNLDRRTGYL---KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR  103 (106)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTSSE---EEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEES
T ss_pred             HHHHHHHhccCCeEEEEEEecCCCCce---eeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCC
Confidence            499999999999999999998877654   789999999999999999999999999999999998654

>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=99.40  E-value=6.3e-13  Score=105.92  Aligned_cols=65  Identities=18%  Similarity=0.228  Sum_probs=58.9

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCC-CCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQN-GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~-g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|+.|| |..|.|+.+..+ +..   +|+|||+|.+.++|.+|| .|||..|+|++|.|.|+....
T Consensus        30 ~~l~~~F~~~G-i~~v~i~~~~~~~g~~---~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~   95 (104)
T 1wi8_A           30 ESIKEFFRGLN-ISAVRLPREPSNPERL---KGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQ   95 (104)
T ss_dssp             HHHHHHTTTSC-EEEEECCBCSSCTTSB---CSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCC
T ss_pred             HHHHHHHHHCC-ceEEEEecCCCCCCCc---CeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccCCC
Confidence            49999999999 999999998765 554   688899999999999999 999999999999999988754

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.39  E-value=5.5e-13  Score=106.05  Aligned_cols=66  Identities=14%  Similarity=0.157  Sum_probs=59.8

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      ++|+++|+.|| |..|.|+.+..++..   +|+|||+|.+.++|.+|| .|||..|+|++|.|.|+....-
T Consensus        30 ~~l~~~F~~~g-i~~v~i~~~~~~g~~---~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2dng_A           30 GDIDAIFKDLS-IRSVRLVRDKDTDKF---KGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQ   95 (103)
T ss_dssp             HHHHHHTTTSC-EEEEEEEECSSSCSE---EEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECCCCCC
T ss_pred             HHHHHHHHhCC-ceEEEEeecCCCCcc---ceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEecCCCC
Confidence            49999999997 999999998877655   789999999999999999 8999999999999999887543

>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=99.39  E-value=5.2e-13  Score=110.53  Aligned_cols=67  Identities=19%  Similarity=0.332  Sum_probs=61.0

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+||+.|||..|+|++|.|.|+....
T Consensus        37 ~~l~~~F~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  103 (126)
T 3ex7_B           37 EDIHDKFAEYGEIKNIHLNLDRRTGYL---KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG  103 (126)
T ss_dssp             HHHHHHHHTTSCEEEEECCBCTTTSSB---CSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESS
T ss_pred             HHHHHHHHhcCCeEEEEEEecCCCCcc---ceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCC
Confidence            499999999999999999998777654   6889999999999999999999999999999999986543

>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=99.39  E-value=8.4e-13  Score=111.85  Aligned_cols=75  Identities=19%  Similarity=0.178  Sum_probs=64.5

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe--cCCCcEEEEEEeCHHHHHHHH-HhcCceecC-
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKFAFVEMRTVEEASNAM-ALDGIIFEG-  248 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~--~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g-  248 (522)
                      ...+|||+||++.+|+++|+++|++||.            |.++.+  ...+|||||+|.+.++|+.|+ .|+|..|.| 
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~------------V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~  112 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGT------------VLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNA  112 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSC------------EEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSS
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCC------------EEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCC
Confidence            3457999999999999999999999998            444443  345789999999999999999 699999966 


Q ss_pred             -ceEEEecCCCC
Q 009944          249 -VAVRVRRPTDY  259 (522)
Q Consensus       249 -~~~~v~~~~~~  259 (522)
                       +.|+|.|++..
T Consensus       113 g~~L~V~~Ak~~  124 (164)
T 1sjr_A          113 CCTLRIDFSKLT  124 (164)
T ss_dssp             CSCEEEEECSSS
T ss_pred             CcEEEEEEecCC
Confidence             99999997754

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.39  E-value=1e-12  Score=106.97  Aligned_cols=65  Identities=17%  Similarity=0.184  Sum_probs=59.5

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|.+||+.||+ .|.|++|.|.|+...
T Consensus        32 ~~l~~~F~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a~~~   96 (116)
T 2cqd_A           32 ASLRKYFEGFGDIEEAVVITDRQTGKS---RGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLG   96 (116)
T ss_dssp             HHHHHHHHTTSCEEEEEESCCSSSCCC---CSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTT
T ss_pred             HHHHHHHHhCCCeeEEEEEEcCCCCcc---ceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEcccC
Confidence            499999999999999999998877665   68999999999999999999999 899999999998653

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.39  E-value=1e-12  Score=110.95  Aligned_cols=63  Identities=17%  Similarity=0.253  Sum_probs=57.9

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEe
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  510 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~  510 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|+|++|+|.|+
T Consensus        78 ~~l~~~f~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           78 KVLHAAFIPFGDITDIQIPLDYETEKH---RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             HHHHHHHGGGSCEEEEECCCCTTTCCC---CSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             HHHHHHHHhcCCEEEEEEeecCCCCCc---CcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            499999999999999999998777654   789999999999999999999999999999999885

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.39  E-value=3.4e-13  Score=109.46  Aligned_cols=73  Identities=26%  Similarity=0.361  Sum_probs=62.1

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||+|||+++|+++|+++|.+||.            |..+.+... |||||+|.+.++|++|| .||+..|.|+.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~gr~   80 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGD------------VCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHE   80 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSC------------EEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEecC-CEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            34679999999999999999999999997            666766655 99999999999999999 59999999988


Q ss_pred             -----EEEecCC
Q 009944          251 -----VRVRRPT  257 (522)
Q Consensus       251 -----~~v~~~~  257 (522)
                           |+|....
T Consensus        81 ~~~~~i~v~~~~   92 (115)
T 3beg_B           81 GETAYIRVKVDG   92 (115)
T ss_dssp             SCCCBCEEEECC
T ss_pred             eeeEEEEeccCC
Confidence                 6666543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.38  E-value=1.1e-12  Score=108.25  Aligned_cols=67  Identities=15%  Similarity=0.261  Sum_probs=61.0

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      ++|+++|+.||.|..|.|+.+. +|..   +|+|||+|.+.++|.+|++.|||..|+|++|+|.|+.....
T Consensus        50 ~~l~~~F~~~G~v~~v~i~~~~-~g~~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  116 (124)
T 2kt5_A           50 ADIQELFAEFGTLKKAAVDYDR-SGRS---LGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID  116 (124)
T ss_dssp             HHHHHHHHTTSCCSEEEEECCS-SSSC---CSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCTTC
T ss_pred             HHHHHHHHhcCCeeEEEEEECC-CCCE---eeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCC
Confidence            4999999999999999999987 6654   68999999999999999999999999999999999887543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.09  E-value=3.3e-14  Score=115.87  Aligned_cols=90  Identities=20%  Similarity=0.226  Sum_probs=70.6

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCC--CCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceec
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAG--PGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~--~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~  247 (522)
                      ..+.++|||+|||..+|+++|+++|..||.|.......  .+.++.+..++.++|||||+|.+.++|.+|+ .|++..|.
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            34567999999999999999999999999875310000  0112333355678999999999999999999 59999999


Q ss_pred             CceEEEecCCCCC
Q 009944          248 GVAVRVRRPTDYN  260 (522)
Q Consensus       248 g~~~~v~~~~~~~  260 (522)
                      |++|.|.++....
T Consensus        84 g~~l~V~~a~~~~   96 (116)
T 2lcw_A           84 GNPIKVSFATRRA   96 (116)
Confidence            9999999876543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=1.2e-13  Score=112.64  Aligned_cols=82  Identities=24%  Similarity=0.264  Sum_probs=65.3

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEE--EecCCCcEEEEEEeCHHHHHHHHHhcCceecC
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV--YINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~--~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g  248 (522)
                      .....+|||+|||+++|+++|+++|.+||.|.+.     +..|.-+  ..++++|||||+|.+.++|++||+.++..|.|
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~-----v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~g   94 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGG-----KEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGK   94 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTG-----GGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTTTTEESSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCC-----cceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeeCC
Confidence            3557899999999999999999999999864200     0012211  34667899999999999999999779999999


Q ss_pred             ceEEEecCC
Q 009944          249 VAVRVRRPT  257 (522)
Q Consensus       249 ~~~~v~~~~  257 (522)
                      +.|.|..+.
T Consensus        95 R~i~V~~a~  103 (123)
T 2dha_A           95 RYIELFRST  103 (123)
T ss_dssp             CEECCEEEC
T ss_pred             eEEEEEECC
Confidence            999997654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.37  E-value=1.1e-12  Score=106.65  Aligned_cols=73  Identities=18%  Similarity=0.125  Sum_probs=61.9

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcE-EEEEEeCHHHHHHHH-HhcCceecC--ce
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKF-AFVEMRTVEEASNAM-ALDGIIFEG--VA  250 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~-afV~f~~~~~a~~a~-~~~~~~~~g--~~  250 (522)
                      ..|||+||++.+|+++|+++|.+||.            |.++.+....|| |||+|.+.++|..|+ .|+|..|.|  +.
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~------------V~~v~i~~~~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~   93 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGK------------VQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCT   93 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSC------------EEEEEEEESSSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSE
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCC------------EEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCeE
Confidence            35889999999999999999999998            444443333586 999999999999999 699999988  68


Q ss_pred             EEEecCCCC
Q 009944          251 VRVRRPTDY  259 (522)
Q Consensus       251 ~~v~~~~~~  259 (522)
                      |+|.+++..
T Consensus        94 l~V~~Ak~~  102 (124)
T 2e5i_A           94 LKIEYARPT  102 (124)
T ss_dssp             EEEECCSCS
T ss_pred             EEEEEecCC
Confidence            999987654

>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=99.36  E-value=1.1e-12  Score=112.80  Aligned_cols=67  Identities=18%  Similarity=0.314  Sum_probs=61.4

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+||+.|||..|+|++|+|.|+....
T Consensus        54 ~~l~~~F~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  120 (156)
T 1h2v_Z           54 EQIYELFSKSGDIKKIIMGLDKMKKTA---CGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK  120 (156)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCC
T ss_pred             HHHHHHHHhcCCeEEEEEEecCCCCcc---ceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            499999999999999999998876654   7899999999999999999999999999999999997643

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.36  E-value=8.1e-13  Score=113.05  Aligned_cols=66  Identities=14%  Similarity=0.171  Sum_probs=61.2

Q ss_pred             HHHHHHhhccC--CeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYG--TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G--~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++|+++|+.||  .|..|.|+.+..+|..   +|||||+|.+.++|.+||+.|||..|+|++|.|.++...
T Consensus        70 ~~L~~~F~~~G~i~v~~v~i~~d~~tg~s---kGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~~  137 (156)
T 3n9u_C           70 QQLIQVIRSIGVYDVVELKFAENRANGQS---KGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ  137 (156)
T ss_dssp             HHHHHHHHHTTCCCEEEEEEEECTTTCCE---EEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCHH
T ss_pred             HHHHHHHHHHCCccEEEEEEEecCCCCcc---ceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCCC
Confidence            49999999999  9999999999878765   789999999999999999999999999999999998754

>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=99.36  E-value=7.7e-13  Score=104.48  Aligned_cols=63  Identities=16%  Similarity=0.184  Sum_probs=57.3

Q ss_pred             HHHHHhhccCCeEEEEecCCC-CCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          446 DMREECGKYGTLVNVVIPRPD-QNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       446 ~l~~~f~~~G~I~~v~i~~~~-~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      +|+++|+.|| |..|.|+.+. .+|..   +|+|||+|.+.++|.+|+ .|||..|+|+.|.|.++...
T Consensus        35 ~l~~~F~~~G-i~~v~i~~~~~~~g~~---~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~~~   98 (100)
T 2j76_E           35 SIKEFFRGLN-ISAVRLPREPSNPERL---KGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQA   98 (100)
T ss_dssp             HHHHHSCSSC-EEEEECSCCTTTTCCC---CSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEECCCS
T ss_pred             HHHHHHHhcC-CeEEEEEecCCcCCcc---CeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEeccCC
Confidence            9999999999 9999999987 45554   688899999999999999 89999999999999998764

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.36  E-value=2.5e-13  Score=103.89  Aligned_cols=64  Identities=16%  Similarity=0.201  Sum_probs=58.0

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|+|+.|++.+..
T Consensus        20 ~~l~~~f~~~G~i~~~~i~~~~~~~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A           20 QDLVKLCQPYGKIVSTKAILDKTTNKC---KGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             HHHHTTSTTTSCEEEEEEECCSSSCSC---CSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             HHHHHHHHhcCCeEEEEEEecCCCCCc---CcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            499999999999999999998777664   6899999999999999999999999999999887643

>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=99.35  E-value=1.7e-12  Score=103.20  Aligned_cols=68  Identities=13%  Similarity=0.226  Sum_probs=60.3

Q ss_pred             HHHHHHhhccCCeEE-EEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccccc
Q 009944          445 EDMREECGKYGTLVN-VVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFN  517 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~-v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~~~  517 (522)
                      ++|+++|++||.|.. |.|+.+ .+|.+   +|+|||+|.+.++|.+||+. ||..|+|+.|.|.+++...+..
T Consensus        30 ~~l~~~F~~~G~v~~~v~i~~~-~~g~~---~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~~~~~~~~   98 (104)
T 1wg5_A           30 EEIVQFFSGLEIVPNGMTLPVD-FQGRS---TGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSRAEVRT   98 (104)
T ss_dssp             HHHHHHTTTCCEEEEEEECCBC-SSSCB---CSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEECTTTSCC
T ss_pred             HHHHHHHHhcCCcceeEEEEEC-CCCCc---ceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEECCHHHHHH
Confidence            499999999999998 888887 56654   68999999999999999997 9999999999999998776543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=6.3e-12  Score=98.47  Aligned_cols=78  Identities=13%  Similarity=0.190  Sum_probs=66.0

Q ss_pred             CCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEE-EecCCCCCCCCCCCccEEEEEecChHhHHHHHHHH
Q 009944          417 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNV-VIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL  495 (522)
Q Consensus       417 ~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v-~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~l  495 (522)
                      ...+.|-+|+..++.+             +|+++|++||.|..| .|+.+..+       |.|||+|.+.++|.+|+..|
T Consensus        15 ~~~l~V~nlp~~~t~~-------------~l~~~F~~~G~v~~~~~i~~~~~~-------~~afV~f~~~~~a~~Ai~~l   74 (96)
T 2e44_A           15 IRKLQIRNIPPHLQWE-------------VLDSLLVQYGVVESCEQVNTDSET-------AVVNVTYSSKDQARQALDKL   74 (96)
T ss_dssp             CCCEEEEEECSSSCHH-------------HHHHHHHHHSCEEEEEEECCSSSS-------EEEEEEESSHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCCHH-------------HHHHHHHhcCCeEEEEEeecCCCC-------CEEEEEECCHHHHHHHHHHh
Confidence            3556677777666654             999999999999999 58776532       45899999999999999999


Q ss_pred             hCCccCCeEEEEEEeCCcc
Q 009944          496 SGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       496 ng~~~~Gr~l~v~~~~~~~  514 (522)
                      ||..|+|++|.|.|+.+..
T Consensus        75 ~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           75 NGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             TTCBCSSCBCEEEECCCCC
T ss_pred             CCCEECCcEEEEEEcCccc
Confidence            9999999999999998764

>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=99.35  E-value=1.6e-12  Score=100.04  Aligned_cols=76  Identities=25%  Similarity=0.445  Sum_probs=58.4

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCcEEEEEEeCHHHHHHHHHhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~-~~~g~afV~f~~~~~a~~a~~~~~~~~~g~  249 (522)
                      .....+|||+|||+++|+++|+++|++||.            |.++.+. .++|||||+|.+.++|.++.. ....+.|+
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~------------i~~v~i~~~srGfaFV~F~~~~~A~~~~~-~~~~~~g~   74 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGE------------VVDVFIPKPFRAFAFVTFADDKVAQSLCG-EDLIIKGI   74 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSC------------EEEEECCSSCCSEEEEEESCHHHHHHHTT-CEEEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCC------------EEEEEEeeCCCCEEEEEECCHHHHHHHcC-CCcccCCE
Confidence            345679999999999999999999999997            5666554 479999999999999985332 13445699


Q ss_pred             eEEEecCCCC
Q 009944          250 AVRVRRPTDY  259 (522)
Q Consensus       250 ~~~v~~~~~~  259 (522)
                      .|.|.++...
T Consensus        75 ~v~v~~a~~k   84 (89)
T 3d2w_A           75 SVHISNAEPK   84 (89)
T ss_dssp             EEEEEECC--
T ss_pred             EEEEEEcCCC
Confidence            9999986543

>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=99.34  E-value=4.5e-13  Score=103.69  Aligned_cols=78  Identities=21%  Similarity=0.230  Sum_probs=65.0

Q ss_pred             ceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCc
Q 009944          420 AKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRK  499 (522)
Q Consensus       420 ~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~  499 (522)
                      ..|.+|+..++++             +|+++|++||.|..|.|+.+..+|..   +|+|||+|.+.+ |.+|+..|||..
T Consensus         4 l~V~nLp~~~t~~-------------~l~~~F~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~-a~~a~~~l~g~~   66 (90)
T 2ki2_A            4 IYVGNLVYSATSE-------------QVKELFSQFGKVFNVKLIYDRETKKP---KGFGFVEMQEES-VSEAIAKLDNTD   66 (90)
T ss_dssp             EEEEEECTTSSHH-------------HHTTTHHHHTCCSEEEECCCSSSCCC---CEEEEEEECTTH-HHHHHHTSCSSC
T ss_pred             EEECCCCCCCCHH-------------HHHHHHHhcCCEEEEEEEEcCCCCCc---ceEEEEEECCHH-HHHHHHHhCCCE
Confidence            4555666665554             99999999999999999998877654   789999999999 999999999999


Q ss_pred             cCCeEEEEEEeCCcc
Q 009944          500 FGGNTVNAFYYPEDK  514 (522)
Q Consensus       500 ~~Gr~l~v~~~~~~~  514 (522)
                      |+|++|+|.++....
T Consensus        67 ~~g~~l~V~~a~~~~   81 (90)
T 2ki2_A           67 FMGRTIRVTEANPKK   81 (90)
T ss_dssp             CSSSSCSEEEC----
T ss_pred             ECCeEEEEEEcCCCC
Confidence            999999999987643

>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=99.34  E-value=1.2e-12  Score=103.45  Aligned_cols=70  Identities=13%  Similarity=0.090  Sum_probs=60.1

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcccccccC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY  520 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~~~~~~  520 (522)
                      ++|+++|++||.| .|.|+.+. ++.+   +|+|||+|.+.++|.+||+ +|+..|+|+.|.|.++....-..+.|
T Consensus        30 ~~l~~~F~~~G~~-~v~i~~d~-~g~~---~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~~~~~~~~~~   99 (102)
T 1wez_A           30 NDIYNFFSPLNPM-RVHIEIGP-DGRV---TGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTSGSGP   99 (102)
T ss_dssp             HHHHHSSCSCCCS-EEEEEESS-SSCE---EEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCCCCCCS
T ss_pred             HHHHHHHHHcCce-EEEEEECC-CCCE---eeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCCCCCCCCCC
Confidence            4999999999955 99999887 6654   7899999999999999995 79999999999999988766554443

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.33  E-value=1e-12  Score=98.41  Aligned_cols=62  Identities=18%  Similarity=0.320  Sum_probs=57.0

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEe
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  510 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~  510 (522)
                      ++|+++|++||.|..|.++.+..+|.+   +|+|||+|.+.++|.+|++.++ ..|+|++|.|.++
T Consensus        15 ~~l~~~F~~~G~v~~v~i~~~~~~~~~---~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A           15 EGLREYFGQFGEVKECLVMRDPLTKRS---RGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             HHHHHHHTTTSCCCCEEEECCCCSSSC---SSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             HHHHHHHHhcCCEEEEEEecCCCCCCc---CceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            399999999999999999998876654   6899999999999999999999 9999999999886

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.33  E-value=2e-12  Score=105.39  Aligned_cols=63  Identities=19%  Similarity=0.289  Sum_probs=56.0

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccE-EEEEecChHhHHHHHHHHhCCccCC--eEEEEEEeCCccc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGK-VFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYYPEDKY  515 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~-afV~F~~~~~A~~Ai~~lng~~~~G--r~l~v~~~~~~~~  515 (522)
                      ++|.++|++||.|.+|.|....        +|+ |||+|.+.++|.+|++.|||..|.|  ++|+|.|+....+
T Consensus        43 ~~L~~lFs~yG~V~~V~i~~~~--------~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l  108 (130)
T 3zzy_A           43 DVLHQIFSKFGTVLKIITFTKN--------NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  108 (130)
T ss_dssp             HHHHHHHTTSSCEEEEEEEEET--------TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSC
T ss_pred             HHHHHHHhCcCCEEEEEEEcCC--------CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCce
Confidence            4999999999999999987632        366 9999999999999999999999988  9999999987543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.33  E-value=2.3e-12  Score=99.88  Aligned_cols=63  Identities=17%  Similarity=0.305  Sum_probs=57.5

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++|+++|+.| .|..|.|+.+ .+|..   +|+|||+|.+.++|.+||. |||..|+|+.|.|.++...
T Consensus        25 ~~l~~~F~~~-~i~~v~i~~~-~~g~~---~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~~   87 (91)
T 2dgw_A           25 KNVMEFLAPL-KPVAIRIVRN-AHGNK---TGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSG   87 (91)
T ss_dssp             HHHHHHHTTS-CCSEEEEEEC-TTSCE---EEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESSC
T ss_pred             HHHHHHHhhC-CceEEEEEEC-CCCCC---ceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCcC
Confidence            4999999999 9999999988 46654   7899999999999999999 9999999999999998765

>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=6.9e-12  Score=100.50  Aligned_cols=76  Identities=14%  Similarity=0.100  Sum_probs=65.1

Q ss_pred             CCCeEEEcCCCCCC----------CHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccC
Q 009944          293 GPDRVFVGGLPYYF----------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (522)
Q Consensus       293 ~~~~l~v~nLp~~~----------t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  362 (522)
                      ++++|.|.||=..-          .+++|+++|++||.|..|.|.++.    ++|+|||+|.+.++|.+|+..|||.+|+
T Consensus         6 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            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            45689999983221          136899999999999999987652    5899999999999999999999999999


Q ss_pred             CeEEEEEEcc
Q 009944          363 DKTLTVRRAT  372 (522)
Q Consensus       363 g~~l~v~~~~  372 (522)
                      |+.|.|.|+.
T Consensus        82 GR~i~v~~~~   91 (114)
T 3s6e_A           82 GKMITAAYVP   91 (114)
T ss_dssp             TEECEEEEEC
T ss_pred             CEEEEEEEEc
Confidence            9999999984

>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=99.30  E-value=1.4e-12  Score=100.39  Aligned_cols=75  Identities=25%  Similarity=0.390  Sum_probs=61.6

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCcEEEEEEeCHHHHHHHHHhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~-~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~  251 (522)
                      ..++|||+|||+.+|+++|+++|.+||.            |..+.+. .++|||||+|.+.++|++|+.. ...+.|+.|
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~~~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l   70 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGD------------VMDVFIPKPFRAFAFVTFADDQIAQSLCGE-DLIIKGISV   70 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSC------------CCEEECCSSCCSCCEEECSCHHHHHHTTTC-EEEETTEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCC------------eeEEEEecCCCCEEEEEECCHHHHHHHhcC-CceeCCEEE
Confidence            4689999999999999999999999997            4455543 3699999999999999876533 456789999


Q ss_pred             EEecCCCCC
Q 009944          252 RVRRPTDYN  260 (522)
Q Consensus       252 ~v~~~~~~~  260 (522)
                      .|.++....
T Consensus        71 ~v~~a~~~~   79 (88)
T 1wf0_A           71 HISNAEPKH   79 (88)
T ss_dssp             EEECCCCCC
T ss_pred             EEEecCCCC
Confidence            999876543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.30  E-value=6.7e-13  Score=105.35  Aligned_cols=74  Identities=22%  Similarity=0.370  Sum_probs=64.0

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCcEEEEEEeCHHHHHHHHHhcCce
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDGII  245 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~a~~~~~~~  245 (522)
                      ....++|||+|||+.+|+++|+++|..||.|            ..+.+     +.++|||||+|.+.++|++|+. ++..
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i------------~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~-~~~~   72 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSV------------KEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-SQIN   72 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCE------------EEEEEEECTTSCEEEEEEEEESSCCCHHHHTT-CCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCe------------EEEEEEECCCCCccceEEEEECCHHHHHHHHh-CCCe
Confidence            3456899999999999999999999999974            34433     4467999999999999999999 9999


Q ss_pred             ecCceEEEecCC
Q 009944          246 FEGVAVRVRRPT  257 (522)
Q Consensus       246 ~~g~~~~v~~~~  257 (522)
                      |.|+.|.|.++.
T Consensus        73 ~~g~~l~v~~a~   84 (102)
T 2xs2_A           73 FHGKKLKLGPAI   84 (102)
T ss_dssp             ETTEECEEEEEE
T ss_pred             ECCEEEEEEECC
Confidence            999999998754

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

Probab=99.30  E-value=2.8e-12  Score=116.42  Aligned_cols=77  Identities=22%  Similarity=0.341  Sum_probs=68.9

Q ss_pred             hcccceeEEeCCCccC---------cHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-H
Q 009944          171 TRHARRVYVGGLPPLA---------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-A  240 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~---------t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~  240 (522)
                      ....++|||+||+..+         ++++|+++|.+||.            |.++.+..++|||||+|.+.++|+.|+ .
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~------------I~~v~v~~~kG~AFV~F~~~~~Ae~A~~a  198 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGD------------IDRIRYVESKNCGFVKFKYQANAEFAKEA  198 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSC------------EEEEEEEGGGTEEEEEESSHHHHHHHHHH
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCC------------EEEEEEECCCCEEEEEeCCHHHHHHHHHH
Confidence            3457899999999998         89999999999997            777777789999999999999999999 7


Q ss_pred             hcCcee------------cCceEEEecCCCC
Q 009944          241 LDGIIF------------EGVAVRVRRPTDY  259 (522)
Q Consensus       241 ~~~~~~------------~g~~~~v~~~~~~  259 (522)
                      |++..|            .|+.|.|.|+...
T Consensus       199 m~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          199 MSNQTLLLPSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             HTTCCCCCTTSTTGGGGGGSCCCEEEECC--
T ss_pred             hCCCEEeccccccccccCCCCEEEEEEccCC
Confidence            999999            8999999998754

>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=99.29  E-value=4.2e-12  Score=103.00  Aligned_cols=64  Identities=13%  Similarity=0.250  Sum_probs=58.2

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCcc--------CCeEEEEEEeCC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF--------GGNTVNAFYYPE  512 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~--------~Gr~l~v~~~~~  512 (522)
                      ++|+++|+.||.|..|.|+.+. ++..   +|+|||+|.+.++|.+|++.|||..|        .|++|.|.|+..
T Consensus        40 ~~l~~~F~~~G~i~~~~i~~~~-~g~~---~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~p  111 (114)
T 1x5o_A           40 QELENMLKPFGQVISTRILRDS-SGTS---RGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGP  111 (114)
T ss_dssp             HHHHHTTTTTSCEEEEEEEECS-SSCE---EEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECCC
T ss_pred             HHHHHHHHhcCCEEEEEEEECC-CCCc---ceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccCC
Confidence            4999999999999999999987 6544   78999999999999999999999999        688899999874

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.29  E-value=2.2e-11  Score=95.08  Aligned_cols=74  Identities=12%  Similarity=0.191  Sum_probs=62.7

Q ss_pred             CeEEEcCCC-------CCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          295 DRVFVGGLP-------YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       295 ~~l~v~nLp-------~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      .+|.|.-..       ..+++++|+++|++||.|..|.|+     +.++|||||+|.+.++|.+|+..+++  +.|++|.
T Consensus        11 ~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~   83 (100)
T 2d9o_A           11 PKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLK   83 (100)
T ss_dssp             CEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCE
T ss_pred             ceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEE
Confidence            456665544       468999999999999999999987     35799999999999999999997544  6799999


Q ss_pred             EEEccCCC
Q 009944          368 VRRATASS  375 (522)
Q Consensus       368 v~~~~~~~  375 (522)
                      |.|+..+.
T Consensus        84 V~~a~~~~   91 (100)
T 2d9o_A           84 ISWLEGQP   91 (100)
T ss_dssp             EECSSCCC
T ss_pred             EEEccCCC
Confidence            99997754

>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=99.29  E-value=4.4e-13  Score=111.77  Aligned_cols=70  Identities=16%  Similarity=0.137  Sum_probs=58.5

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcccccccC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY  520 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~~~~~~  520 (522)
                      ++|+++|++|| |+.|.|+.+.. +.+   +|+|||+|.+.++|.+|| .||+..|+|+.|.|.++.......+.|
T Consensus        61 ~dL~~~F~~~G-i~~v~i~~d~~-g~s---rGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~~~~~~  130 (139)
T 2hgn_A           61 NDIYNFFSPLN-PVRVHIEIGPD-GRV---TGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGASNGAY  130 (139)
T ss_dssp             HHHHHHHCSCC-CSEEECCCSSS-SCS---SCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC-----
T ss_pred             HHHHHHHHhcC-CeEEEEEECCC-CCC---ceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCCCCCCC
Confidence            59999999999 67999999874 654   678899999999999999 789999999999999998877665544

>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=99.28  E-value=1.7e-12  Score=103.90  Aligned_cols=65  Identities=12%  Similarity=0.105  Sum_probs=58.7

Q ss_pred             HHHHHHhhccCC---eEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGT---LVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~---I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|+.||.   |..|.|+.+.. |..   +|+|||+|.+.++|.+||+ |||..|+|+.|.|.++...+
T Consensus        26 ~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~---~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~~~~   93 (107)
T 2lmi_A           26 EDVLNFFSDCRIRNGENGIHFLLNRD-GKR---RGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYEINNED   93 (107)
T ss_dssp             HHHHHHTTTSCBTTTTTTEECCCCTT-STT---CSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEECCHHH
T ss_pred             HHHHHHHHhcCCcCCcceEEEEECCC-CCE---eeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEEECCHHH
Confidence            399999999998   99999999875 654   6899999999999999999 99999999999999987654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.27  E-value=3.6e-12  Score=101.60  Aligned_cols=66  Identities=12%  Similarity=0.105  Sum_probs=58.1

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecC----hHh----HHHHHH--HHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYD----AVG----CATAKN--ALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~----~~~----A~~Ai~--~lng~~~~Gr~l~v~~~~~~  513 (522)
                      .+|+++|+.||+|.+|.++.|+.+|.+   +|+|||+|.+    +++    |.+|+.  .|||..|+|++|+|.+-+..
T Consensus        21 ~~Lk~~Fs~fGeV~~~~li~Dp~Tg~s---lGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           21 ISIKNYFKKYGEISHFEAFNDPNSALP---LHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILNKHS   96 (136)
T ss_dssp             HHHHHHHHTTSCCSEEEEEECTTTCCE---EEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEECCTT
T ss_pred             HHHHHHHHhcCCeEEEEEEecCCCCce---eeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEECccc
Confidence            499999999999999999999999987   7899999996    444    899988  89999999999999986654

>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=99.27  E-value=2.7e-12  Score=117.40  Aligned_cols=66  Identities=15%  Similarity=0.203  Sum_probs=61.2

Q ss_pred             HHHHHHhhccC--CeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYG--TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G--~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++|+++|++||  .|..|.|+++..++..   +|||||+|.+.++|.+||+.|||..|+|++|+|.|+...
T Consensus        83 ~~L~~~F~~~G~~~v~~v~i~~d~~tg~s---kGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~~  150 (229)
T 3q2s_C           83 EDLTEAVHSLGVNDILEIKFFENRANGQS---KGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ  150 (229)
T ss_dssp             HHHHHHHHTTTCCCEEEEEEEECTTTCCE---EEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECCHH
T ss_pred             HHHHHHHHHHCCcceEEEEEEecCCCCcc---ceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECCCC
Confidence            49999999999  9999999999878765   789999999999999999999999999999999998753

>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=99.24  E-value=1.3e-11  Score=118.33  Aligned_cols=76  Identities=21%  Similarity=0.287  Sum_probs=65.2

Q ss_pred             CCCCCeEEEcC--CCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc---CCe-
Q 009944          291 AEGPDRVFVGG--LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM---GDK-  364 (522)
Q Consensus       291 ~~~~~~l~v~n--Lp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~---~g~-  364 (522)
                      ..+..+|||+|  |+..+|+++|+++|++||.|..|.+..      ++|||||+|.+.++|++|++.|||..+   .|+ 
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            45567999999  578999999999999999999987753      479999999999999999999999877   344 


Q ss_pred             -EEEEEEcc
Q 009944          365 -TLTVRRAT  372 (522)
Q Consensus       365 -~l~v~~~~  372 (522)
                       .|.|.|+.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             67788874

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.24  E-value=1.1e-11  Score=100.33  Aligned_cols=75  Identities=21%  Similarity=0.247  Sum_probs=55.5

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe---cCCCcEEEEEEeCHHHHHHHH-HhcCceec
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~---~~~~g~afV~f~~~~~a~~a~-~~~~~~~~  247 (522)
                      ...++|||+|||+.+|+++|+++|.+||.|. ..      .+.+..+   +.++|||||+|.+.++|++|+ .++  .++
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~------~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~   76 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VD------WPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EED   76 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EE------CTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EET
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EE------EeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcC
Confidence            4468999999999999999999999999752 00      0111111   467999999999999999999 562  355


Q ss_pred             CceEEEec
Q 009944          248 GVAVRVRR  255 (522)
Q Consensus       248 g~~~~v~~  255 (522)
                      |+.+.+..
T Consensus        77 G~~~~~~~   84 (114)
T 2dnl_A           77 GKLYLCVS   84 (114)
T ss_dssp             TEEEEEEC
T ss_pred             CcEEEecc
Confidence            55555543

>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=99.24  E-value=8.7e-12  Score=110.85  Aligned_cols=78  Identities=21%  Similarity=0.304  Sum_probs=66.5

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCcEEEEEEeCHHHHHHHHHhcCce
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDGII  245 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~a~~~~~~~  245 (522)
                      ....++|||+|||+.+|+++|.++|.+||.|            ..+.+     +.++|||||+|.+.++|.+|++..+..
T Consensus       106 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v------------~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~~  173 (193)
T 2voo_A          106 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQV------------LNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQK  173 (193)
T ss_dssp             HHHHTEEEEECCCTTCCHHHHHHHHTTSCCE------------EEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTCE
T ss_pred             ccccCEEEecCCCCcCCHHHHHHHHhcCCCE------------EEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCCe
Confidence            3456899999999999999999999999974            44433     446899999999999999999766779


Q ss_pred             ecCceEEEecCCCCC
Q 009944          246 FEGVAVRVRRPTDYN  260 (522)
Q Consensus       246 ~~g~~~~v~~~~~~~  260 (522)
                      |.|+.|.|.+.+.|.
T Consensus       174 ~~Gr~l~V~~~~~y~  188 (193)
T 2voo_A          174 YKETDLLILFKDDYF  188 (193)
T ss_dssp             ETTEECEEEETTTC-
T ss_pred             ECCEEEEEEEhHHHH
Confidence            999999999987764

>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=99.19  E-value=1.4e-11  Score=100.48  Aligned_cols=65  Identities=14%  Similarity=0.303  Sum_probs=56.9

Q ss_pred             HHHHHHhhccCCeE--EEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          445 EDMREECGKYGTLV--NVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       445 ~~l~~~f~~~G~I~--~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      ++|+++|++| .|+  .|.|+.+.. |.+   +|+|||+|.+.++|.+||+. ++..|+|+.|.|.++...++
T Consensus        57 ~dL~~~F~~~-~i~~~~v~i~~d~~-Grs---rGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~a~~~e~  123 (126)
T 2hgm_A           57 EEIVQFFSGL-EIVPNGITLPVDPE-GKI---TGEAFVQFASQELAEKALGK-HKERIGHRYIEVFKSSQEEV  123 (126)
T ss_dssp             HHHHHHTTTS-CEEEEEEECCCCSS-SSS---CSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEEECHHHH
T ss_pred             HHHHHHHhcC-CceeeEEEEEECCC-CCC---ceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEECCHHHh
Confidence            4999999999 666  899999875 654   68999999999999999994 88999999999999876654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.14  E-value=4.5e-10  Score=83.69  Aligned_cols=61  Identities=8%  Similarity=0.305  Sum_probs=54.5

Q ss_pred             HHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCccc
Q 009944          443 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  515 (522)
Q Consensus       443 ~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~  515 (522)
                      +..+|.+.|.+||.|..+++..+           .+||+|.+.++|.+||+ |||..++|+.|+|.+++.+=.
T Consensus        28 l~~~L~~~F~~~G~Vi~vr~~~d-----------~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt~dW~   88 (91)
T 2dnr_A           28 LIDELLQQFASFGEVILIRFVED-----------KMWVTFLEGSSALNVLS-LNGKELLNRTITIALKSPSGP   88 (91)
T ss_dssp             HHHHHHHHHHTTCCEEEEEECSS-----------SEEEEESSHHHHHHGGG-GTTCEETTEEEEEEECCCSSC
T ss_pred             HHHHHHHHHHhCCCeEEEEEecC-----------CEEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCCCCcc
Confidence            44589999999999999999874           35999999999999999 999999999999999987643

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.12  E-value=6.1e-11  Score=92.52  Aligned_cols=60  Identities=17%  Similarity=0.263  Sum_probs=51.9

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+..        .+|||||+|.+.++|..||+.+++  +.|++|+|.|+....
T Consensus        32 ~~L~~~F~~~G~V~~v~i~~~--------~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           32 DVLLRLLQKYGEVLNLVLSSK--------KPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQP   91 (100)
T ss_dssp             HHHHHHHHTTSCEEEEEEESS--------SSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCC
T ss_pred             HHHHHHHHhcCCEEEEEEccC--------CCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCC
Confidence            599999999999999999832        258999999999999999998554  689999999987643

>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=99.04  E-value=3.1e-10  Score=108.72  Aligned_cols=74  Identities=18%  Similarity=0.239  Sum_probs=63.1

Q ss_pred             hcccceeEEeC--CCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceec
Q 009944          171 TRHARRVYVGG--LPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (522)
Q Consensus       171 ~~~~~~v~v~n--lp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~  247 (522)
                      ..++++|||+|  |+..+|+++|+++|.+||.            |..+.+..++|||||+|.+.++|++|+ .|||..+.
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~------------V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~   82 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGL------------VDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSC------------EEEEECCTTCSEEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCC------------eEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCccc
Confidence            34567999999  5788999999999999997            677887789999999999999999999 79998874


Q ss_pred             ---Cc--eEEEecC
Q 009944          248 ---GV--AVRVRRP  256 (522)
Q Consensus       248 ---g~--~~~v~~~  256 (522)
                         |+  .+.|.+.
T Consensus        83 ~~~g~~~~ly~~~~   96 (345)
T 3tht_A           83 DDLGQKITLYLNFV   96 (345)
T ss_dssp             CTTSCEEECEEEEC
T ss_pred             cccCCceEEEEEEe
Confidence               44  5666664

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.00  E-value=8.8e-10  Score=88.10  Aligned_cols=75  Identities=13%  Similarity=0.127  Sum_probs=66.8

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcC-hHHHHHHHHHHc--CCccCCeEE
Q 009944          291 AEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD-PAVTDIACAALN--GLKMGDKTL  366 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~-~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~-~~~A~~Al~~l~--g~~~~g~~l  366 (522)
                      ......|+|+||+.. +++++|+++|+.||.|.+|.++.+..      .|||+|.+ .++|..|+..|+  |..|.|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            344568999999999 99999999999999999999998754      59999999 899999999995  789999999


Q ss_pred             EEEEc
Q 009944          367 TVRRA  371 (522)
Q Consensus       367 ~v~~~  371 (522)
                      ++...
T Consensus        89 ~~evL   93 (121)
T 1owx_A           89 TWEVL   93 (121)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            98875

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.96  E-value=1.9e-09  Score=80.29  Aligned_cols=71  Identities=20%  Similarity=0.302  Sum_probs=60.2

Q ss_pred             CeEEEcCCCC----CCCH----HHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEE
Q 009944          295 DRVFVGGLPY----YFTE----TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (522)
Q Consensus       295 ~~l~v~nLp~----~~t~----~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (522)
                      -||+|.-.+.    .+-.    .+|.+.|++||.|..++++.+.        +||+|.+.++|.+|++ |||..++|+.|
T Consensus         8 ~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr~L   78 (91)
T 2dnr_A            8 GTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNRTI   78 (91)
T ss_dssp             CEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTEEE
T ss_pred             CeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCeEE
Confidence            3777776652    2322    5799999999999999999873        8999999999999999 99999999999


Q ss_pred             EEEEccCC
Q 009944          367 TVRRATAS  374 (522)
Q Consensus       367 ~v~~~~~~  374 (522)
                      +|+++++.
T Consensus        79 kV~lkt~d   86 (91)
T 2dnr_A           79 TIALKSPS   86 (91)
T ss_dssp             EEEECCCS
T ss_pred             EEEeCCCC
Confidence            99998763

>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=98.88  E-value=5.6e-09  Score=95.28  Aligned_cols=67  Identities=16%  Similarity=0.170  Sum_probs=60.5

Q ss_pred             CCHHHHHHHHHhcCCceEEEEeeCC----CCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          306 FTETQIKELLESFGTLHGFDLVKDR----DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       306 ~t~~~l~~~F~~~G~i~~v~~~~~~----~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      -.+++|.+.|++||.|..+.|+.+.    .++.++|++||+|.+.++|.+|+..|||.+|+|++|.|.|..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            3567999999999999999998653    355899999999999999999999999999999999999974

>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=98.86  E-value=3.7e-09  Score=79.08  Aligned_cols=57  Identities=21%  Similarity=0.360  Sum_probs=51.4

Q ss_pred             HHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          443 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       443 ~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                      +..+|.+.|..||+|..++|..+           .+||+|.+.++|.+||+ |||..++|+.|+|.+-.
T Consensus        37 l~~~L~~~F~~~G~Vilvr~v~d-----------~~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           37 LRTELMQTLGSYGTIVLVRINQG-----------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHHHSCCSEEEEETT-----------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHHHHHHCCCEEEEEEecC-----------cEEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccC
Confidence            44689999999999999999875           36999999999999999 99999999999998754

>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=98.78  E-value=1.7e-08  Score=75.52  Aligned_cols=70  Identities=16%  Similarity=0.233  Sum_probs=59.9

Q ss_pred             CeEEEcCCCCC-----C-CH---HHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeE
Q 009944          295 DRVFVGGLPYY-----F-TE---TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT  365 (522)
Q Consensus       295 ~~l~v~nLp~~-----~-t~---~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~  365 (522)
                      -||+|.-++..     + .+   .+|.+.|+.||.|..++++.+.        +||+|.+.++|.+||+ |+|..++|+.
T Consensus        16 ~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~Gr~   86 (95)
T 1ufw_A           16 ATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKGRA   86 (95)
T ss_dssp             CEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEETTEE
T ss_pred             CeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeCCeE
Confidence            48888887643     2 22   5699999999999999999873        9999999999999998 9999999999


Q ss_pred             EEEEEccC
Q 009944          366 LTVRRATA  373 (522)
Q Consensus       366 l~v~~~~~  373 (522)
                      |+|.+..+
T Consensus        87 L~V~~k~~   94 (95)
T 1ufw_A           87 VKISGPSS   94 (95)
T ss_dssp             EEEECCCC
T ss_pred             EEEeccCC
Confidence            99997643

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.58  E-value=3.3e-07  Score=69.79  Aligned_cols=74  Identities=16%  Similarity=0.144  Sum_probs=67.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhc-----CCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESF-----GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-----G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (522)
                      +..++|-|-|||..+++..|+.+++++     |.|..|.+..+.      |-|+|+|.+...|.+|..+|+|..|.|++|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            345789999999999999999999999     999999998874      359999999999999999999999999999


Q ss_pred             EEEEc
Q 009944          367 TVRRA  371 (522)
Q Consensus       367 ~v~~~  371 (522)
                      +|.-.
T Consensus        93 r~gTv   97 (117)
T 2l9w_A           93 RSGTI   97 (117)
T ss_dssp             EEECH
T ss_pred             EecCH
Confidence            99854

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.54  E-value=2.8e-07  Score=73.60  Aligned_cols=58  Identities=10%  Similarity=0.050  Sum_probs=51.8

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecC-hHhHHHHHHHHh--CCccCCeEEEEEEeC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYD-AVGCATAKNALS--GRKFGGNTVNAFYYP  511 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~-~~~A~~Ai~~ln--g~~~~Gr~l~v~~~~  511 (522)
                      ++|+++|++||.|..|.+.++.         -.|||+|.+ .++|..|+.+||  |..|.|..+.+....
T Consensus        34 edLke~F~~~G~V~~Vd~~~g~---------~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~   94 (121)
T 1owx_A           34 EDLHILFSNHGEIKWIDFVRGA---------KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   94 (121)
T ss_dssp             HHHHHHTCSSCCEEEEECCTTC---------SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             HHHHHHHHhcCCEEEEEEecCC---------CEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECC
Confidence            4999999999999999998765         356999999 899999999994  888999999998876

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.47  E-value=3.9e-07  Score=69.37  Aligned_cols=73  Identities=12%  Similarity=0.150  Sum_probs=60.9

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhcc-----CCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHH
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKY-----GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAK  492 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~-----G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai  492 (522)
                      ...-++.|+..++..             .|+.+.++|     |.|.+|.+..+.         |-|+|+|.+...|-+|.
T Consensus        22 rtiaL~~ipDtvnda-------------rIr~lve~~~~i~~g~i~KI~L~pDH---------~GAivef~d~~~AgKas   79 (117)
T 2l9w_A           22 TLICLFPLSDKVSPS-------------LICQFLQEEIHINEKDIRKILLVSDF---------NGAIIIFRDSKFAAKML   79 (117)
T ss_dssp             SCEEEECCCTTCCHH-------------HHHHHHHHHTCCCTTTCSEEEEETTT---------TEEEEECSCHHHHHHHH
T ss_pred             cEEEEecCCCCCCHH-------------HHHHHHhhhhccCccceeEEEEecCC---------CceEEEEccchhhHHHH
Confidence            444455555555554             899999999     999999998875         66999999999999999


Q ss_pred             HHHhCCccCCeEEEEEEeCC
Q 009944          493 NALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       493 ~~lng~~~~Gr~l~v~~~~~  512 (522)
                      -+|+|..|.|++|+|.-+.+
T Consensus        80 LaL~G~ef~gr~Lr~gTv~e   99 (117)
T 2l9w_A           80 MILNGSQFQGKVIRSGTIND   99 (117)
T ss_dssp             HHHSSEEETTEEEEEECHHH
T ss_pred             hhcCCeeecCeEEEecCHHH
Confidence            99999999999999976544

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.09  E-value=1.5e-05  Score=60.32  Aligned_cols=92  Identities=21%  Similarity=0.314  Sum_probs=73.0

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEEE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  253 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~v  253 (522)
                      .++|.|.|||+.+.++.|.-+|+.--       ..-+..|.++....  +-|+|+|.+.+.|+..|+.....|++..|.|
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~r-------rsGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k~~H~L~~~~LsV   78 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRR-------RSGGGPVLSWQRLG--CGGVLTFREPADAERVLAQADHELHGAQLSL   78 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTT-------TTCCCCEEEEEEET--TEEEEEESSHHHHHHHHTCSCCBSSSSBCEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCC-------cCCCceeeEEEEcC--CcEEEEEcChHHHHHHhcCCcceecCeEEEE
Confidence            46899999999999999999998620       01255688887765  8899999999999999987788899999999


Q ss_pred             ecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCC
Q 009944          254 RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFT  307 (522)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t  307 (522)
                      .....                                 ..+.+|++.||++.|+
T Consensus        79 ~P~~~---------------------------------~~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           79 RPAPP---------------------------------RAPARLLLQGLPPGTS   99 (104)
T ss_dssp             EECCC---------------------------------CCCCCCCCCSCCCCCC
T ss_pred             EcCCC---------------------------------CCcceEeeecCCCCCC
Confidence            74221                                 2235899999998875

>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=97.80  E-value=4.6e-05  Score=58.07  Aligned_cols=75  Identities=12%  Similarity=0.097  Sum_probs=63.1

Q ss_pred             CCCeEEEcCCCCCC-C----HHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          293 GPDRVFVGGLPYYF-T----ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       293 ~~~~l~v~nLp~~~-t----~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      -+++|+|.||+..+ .    .+.++++|..|+++....+.+.      -.-..|.|.++++|.+|...||+..|.|..|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS------FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc------ceEEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            45799999998765 2    2578999999999887766654      12479999999999999999999999999999


Q ss_pred             EEEccC
Q 009944          368 VRRATA  373 (522)
Q Consensus       368 v~~~~~  373 (522)
                      |.++.+
T Consensus        78 ~YFgq~   83 (104)
T 1wey_A           78 LYFAQT   83 (104)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999864

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.63  E-value=0.00024  Score=54.14  Aligned_cols=60  Identities=12%  Similarity=0.204  Sum_probs=53.6

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      +.++++|..|+.+......+.         +.-+.|.|.++++|.+|-..|++..|+|+.|+|.|+...
T Consensus        25 ~~~e~Lf~~~~~~~tF~~lkS---------FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~   84 (104)
T 1wey_A           25 AKFESLFRTYDKDTTFQYFKS---------FKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             HHHHHHHHTTCSSCEEEEETT---------TTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             HHHHHHHHhhCcCcceeecCc---------ceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCCC
Confidence            588999999999998888764         467899999999999999999999999999999997643

>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=97.54  E-value=0.00046  Score=51.56  Aligned_cols=54  Identities=19%  Similarity=0.407  Sum_probs=45.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  357 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  357 (522)
                      ..++| ++|+.+...||.++|+.||.| .|.++.|-       .|||.|.+++.|..|+..+.
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            45666 999999999999999999965 46666662       59999999999999999774

>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=97.38  E-value=0.00094  Score=50.05  Aligned_cols=67  Identities=13%  Similarity=0.229  Sum_probs=57.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCC--cceEEEEEEcChHHHHHHHHHHcCCcc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTDIACAALNGLKM  361 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~--~~g~afV~f~~~~~A~~Al~~l~g~~~  361 (522)
                      ++|.|++||+.+||+++.+.++.+..+.....+..+.+..  .-.-|||.|.+.+++..-.+.++|..|
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            4799999999999999999999998888777776553322  346799999999999999999999887

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.29  E-value=0.0023  Score=48.48  Aligned_cols=72  Identities=19%  Similarity=0.243  Sum_probs=59.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHh-----cCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEE
Q 009944          294 PDRVFVGGLPYYFTETQIKELLES-----FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~-----~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (522)
                      ..+|.|.|||+.+.++.|.-+|++     =|.|..|....        +-|+|+|.+.+.|++.|+ -..+.|.+..|.|
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~-k~~H~L~~~~LsV   78 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLA-QADHELHGAQLSL   78 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHT-CSCCBSSSSBCEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhc-CCcceecCeEEEE
Confidence            468999999999999999999996     24588887653        359999999999999877 3357899999999


Q ss_pred             EEccCC
Q 009944          369 RRATAS  374 (522)
Q Consensus       369 ~~~~~~  374 (522)
                      ....+.
T Consensus        79 ~P~~~~   84 (104)
T 2dhx_A           79 RPAPPR   84 (104)
T ss_dssp             EECCCC
T ss_pred             EcCCCC
Confidence            876543

>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=97.08  E-value=0.0022  Score=50.30  Aligned_cols=72  Identities=19%  Similarity=0.295  Sum_probs=58.4

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecC-c
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG-V  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g-~  249 (522)
                      ....+.|.|-+.|+.. ...|...|.+||.            |+............|.|.+..+|++||..||..|.| -
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~------------Iv~~~~~~~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~   87 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGN------------ILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESI   87 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSC------------EEEEEECSSSSEEEEEESSHHHHHHHHTTTTCEETTTE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCc------------EEEeccCCCCCeEEEEeCCHHHHHHHHHhCCeEecCCE
Confidence            4456789999999986 5678889999998            445555556789999999999999999999999985 5


Q ss_pred             eEEEec
Q 009944          250 AVRVRR  255 (522)
Q Consensus       250 ~~~v~~  255 (522)
                      .|-|.+
T Consensus        88 mIGV~p   93 (119)
T 1wwh_A           88 MIGVKP   93 (119)
T ss_dssp             ECEEEE
T ss_pred             EEEEEE
Confidence            566664

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=96.92  E-value=0.0032  Score=49.42  Aligned_cols=72  Identities=17%  Similarity=0.178  Sum_probs=59.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC-eEEEEEEcc
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD-KTLTVRRAT  372 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g-~~l~v~~~~  372 (522)
                      .+.|.|-+.|+.. ...|...|++||.|......    .+  ..+..|.|.+..+|++||. .||..|+| ..|-|.+..
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~~--~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----NT--GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----SS--SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----CC--CCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECC
Confidence            4679999999985 67799999999999887762    12  3479999999999999998 79999974 778888764


Q ss_pred             C
Q 009944          373 A  373 (522)
Q Consensus       373 ~  373 (522)
                      .
T Consensus        96 d   96 (119)
T 1wwh_A           96 D   96 (119)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.85  E-value=0.0019  Score=48.38  Aligned_cols=53  Identities=19%  Similarity=0.410  Sum_probs=45.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHc
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  357 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  357 (522)
                      .++| ++|+.+...||.++|+.||.| .|.++.|-       .|||.|.+++.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            4556 999999999999999999954 57777662       59999999999999999874

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.24  E-value=0.0058  Score=48.62  Aligned_cols=67  Identities=16%  Similarity=0.235  Sum_probs=49.0

Q ss_pred             HHHHHHhhccCCeEE-EEecCCCC--------CCCCC--CCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          445 EDMREECGKYGTLVN-VVIPRPDQ--------NGGET--PGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~-v~i~~~~~--------~g~~~--~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      ..|-++|++||.|.+ +.+.+...        .....  .|.....|+|++..+|.+||.. ||..|+|.-|-|..++.
T Consensus        21 ~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG~ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           21 NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NGAVFNGVLLGVIPYTK   98 (132)
T ss_dssp             HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TTCEETTEECEEEECCH
T ss_pred             HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CCeEeCcEEEEEEECCH
Confidence            478999999999987 33322110        00000  1457899999999999999994 99999999888888764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.91  E-value=0.0079  Score=45.25  Aligned_cols=77  Identities=16%  Similarity=0.147  Sum_probs=55.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCC--cceEEEEEEcChHHHHHHHHHHcCCccC---C--eEEE
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTDIACAALNGLKMG---D--KTLT  367 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~--~~g~afV~f~~~~~A~~Al~~l~g~~~~---g--~~l~  367 (522)
                      -+|.|+.||+.+||+++.+.++.+-.+.+...+..+.+..  .-.-|||.|.+.++...-.+.++|..|-   |  .+..
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a~   89 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPAV   89 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeeeE
Confidence            4899999999999999888887665554433333322211  1235899999999999999999998772   2  3455


Q ss_pred             EEEc
Q 009944          368 VRRA  371 (522)
Q Consensus       368 v~~~  371 (522)
                      |.+|
T Consensus        90 VE~A   93 (97)
T 2l08_A           90 VEFA   93 (97)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            6665

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=95.71  E-value=0.011  Score=44.15  Aligned_cols=62  Identities=16%  Similarity=0.249  Sum_probs=46.8

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE--ecC------CCcEEEEEEeCHHHHHHHH-HhcCce
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY--INH------EKKFAFVEMRTVEEASNAM-ALDGII  245 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~--~~~------~~g~afV~f~~~~~a~~a~-~~~~~~  245 (522)
                      .+|.|++||+.+|++++.+.+..+..            +.-..  -++      .-.-|||.|.+.+++.... .++|..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~------------~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~   69 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPE------------HDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYV   69 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCC------------EEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCccc------------ceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcE
Confidence            57999999999999999988876532            21111  122      1257999999999999999 699988


Q ss_pred             ecC
Q 009944          246 FEG  248 (522)
Q Consensus       246 ~~g  248 (522)
                      |.+
T Consensus        70 F~D   72 (91)
T 1uw4_A           70 FLD   72 (91)
T ss_dssp             EEC
T ss_pred             EEc
Confidence            754

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.55  E-value=0.015  Score=46.29  Aligned_cols=77  Identities=22%  Similarity=0.273  Sum_probs=56.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceE-EEEeeCC-----------C-CC-CcceEEEEEEcChHHHHHHHHHHcCCc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDR-----------D-TG-NSKGYGFCVYQDPAVTDIACAALNGLK  360 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~-v~~~~~~-----------~-~g-~~~g~afV~f~~~~~A~~Al~~l~g~~  360 (522)
                      ..|.|-+.|+..+ ..|.+.|++||.|.+ +.+....           . .+ ....+..|+|.+..+|.+||. .||..
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            4688889976554 558899999999865 2221100           0 00 123578999999999999998 89999


Q ss_pred             cCCeEEEEEEccC
Q 009944          361 MGDKTLTVRRATA  373 (522)
Q Consensus       361 ~~g~~l~v~~~~~  373 (522)
                      |+|.-|-|.+..+
T Consensus        86 i~G~mIGV~Py~~   98 (132)
T 3p3d_A           86 FNGVLLGVIPYTK   98 (132)
T ss_dssp             ETTEECEEEECCH
T ss_pred             eCcEEEEEEECCH
Confidence            9999888888743

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=95.05  E-value=0.086  Score=39.40  Aligned_cols=58  Identities=14%  Similarity=0.122  Sum_probs=41.0

Q ss_pred             CCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHh
Q 009944          417 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  496 (522)
Q Consensus       417 ~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~ln  496 (522)
                      +....|+.|........           .||.++|++||.|. |..+.+          -.|||.|.+++.|..|+..++
T Consensus        13 p~r~HVf~l~FP~ewKt-----------~DI~~lFs~fggv~-I~WidD----------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           13 PKRDHVLHVTFPKEWKT-----------SDLYQLFSAFGNIQ-ISWIDD----------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCSEEEEECCTTCCH-----------HHHHHHHTTTCSCC-CEEEET----------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCeEEEEeCChhhhh-----------HHHHHHhhccCCEE-EEEEcC----------CeEEEEecCHHHHHHHHHhcc
Confidence            34566777733322221           49999999999654 333333          368999999999999999875

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=94.67  E-value=0.02  Score=56.72  Aligned_cols=54  Identities=15%  Similarity=0.242  Sum_probs=41.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHH
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA  354 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~  354 (522)
                      +.|||. .|..+++.+|.++|++||+|..+.+..+  .|   -||.|||.+.+++..++.
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~--~g---~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES--FG---LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS--SS---EEEEEECC---CCHHHHS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc--CC---eEEEEEeCCHHHHHHHHh
Confidence            689997 6999999999999999999999988765  23   599999999999997654

>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=94.41  E-value=0.083  Score=39.61  Aligned_cols=41  Identities=12%  Similarity=0.171  Sum_probs=33.1

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHh
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  496 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~ln  496 (522)
                      .||.++|++||.|. |..+.+          -.|||.|.+++.|..|+..++
T Consensus        20 ~Di~~lFs~fggv~-I~WidD----------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A           20 SDLYQLFSAFGNIQ-ISWIDD----------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             HHHHHHTTTSEEEE-EEEEET----------TEEEEEEEEECHHHHHHHHHT
T ss_pred             HHHHHHHhccCCEE-EEEEcC----------CeEEEEecCHHHHHHHHHhcc
Confidence            49999999999444 444443          368999999999999999875

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=93.82  E-value=0.033  Score=41.89  Aligned_cols=71  Identities=17%  Similarity=0.192  Sum_probs=45.2

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      +-+|.|+.||+.+|++++.+.+..+-.+ +.....++..-.   -...-.-|||.|.+.++..... .++|..|.+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~-d~~~fv~G~~s~---~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAH-DYFEFFAADLSL---YPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSE-EECCCCCCCSSS---CCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCcc-ceEEEeCCccCC---CCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            4589999999999999987666543110 000000000000   0011247999999999999999 699988754

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=93.39  E-value=0.022  Score=56.42  Aligned_cols=60  Identities=18%  Similarity=0.226  Sum_probs=43.2

Q ss_pred             hhhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCc-EEEEEEeCHHHHHHHHHh
Q 009944          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEEASNAMAL  241 (522)
Q Consensus       169 ~~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g-~afV~f~~~~~a~~a~~~  241 (522)
                      ......++|+|. .|..+++.+|.++|++||+            |.++...+++| ||.|+|.+.+.+..++..
T Consensus        48 r~~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~------------i~~~~~~~~~g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           48 RREQAQRTVLIH-CPEKISENKFLKYLSQFGP------------INNHFFYESFGLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHHHHHTEEEEE-ECCC---CHHHHHHGGGSC------------CCCEEEECSSSEEEEEECC---CCHHHHSS
T ss_pred             HHHHhcceEEEE-cCCCCCHHHHHHHHHhcCC------------cceEEEEccCCeEEEEEeCCHHHHHHHHhc
Confidence            345567899998 7999999999999999998            45555555655 999999999999988743

>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=86.09  E-value=1.8  Score=43.75  Aligned_cols=55  Identities=18%  Similarity=0.390  Sum_probs=44.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHc
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  357 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  357 (522)
                      +..++|+ +|..+...+|.++|+.||.| .|.++.+       ..|||.|.+.+.|..++.+++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHHHHH
Confidence            3456665 99999999999999999965 4555544       269999999999999999885

---

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	522
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-23
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-17
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-17
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-16
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-15
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-15
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-14
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-09
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-14
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	4e-06
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-14
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	9e-07
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	6e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-08
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-14
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-11
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-05
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-13
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-13
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-08
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	0.004
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	8e-13
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-10
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	0.002
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	5e-09
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-12
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-05
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-05
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-08
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	4e-06
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	9e-06
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-07
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	1e-09
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-12
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	8e-06
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	5e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	6e-12
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	6e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	6e-12
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-06
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	7e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-06
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-04
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-09
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-11
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	5e-11
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	9e-05
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	9e-08
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	6e-11
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	6e-11
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-11
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	8e-11
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-10
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	9e-04
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	5e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	6e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	5e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-08
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	8e-06
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	5e-09
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	0.001
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	5e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-07
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-08
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	0.001
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-04
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	0.002
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	7e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	8e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	0.001
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	8e-08
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 7e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-04
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	8e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	9e-07
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	0.004
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	4e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	8e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	8e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	2e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.001
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.001
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.002

>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 = 92.4 bits (229), Expect = 3e-23
 Identities = 44/100 (44%), Positives = 60/100 (60%), Gaps = 1/100 (1%)

Query: 421 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFL 480
           +VLCL   +  + L DDEEYEEI+ED+R+EC KYG + ++ IPR   +G E PG GK+F+
Sbjct: 5   EVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPR-PVDGVEVPGCGKIFV 63

Query: 481 EYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 520
           E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct: 64  EFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 103

>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 = 77.7 bits (190), Expect = 3e-17
 Identities = 41/212 (19%), Positives = 73/212 (34%), Gaps = 35/212 (16%)

Query: 173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTV 232
             R++++GGL     ++++ + F Q  T            + +      + F FV   TV
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV------MRDPNTKRSRGFGFVTYATV 58

Query: 233 EEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAE 292
           EE   AM       +G  V  +R      +                          G   
Sbjct: 59  EEVDAAMNARPHKVDGRVVEPKRAVSREDS-----------------------QRPGAHL 95

Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
              ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D    D  
Sbjct: 96  TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 155

Query: 353 CAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
                   +      VR+A      SK E  S
Sbjct: 156 V-IQKYHTVNGHNCEVRKA-----LSKQEMAS 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 = 43.8 bits (102), Expect = 1e-05
 Identities = 14/95 (14%), Positives = 29/95 (30%), Gaps = 6/95 (6%)

Query: 161 MPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH 220
                    A    ++++VGG+     E  +  +F Q             + + +     
Sbjct: 84  SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY------GKIEVIEIMTDRGSGK 137

Query: 221 EKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
           ++ FAFV     +     +        G    VR+
Sbjct: 138 KRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 172

>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 = 74.0 bits (181), Expect = 5e-17
 Identities = 43/89 (48%), Positives = 60/89 (67%), Gaps = 1/89 (1%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M   G   A PG+ V+ V IN +K FAF+E R+V+
Sbjct: 1   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQA-PGNPVLAVQINQDKNFAFLEFRSVD 59

Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNPT 262
           E + AMA DGIIF+G ++++RRP DY P 
Sbjct: 60  ETTQAMAFDGIIFQGQSLKIRRPHDYQPL 88

>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 = 60.1 bits (145), Expect = 4e-12
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 6/81 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDL-----VKDRDTGNSKGYGFCVYQDPAVTD 350
           R++VG +P+  TE  + +   +   L G        V        K + F  ++    T 
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 351 IACAALNGLKMGDKTLTVRRA 371
            A  A +G+    ++L +RR 
Sbjct: 63  QAM-AFDGIIFQGQSLKIRRP 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 = 71.2 bits (174), Expect = 5e-16
 Identities = 45/83 (54%), Positives = 58/83 (69%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A A 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 356 LNGLKMGDKTLTVRRATASSGQS 378
           LNG+++GDK L V+RA+  +  +
Sbjct: 63  LNGMQLGDKKLLVQRASVGAKNA 85

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 2e-08
 Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 7/83 (8%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           A ++++GGLP   N+  +    +              + V +      K +AF E   + 
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSF------GPLKAFNLVKDSATGLSKGYAFCEYVDIN 54

Query: 234 EASNAM-ALDGIIFEGVAVRVRR 255
               A+  L+G+      + V+R
Sbjct: 55  VTDQAIAGLNGMQLGDKKLLVQR 77

>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 = 69.7 bits (170), Expect = 1e-15
 Identities = 16/86 (18%), Positives = 32/86 (37%)

Query: 286 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           GA  G  GP  + V  +P+  +  +I +    +  + G   +K  + G   G     ++ 
Sbjct: 1   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 60

Query: 346 PAVTDIACAALNGLKMGDKTLTVRRA 371
                 A   LN   +G + + +   
Sbjct: 61  RDEATAAVIDLNDRPIGSRKVKLVLG 86

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.4 bits (167), Expect = 5e-15
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCVYQDPAVTDIACA 354
           ++ V  +P+   + +I+EL  +FG L    L K    TG  +G+GF  +        A  
Sbjct: 10  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 355 AL-NGLKMGDKTLTVRRATA 373
           AL +   +  + L +  A +
Sbjct: 70  ALCHSTHLYGRRLVLEWADS 89

>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 = 48.4 bits (115), Expect = 6e-08
 Identities = 15/86 (17%), Positives = 27/86 (31%), Gaps = 7/86 (8%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
           +   ++ V  +P  AN++ I   FS       G                 + F FV+  T
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFSTF-----GELKTVRLPKKMTGTGAHRGFGFVDFIT 60

Query: 232 VEEASNAMA--LDGIIFEGVAVRVRR 255
            ++A  A           G  + +  
Sbjct: 61  KQDAKKAFNALCHSTHLYGRRLVLEW 86

>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 = 66.5 bits (162), Expect = 2e-14
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  T+  ++E    FG +    +++D  T  S+G+GF  + D A  D    A
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD-KVLA 60

Query: 356 LNGLKMGDKTLTVRRA 371
            +  ++  KT+  + A
Sbjct: 61  QSRHELDSKTIDPKVA 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 = 51.9 bits (124), Expect = 2e-09
 Identities = 9/80 (11%), Positives = 24/80 (30%), Gaps = 6/80 (7%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           ++++GGL     ++ +  +F Q               + +      + F FV        
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQF------GEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 55

Query: 236 SNAMALDGIIFEGVAVRVRR 255
              +A      +   +  + 
Sbjct: 56  DKVLAQSRHELDSKTIDPKV 75

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.1 bits (161), Expect = 2e-14
 Identities = 18/76 (23%), Positives = 32/76 (42%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++VG L    TE  + E     G +    + +D  T  S GY +  +Q PA  + A   +
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 357 NGLKMGDKTLTVRRAT 372
           N   +  K + +  + 
Sbjct: 63  NFDVIKGKPVRIMWSQ 78

>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 = 42.6 bits (100), Expect = 4e-06
 Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 7/79 (8%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           +YVG L P   E  +   FS     +            ++       +A+V  +   +A 
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIR------VCRDMITRRSLGYAYVNFQQPADAE 56

Query: 237 NAM-ALDGIIFEGVAVRVR 254
            A+  ++  + +G  VR+ 
Sbjct: 57  RALDTMNFDVIKGKPVRIM 75

>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 = 65.4 bits (159), Expect = 5e-14
 Identities = 25/80 (31%), Positives = 40/80 (50%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+VGGL    +E  + EL    G +    + KDR TG  +GYGF  +      D A   
Sbjct: 11  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 70

Query: 356 LNGLKMGDKTLTVRRATASS 375
           ++ +K+  K + V +A+A +
Sbjct: 71  MDMIKLYGKPIRVNKASAHN 90

>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 = 45.0 bits (106), Expect = 9e-07
 Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 7/90 (7%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             VYVGGL    +E  +   F Q    +  +         +      + + FVE  + E+
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHM------PKDRVTGQHQGYGFVEFLSEED 63

Query: 235 ASNAM-ALDGIIFEGVAVRVRRPTDYNPTL 263
           A  A+  +D I   G  +RV + + +N  L
Sbjct: 64  ADYAIKIMDMIKLYGKPIRVNKASAHNKNL 93

>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 = 65.0 bits (158), Expect = 6e-14
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++V  LP   T+ Q+  +   +G++   ++++D+ TG  +G  F  Y        A +A
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 356 LNG--LKMGDKTLTVRRA 371
           LN    + G + L+VR A
Sbjct: 68  LNNVIPEGGSQPLSVRLA 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 = 48.4 bits (115), Expect = 5e-08
 Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 7/81 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             +YV  LP    +  + T F +  + +  N                +  AFV     EE
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLT------GRPRGVAFVRYNKREE 60

Query: 235 ASNAM-ALDGIIFEGVAVRVR 254
           A  A+ AL+ +I EG +  + 
Sbjct: 61  AQEAISALNNVIPEGGSQPLS 81

>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 = 64.2 bits (156), Expect = 8e-14
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  T+  +K+    FG +    L  D  TG S+G+GF ++++    D     
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVD-KVMD 59

Query: 356 LNGLKMGDKTLTVRRA 371
               K+  K +  +RA
Sbjct: 60  QKEHKLNGKVIDPKRA 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 = 56.1 bits (135), Expect = 7e-11
 Identities = 12/80 (15%), Positives = 26/80 (32%), Gaps = 6/80 (7%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           ++++GGL     ++ +  +FS+    +                   + F FV  +  E  
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPIT------GRSRGFGFVLFKESESV 54

Query: 236 SNAMALDGIIFEGVAVRVRR 255
              M        G  +  +R
Sbjct: 55  DKVMDQKEHKLNGKVIDPKR 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 = 63.5 bits (154), Expect = 2e-13
 Identities = 21/77 (27%), Positives = 36/77 (46%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            + V  LP   T+ ++  L  + G ++   +++D  TG S GY F  +     +  A   
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 356 LNGLKMGDKTLTVRRAT 372
           LNG+ + +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 = 41.5 bits (97), Expect = 1e-05
 Identities = 12/81 (14%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
            + V  LP    ++ +   F  +              + +    +   +AFV+  +  ++
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPIN------TCRIMRDYKTGYSYGYAFVDFTSEMDS 57

Query: 236 SNAM-ALDGIIFEGVAVRVRR 255
             A+  L+GI      ++V  
Sbjct: 58  QRAIKVLNGITVRNKRLKVSY 78

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.2 bits (153), Expect = 3e-13
 Identities = 30/79 (37%), Positives = 41/79 (51%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            + V  LP   T+ + + L  S G +    LV+D+ TG S GYGF  Y DP   + A   
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 356 LNGLKMGDKTLTVRRATAS 374
           LNGL++  KT+ V  A  S
Sbjct: 64  LNGLRLQTKTIKVSYARPS 82

>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 = 40.5 bits (94), Expect = 3e-05
 Identities = 13/86 (15%), Positives = 28/86 (32%), Gaps = 9/86 (10%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             + V  LP    ++   + F  +                         + FV     ++
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKIT------GQSLGYGFVNYIDPKD 56

Query: 235 ASNAM-ALDGIIFEGVAVRVR--RPT 257
           A  A+  L+G+  +   ++V   RP+
Sbjct: 57  AEKAINTLNGLRLQTKTIKVSYARPS 82

>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 = 62.8 bits (152), Expect = 3e-13
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D    D     
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD-KIVI 62

Query: 356 LNGLKMGDKTLTVRRA 371
                +      VR+A
Sbjct: 63  QKYHTVNGHNCEVRKA 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 = 51.6 bits (123), Expect = 2e-09
 Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 6/81 (7%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           ++++VGG+     E  +  +F Q             + + +     ++ FAFV     + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIE------VIEIMTDRGSGKKRGFAFVTFDDHDS 56

Query: 235 ASNAMALDGIIFEGVAVRVRR 255
               +        G    VR+
Sbjct: 57  VDKIVIQKYHTVNGHNCEVRK 77

>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 = 63.1 bits (153), Expect = 3e-13
 Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           E   ++F+GGL +  T+  ++   E +GTL    +++D +T  S+G+GF  Y      D 
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 352 ACAALNGLKMGDKTLTVRRATA 373
           A  A    K+  + +  +RA +
Sbjct: 64  AMNA-RPHKVDGRVVEPKRAVS 84

>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 = 57.7 bits (139), Expect = 3e-11
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTV 232
             R++++GGL     ++++ + F Q        +      + +      + F FV   TV
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQW------GTLTDCVVMRDPNTKRSRGFGFVTYATV 58

Query: 233 EEASNAMALDGIIFEGVAVRVRR 255
           EE   AM       +G  V  +R
Sbjct: 59  EEVDAAMNARPHKVDGRVVEPKR 81

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.9 bits (155), Expect = 3e-13
 Identities = 19/96 (19%), Positives = 41/96 (42%), Gaps = 3/96 (3%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +++  LPY  T  ++ ++   +G +         +T  ++G  + VY+D      AC  L
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKNACDHL 66

Query: 357 NGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 392
           +G  + ++ L V    A+    K + +    Q +  
Sbjct: 67  SGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLL 102

>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 = 49.2 bits (117), Expect = 4e-08
 Identities = 15/81 (18%), Positives = 26/81 (32%), Gaps = 10/81 (12%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           R +Y+  LP     + +   F +          GP   +        +  A+V    + +
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKY---------GPIRQIRVGNTPETRGTAYVVYEDIFD 58

Query: 235 ASNAM-ALDGIIFEGVAVRVR 254
           A NA   L G       + V 
Sbjct: 59  AKNACDHLSGFNVCNRYLVVL 79

>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 = 35.0 bits (80), Expect = 0.004
 Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 6/74 (8%)

Query: 445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 504
           E+M +  GKYG +  + +    +        G  ++ Y D      A + LSG       
Sbjct: 22  EEMYDIFGKYGPIRQIRVGNTPET------RGTAYVVYEDIFDAKNACDHLSGFNVCNRY 75

Query: 505 VNAFYYPEDKYFNK 518
           +   YY  ++ F K
Sbjct: 76  LVVLYYNANRAFQK 89

>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 = 61.5 bits (149), Expect = 8e-13
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL     E +I+E    FG +   +L  D  T   +G+ F  +++          
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 356 LNGLKMGDKTLTVRRA 371
                +G     ++ 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 = 53.4 bits (128), Expect = 5e-10
 Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 6/80 (7%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           +++VGGL P   E+ I  +F               +  ++   N  + F F+  +  E  
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGF------GEVESIELPMDNKTNKRRGFCFITFKEEEPV 54

Query: 236 SNAMALDGIIFEGVAVRVRR 255
              M             ++ 
Sbjct: 55  KKIMEKKYHNVGLSKCEIKV 74

>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 = 61.6 bits (149), Expect = 1e-12
 Identities = 15/84 (17%), Positives = 30/84 (35%), Gaps = 7/84 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++++G L    T   +++L                      GY F  Y D      A   
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKL------PLAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 356 LNG-LKMGDKTLTVRRATASSGQS 378
           L+G +++  K + V  + +   +S
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKLRS 80

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.7 bits (79), Expect = 0.002
 Identities = 14/82 (17%), Positives = 26/82 (31%), Gaps = 14/82 (17%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           ++Y+G L P      +   F                  +   +  +  +AFV+      A
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKL------------PLAGQVLLKSGYAFVDYPDQNWA 50

Query: 236 SNAM-ALDG-IIFEGVAVRVRR 255
             A+  L G +   G  + V  
Sbjct: 51  IRAIETLSGKVELHGKIMEVDY 72

>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 = 61.5 bits (149), Expect = 1e-12
 Identities = 20/76 (26%), Positives = 34/76 (44%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++VG L +Y TE QI EL    G +    +  D+    + G+ F  Y   A  + A   
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 356 LNGLKMGDKTLTVRRA 371
           +NG ++ D+ +     
Sbjct: 69  INGTRLDDRIIRTDWD 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 = 51.5 bits (123), Expect = 5e-09
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 7/87 (8%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++  + +  +YVG L     E+ I   FS+                ++        F FV
Sbjct: 1   EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIK------KIIMGLDKMKKTACGFCFV 54

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV 253
           E  +  +A NAM  ++G   +   +R 
Sbjct: 55  EYYSRADAENAMRYINGTRLDDRIIRT 81

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.3 bits (148), Expect = 2e-12
 Identities = 24/91 (26%), Positives = 40/91 (43%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G  R+FV  L Y  +E  +++L  ++G L       D  T   KG+ F  +  P   
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSKT 380
             A A ++G     + L V  +T     S++
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTIKKEASQS 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 = 40.1 bits (93), Expect = 5e-05
 Identities = 19/83 (22%), Positives = 31/83 (37%), Gaps = 7/83 (8%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           + R++V  L   ++E+ +   FS        +                K FAFV     E
Sbjct: 8   SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL------TKKPKGFAFVTFMFPE 61

Query: 234 EASNAM-ALDGIIFEGVAVRVRR 255
            A  A   +DG +F+G  + V  
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLP 84

>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 = 61.2 bits (148), Expect = 2e-12
 Identities = 24/90 (26%), Positives = 44/90 (48%), Gaps = 2/90 (2%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG       P R+ V  +P+ F +  ++++   FG +   D+    +   SKG+GF  +
Sbjct: 1   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKIL--DVEIIFNERGSKGFGFVTF 58

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATA 373
           ++ A  D A   L+G  +  + + V  ATA
Sbjct: 59  ENSADADRAREKLHGTVVEGRKIEVNNATA 88

>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 = 46.2 bits (109), Expect = 3e-07
 Identities = 17/88 (19%), Positives = 29/88 (32%), Gaps = 9/88 (10%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
           ++    +R++V  +P    +  +   F Q             D  +       K F FV 
Sbjct: 6   ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGK--------ILDVEIIFNERGSKGFGFVT 57

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRVRR 255
                +A  A   L G + EG  + V  
Sbjct: 58  FENSADADRAREKLHGTVVEGRKIEVNN 85

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 2e-12
 Identities = 15/76 (19%), Positives = 31/76 (40%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++VGGL     +  +      FG +    +  D +T   +G+ F  ++       A   
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 356 LNGLKMGDKTLTVRRA 371
           +N  ++  +T+ V  A
Sbjct: 67  MNESELFGRTIRVNLA 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 = 42.0 bits (98), Expect = 1e-05
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           R +YVGGL    +++ +   F                  ++      + FAFVE    E+
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI------PLDYETEKHRGFAFVEFELAED 59

Query: 235 ASNAM-ALDGIIFEGVAVRVRR 255
           A+ A+  ++     G  +RV  
Sbjct: 60  AAAAIDNMNESELFGRTIRVNL 81

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.9 bits (145), Expect = 3e-12
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++ V  L +  ++  I+EL   FGTL    +  DR +G S G     ++  A    A   
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 60

Query: 356 LNGLKMGDKTLTVRRATA 373
            NG+ +  + + ++  T+
Sbjct: 61  YNGVPLDGRPMNIQLVTS 78

>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 = 49.2 bits (117), Expect = 2e-08
 Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 8/80 (10%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           ++ V  L    ++  I   F++  T            V           A V      +A
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAA-------VHYDRSGRSLGTADVHFERKADA 54

Query: 236 SNAM-ALDGIIFEGVAVRVR 254
             AM   +G+  +G  + ++
Sbjct: 55  LKAMKQYNGVPLDGRPMNIQ 74

>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 = 60.4 bits (146), Expect = 3e-12
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACA 354
           F+  L +  TE  +K +    G +    + K ++      S G+GF  Y+ P     A  
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 355 ALNGLKMGDKTLTVRRATASS 375
            L G  +    L VR +  ++
Sbjct: 62  QLQGHTVDGHKLEVRISERAT 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 = 46.9 bits (111), Expect = 2e-07
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 4/79 (5%)

Query: 178 YVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASN 237
           ++  L     E+ +   FS+V        +   +      +     F FVE +  E+A  
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKN---KAGVLLSMGFGFVEYKKPEQAQK 58

Query: 238 AM-ALDGIIFEGVAVRVRR 255
           A+  L G   +G  + VR 
Sbjct: 59  ALKQLQGHTVDGHKLEVRI 77

>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 = 60.8 bits (147), Expect = 3e-12
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  TE  ++   E +G L    +++D  +  S+G+GF  +   A  D A  A
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 80

Query: 356 LNGLKMGDKTLTVRRATA 373
                +  + +  +RA A
Sbjct: 81  ARPHSIDGRVVEPKRAVA 98

>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 = 53.1 bits (127), Expect = 2e-09
 Identities = 16/88 (18%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++     R++++GGL     E+++  ++ Q               + +      + F FV
Sbjct: 14  KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV------MRDPASKRSRGFGFV 67

Query: 228 EMRTVEEASNAMALDGIIFEGVAVRVRR 255
              ++ E   AMA      +G  V  +R
Sbjct: 68  TFSSMAEVDAAMAARPHSIDGRVVEPKR 95

>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 = 60.1 bits (145), Expect = 3e-12
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++V GLP   T+ ++++L   +G +    ++ D+ TG S+G GF  +      + A   
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 356 LNGLKMGDKT--LTVRRA 371
           LNG K    T  +TV+ 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 = 42.7 bits (100), Expect = 4e-06
 Identities = 18/81 (22%), Positives = 27/81 (33%), Gaps = 7/81 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             +YV GLP    ++ +   FSQ      G        V  V     +   F+      E
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQY-----GRIITSRILVDQVTGVS-RGVGFIRFDKRIE 60

Query: 235 ASNAM-ALDGIIFEGVAVRVR 254
           A  A+  L+G    G    + 
Sbjct: 61  AEEAIKGLNGQKPSGATEPIT 81

>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 = 60.1 bits (145), Expect = 3e-12
 Identities = 24/80 (30%), Positives = 35/80 (43%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            + V  L     ET ++EL   FG++    L KD+ TG SKG+ F  +        A A 
Sbjct: 10  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 69

Query: 356 LNGLKMGDKTLTVRRATASS 375
           ++G       L V  A  S+
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 = 42.0 bits (98), Expect = 9e-06
 Identities = 13/82 (15%), Positives = 26/82 (31%), Gaps = 7/82 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             + V  L     E  +   F    +              +      K FAF+     E+
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYL------AKDKTTGQSKGFAFISFHRRED 62

Query: 235 ASNAM-ALDGIIFEGVAVRVRR 255
           A+ A+  + G  ++ + + V  
Sbjct: 63  AARAIAGVSGFGYDHLILNVEW 84

>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 = 60.4 bits (146), Expect = 3e-12
 Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 7/88 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            + V GLP+  TE  +KE   +FG +    + KD  TG+SKG+GF  + +        + 
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 356 LNGLKMGDKTLTVRRATASSGQSKTEQE 383
            + +    +    +        SK  Q+
Sbjct: 70  RHMI--DGRWCDCKLP-----NSKQSQD 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 = 46.5 bits (110), Expect = 2e-07
 Identities = 18/91 (19%), Positives = 31/91 (34%), Gaps = 7/91 (7%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++A +    + V GLP    EQ +  +FS     +            ++   H K F FV
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVL------MVQVKKDLKTGHSKGFGFV 55

Query: 228 EMRTVEEASNAMALDGIIFEGVAVRVRRPTD 258
                E     M+    + +G     + P  
Sbjct: 56  RFTEYETQVKVMS-QRHMIDGRWCDCKLPNS 85

>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 = 19/76 (25%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL    T   +K   E FG +    L+ D+ T   +G+GF  ++   + +  C  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 356 LNGLKMGDKTLTVRRA 371
           ++  ++ +K +  ++A
Sbjct: 60  IHFHEINNKMVECKKA 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 = 52.8 bits (126), Expect = 1e-09
 Identities = 11/80 (13%), Positives = 25/80 (31%), Gaps = 6/80 (7%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           +++VGGL      + +  +F Q               + +   N  + F FV   + +  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVD------DAMLMFDKTTNRHRGFGFVTFESEDIV 54

Query: 236 SNAMALDGIIFEGVAVRVRR 255
                +         V  ++
Sbjct: 55  EKVCEIHFHEINNKMVECKK 74

>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 = 59.8 bits (144), Expect = 5e-12
 Identities = 24/80 (30%), Positives = 45/80 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +++      A  A
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 356 LNGLKMGDKTLTVRRATASS 375
           +NG  +  + + V +A  SS
Sbjct: 67  MNGKSVDGRQIRVDQAGKSS 86

>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 = 42.4 bits (99), Expect = 8e-06
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 7/83 (8%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
             +++VGGL    NEQ++   FS+               V +      + F FV    ++
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVV------VKDRETQRSRGFGFVTFENID 58

Query: 234 EASNAM-ALDGIIFEGVAVRVRR 255
           +A +AM A++G   +G  +RV +
Sbjct: 59  DAKDAMMAMNGKSVDGRQIRVDQ 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 = 59.7 bits (144), Expect = 5e-12
 Identities = 12/81 (14%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLES-FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
            +++  L     + ++K+ L + F        +    +   +G  F ++++ +    A  
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 355 ALNGLKMGDKTLTVRRATASS 375
           ++ G    DK + ++ A   S
Sbjct: 65  SMQGFPFYDKPMRIQYAKTDS 85

>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 = 43.5 bits (102), Expect = 2e-06
 Identities = 15/89 (16%), Positives = 31/89 (34%), Gaps = 14/89 (15%)

Query: 172 RHARRVYVGGLPPLANEQAI----ATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           R    +Y+  L     +  +       FS+               ++       +  AFV
Sbjct: 1   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFG---------QILDILVSRSLKMRGQAFV 51

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRR 255
             + V  A+NA+ ++ G  F    +R++ 
Sbjct: 52  IFKEVSSATNALRSMQGFPFYDKPMRIQY 80

>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 = 59.7 bits (144), Expect = 6e-12
 Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 4/80 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGF--DLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           R+F+GG+P      +I E +                 D   ++G+ F  Y+      +A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 354 AALNG--LKMGDKTLTVRRA 371
             L    +++    + V  A
Sbjct: 63  RKLMPGRIQLWGHQIAVDWA 82

>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 = 42.8 bits (100), Expect = 6e-06
 Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           R+++GG+P +   + I    ++    +                   + FAFVE  +   A
Sbjct: 3   RLFIGGIPKMKKREEILEEIAK----VTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 58

Query: 236 SNA---MALDGIIFEGVAVRVRR 255
           + A   +    I   G  + V  
Sbjct: 59  AMARRKLMPGRIQLWGHQIAVDW 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 = 59.4 bits (143), Expect = 6e-12
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLV-KDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +F+G L     E  + +   +FG +     + +D DTGNSKGY F  +     +D A  A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 356 LNGLKMGDKTLTVRRAT 372
           +NG  + ++ +TV  A 
Sbjct: 61  MNGQYLCNRPITVSYAF 77

>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 = 40.9 bits (95), Expect = 2e-05
 Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 6/80 (7%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           +++G L P  +E+ +   FS       G        + +    + K +AF+   + + + 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAF-----GVILQTPKIMRDPDTGNSKGYAFINFASFDASD 55

Query: 237 NAM-ALDGIIFEGVAVRVRR 255
            A+ A++G       + V  
Sbjct: 56  AAIEAMNGQYLCNRPITVSY 75

>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 = 59.7 bits (144), Expect = 6e-12
 Identities = 23/84 (27%), Positives = 34/84 (40%), Gaps = 2/84 (2%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           P  ++VG L    TE  I +L    G           +  ++  Y F  + +      A 
Sbjct: 8   PRTLYVGNLSRDVTEVLILQLFSQIG--PCKSCKMITEHTSNDPYCFVEFYEHRDAAAAL 65

Query: 354 AALNGLKMGDKTLTVRRATASSGQ 377
           AA+NG K+  K + V  AT  S Q
Sbjct: 66  AAMNGRKILGKEVKVNWATTPSSQ 89

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (100), Expect = 5e-06
 Identities = 20/85 (23%), Positives = 30/85 (35%), Gaps = 9/85 (10%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
              R +YVG L     E  I   FSQ+               +         + FVE   
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCK--------SCKMITEHTSNDPYCFVEFYE 57

Query: 232 VEEASNAM-ALDGIIFEGVAVRVRR 255
             +A+ A+ A++G    G  V+V  
Sbjct: 58  HRDAAAALAAMNGRKILGKEVKVNW 82

>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 = 58.9 bits (142), Expect = 7e-12
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 289 GGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           G    PD    + V GL  Y TE  ++E+   +G +    +V D+ +  S+G+ F  +++
Sbjct: 1   GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 346 PAVTDIACAALNGLKMGDKTLTV 368
                 A    NG+++  + + V
Sbjct: 61  VDDAKEAKERANGMELDGRRIRV 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 = 42.8 bits (100), Expect = 5e-06
 Identities = 14/80 (17%), Positives = 27/80 (33%), Gaps = 7/80 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             + V GL     E+ +   FS+       +      +  +           V    V++
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF------VYFENVDD 63

Query: 235 ASNAM-ALDGIIFEGVAVRV 253
           A  A    +G+  +G  +RV
Sbjct: 64  AKEAKERANGMELDGRRIRV 83

>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 = 58.9 bits (142), Expect = 1e-11
 Identities = 27/94 (28%), Positives = 46/94 (48%), Gaps = 3/94 (3%)

Query: 285 SGAIGG-AEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
            GA G   EGP+   +F+  LP  F +  + ++   FG +    +  D+ T  SK +GF 
Sbjct: 6   IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFV 65

Query: 342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASS 375
            Y +P     A  ++NG ++G K L V+   + +
Sbjct: 66  SYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKN 99

>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 = 39.3 bits (91), Expect = 1e-04
 Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 7/82 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             +++  LP    +Q +   F      +           ++   N  K F FV       
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVV------SAKVFIDKQTNLSKCFGFVSYDNPVS 72

Query: 235 ASNAM-ALDGIIFEGVAVRVRR 255
           A  A+ +++G       ++V+ 
Sbjct: 73  AQAAIQSMNGFQIGMKRLKVQL 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 = 57.7 bits (139), Expect = 4e-11
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VF   L        +++   + G +    ++ DR++  SKG  +  + +          
Sbjct: 20  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP-LAIG 78

Query: 356 LNGLKMGDKTLTVRRATA 373
           L G ++    + V+ + A
Sbjct: 79  LTGQRLLGVPIIVQASQA 96

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 4e-09
 Identities = 21/94 (22%), Positives = 35/94 (37%), Gaps = 7/94 (7%)

Query: 162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
           PV  ++ +  R AR V+   L      + +  FFS V              + +      
Sbjct: 7   PVDNLSPEE-RDARTVFCMQLAARIRPRDLEDFFSAVGKVR------DVRIISDRNSRRS 59

Query: 222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
           K  A+VE   ++    A+ L G    GV + V+ 
Sbjct: 60  KGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQA 93

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.5 bits (138), Expect = 4e-11
 Identities = 18/85 (21%), Positives = 28/85 (32%), Gaps = 8/85 (9%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLV--------KDRDTGNSKGYGFCVYQDPA 347
            ++V GL    T   + +  +  G +               D++TG  KG     Y+DP 
Sbjct: 10  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 69

Query: 348 VTDIACAALNGLKMGDKTLTVRRAT 372
               A    +G       L V  A 
Sbjct: 70  TAKAAVEWFDGKDFQGSKLKVSLAR 94

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 2e-04
 Identities = 20/90 (22%), Positives = 28/90 (31%), Gaps = 3/90 (3%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
             +YV GL        +A FF Q          G     + +     K    A V     
Sbjct: 9   SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 233 EEASNAM-ALDGIIFEGVAVRVRRPTDYNP 261
             A  A+   DG  F+G  ++V       P
Sbjct: 69  PTAKAAVEWFDGKDFQGSKLKVSLARKKPP 98

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.4 bits (138), Expect = 5e-11
 Identities = 18/90 (20%), Positives = 33/90 (36%), Gaps = 5/90 (5%)

Query: 284 ASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G I G  G +  R++VG LP       I+++   +G       +  ++      + F 
Sbjct: 2   GGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYG---AIRDIDLKNRRGGPPFAFV 58

Query: 342 VYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
            ++DP   + A    +G       L V   
Sbjct: 59  EFEDPRDAEDAVYGRDGYDYDGYRLRVEFP 88

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (91), Expect = 9e-05
 Identities = 23/87 (26%), Positives = 34/87 (39%), Gaps = 10/87 (11%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           A  +  R+YVG LPP    + I   F +          G    +          FAFVE 
Sbjct: 10  AGNNDCRIYVGNLPPDIRTKDIEDVFYKY---------GAIRDIDLKNRRGGPPFAFVEF 60

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRVRR 255
               +A +A+   DG  ++G  +RV  
Sbjct: 61  EDPRDAEDAVYGRDGYDYDGYRLRVEF 87

>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 = 56.9 bits (137), Expect = 5e-11
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 6/83 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE ++++L E +G      + KD+       +GF   +   + +IA   
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVE 63

Query: 356 LNGLKMGDKTLTVRRATASSGQS 378
           L+ + +  K L VR A  S+  +
Sbjct: 64  LDNMPLRGKQLRVRFACHSASLT 86

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.7 bits (113), Expect = 9e-08
 Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 13/84 (15%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
            R++VG LPP   E+ +   F +                  V+I+ +K F F+ + T   
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGK------------AGEVFIHKDKGFGFIRLETRTL 56

Query: 235 ASNAM-ALDGIIFEGVAVRVRRPT 257
           A  A   LD +   G  +RVR   
Sbjct: 57  AEIAKVELDNMPLRGKQLRVRFAC 80

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 5e-11
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           G   +F+  L        + +   +FG +    +V D +   SKGYGF  ++     + A
Sbjct: 7   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 64

Query: 353 CAALNGLKMGDKTLTVRRAT 372
              +NG+ + D+ + V R  
Sbjct: 65  IEKMNGMLLNDRKVFVGRFK 84

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (100), Expect = 5e-06
 Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 9/81 (11%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
            +++  L    + +A+   FS                 V    N  K + FV   T E A
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGN--------ILSCKVVCDENGSKGYGFVHFETQEAA 61

Query: 236 SNAM-ALDGIIFEGVAVRVRR 255
             A+  ++G++     V V R
Sbjct: 62  ERAIEKMNGMLLNDRKVFVGR 82

>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 = 6e-11
 Identities = 23/96 (23%), Positives = 39/96 (40%), Gaps = 1/96 (1%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG+      P   F+G LPY  TE  IKE              +  +    KG+G+  +
Sbjct: 5   SSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK 379
           +D      +  +LN   +G+K + V  A  +  +  
Sbjct: 65  EDLDSLL-SALSLNEESLGNKRIRVDVADQAQDKDS 99

>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 = 44.7 bits (105), Expect = 1e-06
 Identities = 14/81 (17%), Positives = 28/81 (34%), Gaps = 6/81 (7%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
              ++G LP    E++I  FF  +  +                    K F + E   ++ 
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISA------VRLPREPSNPERLKGFGYAEFEDLDS 69

Query: 235 ASNAMALDGIIFEGVAVRVRR 255
             +A++L+        +RV  
Sbjct: 70  LLSALSLNEESLGNKRIRVDV 90

>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 = 56.7 bits (136), Expect = 6e-11
 Identities = 23/77 (29%), Positives = 34/77 (44%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FV  +     E +I+E    +G +    L  DR TG SKGY    Y+       A  A
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 356 LNGLKMGDKTLTVRRAT 372
           LNG ++  +T+ V    
Sbjct: 69  LNGAEIMGQTIQVDWCF 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 = 38.9 bits (90), Expect = 1e-04
 Identities = 18/88 (20%), Positives = 30/88 (34%), Gaps = 7/88 (7%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
           Q +     ++V  +   A E  I   F                  ++      K +A VE
Sbjct: 2   QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIK------NIHLNLDRRTGFSKGYALVE 55

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRVRR 255
             T ++A  A  AL+G    G  ++V  
Sbjct: 56  YETHKQALAAKEALNGAEIMGQTIQVDW 83

>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 = 56.7 bits (136), Expect = 7e-11
 Identities = 17/83 (20%), Positives = 30/83 (36%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +++  L    TE  +  L   F    G  +     TG  +G  F  + +  +   A   
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 356 LNGLKMGDKTLTVRRATASSGQS 378
           +NG K+  K L +        +S
Sbjct: 80  VNGYKLYGKILVIEFGKNKKQRS 102

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.7 bits (136), Expect = 8e-11
 Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGLPY+ T+  +++  E FG +    ++ DR TG S+GYGF    D A  + AC  
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 356 LNGLKMGDKTLTVRRATASS 375
            N   +  +   V  A   +
Sbjct: 72  PNP-IIDGRKANVNLAYLGA 90

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 2e-05
 Identities = 14/81 (17%), Positives = 26/81 (32%), Gaps = 6/81 (7%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
            +++VGGLP    + ++  +F                 + +      + + FV M     
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGF------GDIEEAVVITDRQTGKSRGYGFVTMADRAA 64

Query: 235 ASNAMALDGIIFEGVAVRVRR 255
           A  A      I +G    V  
Sbjct: 65  AERACKDPNPIIDGRKANVNL 85

>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 = 56.1 bits (135), Expect = 1e-10
 Identities = 22/97 (22%), Positives = 36/97 (37%), Gaps = 9/97 (9%)

Query: 421 KVLCLTEAIT-ADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVF 479
           +V+ +       D   D     EI ED+R EC K+G +  +++     +       G   
Sbjct: 9   RVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPD-------GVAS 61

Query: 480 LEYYDAVGCATAKNALSGRKFGGNTVNA-FYYPEDKY 515
           + + D          L GR FGG  + A  +     Y
Sbjct: 62  VSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDY 98

>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 = 38.0 bits (88), Expect = 3e-04
 Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 4/87 (4%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKFAFVE 228
            RH R V +  +    + +      +++   +          +  + +   H    A V 
Sbjct: 5   MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLR-VECSKFGQIRKLLLFDRHPDGVASVS 63

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRVR 254
            R  EEA   +  LDG  F G  +  +
Sbjct: 64  FRDPEEADYCIQTLDGRWFGGRQITAQ 90

>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 = 36.4 bits (84), Expect = 9e-04
 Identities = 9/59 (15%), Positives = 18/59 (30%), Gaps = 1/59 (1%)

Query: 313 ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
           +L            +      +  G     ++DP   D     L+G   G + +T +  
Sbjct: 35  DLRVECSKFGQIRKLL-LFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

>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 = 56.2 bits (135), Expect = 1e-10
 Identities = 13/83 (15%), Positives = 30/83 (36%), Gaps = 5/83 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +    L +  TE ++KE+ E    +           G SKG  +  ++  A  +     
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 356 LNGLKMGDKTLTVRRATASSGQS 378
             G ++  +++++       G  
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGGTR 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 = 46.6 bits (110), Expect = 3e-07
 Identities = 15/89 (16%), Positives = 29/89 (32%), Gaps = 12/89 (13%)

Query: 167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAF 226
           T +  R AR +    L     E  +   F   +     +  G             K  A+
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDG-----------KSKGIAY 57

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRVR 254
           +E ++  +A   +    G   +G +V + 
Sbjct: 58  IEFKSEADAEKNLEEKQGAEIDGRSVSLY 86

>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 = 54.2 bits (130), Expect = 5e-10
 Identities = 20/89 (22%), Positives = 39/89 (43%), Gaps = 13/89 (14%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFA 225
           +  Q++     VY GG+     +Q +   FS                ++ + +  EK ++
Sbjct: 10  VVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQ------------IMEIRVFPEKGYS 57

Query: 226 FVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           FV   T E A++A+ +++G   EG  V+ 
Sbjct: 58  FVRFSTHESAAHAIVSVNGTTIEGHVVKC 86

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.7 bits (121), Expect = 1e-08
 Identities = 11/76 (14%), Positives = 26/76 (34%), Gaps = 6/76 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+ GG+    T+  +++    FG +    +  ++       Y F  +        A  +
Sbjct: 20  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHAIVS 73

Query: 356 LNGLKMGDKTLTVRRA 371
           +NG  +    +     
Sbjct: 74  VNGTTIEGHVVKCYWG 89

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.6 bits (128), Expect = 6e-10
 Identities = 17/93 (18%), Positives = 28/93 (30%), Gaps = 11/93 (11%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   + V  LP      ++ +LL+ +         K      +K   F    +    
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQA 53

Query: 350 DIACAALNGLKMGDKTLTVRRAT----ASSGQS 378
             A    +      K L V+         SG S
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQPTDALLCSGPS 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 = 53.7 bits (129), Expect = 7e-10
 Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 9/78 (11%)

Query: 296 RVFVGGLPYYFT-ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           RVF+G L      ++ ++ +   +G +              KG+ F  Y +      A A
Sbjct: 17  RVFIGNLNTLVVKKSDVEAIFSKYGKI--------VGCSVHKGFAFVQYVNERNARAAVA 68

Query: 355 ALNGLKMGDKTLTVRRAT 372
             +G  +  + L +  A 
Sbjct: 69  GEDGRMIAGQVLDINLAA 86

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.4 bits (97), Expect = 2e-05
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 16/83 (19%)

Query: 175 RRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
            RV++G L   +  +  +   FS+          G    +V   ++    FAFV+     
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKY---------GK---IVGCSVHK--GFAFVQYVNER 61

Query: 234 EASNAM-ALDGIIFEGVAVRVRR 255
            A  A+   DG +  G  + +  
Sbjct: 62  NARAAVAGEDGRMIAGQVLDINL 84

>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 = 53.3 bits (127), Expect = 9e-10
 Identities = 13/76 (17%), Positives = 29/76 (38%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +++   P  +T+  I++LL+    +     +       S+ + +               
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 356 LNGLKMGDKTLTVRRA 371
           LNGLK+   TL  + +
Sbjct: 63  LNGLKIEGYTLVTKVS 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 = 36.7 bits (84), Expect = 5e-04
 Identities = 13/81 (16%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             +++   PP   ++ I      +      N       + ++  N  ++FA++++ + E+
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDI------NVVALSIRLPSLRFNTSRRFAYIDVTSKED 55

Query: 235 ASNAM-ALDGIIFEGVAVRVR 254
           A   +  L+G+  EG  +  +
Sbjct: 56  ARYCVEKLNGLKIEGYTLVTK 76

>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 = 53.1 bits (127), Expect = 1e-09
 Identities = 13/76 (17%), Positives = 24/76 (31%), Gaps = 6/76 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++V  L    +E  I++   +                  + Y F  + +      A  A
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKP------GAVERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 356 LNGLKMGDKTLTVRRA 371
           LNG  +    + V  A
Sbjct: 64  LNGKVLDGSPIEVTLA 79

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 1e-08
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 13/82 (15%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           + +YV  L    +E+ I   F+ +                   +   + +AFV     E+
Sbjct: 9   KILYVRNLMLSTSEEMIEKEFNNIKP------------GAVERVKKIRDYAFVHFSNRED 56

Query: 235 ASNAM-ALDGIIFEGVAVRVRR 255
           A  AM AL+G + +G  + V  
Sbjct: 57  AVEAMKALNGKVLDGSPIEVTL 78

>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 = 34/87 (39%), Positives = 46/87 (52%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC YQD      A   
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 356 LNGLKMGDKTLTVRRATASSGQSKTEQ 382
           LNG +   + L V  A +   + + + 
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKS 96

>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 = 42.4 bits (99), Expect = 8e-06
 Identities = 31/103 (30%), Positives = 46/103 (44%), Gaps = 8/103 (7%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
           R  R V+VG +P  A E+ +   FS+V   +          V +      K + F E + 
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRL------VYDRETGKPKGYGFCEYQD 59

Query: 232 VEEASNAM-ALDGIIFEGVAVRVRR-PTDYNPTLAAALGPGQP 272
            E A +AM  L+G  F G A+RV    ++ N     +LG G P
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 2e-09
 Identities = 15/90 (16%), Positives = 31/90 (34%), Gaps = 7/90 (7%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   VFVG      TE +++E    +G      ++        + + F  + D  + 
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGD-----VMDVFIPKPFRAFAFVTFADDQIA 55

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSK 379
              C     L +   ++ +  A      + 
Sbjct: 56  QSLCG--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 = 41.9 bits (98), Expect = 8e-06
 Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 12/81 (14%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             V+VG       E  +  FFSQ            GD +        + FAFV     + 
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQY-----------GDVMDVFIPKPFRAFAFVTFADDQI 54

Query: 235 ASNAMALDGIIFEGVAVRVRR 255
           A +    + +I +G++V +  
Sbjct: 55  AQSLCG-EDLIIKGISVHISN 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 = 51.1 bits (122), Expect = 5e-09
 Identities = 13/83 (15%), Positives = 29/83 (34%), Gaps = 14/83 (16%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           V V G P  +    +  F                   +   +++   +  +  ++  +A 
Sbjct: 7   VTVFGFPQASASYILLQFAQYGNI-------------LKHVMSNTGNWMHIRYQSKLQAR 53

Query: 237 NAMALDGIIFEG-VAVRVRRPTD 258
            A++ DG IF   + + V+   D
Sbjct: 54  KALSKDGRIFGESIMIGVKPCID 76

>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 = 35.7 bits (82), Expect = 0.001
 Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 9/77 (11%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V V G P          +L  F     +  +      N+  +    YQ       A  + 
Sbjct: 7   VTVFGFPQASAS----YILLQF---AQYGNILKHVMSNTGNWMHIRYQSKLQARKAL-SK 58

Query: 357 NGLKMGDKT-LTVRRAT 372
           +G   G+   + V+   
Sbjct: 59  DGRIFGESIMIGVKPCI 75

>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 = 51.3 bits (122), Expect = 5e-09
 Identities = 15/85 (17%), Positives = 26/85 (30%), Gaps = 7/85 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           R VY+ G P  A    I  +       +          +        K   FV   ++E 
Sbjct: 7   RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-------MRRTLHKAFKGSIFVVFDSIES 59

Query: 235 ASNAMALDGIIFEGVAVRVRRPTDY 259
           A   +   G  ++   + +    DY
Sbjct: 60  AKKFVETPGQKYKETDLLILFKDDY 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 = 47.4 bits (112), Expect = 1e-07
 Identities = 17/76 (22%), Positives = 25/76 (32%), Gaps = 2/76 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V++ G P   T   IKE LE  G +     ++       KG  F V+            
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFV-E 65

Query: 356 LNGLKMGDKTLTVRRA 371
             G K  +  L +   
Sbjct: 66  TPGQKYKETDLLILFK 81

>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 = 50.2 bits (119), Expect = 1e-08
 Identities = 11/76 (14%), Positives = 25/76 (32%), Gaps = 1/76 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
             +  +P+  T+  + + LE          V   + G   G     +++      +   L
Sbjct: 11  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-RL 69

Query: 357 NGLKMGDKTLTVRRAT 372
           +  K+  +   V   T
Sbjct: 70  HRKKLNGREAFVHVVT 85

>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 = 36.7 bits (84), Expect = 0.001
 Identities = 10/84 (11%), Positives = 22/84 (26%), Gaps = 6/84 (7%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
              ++  +P    +  +  F   +              V+          A V+ +  ++
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDE------NAVHVLVDNNGQGLGQALVQFKNEDD 62

Query: 235 ASNAMALDGIIFEGVAVRVRRPTD 258
           A  +  L      G    V   T 
Sbjct: 63  ARKSERLHRKKLNGREAFVHVVTL 86

>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 = 1e-08
 Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 6/79 (7%)

Query: 296 RVFVGGLPYYFTETQI---KELLESFGTLHGFDLVKDRDTGNS---KGYGFCVYQDPAVT 349
            VFV GL     + ++    E    FG +H   +        S       +  Y      
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 350 DIACAALNGLKMGDKTLTV 368
             A   +N + +  +TL  
Sbjct: 70  LRAIQCVNNVVVDGRTLKA 88

>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 = 2e-08
 Identities = 9/76 (11%), Positives = 22/76 (28%), Gaps = 3/76 (3%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V V  LP  + + ++ +  +  G +   D+        +  +    +             
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALA-AITK 59

Query: 357 NGLKMGDKTLTVRRAT 372
               +G   + V   T
Sbjct: 60  THKVVGQNEIIVSHLT 75

>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 = 43.7 bits (102), Expect = 2e-06
 Identities = 15/81 (18%), Positives = 25/81 (30%), Gaps = 8/81 (9%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           V V  LP   N+  +  +F      I           V   +    +FA +E    + A 
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPII--------HVDVADSLKKNFRFARIEFARYDGAL 54

Query: 237 NAMALDGIIFEGVAVRVRRPT 257
            A+     +     + V   T
Sbjct: 55  AAITKTHKVVGQNEIIVSHLT 75

>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 = 51.1 bits (121), Expect = 2e-08
 Identities = 26/81 (32%), Positives = 41/81 (50%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           +    + V  +P    E Q+++L E +G +    +V DR+T  S+GYGF  +Q  +    
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 352 ACAALNGLKMGDKTLTVRRAT 372
           A A LNG  + +K L V  A 
Sbjct: 100 AIAGLNGFNILNKRLKVALAA 120

>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 = 39.5 bits (91), Expect = 2e-04
 Identities = 26/143 (18%), Positives = 48/143 (33%), Gaps = 17/143 (11%)

Query: 138 SAVPEMAQNMLPFGAT------QLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAI 191
           S +P ++Q   P+G T      Q      +P            R + V  +P   +E  +
Sbjct: 2   SQIPLVSQYD-PYGQTAQLQQLQQQQQQHIPPT-QMNPEPDVLRNLMVNYIPTTVDEVQL 59

Query: 192 ATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA 250
              F +               V +      + + FV+ ++   A  A+  L+G       
Sbjct: 60  RQLFERYGPIE------SVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR 113

Query: 251 VRVR--RPTDYNPTLAAALGPGQ 271
           ++V         P +A A+G G 
Sbjct: 114 LKVALAASGHQRPGIAGAVGDGN 136

>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 = 50.0 bits (119), Expect = 2e-08
 Identities = 19/99 (19%), Positives = 34/99 (34%), Gaps = 6/99 (6%)

Query: 288 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 347
           + G     R+ V  L Y  T   + ++   FGT+             ++      Y DP 
Sbjct: 1   MAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPV 56

Query: 348 VTDIACAALNG--LKMGDKTLTVRRATASSGQSKTEQES 384
               A  +L+G  +     TL +  +  +S   K   + 
Sbjct: 57  SAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDK 95

>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 = 35.4 bits (81), Expect = 0.002
 Identities = 16/92 (17%), Positives = 29/92 (31%), Gaps = 17/92 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVE 233
            R+ V  L        +   FS+            G  +  +      +  A ++     
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSK-----------FGTVLKIITFTKNNQFQALLQYADPV 56

Query: 234 EASNAM-ALDG--IIFEGVAVRVR--RPTDYN 260
            A +A  +LDG  I      +R+   + T  N
Sbjct: 57  SAQHAKLSLDGQNIYNACCTLRIDFSKLTSLN 88

>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 = 47.6 bits (112), Expect = 7e-08
 Identities = 12/79 (15%), Positives = 29/79 (36%), Gaps = 7/79 (8%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + + GLP   T  ++ +LL  +   +             KG  F    +    + A    
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKY-------CFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 357 NGLKMGDKTLTVRRATASS 375
           +  ++ ++ L+V+     +
Sbjct: 54  HQSRLRERELSVQLQPTDA 72

>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 = 48.3 bits (114), Expect = 8e-08
 Identities = 24/83 (28%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VF+  L +   E  + E+L+ FG L    +V   DT +SKG  F  +          AA
Sbjct: 10  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 69

Query: 356 LN------GLKMGDKTLTVRRAT 372
            +      GLK+  + L V  A 
Sbjct: 70  ASLEAEGGGLKLDGRQLKVDLAV 92

>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 = 36.3 bits (83), Expect = 0.001
 Identities = 17/92 (18%), Positives = 31/92 (33%), Gaps = 13/92 (14%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
               + V++  L   + E+A+     Q               V++    H K  AF +  
Sbjct: 5   VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRV------VLHPDTEHSKGCAFAQFM 58

Query: 231 TVEEASNAMA-------LDGIIFEGVAVRVRR 255
           T E A   +A         G+  +G  ++V  
Sbjct: 59  TQEAAQKCLAAASLEAEGGGLKLDGRQLKVDL 90

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.8 bits (113), Expect = 8e-08
 Identities = 12/86 (13%), Positives = 25/86 (29%), Gaps = 6/86 (6%)

Query: 171 TRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           T   R + +  L   L +E  +   F    +    N             +     AF+  
Sbjct: 1   TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQK-----EHSFNNCCAFMVF 55

Query: 230 RTVEEASNAMALDGIIFEGVAVRVRR 255
              + A  A+ ++  +     + V  
Sbjct: 56  ENKDSAERALQMNRSLLGNREISVSL 81

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.5 bits (107), Expect = 4e-07
 Identities = 8/79 (10%), Positives = 25/79 (31%), Gaps = 3/79 (3%)

Query: 296 RVFVGGLPYYFTETQIKELL--ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
            + +  L     +  +                    ++   +    F V+++    + A 
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 354 AALNGLKMGDKTLTVRRAT 372
             +N   +G++ ++V  A 
Sbjct: 66  -QMNRSLLGNREISVSLAD 83

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 1e-07
 Identities = 16/70 (22%), Positives = 31/70 (44%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +++ GL    T+  + +L + +G +     + D+ T   KGYGF  +  P+    A  AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 357 NGLKMGDKTL 366
               +  +  
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 = 37.8 bits (87), Expect = 2e-04
 Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 7/77 (9%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           +Y+ GL P   +Q +          +   +      +++   N  K + FV+  +   A 
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKA------ILDKTTNKCKGYGFVDFDSPSAAQ 54

Query: 237 NAM-ALDGIIFEGVAVR 252
            A+ AL     +    +
Sbjct: 55  KAVTALKASGVQAQMAK 71

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 2e-07
 Identities = 12/85 (14%), Positives = 27/85 (31%), Gaps = 1/85 (1%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +  A G       V +      F E    E+ E +G +   ++  +    +  G  +  +
Sbjct: 17  SQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKF 75

Query: 344 QDPAVTDIACAALNGLKMGDKTLTV 368
           +     + A   LN      + +  
Sbjct: 76  RREEDAEKAVIDLNNRWFNGQPIHA 100

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 7e-07
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 5/76 (6%)

Query: 437 DEEYEEILEDMREEC-GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL 495
            E Y+E  E++  E   KYG +  + +     +          ++++        A   L
Sbjct: 33  QEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNV----YVKFRREEDAEKAVIDL 88

Query: 496 SGRKFGGNTVNAFYYP 511
           + R F G  ++A   P
Sbjct: 89  NNRWFNGQPIHAELSP 104

>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 = 46.4 bits (109), Expect = 4e-07
 Identities = 12/95 (12%), Positives = 36/95 (37%), Gaps = 1/95 (1%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG          V + GLP+  ++ +I +       +     +     G S G  F  +
Sbjct: 5   SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQS 378
               + +      +  ++G + + + +++ +  ++
Sbjct: 65  ASQEIAE-KALKKHKERIGHRYIEIFKSSRAEVRT 98

>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 = 45.9 bits (108), Expect = 6e-07
 Identities = 16/93 (17%), Positives = 32/93 (34%), Gaps = 6/93 (6%)

Query: 293 GPDRVFVGGL-PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           G   + V  L P   T   +  L   +G +    ++ ++              D     +
Sbjct: 1   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQL 55

Query: 352 ACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
           A + LNG K+  K + +  +   + Q   E + 
Sbjct: 56  AMSHLNGHKLHGKPIRITLSKHQNVQLPREGQE 88

>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 = 45.5 bits (107), Expect = 7e-07
 Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 1/80 (1%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           + P  +++  LP    E +++ +L+ FG       +    +G S+G GF   +     + 
Sbjct: 16  QDPTNLYISNLPLSMDEQELENMLKPFGQ-VISTRILRDSSGTSRGVGFARMESTEKCEA 74

Query: 352 ACAALNGLKMGDKTLTVRRA 371
                NG  +          
Sbjct: 75  VIGHFNGKFIKTPPGVSAPT 94

>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 = 38.6 bits (89), Expect = 2e-04
 Identities = 12/90 (13%), Positives = 26/90 (28%), Gaps = 8/90 (8%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFA 225
           M +Q  +    +Y+  LP   +EQ +          I          ++       +   
Sbjct: 10  MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTR-------ILRDSSGTSRGVG 62

Query: 226 FVEMRTVEEASNAM-ALDGIIFEGVAVRVR 254
           F  M + E+    +   +G   +       
Sbjct: 63  FARMESTEKCEAVIGHFNGKFIKTPPGVSA 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 = 44.6 bits (105), Expect = 8e-07
 Identities = 18/77 (23%), Positives = 27/77 (35%), Gaps = 8/77 (10%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++V G     T T ++     FG +       D      +   F  Y+     D A A 
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNII------DLSMDPPRNCAFVTYEKMESADQAVAE 58

Query: 356 LNGLKMGDKTLTVRRAT 372
           LNG ++    L V  A 
Sbjct: 59  LNGTQVESVQLKVNIAR 75

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 19/92 (20%), Positives = 35/92 (38%), Gaps = 19/92 (20%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           A R    +YV G         +   FS                ++++ ++  +  AFV  
Sbjct: 1   APRKGNTLYVYGED--MTPTLLRGAFSPF------------GNIIDLSMDPPRNCAFVTY 46

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV----RRP 256
             +E A  A+  L+G   E V ++V    ++P
Sbjct: 47  EKMESADQAVAELNGTQVESVQLKVNIARKQP 78

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 44.9 bits (105), Expect = 9e-07
 Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
             P  +F+G L    +  ++K  +      +   +V  R TG ++ +G+  ++     + 
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEK 69

Query: 352 ACAALNGLKMGDKTLTVRRAT 372
           A   L GLK+    + + +  
Sbjct: 70  AL-ELTGLKVFGNEIKLEKPK 89

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 34.5 bits (78), Expect = 0.004
 Identities = 12/81 (14%), Positives = 30/81 (37%), Gaps = 7/81 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             +++G L P  +   +    S++                       +KF +V+  + E+
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-------GTNRKFGYVDFESAED 66

Query: 235 ASNAMALDGIIFEGVAVRVRR 255
              A+ L G+   G  +++ +
Sbjct: 67  LEKALELTGLKVFGNEIKLEK 87

>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 = 44.4 bits (104), Expect = 2e-06
 Identities = 20/92 (21%), Positives = 30/92 (32%), Gaps = 13/92 (14%)

Query: 286 GAIGGAEGPD------RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYG 339
           G+ G + GP       RV V GLP   +   +K+ +   G +   D+ KD         G
Sbjct: 1   GSSGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MG 53

Query: 340 FCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
              Y      + A   L+  K           
Sbjct: 54  MVEYLRKEDMEYALRKLDDTKFRSHEGETSYI 85

>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 = 39.4 bits (91), Expect = 1e-04
 Identities = 17/87 (19%), Positives = 23/87 (26%), Gaps = 14/87 (16%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
             R   RV V GLPP  + Q +     +                V      +     VE 
Sbjct: 11  TRRSDFRVLVSGLPPSGSWQDLKDHMREAGD-------------VCYADVQKDGMGMVEY 57

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRVRR 255
              E+   A+  LD   F         
Sbjct: 58  LRKEDMEYALRKLDDTKFRSHEGETSY 84

>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 = 44.4 bits (104), Expect = 2e-06
 Identities = 13/83 (15%), Positives = 23/83 (27%), Gaps = 3/83 (3%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V + GLPY  TE  I               ++    G   G     +        A  A 
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLN--PMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AK 74

Query: 357 NGLKMGDKTLTVRRATASSGQSK 379
           +   M  + + +   + +     
Sbjct: 75  DKANMQHRYVELFLNSTAGTSGS 97

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 4e-05
 Identities = 21/81 (25%), Positives = 29/81 (35%), Gaps = 8/81 (9%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           V++ GLP  A E  I  FFS +              +           A VE  T E+A 
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNP--------MRVHIEIGPDGRVTGEADVEFATHEDAV 69

Query: 237 NAMALDGIIFEGVAVRVRRPT 257
            AMA D    +   V +   +
Sbjct: 70  AAMAKDKANMQHRYVELFLNS 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 = 43.6 bits (102), Expect = 4e-06
 Identities = 15/106 (14%), Positives = 27/106 (25%), Gaps = 5/106 (4%)

Query: 286 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           G++    G    F G L        +  L  + G +   D V+    G          + 
Sbjct: 3   GSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIIL-----FKEK 57

Query: 346 PAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQ 391
                      N   +  +   V          K   + I+   Q+
Sbjct: 58  AKEALGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQE 103

>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 = 42.4 bits (99), Expect = 7e-06
 Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 12/99 (12%)

Query: 284 ASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
           +SG IG  +     R++VGGL    +   +    + FG++   D VK         + + 
Sbjct: 5   SSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYI 58

Query: 342 VYQDPAVTDIACAALNGLKMGDKTLTVR----RATASSG 376
            Y+       ACA + G  +G     +R    ++  SSG
Sbjct: 59  QYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSSG 97

>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 = 40.8 bits (95), Expect = 3e-05
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 13/81 (16%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
            R++VGGL P  +  A+A  F +              ++  +       FA+++  +++ 
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRF------------GSIRTIDHVKGDSFAYIQYESLDA 65

Query: 235 ASNAM-ALDGIIFEGVAVRVR 254
           A  A   + G    G   R+R
Sbjct: 66  AQAACAKMRGFPLGGPDRRLR 86

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.7 bits (94), Expect = 4e-05
 Identities = 16/99 (16%), Positives = 27/99 (27%), Gaps = 10/99 (10%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +    LP      +I+E      T   F  +               + +P     A   L
Sbjct: 13  ILAKNLPAGTLAAEIQE------TFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHL 66

Query: 357 NGLKMGDKTLTVRRAT----ASSGQSKTEQESILAQAQQ 391
              K     L +  A      ++ Q K  Q    A+  +
Sbjct: 67  AYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAE 105

>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 = 39.9 bits (92), Expect = 8e-05
 Identities = 15/86 (17%), Positives = 32/86 (37%), Gaps = 1/86 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V++ GLP+      + +  +    +     +     G + G GF  +++ A    A    
Sbjct: 21  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYK-AALCR 79

Query: 357 NGLKMGDKTLTVRRATASSGQSKTEQ 382
           +   MG++ + V   T      K + 
Sbjct: 80  HKQYMGNRFIQVHPITKKGMLEKIDM 105

>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 = 37.2 bits (85), Expect = 8e-04
 Identities = 15/86 (17%), Positives = 25/86 (29%), Gaps = 6/86 (6%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
                VY+ GLP  A  + +  FF ++              +            FVE R 
Sbjct: 16  EAGFCVYLKGLPFEAENKHVIDFFKKLDIVE------DSIYIAYGPNGKATGEGFVEFRN 69

Query: 232 VEEASNAMALDGIIFEGVAVRVRRPT 257
             +   A+           ++V   T
Sbjct: 70  EADYKAALCRHKQYMGNRFIQVHPIT 95

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 15/87 (17%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
            AT+    V  GGL    +   +     +               V  + +   K ++F  
Sbjct: 16  YATQS-LVVANGGLGNGVSRNQLLPVLEKC------------GLVDALLMPPNKPYSFAR 62

Query: 229 MRTVEEASNAM-ALDG-IIFEGVAVRV 253
            RT EE+  A   L+G  + + +  ++
Sbjct: 63  YRTTEESKRAYVTLNGKEVVDDLGQKI 89

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 6/68 (8%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V  GGL    +  Q+  +LE  G +    +  ++       Y F  Y+    +  A   L
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYVTL 76

Query: 357 NGLKMGDK 364
           NG ++ D 
Sbjct: 77  NGKEVVDD 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 = 38.2 bits (88), Expect = 2e-04
 Identities = 12/76 (15%), Positives = 24/76 (31%), Gaps = 5/76 (6%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + +  +P   +E  +K L  S G +        +D    +               A   L
Sbjct: 13  LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDL 68

Query: 357 NGLKMGD-KTLTVRRA 371
           +   +G+   L V  +
Sbjct: 69  HNHDLGENHHLRVSFS 84

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.2 bits (88), Expect = 3e-04
 Identities = 16/104 (15%), Positives = 29/104 (27%), Gaps = 11/104 (10%)

Query: 284 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G          V V GL     E  + E       L  F  +        K    
Sbjct: 2   SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEA------LEKFGTICYVMMMPFKRQAL 55

Query: 341 CVYQDP--AVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQ 382
             +++   A   +  AA   + +  +      +T+         
Sbjct: 56  VEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNS 99

>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 = 36.3 bits (83), Expect = 0.001
 Identities = 16/99 (16%), Positives = 27/99 (27%), Gaps = 23/99 (23%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             V+V GL     E  +     +               +  V +   K+ A VE   ++ 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKF------------GTICYVMMMPFKRQALVEFENIDS 63

Query: 235 ASNA---MALDGIIFEGVAVRV--------RRPTDYNPT 262
           A       A   +   G              RP +  P+
Sbjct: 64  AKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPS 102

>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 = 36.0 bits (82), Expect = 0.001
 Identities = 14/89 (15%), Positives = 25/89 (28%), Gaps = 7/89 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           RV V GLP   +   +K+ +   G +   D+ +D         G   +        A   
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAVRK 54

Query: 356 LNGLKMGDKTLTVRRATASSGQSKTEQES 384
           L+  K                  ++    
Sbjct: 55  LDNTKFRSHEGETAYIRVKVDGPRSPSYG 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 = 35.6 bits (81), Expect = 0.002
 Identities = 11/77 (14%), Positives = 33/77 (42%), Gaps = 4/77 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            + +  LP   TET++  L   FG +    ++K ++      +     ++ A+T +   +
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQ----AFLELATEEAAITMVNYYS 65

Query: 356 LNGLKMGDKTLTVRRAT 372
                + ++ + ++ + 
Sbjct: 66  AVTPHLRNQPIYIQYSN 82

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	522
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.96
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.94
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.84
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.82
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.81
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.81
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.81
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.81
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.81
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.8
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.8
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.8
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.8
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.79
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.79
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.79
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.79
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.78
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.78
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.78
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.77
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.77
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.77
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.77
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.76
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.76
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.75
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.75
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.75
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.75
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.74
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.74
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.73
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.73
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.73
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.72
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.72
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.71
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.71
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.7
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.7
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.7
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.7
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.69
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.69
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.69
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.69
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.69
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.69
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.69
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.68
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.68
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.67
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.67
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.67
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.67
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.66
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.66
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.66
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.65
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.65
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.64
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.64
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.64
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.64
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.64
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.63
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.63
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.63
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.63
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.63
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.62
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.62
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.62
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.62
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.62
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.62
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.6
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.6
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.6
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.6
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.6
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.6
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.59
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.59
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.59
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.59
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.59
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.59
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.59
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.58
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.58
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.58
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.58
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.58
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.58
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.57
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.57
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.57
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.57
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.56
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.56
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.56
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.56
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.56
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.56
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.56
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.56
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.56
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.55
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.55
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.55
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.55
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.54
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.54
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.54
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.54
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.54
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.54
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.53
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.53
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.53
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.53
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.53
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.52
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.52
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.52
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.52
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.52
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.52
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.52
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.52
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.51
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.51
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.51
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	99.5
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.5
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.49
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.49
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.49
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.49
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.48
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.46
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.46
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.45
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.44
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.44
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.44
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.42
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.42
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.41
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.4
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.39
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.35
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.34
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.34
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.31
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.28
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.16
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.34
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.92
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.7
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.39
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.33
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.19
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	94.46
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	87.94

>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=2.8e-29  Score=222.10  Aligned_cols=171  Identities=22%  Similarity=0.398  Sum_probs=142.0

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~  252 (522)
                      ..++|||+|||+.+|+++|+++|++||.|....      ++.+..++.++|||||+|.+.++|.+|+.+.+..+.++.+.
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~------~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~   78 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV------VMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE   78 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEE------eeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchh
Confidence            457999999999999999999999999753210      11111245668999999999999999999899999999988


Q ss_pred             EecCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCC
Q 009944          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (522)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~  332 (522)
                      +.+.........                       .......++|||+|||..+|+++|+++|+.||.|..+.++.+..+
T Consensus        79 ~~~~~~~~~~~~-----------------------~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~  135 (183)
T d1u1qa_          79 PKRAVSREDSQR-----------------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS  135 (183)
T ss_dssp             EEECCCTTGGGS-----------------------TTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTT
T ss_pred             hhhhhhcccccc-----------------------cccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeeccccc
Confidence            876443322110                       112334578999999999999999999999999999999999889


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      |.++|||||+|.+.++|.+||+ +++..|.|+.|.|.+|.+
T Consensus       136 ~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         136 GKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALS  175 (183)
T ss_dssp             CCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCC
T ss_pred             CccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCC
Confidence            9999999999999999999997 788999999999999865

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=3.6e-26  Score=201.85  Aligned_cols=169  Identities=19%  Similarity=0.306  Sum_probs=138.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      ++|||+|||+.+|+++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|.+|+. +++..+.++.+.+......
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCCT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhhc
Confidence            689999999999999999999999999999999999999999999999999999999988 5667788888888876542


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHHhhccCCccCCCCcCCCCCCcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhcc
Q 009944          375 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  454 (522)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~  454 (522)
                      ......                               ........+.|.+|+..++.             ++|+++|+.|
T Consensus        86 ~~~~~~-------------------------------~~~~~~~~i~V~~lp~~~te-------------~~L~~~f~~~  121 (183)
T d1u1qa_          86 EDSQRP-------------------------------GAHLTVKKIFVGGIKEDTEE-------------HHLRDYFEQY  121 (183)
T ss_dssp             TGGGST-------------------------------TTTCCCSEEEEECCCTTCCH-------------HHHHHHHGGG
T ss_pred             cccccc-------------------------------ccccccceeEEccCCCcCCH-------------HHHhhhhccC
Confidence            211000                               00111133445555554444             3999999999


Q ss_pred             CCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          455 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       455 G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      |.|..+.|+.+..+|.+   +|+|||+|.+.++|.+||+ +++..|+|++|.|.++..
T Consensus       122 G~v~~~~i~~~~~~~~~---~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         122 GKIEVIEIMTDRGSGKK---RGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALS  175 (183)
T ss_dssp             SCEEEEEEEECTTTCCE---EEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCC
T ss_pred             CceeeeeeecccccCcc---ceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCC
Confidence            99999999998877765   7899999999999999997 799999999999999754

>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=99.84  E-value=4e-21  Score=150.74  Aligned_cols=102  Identities=42%  Similarity=0.821  Sum_probs=95.0

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhC
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  497 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng  497 (522)
                      .|++|++|.|++++++|.++.+|+++.+||++.|++||.|++|.|+++..+.. ..+.|+|||+|.+.++|.+|+..|||
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~-~~~~g~vfV~f~~~e~A~~A~~~l~G   80 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVE-VPGCGKIFVEFTSVFDCQKAMQGLTG   80 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSS-CTTCCEEEEEESCHHHHHHHHHHHSS
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCc-cCCceEEEEEECCHHHHHHHHHHHCC
Confidence            67999999999999999999999999999999999999999999998765433 35568999999999999999999999


Q ss_pred             CccCCeEEEEEEeCCcccccccC
Q 009944          498 RKFGGNTVNAFYYPEDKYFNKDY  520 (522)
Q Consensus       498 ~~~~Gr~l~v~~~~~~~~~~~~~  520 (522)
                      +.|+||+|.|.|+++++|.+++|
T Consensus        81 r~f~gR~v~v~f~~~~~y~~~~f  103 (104)
T d1o0pa_          81 RKFANRVVVTKYCDPDSYHRRDF  103 (104)
T ss_dssp             CCSSSSCCEEEEECHHHHHHTSC
T ss_pred             CEECCeEEEEEEcCHHHhhhccC
Confidence            99999999999999999999987

>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=99.82  E-value=1.5e-20  Score=141.31  Aligned_cols=79  Identities=27%  Similarity=0.452  Sum_probs=76.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      ++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++||..|||..|.|+.|+|.|+.|
T Consensus         3 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           3 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            5899999999999999999999999999999999988999999999999999999999999999999999999999965

>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=99.82  E-value=3.2e-20  Score=141.04  Aligned_cols=81  Identities=28%  Similarity=0.350  Sum_probs=78.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      ..+|||+|||..+++++|.++|+.||.|..|.++.++.+|.++|||||+|.+.++|++|+..|||..|.|+.|.|.||.+
T Consensus         7 ~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~   86 (88)
T d1rk8a_           7 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV   86 (88)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             C
Q 009944          374 S  374 (522)
Q Consensus       374 ~  374 (522)
                      +
T Consensus        87 k   87 (88)
T d1rk8a_          87 K   87 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.82  E-value=5.7e-20  Score=138.11  Aligned_cols=79  Identities=37%  Similarity=0.606  Sum_probs=76.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      ++|||+|||..+++++|+++|++||.|..|.++.+..+|.++|||||+|.+.++|++|++.|||..|.|+.|.|.||.|
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            5799999999999999999999999999999999988999999999999999999999999999999999999999965

>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=99.81  E-value=2.8e-20  Score=141.78  Aligned_cols=81  Identities=19%  Similarity=0.336  Sum_probs=78.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||+.+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.++.+
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p   84 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP   84 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             C
Q 009944          374 S  374 (522)
Q Consensus       374 ~  374 (522)
                      +
T Consensus        85 ~   85 (89)
T d2cqba1          85 M   85 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.81  E-value=3.1e-20  Score=142.63  Aligned_cols=83  Identities=30%  Similarity=0.455  Sum_probs=79.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++|++.|||..|.|+.|+|.||.
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            34689999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 009944          373 ASS  375 (522)
Q Consensus       373 ~~~  375 (522)
                      ++.
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            753

>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=99.81  E-value=3.8e-20  Score=141.33  Aligned_cols=82  Identities=29%  Similarity=0.429  Sum_probs=78.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ...+|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.|+.
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            34689999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             CC
Q 009944          373 AS  374 (522)
Q Consensus       373 ~~  374 (522)
                      ++
T Consensus        87 p~   88 (90)
T d2cq0a1          87 PS   88 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.81  E-value=4.5e-20  Score=137.55  Aligned_cols=77  Identities=23%  Similarity=0.327  Sum_probs=75.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      .|||+|||+.+|+++|.++|+.||+|..|+|+.++.+|.++|||||+|.+.++|.+|++.|+|..|.|++|+|.|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            59999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.81  E-value=8.8e-20  Score=142.10  Aligned_cols=84  Identities=26%  Similarity=0.440  Sum_probs=79.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            44568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      ..+.
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8753

>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=8.5e-20  Score=137.24  Aligned_cols=77  Identities=22%  Similarity=0.442  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (522)
                      .+.++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|+|
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            34468999999999999999999999999999999999989999999999999999999999999999999999987

>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=99.80  E-value=1.3e-19  Score=141.69  Aligned_cols=83  Identities=25%  Similarity=0.493  Sum_probs=78.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      +.++|||+|||+.+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|..||+.|||..|+|+.|.|.|+.
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            34679999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 009944          373 ASS  375 (522)
Q Consensus       373 ~~~  375 (522)
                      ++.
T Consensus        97 ~k~   99 (102)
T d2cpza1          97 SKN   99 (102)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            754

>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=99.80  E-value=1.5e-19  Score=138.73  Aligned_cols=82  Identities=24%  Similarity=0.399  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||..+|+++|+++|++||.|.+|.++.++.+|.++|||||+|.+.++|..|++.|||..|.|+.|.|.|+
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            34579999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 009944          372 TA  373 (522)
Q Consensus       372 ~~  373 (522)
                      ..
T Consensus        85 ~~   86 (93)
T d1h2vz_          85 AG   86 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.80  E-value=4.9e-20  Score=138.90  Aligned_cols=81  Identities=56%  Similarity=0.965  Sum_probs=77.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      .+|||+|||..+|+++|+++|++||+|..|+|+.++.+|.++|||||+|.++++|..|+..|||..|.|+.|.|.++.+.
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            47999999999999999999999999999999999999999999999999999999999999999999999999999764


Q ss_pred             C
Q 009944          375 S  375 (522)
Q Consensus       375 ~  375 (522)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.80  E-value=1.7e-19  Score=136.15  Aligned_cols=79  Identities=25%  Similarity=0.458  Sum_probs=74.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC--eEEEEEE
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRR  370 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~  370 (522)
                      ..++|||+|||..+++++|+++|++||.|..++++.++.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|.|.|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            34679999999999999999999999999999999999999999999999999999999999999998876  8899998


Q ss_pred             c
Q 009944          371 A  371 (522)
Q Consensus       371 ~  371 (522)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=3.6e-19  Score=135.21  Aligned_cols=83  Identities=23%  Similarity=0.388  Sum_probs=76.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      +..++|||+|||+.+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.  +..|.|+.|.|.++
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            4457899999999999999999999999999999999999999999999999999999999984  45899999999999


Q ss_pred             cCCCC
Q 009944          372 TASSG  376 (522)
Q Consensus       372 ~~~~~  376 (522)
                      .++..
T Consensus        84 ~~k~~   88 (90)
T d2cqga1          84 NSKQS   88 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            87543

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=1.9e-19  Score=133.31  Aligned_cols=76  Identities=25%  Similarity=0.413  Sum_probs=73.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      +|||+|||+.+++++|+++|++||.|..+.|+.++ +|.++|||||+|.+.++|.+|++.|||..|.|++|.|.+++
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            69999999999999999999999999999999885 89999999999999999999999999999999999999985

>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=99.79  E-value=2.2e-19  Score=135.35  Aligned_cols=77  Identities=29%  Similarity=0.509  Sum_probs=73.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC--eEEEEEEc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  371 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~  371 (522)
                      ++|||+|||+.+|+++|+++|++||.|..++++.++.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|.|.||
T Consensus         7 ~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           7 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            579999999999999999999999999999999999899999999999999999999999999999987  56999886

>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=2.2e-19  Score=137.34  Aligned_cols=83  Identities=29%  Similarity=0.569  Sum_probs=78.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ...+|||+|||+.+++++|.++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|+|..|.|+.|.|.++.
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            34689999999999999999999999999999999988899999999999999999999999999999999999999997


Q ss_pred             CCC
Q 009944          373 ASS  375 (522)
Q Consensus       373 ~~~  375 (522)
                      ++.
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.78  E-value=7.3e-19  Score=134.10  Aligned_cols=82  Identities=27%  Similarity=0.406  Sum_probs=75.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ..+++|||+|||..+++++|+++|+.||.|..|.++.+..+  .+|||||+|.+.++|.+|+..|+|..|.|+.|+|.|+
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 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34579999999999999999999999999999999988644  4789999999999999999999999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      .++.
T Consensus        84 ~~~~   87 (90)
T d2cqia1          84 TTPS   87 (90)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            7653

>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=99.78  E-value=2e-19  Score=134.58  Aligned_cols=79  Identities=16%  Similarity=0.257  Sum_probs=69.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      ++|||+|||+.+|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|++.|||..|.|++|.|.++.|
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            5899999999999999999999999999888888878999999999999999999999999999999999999999975

>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=99.78  E-value=3.9e-19  Score=136.63  Aligned_cols=83  Identities=24%  Similarity=0.458  Sum_probs=76.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCC-CCCcceEEEEEEcChHHHHHHHHHH-cCCccCCeEEEEEE
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVRR  370 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~-~g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v~~  370 (522)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.+.. +|.++|||||+|.+.++|.+||+.| ||..|.|+.|.|.|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            446899999999999999999999999999999988753 8999999999999999999999998 89999999999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      |....
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            97653

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=3.9e-19  Score=133.41  Aligned_cols=79  Identities=27%  Similarity=0.518  Sum_probs=74.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||+ +++..|.|+.|.|..|.
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            34689999999999999999999999999999999999999999999999999999999997 69999999999999874

>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=99.78  E-value=8.4e-19  Score=134.55  Aligned_cols=83  Identities=25%  Similarity=0.574  Sum_probs=76.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ...+++|||+|||+.+++++|+++|+.||.|..|.++.+.  +.++|||||+|.+.++|.+|+..|||..|.|+.|.|.+
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 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4456789999999999999999999999999999999884  44789999999999999999999999999999999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      |.++.
T Consensus        86 A~~r~   90 (93)
T d2cq3a1          86 ATARV   90 (93)
T ss_dssp             CCSSC
T ss_pred             cCcCC
Confidence            98753

>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=1.1e-18  Score=145.22  Aligned_cols=84  Identities=31%  Similarity=0.536  Sum_probs=79.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||.++++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|+|+.|.|.++
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            44578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      ....
T Consensus       120 ~~~~  123 (139)
T d1u6fa1         120 ASGH  123 (139)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7654

>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=99.77  E-value=1.3e-19  Score=133.47  Aligned_cols=76  Identities=28%  Similarity=0.496  Sum_probs=73.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ++|||+|||+++|+++|+++|++||.|..+.|+.++.+|.++|||||+|.+.++|.+||+ +++..|+|+.|.|..|
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            479999999999999999999999999999999999999999999999999999999997 7999999999999876

>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=99.77  E-value=3e-19  Score=134.28  Aligned_cols=79  Identities=30%  Similarity=0.515  Sum_probs=74.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCceE-EEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCCC
Q 009944          297 VFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (522)
Q Consensus       297 l~v~nLp~~~t~~~l~~~F~~~G~i~~-v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (522)
                      |||+|||+++++++|+++|++||.|.. +.++.++.+|.++|||||+|.+.++|.+||+.|+|..|.|++|.|.++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            799999999999999999999999865 4788888899999999999999999999999999999999999999997653

>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=99.77  E-value=4.1e-19  Score=138.06  Aligned_cols=78  Identities=17%  Similarity=0.359  Sum_probs=74.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      .++|||+|||+.+++++|+++|+.||.|..|.|+.+..+|.++|||||+|.+.++|.+|+. |||..|.|+.|.|.++.
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~   95 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            3689999999999999999999999999999999999999999999999999999999995 99999999999999974

>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=99.77  E-value=3.8e-19  Score=139.90  Aligned_cols=79  Identities=43%  Similarity=0.754  Sum_probs=76.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      ++|||+|||..+++++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.++.+
T Consensus         9 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_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            5899999999999999999999999999999999999999999999999999999999999999999999999999865

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=3.3e-19  Score=130.75  Aligned_cols=75  Identities=28%  Similarity=0.570  Sum_probs=71.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      +|||+|||+.+++++|+++|++||.|..+.|+.++.+|.++|||||+|.+.++|++||+ +++..|.|+.|.|..|
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            48999999999999999999999999999999999999999999999999999999997 7999999999998754

>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=99.76  E-value=8.2e-19  Score=132.49  Aligned_cols=78  Identities=24%  Similarity=0.479  Sum_probs=72.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCC---CcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG---NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       297 l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g---~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      |||+|||..+|+++|+++|++||.|..|.|+.++.++   .++|||||+|.+.++|.+|++.|||..|.|+.|.|.++..
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            7999999999999999999999999999999886655   4689999999999999999999999999999999999865


Q ss_pred             C
Q 009944          374 S  374 (522)
Q Consensus       374 ~  374 (522)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.2e-18  Score=136.36  Aligned_cols=80  Identities=34%  Similarity=0.634  Sum_probs=75.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||+.+++++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|.+||+.+++ .|.|+.|.|.++..
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~   88 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYL   88 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTT
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCC
Confidence            36799999999999999999999999999999999999999999999999999999999998876 79999999999875


Q ss_pred             C
Q 009944          374 S  374 (522)
Q Consensus       374 ~  374 (522)
                      +
T Consensus        89 ~   89 (103)
T d2cqda1          89 G   89 (103)
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=3.9e-19  Score=129.81  Aligned_cols=75  Identities=23%  Similarity=0.432  Sum_probs=71.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      +|||+|||+++|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++||+ +++..|+|+.|.|..|
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            59999999999999999999999999999999999999999999999999999999997 5778999999999864

>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=99.75  E-value=1.2e-18  Score=135.79  Aligned_cols=80  Identities=26%  Similarity=0.519  Sum_probs=76.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      ++|||+|||+++++++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|.+||+ ++|..|.|+.|.|.+|.++
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            689999999999999999999999999999999999999999999999999999999996 7999999999999999875


Q ss_pred             C
Q 009944          375 S  375 (522)
Q Consensus       375 ~  375 (522)
                      .
T Consensus       100 e  100 (103)
T d1x4ba1         100 E  100 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.75  E-value=2.6e-18  Score=127.79  Aligned_cols=76  Identities=22%  Similarity=0.530  Sum_probs=72.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++ ++|..|.|+.|.|..|
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            689999999999999999999999999999999999999999999999999999999986 8999999999999876

>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=99.75  E-value=3.7e-18  Score=132.88  Aligned_cols=84  Identities=29%  Similarity=0.428  Sum_probs=77.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHc------CCccCCeE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN------GLKMGDKT  365 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~------g~~~~g~~  365 (522)
                      ...++|||+|||+.+|+++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+||+.|+      |..|.|+.
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            445789999999999999999999999999999999998899999999999999999999999987      57789999


Q ss_pred             EEEEEccCCC
Q 009944          366 LTVRRATASS  375 (522)
Q Consensus       366 l~v~~~~~~~  375 (522)
                      |.|.++.++.
T Consensus        86 l~v~~a~~k~   95 (98)
T d1x4ha1          86 LKVDLAVTRD   95 (98)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCC
Confidence            9999998754

>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=99.75  E-value=1.2e-18  Score=131.51  Aligned_cols=80  Identities=16%  Similarity=0.360  Sum_probs=70.2

Q ss_pred             CCeEEEcCCCCCCC-HHHHHHHHHhcCCceEEEEeeC-CCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          294 PDRVFVGGLPYYFT-ETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       294 ~~~l~v~nLp~~~t-~~~l~~~F~~~G~i~~v~~~~~-~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      .++|||+|||++++ +++|+++|++||.|..|.|+.+ ..+|.++|||||+|.+.++|.+||+ |||..|+|+.|.|.++
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEEC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEc
Confidence            46999999999976 5669999999999999998764 4689999999999999999999996 9999999999999999


Q ss_pred             cCC
Q 009944          372 TAS  374 (522)
Q Consensus       372 ~~~  374 (522)
                      .++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.75  E-value=1.1e-18  Score=132.82  Aligned_cols=79  Identities=23%  Similarity=0.469  Sum_probs=73.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      ..+|||+|||+.+++++|+++|+.||.|..+.|+.+.  +.++|||||+|.+.++|++||+.|||..|+|+.|.|.++.+
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 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            3589999999999999999999999999999999885  44789999999999999999999999999999999999976


Q ss_pred             C
Q 009944          374 S  374 (522)
Q Consensus       374 ~  374 (522)
                      +
T Consensus        86 ~   86 (89)
T d1cvja2          86 R   86 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=1.3e-18  Score=128.12  Aligned_cols=75  Identities=25%  Similarity=0.585  Sum_probs=72.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      +|||+|||+++|+++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+|++ +||..|.|+.|.|.+|
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            58999999999999999999999999999999998899999999999999999999997 9999999999999876

>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=99.74  E-value=5.6e-18  Score=132.63  Aligned_cols=83  Identities=22%  Similarity=0.383  Sum_probs=76.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCce--------EEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCe
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK  364 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~--------~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~  364 (522)
                      ..++|||+|||..+|+++|.++|+.||.|.        .+.+..+..+|.++|||||+|.+.++|.+||+.|||..|.|+
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr   86 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGS   86 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCE
Confidence            457999999999999999999999999874        567777888899999999999999999999999999999999


Q ss_pred             EEEEEEccCCC
Q 009944          365 TLTVRRATASS  375 (522)
Q Consensus       365 ~l~v~~~~~~~  375 (522)
                      .|.|.++.++.
T Consensus        87 ~i~V~~a~~~~   97 (101)
T d2cpea1          87 KLKVSLARKKP   97 (101)
T ss_dssp             ECEEECSSCCC
T ss_pred             EEEEEEcCCCC
Confidence            99999997753

>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=2.9e-18  Score=129.76  Aligned_cols=79  Identities=16%  Similarity=0.338  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEE-EEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGF-DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v-~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ...++|||+|||+.+++++|+++|+.||.|... .+..+ .+|.++|+|||+|.+.++|.+|+..|||..|+|++|+|.+
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC-CCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345679999999999999999999999998764 44444 6899999999999999999999999999999999999987


Q ss_pred             c
Q 009944          371 A  371 (522)
Q Consensus       371 ~  371 (522)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.73  E-value=9.7e-18  Score=134.27  Aligned_cols=78  Identities=22%  Similarity=0.448  Sum_probs=72.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||..+++++|.++|++||.|..|.+..   ++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.++.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            347899999999999999999999999999999875   46679999999999999999999999999999999999986


Q ss_pred             C
Q 009944          373 A  373 (522)
Q Consensus       373 ~  373 (522)
                      .
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.73  E-value=9.4e-19  Score=133.38  Aligned_cols=80  Identities=18%  Similarity=0.336  Sum_probs=73.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ....+|||+|||+.+++++|+++|+.||.|..+.|+.+ .+|.++|||||+|.+.++|++||+ |||..|.|+.|.|.++
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            34568999999999999999999999999998888655 589999999999999999999996 9999999999999998


Q ss_pred             cC
Q 009944          372 TA  373 (522)
Q Consensus       372 ~~  373 (522)
                      ..
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.72  E-value=1.7e-18  Score=135.87  Aligned_cols=84  Identities=20%  Similarity=0.265  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      .+.++|||+|||..+++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.|+
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            34578999999999999999999999999999988888778999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      .++.
T Consensus        96 k~k~   99 (102)
T d2cpxa1          96 KNKK   99 (102)
T ss_dssp             CCCS
T ss_pred             CCcc
Confidence            8754

>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=99.72  E-value=1.6e-17  Score=127.81  Aligned_cols=76  Identities=18%  Similarity=0.393  Sum_probs=71.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+++++|+++|++||.|..|+++.+      +|||||+|.+.++|.+|+..|||..|.|+.|+|.|+.+
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            368999999999999999999999999999999865      68999999999999999999999999999999999976


Q ss_pred             CC
Q 009944          374 SS  375 (522)
Q Consensus       374 ~~  375 (522)
                      .+
T Consensus        92 ~p   93 (96)
T d1x4ga1          92 SP   93 (96)
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=99.71  E-value=1.6e-17  Score=124.72  Aligned_cols=76  Identities=22%  Similarity=0.270  Sum_probs=72.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ++|||+|||..+|+++|+++|+.||+|..|.|..+. +|.++|||||+|.+.++|.+||+ ++|..|.|+.|.|.+..
T Consensus         7 rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           7 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            689999999999999999999999999999998875 89999999999999999999996 79999999999999864

>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=99.71  E-value=3.4e-17  Score=126.05  Aligned_cols=79  Identities=20%  Similarity=0.406  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...++|||+|||+.+++++|+++|+.||.|..+.+..+   +.++|||||+|.+.++|++||+.|||..|.|+.|.|.|+
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            44568999999999999999999999999999887654   457899999999999999999999999999999999998


Q ss_pred             cC
Q 009944          372 TA  373 (522)
Q Consensus       372 ~~  373 (522)
                      ..
T Consensus        89 ~~   90 (95)
T d1x4aa1          89 RS   90 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            65

>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=99.71  E-value=7.1e-18  Score=131.49  Aligned_cols=81  Identities=19%  Similarity=0.440  Sum_probs=74.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ..+++|||+|||..+++++|+++|+.||.|..+.+..+. ++.++|||||+|.+.++|.+||+.|||..|.|+++.|.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            345789999999999999999999999999999998884 8899999999999999999999999999999999888776


Q ss_pred             cC
Q 009944          372 TA  373 (522)
Q Consensus       372 ~~  373 (522)
                      .|
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            44

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=1e-17  Score=126.99  Aligned_cols=76  Identities=20%  Similarity=0.327  Sum_probs=69.8

Q ss_pred             CCeEEEcCCCCCCCHHHH---HHHHHhcCCceEEEEeeCCCCCCc---ceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          294 PDRVFVGGLPYYFTETQI---KELLESFGTLHGFDLVKDRDTGNS---KGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l---~~~F~~~G~i~~v~~~~~~~~g~~---~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      .++|||+|||+.+++++|   .++|++||.|..|.+++++.++.+   .|||||+|.+.++|.+|++.|||..|.|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            468999999999999999   778999999999999998766654   49999999999999999999999999999999


Q ss_pred             EE
Q 009944          368 VR  369 (522)
Q Consensus       368 v~  369 (522)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>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=6.6e-17  Score=122.05  Aligned_cols=77  Identities=18%  Similarity=0.185  Sum_probs=70.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||+.+++++|+++|+.||.|..+.+..      ++|||||+|.+.++|..|+..|||..|.|+.|.|.|+.
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            346899999999999999999999999998777644      47899999999999999999999999999999999998


Q ss_pred             CCC
Q 009944          373 ASS  375 (522)
Q Consensus       373 ~~~  375 (522)
                      |+.
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.70  E-value=2.1e-17  Score=124.41  Aligned_cols=76  Identities=34%  Similarity=0.568  Sum_probs=71.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||..+++++|+++|+.||.|..|.+.++      +|||||+|.+.++|.+|+..|||..|.|+.|+|.||..
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 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            357999999999999999999999999999999865      57999999999999999999999999999999999977


Q ss_pred             CC
Q 009944          374 SS  375 (522)
Q Consensus       374 ~~  375 (522)
                      +.
T Consensus        82 ~~   83 (86)
T d2cpja1          82 SA   83 (86)
T ss_dssp             CS
T ss_pred             cC
Confidence            53

>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=99.70  E-value=2.1e-17  Score=127.57  Aligned_cols=81  Identities=16%  Similarity=0.327  Sum_probs=72.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      ....++|||+|||..+++++|+++|+.||.|..+.     .++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34457999999999999999999999999886654     2678899999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009944          371 ATASSG  376 (522)
Q Consensus       371 ~~~~~~  376 (522)
                      +.++..
T Consensus        88 a~~k~~   93 (96)
T d1fjca_          88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             eCCCCC
Confidence            987643

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=4.4e-18  Score=123.93  Aligned_cols=71  Identities=23%  Similarity=0.452  Sum_probs=68.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       297 l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      |||+|||.++|+++|.++|++||.|..++++.++.++.++|||||+|.+.++|++|++.|||..|.|+.|+
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            79999999999999999999999999999999999999999999999999999999999999999998753

>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=99.69  E-value=1.7e-17  Score=123.10  Aligned_cols=75  Identities=19%  Similarity=0.317  Sum_probs=68.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCC-ccCCeEEEEEEccC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL-KMGDKTLTVRRATA  373 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~-~~~g~~l~v~~~~~  373 (522)
                      ++|||+|||..+|+++|+++|++||.|..+.+..      ++|||||+|.+.++|.+|++.|||. .|.|+.|.|.|+.+
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 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4799999999999999999999999998776665      3689999999999999999999995 69999999999987


Q ss_pred             CC
Q 009944          374 SS  375 (522)
Q Consensus       374 ~~  375 (522)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=3.6e-17  Score=128.25  Aligned_cols=84  Identities=13%  Similarity=0.245  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      .....+|||+|||+++|+++|+++|..||.|..+.++.+..++.++|||||+|.+.++|++|++ +|+..|+|+.|.|.+
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            3445689999999999999999999999998876666666789999999999999999999996 999999999999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      +.+..
T Consensus        91 ~~~~~   95 (104)
T d1wg5a_          91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            97754

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=2.9e-17  Score=129.04  Aligned_cols=82  Identities=28%  Similarity=0.502  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCC-CCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~-~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      .++.+|||+|||+.+++++|+++|+.|| |..+.++.+. .++.++|||||+|.+.++|++|++ |||..|.|+.|.|.+
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            4557999999999999999999999999 6677776654 478899999999999999987774 999999999999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      +.++.
T Consensus        91 a~~~~   95 (104)
T d1wi8a_          91 ADQAQ   95 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            97754

>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=99.69  E-value=4.1e-17  Score=119.21  Aligned_cols=74  Identities=12%  Similarity=0.188  Sum_probs=68.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ++|||+|||+.+++++|+++|+.||.|..|.++.++.  ..+|||||+|.+.++|.+||. +++..|+|+.|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            4899999999999999999999999999999999853  346899999999999999986 8999999999999875

>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=99.69  E-value=4.2e-17  Score=122.09  Aligned_cols=75  Identities=20%  Similarity=0.318  Sum_probs=68.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc-CCeEEEEEEc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-GDKTLTVRRA  371 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~-~g~~l~v~~~  371 (522)
                      +.++|||+|||..+++++|.++|+.||.|..|.++.+     .+|||||+|.+.++|..|+..|||..| +|+.|.|.|+
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~a   81 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA   81 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEe
Confidence            3468999999999999999999999999999999764     368999999999999999999999888 5789999998


Q ss_pred             c
Q 009944          372 T  372 (522)
Q Consensus       372 ~  372 (522)
                      .
T Consensus        82 k   82 (83)
T d2b0ga1          82 K   82 (83)
T ss_dssp             C
T ss_pred             c
Confidence            5

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.69  E-value=7.4e-17  Score=122.70  Aligned_cols=80  Identities=20%  Similarity=0.426  Sum_probs=72.0

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceE
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~  251 (522)
                      ....+|||+|||+.+|+++|+++|..||.|..+.       |.+..++.++|||||+|.+.++|++||++++..|.|++|
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~-------v~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i   83 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-------VVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEI   83 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCC-------CCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEE
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEee-------eeecCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEE
Confidence            3456899999999999999999999999987643       456678999999999999999999999999999999999


Q ss_pred             EEecCCC
Q 009944          252 RVRRPTD  258 (522)
Q Consensus       252 ~v~~~~~  258 (522)
                      +|.+++.
T Consensus        84 ~V~~ak~   90 (91)
T d1fjeb1          84 KLEKPKG   90 (91)
T ss_dssp             EEECCCC
T ss_pred             EEEecCC
Confidence            9998653

>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=99.68  E-value=4e-17  Score=120.85  Aligned_cols=74  Identities=23%  Similarity=0.369  Sum_probs=68.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+||+  +|+++|+++|++||.|..|.+.++      +|||||+|.+.++|.+|+..|||..|.|+.|+|.|+.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            45799999996  899999999999999999998754      5799999999999999999999999999999999997


Q ss_pred             CC
Q 009944          373 AS  374 (522)
Q Consensus       373 ~~  374 (522)
                      ++
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>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=99.68  E-value=8.7e-17  Score=121.94  Aligned_cols=77  Identities=13%  Similarity=0.098  Sum_probs=69.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc-CCeEEEEEEc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-GDKTLTVRRA  371 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~-~g~~l~v~~~  371 (522)
                      ++++|||+|||..+++++|+++|+.||.|..+.+...    .++|||||+|.+.++|.+|+..|||..+ .|+.|+|.|+
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            3568999999999999999999999999988776643    4578999999999999999999999988 5899999998


Q ss_pred             cC
Q 009944          372 TA  373 (522)
Q Consensus       372 ~~  373 (522)
                      ++
T Consensus        85 k~   86 (88)
T d2adca2          85 KS   86 (88)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>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=99.67  E-value=5.5e-17  Score=125.20  Aligned_cols=81  Identities=19%  Similarity=0.322  Sum_probs=72.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCC-ceEEEEeeCC-CCCCcceEEEEEEcChHHHHHHHHHHcC--CccCCeEEEEEE
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDR-DTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVRR  370 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~-i~~v~~~~~~-~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v~~  370 (522)
                      ++|||+|||..+++++|+++|+.||. |..|.++.+. .+|.++|||||+|.+.++|..|++.|++  ..+.|+.|.|.|
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            47999999999999999999999996 8999998875 4688999999999999999999999864  566899999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      |.++.
T Consensus        82 A~p~~   86 (96)
T d2disa1          82 AEPEI   86 (96)
T ss_dssp             SCSSC
T ss_pred             cCCCC
Confidence            97753

>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=99.67  E-value=6.1e-17  Score=124.95  Aligned_cols=74  Identities=22%  Similarity=0.459  Sum_probs=67.5

Q ss_pred             CCCeEEEcCCC-CCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          293 GPDRVFVGGLP-YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       293 ~~~~l~v~nLp-~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ...+|||+||| ..+++++|+++|++||.|..|.|.        +|||||+|.+.++|.+||..|||..|.|+.|.|.|+
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   85 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34679999997 568899999999999999999883        689999999999999999999999999999999999


Q ss_pred             cCC
Q 009944          372 TAS  374 (522)
Q Consensus       372 ~~~  374 (522)
                      .++
T Consensus        86 ~~~   88 (98)
T d1wf2a_          86 AEP   88 (98)
T ss_dssp             TSC
T ss_pred             CCC
Confidence            764

>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=99.67  E-value=7e-17  Score=128.17  Aligned_cols=77  Identities=17%  Similarity=0.270  Sum_probs=70.3

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          294 PDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       294 ~~~l~v~nLp~-~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      .++|||+|||+ .+++++|+++|+.||.|..|.|+.++     +|||||+|.+.++|.+|++.|||..|.|+.|.|.|+.
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            36899999965 59999999999999999999998763     6899999999999999999999999999999999986


Q ss_pred             CCC
Q 009944          373 ASS  375 (522)
Q Consensus       373 ~~~  375 (522)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.67  E-value=4.2e-17  Score=124.41  Aligned_cols=78  Identities=14%  Similarity=0.379  Sum_probs=70.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHH----HHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEE
Q 009944          294 PDRVFVGGLPYYFTETQIKE----LLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~----~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (522)
                      .++|||+|||..+++++|++    +|++||.|..|.+..   ++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            46899999999999998864    689999999988764   56789999999999999999999999999999999999


Q ss_pred             EccCC
Q 009944          370 RATAS  374 (522)
Q Consensus       370 ~~~~~  374 (522)
                      |+..+
T Consensus        80 ~ak~~   84 (91)
T d1nu4a_          80 YAKTD   84 (91)
T ss_dssp             ECSSC
T ss_pred             EeCCC
Confidence            99764

>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=99.66  E-value=8.3e-17  Score=128.24  Aligned_cols=76  Identities=18%  Similarity=0.166  Sum_probs=69.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccC
Q 009944          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (522)
Q Consensus       294 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (522)
                      .++|||+|||+.+++++|+++|+.||.|..|.|..      ++|||||+|.+.++|.+||+.|||..|.|+.|.|.|+..
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            36899999999999999999999999999998743      478999999999999999999999999999999999876


Q ss_pred             CC
Q 009944          374 SS  375 (522)
Q Consensus       374 ~~  375 (522)
                      ..
T Consensus        84 ~~   85 (111)
T d1whxa_          84 GV   85 (111)
T ss_dssp             TT
T ss_pred             Cc
Confidence            54

>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=99.66  E-value=5.9e-17  Score=126.90  Aligned_cols=81  Identities=14%  Similarity=0.175  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ....+|||+|||+.+|+++|.++|..||.|..+.++....+|.++|||||+|.+.++|.+||+ |||..|.|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            344689999999999999999999999998775555555699999999999999999999996 9999999999999987


Q ss_pred             cC
Q 009944          372 TA  373 (522)
Q Consensus       372 ~~  373 (522)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            43

>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=99.66  E-value=1e-16  Score=125.05  Aligned_cols=81  Identities=16%  Similarity=0.204  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ....+|||+|||+++|+++|+++|+.||.+ .|.++.+. +|..+|||||+|.+.++|++|++ ||+..|+|+.|.|.++
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCcc-eeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            344689999999999999999999999854 67777774 68999999999999999999986 8999999999999998


Q ss_pred             cCCC
Q 009944          372 TASS  375 (522)
Q Consensus       372 ~~~~  375 (522)
                      ....
T Consensus        90 ~~~~   93 (102)
T d1weza_          90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.8e-17  Score=125.21  Aligned_cols=73  Identities=21%  Similarity=0.246  Sum_probs=67.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      ++|||+|||+.+++++|+++|++||.|..+.+..+       |||||+|.+.++|++||..|||..|.|+.|.|.++...
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            37999999999999999999999999999988643       79999999999999999999999999999999887543

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.4e-16  Score=120.37  Aligned_cols=76  Identities=16%  Similarity=0.233  Sum_probs=66.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||+++++++|+++|++||. ..+.+      +..+|||||+|.+.++|++|++.|||..|.|+.|.|.++.
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            3468999999999999999999999993 22333      3457899999999999999999999999999999999996


Q ss_pred             CCC
Q 009944          373 ASS  375 (522)
Q Consensus       373 ~~~  375 (522)
                      .+.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=7.4e-17  Score=122.13  Aligned_cols=77  Identities=19%  Similarity=0.427  Sum_probs=68.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      ..++|||+|||..+|+++|+++|++||.|..|++..     .++|||||+|.+.++|++||.  +++.|.|++|.|.++.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            457999999999999999999999999999987654     367899999999999999985  7889999999999997


Q ss_pred             CCCC
Q 009944          373 ASSG  376 (522)
Q Consensus       373 ~~~~  376 (522)
                      ++..
T Consensus        77 ~k~~   80 (88)
T d1wf0a_          77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>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=99.64  E-value=3.4e-17  Score=124.85  Aligned_cols=87  Identities=49%  Similarity=0.887  Sum_probs=77.3

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEEE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  253 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~v  253 (522)
                      .++|||+|||+.+|+++|+++|+.||.+....+. ....+.+..++.++|||||+|.+.++|+.|++|||..|.|+.|+|
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~-~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V   79 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQA-PGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKI   79 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCS-SSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCC
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEe-ccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEE
Confidence            3789999999999999999999999998776553 344577788899999999999999999999999999999999999


Q ss_pred             ecCCCCCc
Q 009944          254 RRPTDYNP  261 (522)
Q Consensus       254 ~~~~~~~~  261 (522)
                      .+++.+.+
T Consensus        80 ~r~k~~~p   87 (90)
T d1u2fa_          80 RRPHDYQP   87 (90)
T ss_dssp             BCTTCCSC
T ss_pred             CCCCCCCC
Confidence            98887753

>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=99.64  E-value=2.6e-16  Score=124.17  Aligned_cols=79  Identities=22%  Similarity=0.259  Sum_probs=71.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc--CCeEEEEEE
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVRR  370 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--~g~~l~v~~  370 (522)
                      +..+|||+|||+.+|+++|+++|++||.|..|.++.++    ++|||||+|.+.++|++|+..|||..|  .|+.|.|.|
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            34579999999999999999999999999999998763    589999999999999999999999888  688999999


Q ss_pred             ccCCC
Q 009944          371 ATASS  375 (522)
Q Consensus       371 ~~~~~  375 (522)
                      +.+..
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            87653

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=5.2e-16  Score=119.23  Aligned_cols=75  Identities=25%  Similarity=0.431  Sum_probs=69.5

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||+|||..+++++|+++|.+||.            |.++.+..++|||||+|.+.++|..|+ .|++..|.|+.
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~------------i~~v~i~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~   83 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQ------------IMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHV   83 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCC------------ceEEEEEecceEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            34578999999999999999999999997            788888899999999999999999999 79999999999


Q ss_pred             EEEecCCC
Q 009944          251 VRVRRPTD  258 (522)
Q Consensus       251 ~~v~~~~~  258 (522)
                      |+|.|++.
T Consensus        84 l~v~~ak~   91 (96)
T d1x4ga1          84 VKCYWGKE   91 (96)
T ss_dssp             CEEECCCC
T ss_pred             EEEEEcCC
Confidence            99999764

>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=7.9e-17  Score=127.92  Aligned_cols=82  Identities=18%  Similarity=0.309  Sum_probs=73.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (522)
                      .....+|||+|||+.+|+++|.++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+||. |||..|+|+.|.|..
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            3456799999999999999999999999998776566655699999999999999999999996 999999999999998


Q ss_pred             ccC
Q 009944          371 ATA  373 (522)
Q Consensus       371 ~~~  373 (522)
                      +..
T Consensus        94 ~~~   96 (112)
T d1wela1          94 ITK   96 (112)
T ss_dssp             ECH
T ss_pred             cCh
Confidence            854

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=4.8e-16  Score=119.91  Aligned_cols=76  Identities=25%  Similarity=0.511  Sum_probs=69.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCC--eEEEEEE
Q 009944          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRR  370 (522)
Q Consensus       293 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~  370 (522)
                      +.++|||+|||+.+++++|+++|++||.|..|.+.++      ++||||+|.+.++|.+|++.|||..|.|  +.|+|.|
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            4578999999999999999999999999999998764      5799999999999999999999999976  5899999


Q ss_pred             ccCC
Q 009944          371 ATAS  374 (522)
Q Consensus       371 ~~~~  374 (522)
                      +.+.
T Consensus        90 ak~~   93 (97)
T d1whya_          90 AKSG   93 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9764

>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=99.63  E-value=5.2e-16  Score=113.21  Aligned_cols=71  Identities=18%  Similarity=0.355  Sum_probs=63.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEccCC
Q 009944          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (522)
Q Consensus       297 l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (522)
                      |||+|||+++++++|+++|++|| +..+.+      +.++|||||+|.+.++|.+|+..|||..+.|++|.|.|+...
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 444443      446899999999999999999999999999999999999654

>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=99.63  E-value=1.1e-15  Score=119.60  Aligned_cols=79  Identities=16%  Similarity=0.138  Sum_probs=70.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHH--cCCccCCeEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLTV  368 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l--~g~~~~g~~l~v  368 (522)
                      ..+..+|||+|||..+++++|.++|++||.|..|.+.+.      +|+|||+|.+.++|+.|+..|  ++..++|++|.|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            445679999999999999999999999999999998754      679999999999999999988  457789999999


Q ss_pred             EEccCCC
Q 009944          369 RRATASS  375 (522)
Q Consensus       369 ~~~~~~~  375 (522)
                      .|+..+.
T Consensus        86 ~~s~~~~   92 (104)
T d1wexa_          86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEcCCCc
Confidence            9997643

>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=99.63  E-value=8.3e-16  Score=116.38  Aligned_cols=79  Identities=14%  Similarity=0.160  Sum_probs=70.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHH--cCCccCCeEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLTV  368 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l--~g~~~~g~~l~v  368 (522)
                      ..+.++|||+|||..+++++|.++|++||.|..+.+..+      +|||||+|.+.++|.+|++.+  ++..+.|++|.|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            345679999999999999999999999999999998764      479999999999999999876  567899999999


Q ss_pred             EEccCCC
Q 009944          369 RRATASS  375 (522)
Q Consensus       369 ~~~~~~~  375 (522)
                      .|+..+.
T Consensus        79 ~~sk~~~   85 (88)
T d2cq1a1          79 QYSNHKE   85 (88)
T ss_dssp             EECSCSS
T ss_pred             EECCCCC
Confidence            9997653

>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=99.63  E-value=3.3e-16  Score=120.78  Aligned_cols=76  Identities=21%  Similarity=0.221  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       292 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      ....+|||+|||+.+++++|+++|+.||.|..+.+..       +|||||+|.+.++|++||+.|||..|.|+.|.|.++
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            3456899999999999999999999999999998863       489999999999999999999999999999999998


Q ss_pred             cCC
Q 009944          372 TAS  374 (522)
Q Consensus       372 ~~~  374 (522)
                      ...
T Consensus        86 ~~~   88 (98)
T d1wg4a_          86 RVY   88 (98)
T ss_dssp             EEE
T ss_pred             ecC
Confidence            653

>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=99.62  E-value=6.2e-17  Score=121.18  Aligned_cols=78  Identities=24%  Similarity=0.373  Sum_probs=64.6

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~  252 (522)
                      ..++|||+|||+++|+++|.++|+.||.|....      ++.+..++.++|||||+|.+.++|.+|+++++..|.|+.|+
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~------i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~   78 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV------VMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE   78 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhcccccee------ecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEE
Confidence            457899999999999999999999999853211      11112235678999999999999999999999999999999


Q ss_pred             EecC
Q 009944          253 VRRP  256 (522)
Q Consensus       253 v~~~  256 (522)
                      |+++
T Consensus        79 V~~A   82 (84)
T d1l3ka1          79 PKRA   82 (84)
T ss_dssp             EEEC
T ss_pred             EEee
Confidence            9875

>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=99.62  E-value=6.6e-17  Score=125.78  Aligned_cols=84  Identities=19%  Similarity=0.333  Sum_probs=68.3

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCce
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~  250 (522)
                      ....++|||+|||+++|+++|+++|.+||.|....      ++.+..++.++|||||+|.+.++|.+|+++++..|.|+.
T Consensus        17 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~------i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~   90 (103)
T d1x4ba1          17 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCV------VMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRV   90 (103)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEE------EECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEE
T ss_pred             cCCCCEEEEeCCCCcCCHHHHHHHHHhhCccccee------ecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEE
Confidence            34457999999999999999999999999854211      011112356789999999999999999999999999999


Q ss_pred             EEEecCCCCC
Q 009944          251 VRVRRPTDYN  260 (522)
Q Consensus       251 ~~v~~~~~~~  260 (522)
                      |.|.++.+.+
T Consensus        91 i~V~~a~~ke  100 (103)
T d1x4ba1          91 VEPKRAVARE  100 (103)
T ss_dssp             EEEECCSSCC
T ss_pred             EEEEECcccC
Confidence            9999876543

>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=99.62  E-value=6.1e-16  Score=116.63  Aligned_cols=75  Identities=24%  Similarity=0.383  Sum_probs=67.0

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~  251 (522)
                      ..++|||+|||+.+|+++|+++|.+||.            +..+.+..++|||||+|.+.++|..|+ .|++..|.|+.|
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~------------i~~~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i   74 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKP------------GAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPI   74 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTST------------TCEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccce------------eeeEEEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEE
Confidence            3578999999999999999999999987            344556778999999999999999999 699999999999


Q ss_pred             EEecCCCC
Q 009944          252 RVRRPTDY  259 (522)
Q Consensus       252 ~v~~~~~~  259 (522)
                      .|.|+++.
T Consensus        75 ~V~~akP~   82 (86)
T d2cpda1          75 EVTLAKPV   82 (86)
T ss_dssp             EEECCCCC
T ss_pred             EEEeccCC
Confidence            99997644

>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=99.62  E-value=8.3e-17  Score=117.71  Aligned_cols=74  Identities=16%  Similarity=0.356  Sum_probs=62.0

Q ss_pred             eeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEEEec
Q 009944          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (522)
Q Consensus       176 ~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~v~~  255 (522)
                      +|||+|||+++|+++|.++|.+||.|....+      +.+..+++++|||||+|.+.++|++|+++++..|.|+.|.|++
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 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTL------KLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEEC------CCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhcccccccc------ccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeE
Confidence            5999999999999999999999998533211      1222335678999999999999999999999999999999975

>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=99.62  E-value=9.7e-16  Score=118.20  Aligned_cols=88  Identities=23%  Similarity=0.388  Sum_probs=78.7

Q ss_pred             CcceEEEeeCCCCcCcCC-ChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHh
Q 009944          418 TLAKVLCLTEAITADALA-DDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  496 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~-~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~ln  496 (522)
                      ...+++.|.|++++.++. +++.+.++.++|++.|++||.|..|.++.+..       .|+|||+|.+.++|.+|+..||
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~-------~G~~fV~f~~~e~A~~A~~~ln   78 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHP-------DGVASVSFRDPEEADYCIQTLD   78 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCT-------TCEEEEECSCHHHHHHHHHHST
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCC-------ccEEEEEECCHHHHHHHHHHhC
Confidence            667899999999988764 45668999999999999999999999987642       4899999999999999999999


Q ss_pred             CCccCCeEEEEEEeCC
Q 009944          497 GRKFGGNTVNAFYYPE  512 (522)
Q Consensus       497 g~~~~Gr~l~v~~~~~  512 (522)
                      |+.|+|++|.|.|++.
T Consensus        79 g~~~~gr~i~v~~~~g   94 (99)
T d2dita1          79 GRWFGGRQITAQAWDG   94 (99)
T ss_dssp             TCEETTEECEEEECCS
T ss_pred             CcEECCEEEEEEEeCC
Confidence            9999999999999864

>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=99.62  E-value=2.3e-16  Score=117.55  Aligned_cols=78  Identities=15%  Similarity=0.374  Sum_probs=62.2

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEEE
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~v  253 (522)
                      ++|||+|||+++|+++|+++|+.||.|...      ..+.+...+.++|||||+|.+.++|.+|+ .|||..|.|++|.|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~------~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V   75 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALS------IRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVT   75 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCE------EECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEee------eeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            689999999999999999999999986321      11233345778999999999999999999 69999999999999


Q ss_pred             ecCCC
Q 009944          254 RRPTD  258 (522)
Q Consensus       254 ~~~~~  258 (522)
                      +++++
T Consensus        76 ~~a~P   80 (81)
T d2ghpa1          76 KVSNP   80 (81)
T ss_dssp             EECCC
T ss_pred             EEccC
Confidence            98653

>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=99.61  E-value=3e-17  Score=120.48  Aligned_cols=76  Identities=12%  Similarity=0.243  Sum_probs=65.3

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEEEe
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVR  254 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~v~  254 (522)
                      |+|||+|||+++|+++|+++|.+||.|...      .++.+..++.++|||||+|.+.++|++|+++++..|+|+.|.|+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v------~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~   74 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKEC------LVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK   74 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCE------EEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCccee------eeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEE
Confidence            689999999999999999999999986431      12333445778999999999999999999999999999999998


Q ss_pred             cC
Q 009944          255 RP  256 (522)
Q Consensus       255 ~~  256 (522)
                      .+
T Consensus        75 ~A   76 (77)
T d1uawa_          75 VA   76 (77)
T ss_dssp             EC
T ss_pred             EC
Confidence            53

>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=99.60  E-value=8.5e-17  Score=124.76  Aligned_cols=79  Identities=24%  Similarity=0.329  Sum_probs=65.7

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceE
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~  251 (522)
                      ...++|||+|||+.+|+++|+++|..||.|....      ++.+..++.++|||||+|.+.++|.+|++|+|..|.|+.|
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~------i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l   89 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVR------IISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPI   89 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEE------ECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEE------eeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEE
Confidence            3457899999999999999999999999853211      1222234678999999999999999999999999999999


Q ss_pred             EEecC
Q 009944          252 RVRRP  256 (522)
Q Consensus       252 ~v~~~  256 (522)
                      .|+++
T Consensus        90 ~V~~a   94 (101)
T d2cq4a1          90 IVQAS   94 (101)
T ss_dssp             EEEEH
T ss_pred             EEEEC
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=99.60  E-value=6.3e-15  Score=122.06  Aligned_cols=82  Identities=16%  Similarity=0.243  Sum_probs=66.4

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||+|||+++|+++|+++|++||.|....      ++.+..++.++|||||+|.+.++|..|+ .||+..|.|+.
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~------i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~  113 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVK------IVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR  113 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEE------EEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccc------cccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEE
Confidence            3456899999999999999999999999853210      1111123556899999999999999999 69999999999


Q ss_pred             EEEecCCCC
Q 009944          251 VRVRRPTDY  259 (522)
Q Consensus       251 ~~v~~~~~~  259 (522)
                      |+|.++...
T Consensus       114 l~V~~a~~~  122 (139)
T d1u6fa1         114 LKVALAASG  122 (139)
T ss_dssp             EEEEESSCC
T ss_pred             EEEEEcCCC
Confidence            999987644

>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=99.60  E-value=1.4e-15  Score=118.93  Aligned_cols=82  Identities=16%  Similarity=0.270  Sum_probs=72.6

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~  251 (522)
                      ++++|||+|||..+|+++|+++|..||.|....      .+.+...+.++|||||+|.+.++|..|+ .|+|..|.|++|
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~------~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l   90 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPP------IQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKIL   90 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSC------CEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEE------eecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEE
Confidence            457899999999999999999999999986543      3566677889999999999999999999 699999999999


Q ss_pred             EEecCCCCC
Q 009944          252 RVRRPTDYN  260 (522)
Q Consensus       252 ~v~~~~~~~  260 (522)
                      +|.|++...
T Consensus        91 ~V~~ak~k~   99 (102)
T d2cpxa1          91 VIEFGKNKK   99 (102)
T ss_dssp             EEEECCCCS
T ss_pred             EEEeCCCcc
Confidence            999987543

>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=99.60  E-value=6.4e-16  Score=115.47  Aligned_cols=79  Identities=18%  Similarity=0.222  Sum_probs=68.5

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhC
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  497 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng  497 (522)
                      +.+.|.+|+..++++             +|+++|++||.|..|.|+++..+|.+   +|+|||+|.+.++|++||+.|||
T Consensus         3 t~l~V~nLp~~~t~~-------------~l~~~F~~~G~v~~~~i~~~~~~g~~---~g~afV~f~~~~~A~~ai~~lng   66 (82)
T d1b7fa1           3 TNLIVNYLPQDMTDR-------------ELYALFRAIGPINTCRIMRDYKTGYS---YGYAFVDFTSEMDSQRAIKVLNG   66 (82)
T ss_dssp             SEEEEECCCTTCCHH-------------HHHHHHHTTSCEEEEECCEETTTTEE---CSEEEEEESSHHHHHHHHHHHTT
T ss_pred             CEEEEeCCCCCCCHH-------------HHHHHHHHhCCcceeeeeeecccCCc---cccceEEECCHHHHHHHHHHhCC
Confidence            445566666665554             99999999999999999988877765   78999999999999999999999


Q ss_pred             CccCCeEEEEEEeCC
Q 009944          498 RKFGGNTVNAFYYPE  512 (522)
Q Consensus       498 ~~~~Gr~l~v~~~~~  512 (522)
                      ..|+|++|+|.|+.+
T Consensus        67 ~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          67 ITVRNKRLKVSYARP   81 (82)
T ss_dssp             CEETTEECEEEECCC
T ss_pred             CEECCEEEEEEEcCC
Confidence            999999999999875

>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=99.60  E-value=2.4e-15  Score=114.21  Aligned_cols=75  Identities=28%  Similarity=0.426  Sum_probs=65.3

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCcEEEEEEeCHHHHHHHH-HhcCcee
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~----~~~~g~afV~f~~~~~a~~a~-~~~~~~~  246 (522)
                      ...++|||+|||..+|+++|+++|+.||.            |..+.+    ...+|||||+|.+.++|..|+ .+++..|
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~   73 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGP------------CKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKI   73 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSC------------EEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCC------------ceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEE
Confidence            34679999999999999999999999997            444443    335789999999999999999 6999999


Q ss_pred             cCceEEEecCCC
Q 009944          247 EGVAVRVRRPTD  258 (522)
Q Consensus       247 ~g~~~~v~~~~~  258 (522)
                      .|+.|+|.|++.
T Consensus        74 ~g~~i~v~~a~~   85 (90)
T d2cqia1          74 LGKEVKVNWATT   85 (90)
T ss_dssp             TTEEEEEEECCC
T ss_pred             CCEEEEEEEcCC
Confidence            999999999754

>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=99.60  E-value=1.4e-16  Score=118.22  Aligned_cols=77  Identities=17%  Similarity=0.292  Sum_probs=63.1

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEEE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  253 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~v  253 (522)
                      .++|||+|||+++|+++|+++|++||.+....      .+.+...+.++|||||+|.+.++|.+|+++++..|.|++|+|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~------~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V   75 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE------IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV   75 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEE
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccc------cccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEE
Confidence            47899999999999999999999999853210      011112345679999999999999999999999999999999


Q ss_pred             ecC
Q 009944          254 RRP  256 (522)
Q Consensus       254 ~~~  256 (522)
                      +++
T Consensus        76 ~~A   78 (79)
T d1l3ka2          76 RKA   78 (79)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            863

>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=99.59  E-value=1.7e-16  Score=120.90  Aligned_cols=80  Identities=26%  Similarity=0.441  Sum_probs=66.1

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~  251 (522)
                      +.++|||+|||+++|+++|+++|.+||.|..+.      .+.....+.++|||||+|.++++|+.|+ .|++..|.|++|
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~------~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l   77 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVV------VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQI   77 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEE------ECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCC
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhcccccccee------eccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            457899999999999999999999999854311      1112234567899999999999999999 799999999999


Q ss_pred             EEecCCC
Q 009944          252 RVRRPTD  258 (522)
Q Consensus       252 ~v~~~~~  258 (522)
                      +|.++..
T Consensus        78 ~V~~a~~   84 (90)
T d1x5sa1          78 RVDQAGK   84 (90)
T ss_dssp             EEEEEEC
T ss_pred             EEEEcCC
Confidence            9998643

>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=99.59  E-value=5.3e-16  Score=115.08  Aligned_cols=66  Identities=12%  Similarity=0.247  Sum_probs=61.2

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  513 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~  513 (522)
                      ++|+++|++||.|.+|+|+++..+|.+   +|+|||+|.++++|..|++.|||..|+|++|+|.|+..+
T Consensus        15 ~~l~~~F~~~G~i~~v~i~~d~~tg~~---~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~d   80 (80)
T d1cvja1          15 AMLYEKFSPAGPILSIRVCRDMITRRS---LGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD   80 (80)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCCC
T ss_pred             HHHHHHHHHhCCEeEEEEEecccccCC---CCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            499999999999999999999877765   789999999999999999999999999999999998653

>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=99.59  E-value=3.6e-16  Score=115.84  Aligned_cols=73  Identities=19%  Similarity=0.337  Sum_probs=63.3

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCc-eecCceEE
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI-IFEGVAVR  252 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~-~~~g~~~~  252 (522)
                      ++|||+|||+++|+++|+++|.+||.+            .++.+..++|||||+|.+.++|..|+ .|||. .|.|++|.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i------------~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~   69 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLP------------LAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIME   69 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCC------------CSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcE------------EEeEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEE
Confidence            479999999999999999999999974            33334456899999999999999999 69985 69999999


Q ss_pred             EecCCCC
Q 009944          253 VRRPTDY  259 (522)
Q Consensus       253 v~~~~~~  259 (522)
                      |.|+.+.
T Consensus        70 V~~a~~k   76 (80)
T d2cqha1          70 VDYSVSK   76 (80)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCc
Confidence            9997654

>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=99.59  E-value=2.4e-16  Score=115.77  Aligned_cols=75  Identities=15%  Similarity=0.284  Sum_probs=63.8

Q ss_pred             eeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEEEec
Q 009944          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (522)
Q Consensus       176 ~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~v~~  255 (522)
                      +|||+|||+++|+++|+++|+.||.+....      .+.+..++..+|||||+|.+.++|.+|+++++..|.|++|.|++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~------~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~   74 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAM------LMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEEC------CBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceee------eeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEE
Confidence            599999999999999999999999865322      12223346678999999999999999999999999999999986


Q ss_pred             C
Q 009944          256 P  256 (522)
Q Consensus       256 ~  256 (522)
                      +
T Consensus        75 A   75 (75)
T d2msta_          75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=4.2e-16  Score=117.95  Aligned_cols=81  Identities=21%  Similarity=0.313  Sum_probs=65.2

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceE
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~  251 (522)
                      ...++|||+|||+++|+++|+++|+.||.|..+.      ++.+..++.++|||||+|.+.++|.+||+ +...|.|+.|
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~------i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~~~l~Gr~i   78 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQ------VKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWC   78 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEE------EEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEE
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceee------eccCCCCcccCCEEEEEECCHHHHHHHHh-cCCccCCEEe
Confidence            4567899999999999999999999999854311      12222346778999999999999999996 4458999999


Q ss_pred             EEecCCCC
Q 009944          252 RVRRPTDY  259 (522)
Q Consensus       252 ~v~~~~~~  259 (522)
                      .|+++...
T Consensus        79 ~v~~a~~k   86 (90)
T d2cqga1          79 DCKLPNSK   86 (90)
T ss_dssp             EEECCCTT
T ss_pred             EEEeCCCC
Confidence            99987654

>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=99.59  E-value=1.8e-16  Score=118.86  Aligned_cols=80  Identities=19%  Similarity=0.267  Sum_probs=65.2

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~  252 (522)
                      ..++|||+|||.++|+++|+++|+.||.|..+.       +..-..+.++|||||+|.++++|.+|+++++..+.|+.|.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~-------l~~~~~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~   77 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-------MRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLL   77 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEE-------EEECTTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECE
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccce-------eeeeccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEE
Confidence            467999999999999999999999999753210       1111224557999999999999999999999999999999


Q ss_pred             EecCCCC
Q 009944          253 VRRPTDY  259 (522)
Q Consensus       253 v~~~~~~  259 (522)
                      |.+..+|
T Consensus        78 v~~~~dy   84 (85)
T d1zh5a2          78 ILFKDDY   84 (85)
T ss_dssp             EEEGGGC
T ss_pred             EEEcCCC
Confidence            9985543

>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=99.59  E-value=1.6e-15  Score=115.84  Aligned_cols=67  Identities=18%  Similarity=0.203  Sum_probs=62.0

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|.+|.|+.+..+|..   +|+|||+|.+.++|.+||+.|||..|+|++|+|.|+....
T Consensus        24 ~~l~~~F~~~G~v~~v~~~~d~~tg~~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~   90 (93)
T d1x5ua1          24 PLLWELFLQAGPVVNTHMPKDRVTGQH---QGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN   90 (93)
T ss_dssp             HHHHHHHHTTSCEEEEECCBCSSSCSB---CSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             HHHHHHHHHhCCccccceeeccccccc---ccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            399999999999999999998877765   6889999999999999999999999999999999998754

>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=99.58  E-value=1.9e-16  Score=115.29  Aligned_cols=74  Identities=18%  Similarity=0.279  Sum_probs=61.1

Q ss_pred             eeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEEEec
Q 009944          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (522)
Q Consensus       176 ~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~v~~  255 (522)
                      +|||+|||+++|+++|+++|++||.|....+      +.+-.++.++|||||+|.+.++|++|+++++..|.|+.|.|+.
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIEL------PMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKV   74 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEEC------CCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEEC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccc------cccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEE
Confidence            5999999999999999999999998432111      1112235678999999999999999998888999999999975

>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=99.58  E-value=1.3e-15  Score=117.11  Aligned_cols=78  Identities=28%  Similarity=0.434  Sum_probs=65.7

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      ...++|||+|||+++|+++|+++|..||.|..         +........++||||+|.+.++|+.|+ .|++..|.|++
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~---------~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~   82 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRD---------IDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYR   82 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEE---------EEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEE---------EEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            34568999999999999999999999997421         222223456899999999999999999 69999999999


Q ss_pred             EEEecCCC
Q 009944          251 VRVRRPTD  258 (522)
Q Consensus       251 ~~v~~~~~  258 (522)
                      |+|.+++.
T Consensus        83 l~V~~a~~   90 (95)
T d1x4aa1          83 LRVEFPRS   90 (95)
T ss_dssp             CEEECCCC
T ss_pred             EEEEeccC
Confidence            99999764

>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=99.58  E-value=1.5e-15  Score=110.66  Aligned_cols=68  Identities=19%  Similarity=0.295  Sum_probs=63.8

Q ss_pred             eEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEEEec
Q 009944          177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRR  255 (522)
Q Consensus       177 v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~v~~  255 (522)
                      |||+|||+++|+++|+++|.+||             +..+.++..+|||||+|.+.++|.+|+ .||+..+.|++|+|++
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-------------~~~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~   67 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-------------LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQL   67 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-------------ccceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEE
Confidence            79999999999999999999997             567778899999999999999999999 7999999999999998


Q ss_pred             CC
Q 009944          256 PT  257 (522)
Q Consensus       256 ~~  257 (522)
                      ++
T Consensus        68 a~   69 (75)
T d1wi6a1          68 QP   69 (75)
T ss_dssp             CC
T ss_pred             eC
Confidence            64

>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=99.58  E-value=1.3e-15  Score=121.73  Aligned_cols=76  Identities=17%  Similarity=0.138  Sum_probs=65.6

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~  251 (522)
                      .+++|||+|||..+|+++|.++|..||.|..         |.....+.++|||||+|.+.++|..|+ .|+|..|.|+.|
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~---------i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   76 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---------IRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYL   76 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEE---------EEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEe---------ecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            3578999999999999999999999998532         333334567899999999999999999 799999999999


Q ss_pred             EEecCC
Q 009944          252 RVRRPT  257 (522)
Q Consensus       252 ~v~~~~  257 (522)
                      .|.++.
T Consensus        77 ~V~~a~   82 (114)
T d2f9da1          77 VVLYYN   82 (114)
T ss_dssp             EEEECC
T ss_pred             EEEEcC
Confidence            999754

>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=99.58  E-value=2.3e-15  Score=113.65  Aligned_cols=78  Identities=14%  Similarity=0.092  Sum_probs=69.4

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHH--cCCccCCeEEE
Q 009944          291 AEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLT  367 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~-~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l--~g~~~~g~~l~  367 (522)
                      .+++++|||+|||.. +|++||.++|++||.|..|.++.+      +++|||+|.+.++|..|++.|  ++..+.|++|.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            355679999999986 889999999999999999999865      468999999999999999976  57789999999


Q ss_pred             EEEccCC
Q 009944          368 VRRATAS  374 (522)
Q Consensus       368 v~~~~~~  374 (522)
                      |.|++..
T Consensus        79 V~~s~~~   85 (89)
T d1x4da1          79 VHLSQKY   85 (89)
T ss_dssp             EEEECCC
T ss_pred             EEECCCc
Confidence            9999753

>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=99.58  E-value=2e-15  Score=114.47  Aligned_cols=75  Identities=21%  Similarity=0.364  Sum_probs=64.9

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCcEEEEEEeCHHHHHHHH-HhcCceec
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~----~~~~g~afV~f~~~~~a~~a~-~~~~~~~~  247 (522)
                      ...+|||+|||+++|+++|+++|.+||.            |..+.+    +.++|||||+|.+.++|.+|+ .|+|..|.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~   74 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGN------------ILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN   74 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSC------------EEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCC------------ceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEEC
Confidence            3457999999999999999999999997            444443    335799999999999999999 69999999


Q ss_pred             CceEEEecCCCC
Q 009944          248 GVAVRVRRPTDY  259 (522)
Q Consensus       248 g~~~~v~~~~~~  259 (522)
                      |+.|.|.+++..
T Consensus        75 g~~i~V~~a~~~   86 (89)
T d1cvja2          75 DRKVFVGRFKSR   86 (89)
T ss_dssp             TEEEEEEECCCT
T ss_pred             CEEEEEEECCCC
Confidence            999999987643

>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=99.58  E-value=5.9e-16  Score=116.31  Aligned_cols=73  Identities=30%  Similarity=0.520  Sum_probs=67.3

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~  252 (522)
                      .++|||+|||.++++++|+++|.+||.            |..+.+..++|||||+|.+.++|..|+ .|++..|.|+.|+
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~------------i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~   75 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGK------------AGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLR   75 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCC------------CSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCC------------ceEeeeecccceEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            457999999999999999999999997            677788889999999999999999999 6999999999999


Q ss_pred             EecCCC
Q 009944          253 VRRPTD  258 (522)
Q Consensus       253 v~~~~~  258 (522)
                      |+|+..
T Consensus        76 V~~A~~   81 (86)
T d2cpja1          76 VRFACH   81 (86)
T ss_dssp             EEESSC
T ss_pred             EEECCC
Confidence            998653

>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=99.57  E-value=1e-15  Score=121.75  Aligned_cols=76  Identities=21%  Similarity=0.153  Sum_probs=69.6

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++|||+|||+.+|+++|+++|..||.            |..+.+...+|||||+|.+.++|.+|+ .|||..|.|+
T Consensus         7 ~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~------------I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr   74 (111)
T d1whxa_           7 GRSKTVILAKNLPAGTLAAEIQETFSRFGS------------LGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHV   74 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhhccCC------------ccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCCC
Confidence            345679999999999999999999999997            788888999999999999999999999 7999999999


Q ss_pred             eEEEecCCC
Q 009944          250 AVRVRRPTD  258 (522)
Q Consensus       250 ~~~v~~~~~  258 (522)
                      +|.|.|+..
T Consensus        75 ~l~v~~a~~   83 (111)
T d1whxa_          75 PLYLEWAPI   83 (111)
T ss_dssp             BCEEEEEET
T ss_pred             eEEEEECCC
Confidence            999998643

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=6.4e-16  Score=115.69  Aligned_cols=78  Identities=17%  Similarity=0.318  Sum_probs=64.5

Q ss_pred             eEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEEEec
Q 009944          177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRR  255 (522)
Q Consensus       177 v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~v~~  255 (522)
                      |||+|||+++|+++|+++|.+||.|...     ..++.+..++.++|||||+|.+.++|..|+ .+++..|.|++|+|.+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~-----~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~   75 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQT-----PKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   75 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSC-----CEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeee-----EEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEE
Confidence            7999999999999999999999986431     001222234677899999999999999999 6999999999999998


Q ss_pred             CCCC
Q 009944          256 PTDY  259 (522)
Q Consensus       256 ~~~~  259 (522)
                      +...
T Consensus        76 a~~k   79 (83)
T d1x5ta1          76 AFKK   79 (83)
T ss_dssp             SCCC
T ss_pred             ecCC
Confidence            6643

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=2.8e-15  Score=110.45  Aligned_cols=63  Identities=17%  Similarity=0.308  Sum_probs=58.2

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                      ++|+++|++||.|..|.|+.+. +|.+   +|+|||+|.+.++|.+|++.|||..|+|++|+|.+++
T Consensus        15 ~~l~~~F~~~G~v~~~~i~~~~-~g~~---~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_          15 ADIQELFAEFGTLKKAAVHYDR-SGRS---LGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             HHHHHHHHHHSCEEEEEESCSS-CCCS---CCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHHHHhCCCeEEEEEEee-cccc---ceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            4999999999999999999886 5554   6899999999999999999999999999999999986

>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=99.57  E-value=1.1e-15  Score=112.89  Aligned_cols=72  Identities=22%  Similarity=0.373  Sum_probs=65.6

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~  251 (522)
                      ..++|||+||+  +|+++|+++|++||.            |.++.+.+.+|||||+|.+.++|..|+ +||+..|.|++|
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~------------I~~v~~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   69 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGN------------IIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQL   69 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCC------------CSCEEEETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCc------------cceeeeccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEE
Confidence            45789999995  899999999999997            667778889999999999999999999 799999999999


Q ss_pred             EEecCCC
Q 009944          252 RVRRPTD  258 (522)
Q Consensus       252 ~v~~~~~  258 (522)
                      +|.|++.
T Consensus        70 ~V~~a~~   76 (79)
T d2bz2a1          70 KVNIARK   76 (79)
T ss_dssp             EEEECCS
T ss_pred             EEEEecC
Confidence            9999753

>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=99.57  E-value=9.2e-16  Score=118.14  Aligned_cols=79  Identities=16%  Similarity=0.254  Sum_probs=68.2

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      .....++|||+|||+++|+++|+++|.+||.+.           .....+.++|||||+|.+.++|..|+ .|++..|.|
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~-----------~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g   80 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----------LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG   80 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEEC-----------CEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccce-----------eeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECC
Confidence            345578999999999999999999999999742           22345678999999999999999999 699999999


Q ss_pred             ceEEEecCCCC
Q 009944          249 VAVRVRRPTDY  259 (522)
Q Consensus       249 ~~~~v~~~~~~  259 (522)
                      ++|+|.|+.+.
T Consensus        81 r~i~V~~a~~k   91 (96)
T d1fjca_          81 RSVSLYYTGEK   91 (96)
T ss_dssp             EEEEEEECSSS
T ss_pred             EEEEEEEeCCC
Confidence            99999987654

>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=99.56  E-value=8.7e-16  Score=115.94  Aligned_cols=72  Identities=24%  Similarity=0.344  Sum_probs=64.7

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~  252 (522)
                      .++|||+|||+++|+++|+++|.+||.             ..+.+...+|||||+|.+.++|+.|+ .||+..|.|++|.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G~-------------~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~   71 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYDL-------------KYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLI   71 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSCC-------------CCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcCc-------------eeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            468999999999999999999999972             33556778999999999999999999 7999999999999


Q ss_pred             EecCCC
Q 009944          253 VRRPTD  258 (522)
Q Consensus       253 v~~~~~  258 (522)
                      |++++.
T Consensus        72 V~~a~~   77 (88)
T d1wg1a_          72 VQLQPT   77 (88)
T ss_dssp             EEECCC
T ss_pred             EEEcCC
Confidence            998654

>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=99.56  E-value=2.9e-16  Score=123.16  Aligned_cols=83  Identities=31%  Similarity=0.444  Sum_probs=67.4

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCc
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~  249 (522)
                      ....++|||+|||+++|+++|+++|++||.|..+.      ++.+..++.++|||||+|.+.++|+.|+ .|++..|.|+
T Consensus         5 ~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~------i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~   78 (104)
T d1p1ta_           5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFR------LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGR   78 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEE------EEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSS
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHhhhccccccccc------cccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCE
Confidence            34567899999999999999999999999854311      1111223556899999999999999999 6999999999


Q ss_pred             eEEEecCCCC
Q 009944          250 AVRVRRPTDY  259 (522)
Q Consensus       250 ~~~v~~~~~~  259 (522)
                      +|+|.++...
T Consensus        79 ~i~V~~a~~~   88 (104)
T d1p1ta_          79 ALRVDNAASE   88 (104)
T ss_dssp             CBEEEETTCT
T ss_pred             EEEEEECCCC
Confidence            9999987654

>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=99.56  E-value=2.9e-15  Score=115.71  Aligned_cols=77  Identities=14%  Similarity=0.231  Sum_probs=68.9

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHH--HHcCCccCCeEEEE
Q 009944          292 EGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA--ALNGLKMGDKTLTV  368 (522)
Q Consensus       292 ~~~~~l~v~nLp~~-~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~--~l~g~~~~g~~l~v  368 (522)
                      ...++|||+|||.. +|+++|.++|+.||.|..|.+..+      +|+|||+|.+.++|..|++  .+++..|.|+.|.|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            34578999999985 899999999999999999998764      5799999999999999998  47788999999999


Q ss_pred             EEccCC
Q 009944          369 RRATAS  374 (522)
Q Consensus       369 ~~~~~~  374 (522)
                      .|++.+
T Consensus        90 ~~s~~~   95 (99)
T d1x4fa1          90 DLSEKY   95 (99)
T ss_dssp             EEECSC
T ss_pred             EEcCCc
Confidence            999764

>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=99.56  E-value=2.6e-15  Score=113.66  Aligned_cols=76  Identities=22%  Similarity=0.363  Sum_probs=64.9

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCcee-cCce
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF-EGVA  250 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~-~g~~  250 (522)
                      ++++|||+|||+.+|+++|+++|..||.+.          ......+.++|||||+|.+.++|.+|+ +|++..| .|++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~----------~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~   78 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVV----------KGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHH   78 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCE----------EEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEE----------EEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCE
Confidence            357899999999999999999999999742          223345677899999999999999999 7999888 5899


Q ss_pred             EEEecCCC
Q 009944          251 VRVRRPTD  258 (522)
Q Consensus       251 ~~v~~~~~  258 (522)
                      |+|.+++.
T Consensus        79 l~v~~sk~   86 (88)
T d2adca2          79 LRVSFSKS   86 (88)
T ss_dssp             CEEEECSS
T ss_pred             EEEEeCCC
Confidence            99998654

>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=99.56  E-value=3e-15  Score=111.75  Aligned_cols=78  Identities=23%  Similarity=0.359  Sum_probs=67.0

Q ss_pred             cceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCC
Q 009944          419 LAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGR  498 (522)
Q Consensus       419 ~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~  498 (522)
                      .+.|-+|+..++++             +|+++|++||.|..|.|+++..++..   +|+|||+|.+.++|++|++.|||.
T Consensus         4 ~l~V~nLp~~~te~-------------~l~~~f~~~G~v~~v~i~~~~~~~~~---~g~afv~f~~~~~a~~a~~~l~g~   67 (82)
T d1fxla1           4 NLIVNYLPQNMTQE-------------EFRSLFGSIGEIESCKLVRDKITGQS---LGYGFVNYIDPKDAEKAINTLNGL   67 (82)
T ss_dssp             EEEEESCCTTCCHH-------------HHHHHHHTTSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEEECCCCCCCHH-------------HHHHHHHHhCCcccccceeeccCCCc---eeeEEEEECCHHHHHHHHHHhCCC
Confidence            34555565555554             99999999999999999988777654   789999999999999999999999


Q ss_pred             ccCCeEEEEEEeCC
Q 009944          499 KFGGNTVNAFYYPE  512 (522)
Q Consensus       499 ~~~Gr~l~v~~~~~  512 (522)
                      .|+|++|+|.|+.+
T Consensus        68 ~~~g~~l~v~~AkP   81 (82)
T d1fxla1          68 RLQTKTIKVSYARP   81 (82)
T ss_dssp             EETTEECEEEECCC
T ss_pred             EECCEEEEEEEeeC
Confidence            99999999999864

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.56  E-value=2.7e-15  Score=112.80  Aligned_cols=81  Identities=12%  Similarity=0.120  Sum_probs=62.8

Q ss_pred             ccceeEEeCCCccCc-HHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceE
Q 009944          173 HARRVYVGGLPPLAN-EQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t-~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~  251 (522)
                      +.++|||+|||+++| +++|+++|++||.|....+.     ..+...+.++|||||+|.+.++|.+|+++|+..|.|+.|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~-----~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l   77 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIP-----AGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREI   77 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECC-----SCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeee-----cccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEE
Confidence            467999999999986 56699999999985321110     001123456899999999999999999999999999999


Q ss_pred             EEecCCC
Q 009944          252 RVRRPTD  258 (522)
Q Consensus       252 ~v~~~~~  258 (522)
                      +|.+++.
T Consensus        78 ~V~~a~~   84 (86)
T d2ghpa3          78 SVSLADK   84 (86)
T ss_dssp             EEEECCC
T ss_pred             EEEEcCC
Confidence            9998653

>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=99.56  E-value=2.9e-15  Score=113.50  Aligned_cols=81  Identities=17%  Similarity=0.215  Sum_probs=69.3

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhC
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  497 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng  497 (522)
                      ..+.|-+|+..++++             +|+++|++||.|.+|.|+.+..+|.+   +|+|||+|.+.++|.+|++.|||
T Consensus         6 ~tlfV~nLp~~~te~-------------~l~~~F~~~G~i~~v~i~~d~~~~~~---kg~afV~f~~~~~A~~ai~~l~~   69 (89)
T d2cqba1           6 RVLYVGGLAEEVDDK-------------VLHAAFIPFGDITDIQIPLDYETEKH---RGFAFVEFELAEDAAAAIDNMNE   69 (89)
T ss_dssp             SCEEEESCCSSCCHH-------------HHHHHHTTTSCCCCEECCCCSSSCCC---SSEEEECCSSHHHHHHHHHHHTT
T ss_pred             cEEEEeCCCCcCCHH-------------HHHHHHhhCCeEEecccccccccccc---cceeEEEECCHHHHHHHHHHcCC
Confidence            344555565555544             99999999999999999999877765   68999999999999999999999


Q ss_pred             CccCCeEEEEEEeCCcc
Q 009944          498 RKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       498 ~~~~Gr~l~v~~~~~~~  514 (522)
                      ..|+|++|.|.|+...+
T Consensus        70 ~~i~g~~l~v~~a~p~~   86 (89)
T d2cqba1          70 SELFGRTIRVNLAKPMR   86 (89)
T ss_dssp             EEETTEEEEEEECCCCC
T ss_pred             CEECCEEEEEEEeCCCC
Confidence            99999999999987654

>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=99.56  E-value=6e-15  Score=114.23  Aligned_cols=67  Identities=19%  Similarity=0.293  Sum_probs=62.1

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+.+..++.+   +|+|||+|.+.++|..||+.|||..|+|++|+|.++....
T Consensus        23 ~~l~~~F~~~g~v~~v~i~~d~~tg~~---~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~   89 (99)
T d1whwa_          23 EDLEKLFSAYGPLSELHYPIDSLTKKP---KGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKK   89 (99)
T ss_dssp             HHHHHHHHTTSCEEEEECCCCTTTCCC---CSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCS
T ss_pred             HHHHHHHHhcCCceeeeeccccccccc---CcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            499999999999999999999878765   7899999999999999999999999999999999988654

>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=99.56  E-value=2.8e-15  Score=113.21  Aligned_cols=65  Identities=23%  Similarity=0.370  Sum_probs=60.4

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      ++|+++|++||.|.+|.|+.+..+|.+   +|+|||+|.+.++|++|+..|||..|+|++|+|.|+..
T Consensus        22 ~~l~~~F~~~G~i~~v~i~~d~~tg~~---~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~   86 (88)
T d1rk8a_          22 DEIQEKFCDYGEIKNIHLNLDRRTGFS---KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV   86 (88)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTSSE---EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             HHHHHHHHHcCCccccccccccccccc---ccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecC
Confidence            499999999999999999998877765   78999999999999999999999999999999999864

>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=99.55  E-value=8.3e-15  Score=112.02  Aligned_cols=67  Identities=21%  Similarity=0.339  Sum_probs=59.9

Q ss_pred             HHHHHHhhccCCeEEEEecCCCC-CCCCCCCccEEEEEecChHhHHHHHHHH-hCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQ-NGGETPGVGKVFLEYYDAVGCATAKNAL-SGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~-~g~~~~g~G~afV~F~~~~~A~~Ai~~l-ng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|+++.. +|..   +|+|||+|.+.++|.+||+.| ||..|.|++|.|.|+..+.
T Consensus        23 ~~l~~~F~~~G~i~~v~i~~~~~~~g~~---rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~~   91 (94)
T d2cpha1          23 REIRELFSTFGELKTVRLPKKMTGTGAH---RGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV   91 (94)
T ss_dssp             HHHHHHHHTTSCEEEEECCCCCSSSCSS---CSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCC
T ss_pred             HHHHHHHHHhCCceEEEEEeccccCCCc---ccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCCC
Confidence            39999999999999999988753 4544   689999999999999999998 8999999999999998764

>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=99.55  E-value=2.2e-15  Score=117.58  Aligned_cols=89  Identities=21%  Similarity=0.219  Sum_probs=69.3

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCc--eEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDA--VVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~--v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      ...++|||+|||..+|+++|+++|..||.|..+........  ..+..++..+|||||+|.+.++|..|+ .|+|..|.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            45679999999999999999999999998754322111110  111123566899999999999999999 699999999


Q ss_pred             ceEEEecCCCCC
Q 009944          249 VAVRVRRPTDYN  260 (522)
Q Consensus       249 ~~~~v~~~~~~~  260 (522)
                      +.|+|.+++...
T Consensus        86 r~i~V~~a~~~~   97 (101)
T d2cpea1          86 SKLKVSLARKKP   97 (101)
T ss_dssp             EECEEECSSCCC
T ss_pred             EEEEEEEcCCCC
Confidence            999999976543

>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=99.55  E-value=1e-14  Score=110.17  Aligned_cols=78  Identities=21%  Similarity=0.335  Sum_probs=67.8

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHH---HHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHH
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDM---REECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA  494 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l---~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~  494 (522)
                      ...+|.+|+..++.+             +|   .++|++||.|..|.|+++..++......|+|||+|.+.++|.+|++.
T Consensus         9 n~vyV~nLp~~~t~~-------------~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~   75 (89)
T d2cpia1           9 NLVFVVGLSQRLADP-------------EVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQC   75 (89)
T ss_dssp             SCEEEEEECTTTCCH-------------HHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHH
T ss_pred             CEEEEECCCCccCHH-------------HHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHH
Confidence            456788888887776             67   77899999999999999887765544568999999999999999999


Q ss_pred             HhCCccCCeEEEEE
Q 009944          495 LSGRKFGGNTVNAF  508 (522)
Q Consensus       495 lng~~~~Gr~l~v~  508 (522)
                      |||..|+|++|+|+
T Consensus        76 lng~~~~gr~lkvS   89 (89)
T d2cpia1          76 VNNVVVDGRTLKAS   89 (89)
T ss_dssp             HTTEEETTEEEEEE
T ss_pred             hCCCEECCEEEEEC
Confidence            99999999999986

>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=99.55  E-value=4.4e-15  Score=111.27  Aligned_cols=79  Identities=19%  Similarity=0.215  Sum_probs=69.5

Q ss_pred             cceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCC
Q 009944          419 LAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGR  498 (522)
Q Consensus       419 ~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~  498 (522)
                      ...|-+|+..++++             +|+++|++||+|..|+|+++..+|..   +|+|||+|.++++|..|++.|||.
T Consensus         3 rlfV~nlp~~~te~-------------~l~~~F~~~G~v~~v~i~~d~~tg~~---rg~aFV~f~~~~~A~~a~~~l~~~   66 (85)
T d2u2fa_           3 KLFIGGLPNYLNDD-------------QVKELLTSFGPLKAFNLVKDSATGLS---KGYAFCEYVDINVTDQAIAGLNGM   66 (85)
T ss_dssp             CEEEETCCSSCCSH-------------HHHHHHTSSSCEEEEEEECCCSSSCC---CCEEEEEESSSHHHHHHHHTSSSC
T ss_pred             EEEEECCCCCCCHH-------------HHHHHHHhcCccceEEeecccccccc---ceeEEEEECCHHHHHHHHHHhCCC
Confidence            34566676666665             99999999999999999999887765   789999999999999999999999


Q ss_pred             ccCCeEEEEEEeCCc
Q 009944          499 KFGGNTVNAFYYPED  513 (522)
Q Consensus       499 ~~~Gr~l~v~~~~~~  513 (522)
                      .|+|++|.|.|++..
T Consensus        67 ~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_          67 QLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCSSSCCEEEECCCC
T ss_pred             EECCEEEEEEECCCC
Confidence            999999999999754

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=8.8e-15  Score=113.97  Aligned_cols=81  Identities=17%  Similarity=0.276  Sum_probs=63.0

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceE
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~  251 (522)
                      ...++|||+|||+.+|+++|+++|++||.|....      ++.+..++.++|||||+|.+.++|.+|++..+..|.|++|
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~------i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l   81 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAV------VITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKA   81 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEE------ESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEEC
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhccccccee------ccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEE
Confidence            3456899999999999999999999999743211      0111123567899999999999999999533457999999


Q ss_pred             EEecCCC
Q 009944          252 RVRRPTD  258 (522)
Q Consensus       252 ~v~~~~~  258 (522)
                      .|.++..
T Consensus        82 ~V~~a~~   88 (103)
T d2cqda1          82 NVNLAYL   88 (103)
T ss_dssp             EEEESTT
T ss_pred             EEEEcCC
Confidence            9988654

>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=99.54  E-value=5.4e-15  Score=114.96  Aligned_cols=81  Identities=14%  Similarity=0.162  Sum_probs=68.6

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhC
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  497 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng  497 (522)
                      ..+.|.+|+..++++             +|+++|+.||.|..|.++.+..+|..   +|+|||+|.+.++|..||+.|||
T Consensus        19 ~~l~V~nLp~~~te~-------------~l~~~F~~~G~i~~~~~~~~~~~g~~---kG~afV~f~~~~~A~~Ai~~lng   82 (102)
T d2cpza1          19 ANLFIYHLPQEFGDQ-------------DLLQMFMPFGNVVSAKVFIDKQTNLS---KCFGFVSYDNPVSAQAAIQSMNG   82 (102)
T ss_dssp             CCEEEESCCSSCCHH-------------HHHHHHGGGSCCSEEEEEECSSSCSE---EEEEEEECSSHHHHHHHHHHHTT
T ss_pred             CEEEEeCCCCCCCHH-------------HHHHHHHhhccccccceeeecccCCC---ccceEEEeCCHHHHHHHHHHhCC
Confidence            344555565555554             99999999999999999988877755   78999999999999999999999


Q ss_pred             CccCCeEEEEEEeCCcc
Q 009944          498 RKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       498 ~~~~Gr~l~v~~~~~~~  514 (522)
                      ..|+|++|+|.|+....
T Consensus        83 ~~~~g~~i~V~~a~~k~   99 (102)
T d2cpza1          83 FQIGMKRLKVQLKRSKN   99 (102)
T ss_dssp             CEETTEECEEECCCCSC
T ss_pred             CEECCEEEEEEEeCCCC
Confidence            99999999999987543

>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=99.54  E-value=2.9e-15  Score=113.74  Aligned_cols=65  Identities=17%  Similarity=0.313  Sum_probs=60.3

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      ++|+++|+.||.|..|.|+.+..+|..   +|+|||+|.+.++|.+||+.|||..|+|++|+|.|+..
T Consensus        23 ~~l~~~f~~~G~v~~v~i~~d~~t~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp   87 (90)
T d2cq0a1          23 TDLQELFRPFGSISRIYLAKDKTTGQS---KGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKP   87 (90)
T ss_dssp             HHHHTTSTTTCCEEEEEEEECSSSCSE---EEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSC
T ss_pred             HHHHHHHHHhccccccccccccccccc---ccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeC
Confidence            399999999999999999998877755   78999999999999999999999999999999999865

>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=99.54  E-value=1.4e-16  Score=121.40  Aligned_cols=78  Identities=22%  Similarity=0.439  Sum_probs=68.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEe-----eCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEE
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLV-----KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~-----~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (522)
                      ++|||+|||..+|+++|+++|+.||.|..+.+.     .+..++.++|||||+|.+.++|++|+. |||..|.|+.|+|.
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            589999999999999999999999987765543     344578899999999999999999985 99999999999998


Q ss_pred             EccC
Q 009944          370 RATA  373 (522)
Q Consensus       370 ~~~~  373 (522)
                      .+..
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6543

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=5.9e-15  Score=110.28  Aligned_cols=60  Identities=25%  Similarity=0.417  Sum_probs=55.9

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEE
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNA  507 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v  507 (522)
                      ++|+++|++||.|.+|.|+.+..++.+   +|+|||+|.+.++|.+|++.|||..|+|++|+|
T Consensus        24 ~~l~~~F~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          24 RDLREVFSKYGPIADVSIVYDQQSRRS---RGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             HHHHHHHHTTSCEEEEEEEECSSSSSE---EEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             HHHHHHHHHhCCCcccccccccccccc---ccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            499999999999999999998877765   789999999999999999999999999999987

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.54  E-value=2.7e-15  Score=116.37  Aligned_cols=82  Identities=21%  Similarity=0.282  Sum_probs=64.2

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-Hhc------Cc
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD------GI  244 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~------~~  244 (522)
                      .+.++|||+|||+++|+++|+++|.+||.+....      .+.+...+.++|||||+|.+.++|.+|+ .++      +.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~------~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~   79 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVR------VVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL   79 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEE------CCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeee------eccccccccccceEEEEEcCHHHHHHHHHHcccccccCCc
Confidence            3467899999999999999999999999742111      0111123446899999999999999999 454      67


Q ss_pred             eecCceEEEecCCCC
Q 009944          245 IFEGVAVRVRRPTDY  259 (522)
Q Consensus       245 ~~~g~~~~v~~~~~~  259 (522)
                      .|.|+.|+|.++.+.
T Consensus        80 ~~~gr~l~v~~a~~k   94 (98)
T d1x4ha1          80 KLDGRQLKVDLAVTR   94 (98)
T ss_dssp             ESSSCEEEEECCCCC
T ss_pred             EECCEEEEEEECCCC
Confidence            899999999987654

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=6.9e-15  Score=112.24  Aligned_cols=65  Identities=17%  Similarity=0.331  Sum_probs=60.7

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      ++|+++|++||.|.+|.|+++..++.+   +|+|||+|.+.++|..|++.|||..|+|++|+|.|+..
T Consensus        22 ~~l~~~F~~~G~i~~v~i~~~~~~~~~---kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~   86 (93)
T d1h2vz_          22 EQIYELFSKSGDIKKIIMGLDKMKKTA---CGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG   86 (93)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESC
T ss_pred             HHHHHHHHHHCCcceeccccccccccc---cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            499999999999999999998877765   78999999999999999999999999999999999864

>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=99.53  E-value=2.1e-14  Score=109.62  Aligned_cols=65  Identities=18%  Similarity=0.360  Sum_probs=59.0

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|+.||.|..|.++.+...     .+|+|||+|.+.++|.+||+.|||..|+|++|+|.|+.+..
T Consensus        26 ~~L~~~F~~~G~v~~v~~~~~~~~-----~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~   90 (93)
T d2cq3a1          26 PDLRQMFGQFGKILDVEIIFNERG-----SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV   90 (93)
T ss_dssp             HHHHHHGGGTSCEEEEEEECCTTT-----TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSC
T ss_pred             HHHHHHHhhcceeeeccccccccC-----CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCC
Confidence            499999999999999999987632     25899999999999999999999999999999999998754

>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=99.53  E-value=7.1e-15  Score=109.70  Aligned_cols=74  Identities=23%  Similarity=0.337  Sum_probs=64.4

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCcEEEEEEeCHHHHHHHH-HhcCceec-C
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAM-ALDGIIFE-G  248 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~-~~~g~afV~f~~~~~a~~a~-~~~~~~~~-g  248 (522)
                      .++++|||+|||..+|+++|.++|..||.            |..+.+. ..+|||||+|.+.++|..|+ .|+|..|. |
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~------------i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~   73 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPG------------FKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPT   73 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTT------------EEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTT
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCcc------------EEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCC
Confidence            34679999999999999999999999997            6666554 45789999999999999999 69998884 6


Q ss_pred             ceEEEecCC
Q 009944          249 VAVRVRRPT  257 (522)
Q Consensus       249 ~~~~v~~~~  257 (522)
                      ++|+|.|++
T Consensus        74 ~~i~v~~ak   82 (83)
T d2b0ga1          74 HAMKITFAK   82 (83)
T ss_dssp             CBCEEEECC
T ss_pred             cEEEEEEec
Confidence            899999865

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=3.6e-15  Score=115.87  Aligned_cols=77  Identities=13%  Similarity=0.092  Sum_probs=68.3

Q ss_pred             CCCeEEEcCCCCCC-C----HHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEE
Q 009944          293 GPDRVFVGGLPYYF-T----ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (522)
Q Consensus       293 ~~~~l~v~nLp~~~-t----~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (522)
                      +.++|||+||+..+ +    +++|.++|+.||.|..+.+.+      ++|||||+|.+.++|.+|+..|||..|.|+.|.
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            45789999999876 3    357999999999999999875      467999999999999999999999999999999


Q ss_pred             EEEccCCC
Q 009944          368 VRRATASS  375 (522)
Q Consensus       368 v~~~~~~~  375 (522)
                      |.|+.+..
T Consensus        78 v~~a~~~~   85 (104)
T d1weya_          78 LYFAQTLH   85 (104)
T ss_dssp             EECCCCSS
T ss_pred             EeecccCC
Confidence            99997653

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=3.1e-15  Score=113.02  Aligned_cols=75  Identities=24%  Similarity=0.392  Sum_probs=64.7

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE-ecCCCcEEEEEEeCHHHHHHHHHhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY-INHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~-~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~  251 (522)
                      .+++|||+|||+.+|+++|+++|.+||.            |.++. ...++|||||+|.+.++|++|+. ++..|.|++|
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~------------v~~v~~~~~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l   70 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGD------------VMDVFIPKPFRAFAFVTFADDQIAQSLCG-EDLIIKGISV   70 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSC------------CCEEECCSSCCSCCEEECSCHHHHHHTTT-CEEEETTEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCC------------ceEEEEeeccCceEEEEECCHHHHHHHHh-CCCEECCEEe
Confidence            4679999999999999999999999997            44444 35578999999999999999994 7889999999


Q ss_pred             EEecCCCCC
Q 009944          252 RVRRPTDYN  260 (522)
Q Consensus       252 ~v~~~~~~~  260 (522)
                      .|.++.+..
T Consensus        71 ~v~~a~~k~   79 (88)
T d1wf0a_          71 HISNAEPKH   79 (88)
T ss_dssp             EEECCCCCC
T ss_pred             EEEeCCCCC
Confidence            999876543

>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=99.52  E-value=3.5e-15  Score=112.18  Aligned_cols=68  Identities=19%  Similarity=0.311  Sum_probs=60.2

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      ++|+++|++||.|.+|.|+++..++.....+|+|||+|.+.++|.+|++.|||..|+|++|.|.|+..
T Consensus        13 ~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1          13 ETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             HHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             HHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            49999999999999999998876554333478999999999999999999999999999999999854

>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=99.52  E-value=9e-15  Score=109.73  Aligned_cols=63  Identities=24%  Similarity=0.332  Sum_probs=58.2

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCC--eEEEEEEe
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYY  510 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~G--r~l~v~~~  510 (522)
                      ++|+++|++||.|..|.|+++..+|.+   +|+|||+|.+.++|.+||+.|||..+.|  ++|+|.||
T Consensus        21 ~~l~~~F~~~G~i~~~~~~~d~~~g~~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          21 DQLDTIFGKYGSIVQKNILRDKLTGRP---RGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             HHHHHHHTSSSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHhhCCEeeeeeecccccccC---ceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            399999999999999999998877765   7899999999999999999999999976  88999986

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=1.9e-14  Score=112.39  Aligned_cols=78  Identities=18%  Similarity=0.152  Sum_probs=69.1

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-Hh--cCceec
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-AL--DGIIFE  247 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~--~~~~~~  247 (522)
                      ..++++|||+|||+.+|+++|.++|..||.            |..+.+.+.++||||+|.+.++|+.|+ .+  ++..+.
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~------------I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~   79 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGT------------ICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIA   79 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhccc------------ceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEe
Confidence            345779999999999999999999999997            788888899999999999999999999 44  677899


Q ss_pred             CceEEEecCCCCC
Q 009944          248 GVAVRVRRPTDYN  260 (522)
Q Consensus       248 g~~~~v~~~~~~~  260 (522)
                      |++|+|.+++...
T Consensus        80 g~~l~v~~s~~~~   92 (104)
T d1wexa_          80 GQQAFFNYSTSKR   92 (104)
T ss_dssp             SSBCEEEECSSSS
T ss_pred             eEEEEEEEcCCCc
Confidence            9999999976543

>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=99.52  E-value=7.9e-15  Score=109.92  Aligned_cols=77  Identities=18%  Similarity=0.308  Sum_probs=65.1

Q ss_pred             CcceEEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhC
Q 009944          418 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  497 (522)
Q Consensus       418 ~~~~v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng  497 (522)
                      ..+.|.+|+..++++             +|+++|++||.|.+|.|+.+..+|..   +|+|||+|.+.++|.+|++.|||
T Consensus         7 ~~lfV~nLp~~~te~-------------~L~~~F~~~G~v~~v~i~~d~~~g~~---kg~afV~f~~~~~a~~Ai~~lng   70 (85)
T d1fxla2           7 ANLYVSGLPKTMTQK-------------ELEQLFSQYGRIITSRILVDQVTGVS---RGVGFIRFDKRIEAEEAIKGLNG   70 (85)
T ss_dssp             CEEEEESCCTTCCHH-------------HHHHHHGGGSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CEEEEeCCCCCCCHH-------------HHHHHHHHhCCccccccccccccccC---CCeeEEEEcCHHHHHHHHHHhCC
Confidence            345555566555554             99999999999999999998877655   78999999999999999999999


Q ss_pred             CccCC--eEEEEEEe
Q 009944          498 RKFGG--NTVNAFYY  510 (522)
Q Consensus       498 ~~~~G--r~l~v~~~  510 (522)
                      ..++|  ++|.|.|+
T Consensus        71 ~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          71 QKPSGATEPITVKFA   85 (85)
T ss_dssp             CCCTTCSSCCEEEEC
T ss_pred             CEeCCCCEEEEEEeC
Confidence            99998  55999886

>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=99.52  E-value=9.4e-15  Score=106.39  Aligned_cols=69  Identities=19%  Similarity=0.273  Sum_probs=60.7

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCcEEEEEEeCHHHHHHHHHhcCceecCce
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~----~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~  250 (522)
                      .+|||+|||+++++++|+++|..||.|            ..+.+    +..++||||+|.++++|.+|+.+++..|+|++
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I------------~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~~~~~~i~g~~   68 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPI------------IHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNE   68 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCE------------EEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEETTEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCce------------EEEEEEeeccccceEEEEEEcchHHhHHHHHhcCcEECCEE
Confidence            379999999999999999999999984            44443    23467999999999999999999999999999


Q ss_pred             EEEec
Q 009944          251 VRVRR  255 (522)
Q Consensus       251 ~~v~~  255 (522)
                      |.|..
T Consensus        69 i~V~~   73 (75)
T d2ghpa2          69 IIVSH   73 (75)
T ss_dssp             CEEEE
T ss_pred             EEEEE
Confidence            99975

>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=99.52  E-value=1e-14  Score=110.22  Aligned_cols=76  Identities=17%  Similarity=0.164  Sum_probs=68.5

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHH---hcCceecC
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIFEG  248 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~---~~~~~~~g  248 (522)
                      .++++|||+|||+.+|+++|+++|++||.            |..+.+..+++||||+|.+.++|..|++   +++..+.|
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~------------i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g   73 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGK------------VTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRN   73 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcccc------------cccccccccceEEEEEeCCHHHHHHHHHHHccCCCccCC
Confidence            45789999999999999999999999987            7888888999999999999999999993   47889999


Q ss_pred             ceEEEecCCCC
Q 009944          249 VAVRVRRPTDY  259 (522)
Q Consensus       249 ~~~~v~~~~~~  259 (522)
                      ++|+|.+++..
T Consensus        74 ~~l~v~~sk~~   84 (88)
T d2cq1a1          74 QPIYIQYSNHK   84 (88)
T ss_dssp             EECEEEECSCS
T ss_pred             CEEEEEECCCC
Confidence            99999987643

>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=99.52  E-value=1.3e-14  Score=113.65  Aligned_cols=80  Identities=18%  Similarity=0.262  Sum_probs=63.7

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEE-EecCCCcEEEEEEeCHHHHHHHHHhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV-YINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~-~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~  251 (522)
                      +.++|||+|||+++|+++|+++|..||.+ ...      .+.+. ..+..+|||||+|.+.++|++|+++++..|.|+.|
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g~~-~~~------~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l   86 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLNIS-AVR------LPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRI   86 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSCEE-EEE------CCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhccc-cce------eeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEE
Confidence            35789999999999999999999999832 100      01111 13456789999999999999888999999999999


Q ss_pred             EEecCCCC
Q 009944          252 RVRRPTDY  259 (522)
Q Consensus       252 ~v~~~~~~  259 (522)
                      +|.++...
T Consensus        87 ~V~~a~~~   94 (104)
T d1wi8a_          87 RVDVADQA   94 (104)
T ss_dssp             EEEECCCC
T ss_pred             EEEECCCC
Confidence            99987654

>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=99.52  E-value=1.5e-14  Score=111.39  Aligned_cols=74  Identities=23%  Similarity=0.404  Sum_probs=67.4

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC--c
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--V  249 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g--~  249 (522)
                      +.++|||+|||+++|+++|+++|++||.            |..+.+...++||||+|.+.++|+.|+ .|++..|.|  +
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~------------i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~   83 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGS------------IRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDR   83 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSC------------EEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcc------------cceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCce
Confidence            3578999999999999999999999987            788888889999999999999999999 799999987  5


Q ss_pred             eEEEecCCC
Q 009944          250 AVRVRRPTD  258 (522)
Q Consensus       250 ~~~v~~~~~  258 (522)
                      +|+|.|++.
T Consensus        84 ~l~v~~ak~   92 (97)
T d1whya_          84 RLRVDFAKS   92 (97)
T ss_dssp             BCEEEECCC
T ss_pred             EEEEEeCCC
Confidence            899998764

>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=99.51  E-value=9.9e-16  Score=119.09  Aligned_cols=80  Identities=13%  Similarity=0.256  Sum_probs=64.4

Q ss_pred             hhcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecC
Q 009944          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g  248 (522)
                      .....++|||+|||+++|+++|+++|.+||.|....       +.....+.++|||||+|.+.++|.+|+ .|||..|.|
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~-------~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~g   86 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTR-------ILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKT   86 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEE-------EEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCC
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhccccccee-------eecccccccccceeEEeCCHHHHHHHHHHhCCCEECC
Confidence            344567899999999999999999999999853210       111123456799999999999999999 699999999


Q ss_pred             ceEEEecC
Q 009944          249 VAVRVRRP  256 (522)
Q Consensus       249 ~~~~v~~~  256 (522)
                      +++.|.++
T Consensus        87 r~~~v~~~   94 (101)
T d1x5oa1          87 PPGVSAPT   94 (101)
T ss_dssp             CTTSCCCS
T ss_pred             cCCccCCC
Confidence            99988754

>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=99.51  E-value=3.9e-14  Score=111.99  Aligned_cols=74  Identities=26%  Similarity=0.307  Sum_probs=64.9

Q ss_pred             cceeEEeCCCc-cCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCcEEEEEEeCHHHHHHHH-HhcCceecCce
Q 009944          174 ARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (522)
Q Consensus       174 ~~~v~v~nlp~-~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~-~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~  250 (522)
                      +++|||+|||+ .+|+++|+++|+.||.            |..+.+.. .+|||||+|.+.++|.+|+ .|++..|.|+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~------------I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~   69 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGD------------VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKP   69 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTC------------EEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSB
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccc------------cceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            46899999966 5999999999999997            66666543 5799999999999999999 79999999999


Q ss_pred             EEEecCCCC
Q 009944          251 VRVRRPTDY  259 (522)
Q Consensus       251 ~~v~~~~~~  259 (522)
                      |+|.+++..
T Consensus        70 l~v~~s~~~   78 (109)
T d2adca1          70 IRITLSKHQ   78 (109)
T ss_dssp             CEEECCSCC
T ss_pred             EEEEECCCC
Confidence            999997643

>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=99.51  E-value=4.1e-15  Score=113.16  Aligned_cols=76  Identities=18%  Similarity=0.381  Sum_probs=64.3

Q ss_pred             ccceeEEeCCCccCcHHHHHH----HHHHHHHhhcCCCCCCCCceEEEEe---cCCCcEEEEEEeCHHHHHHHH-HhcCc
Q 009944          173 HARRVYVGGLPPLANEQAIAT----FFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGI  244 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~----~f~~~g~~~~~~~~~~~~~v~~~~~---~~~~g~afV~f~~~~~a~~a~-~~~~~  244 (522)
                      ++++|||+|||+.+|+++|++    +|.+||.            |..+.+   +.++|||||+|.+.++|..|+ .+++.
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~------------i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~   69 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQ------------ILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGF   69 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSC------------EEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccccc------------ccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCC
Confidence            467999999999999999875    4677776            555554   446899999999999999999 69999


Q ss_pred             eecCceEEEecCCCCC
Q 009944          245 IFEGVAVRVRRPTDYN  260 (522)
Q Consensus       245 ~~~g~~~~v~~~~~~~  260 (522)
                      .|.|+.|.|.|++...
T Consensus        70 ~~~g~~l~v~~ak~~~   85 (91)
T d1nu4a_          70 PFYDKPMRIQYAKTDS   85 (91)
T ss_dssp             EETTEECEEEECSSCC
T ss_pred             EECCEEEEEEEeCCCc
Confidence            9999999999976543

>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=99.50  E-value=1.7e-15  Score=117.82  Aligned_cols=75  Identities=13%  Similarity=0.163  Sum_probs=70.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEc
Q 009944          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (522)
Q Consensus       296 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (522)
                      .++|.+++..+++++|.++|++||.|..|.|+.+ .+|.++|+|||+|.+.++|.+|+..|||.+|.|++|.|.|.
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 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            5788899999999999999999999999999877 58999999999999999999999999999999999999985

>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=99.50  E-value=2.4e-14  Score=111.15  Aligned_cols=67  Identities=24%  Similarity=0.291  Sum_probs=59.3

Q ss_pred             HHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeC
Q 009944          441 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  511 (522)
Q Consensus       441 ~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~  511 (522)
                      +..+++|+++|++||.|.+|.|+++. ++.+   +|+|||+|.+.++|.+|++.|||+.|+|++|.|.|.|
T Consensus        38 ~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~---~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~sP  104 (104)
T d1jmta_          38 EFFEEVFTEMEEKYGEVEEMNVCDNL-GDHL---VGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP  104 (104)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEEECCSS-SSSS---EEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEECC
T ss_pred             hhhHHHHHHHhccCCCEEEEEeecCC-CCCE---eeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEECC
Confidence            33456799999999999999998775 5554   7899999999999999999999999999999999976

>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=99.49  E-value=6.4e-15  Score=110.98  Aligned_cols=69  Identities=23%  Similarity=0.262  Sum_probs=61.9

Q ss_pred             ceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEEE
Q 009944          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (522)
Q Consensus       175 ~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~v  253 (522)
                      ++|||+|||+++|+++|+++|++||.            |..+.+. ..|||||+|.+.++|+.|| .|++..|.|+.|+|
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~------------v~~~~i~-~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v   67 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGD------------VCYADVY-RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGET   67 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSC------------EEEEEEC-TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCC
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcc------------ccccccc-ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEE
Confidence            36999999999999999999999997            6666654 4599999999999999999 79999999999988


Q ss_pred             ecC
Q 009944          254 RRP  256 (522)
Q Consensus       254 ~~~  256 (522)
                      .+.
T Consensus        68 ~~~   70 (87)
T d3begb1          68 AYI   70 (87)
T ss_dssp             CBC
T ss_pred             eEE
Confidence            764

>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=99.49  E-value=6.9e-15  Score=110.77  Aligned_cols=76  Identities=17%  Similarity=0.134  Sum_probs=64.6

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceEE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~~  252 (522)
                      ...|||+|||+++++++|+++|..||.+...      ..+.....+.++|||||+|.+.++|.+|+ +||+..|.|++|+
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~------~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~   82 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGS------VCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   82 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTT------CEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeE------EEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEE
Confidence            3469999999999999999999999876431      12344455677899999999999999999 6999999999999


Q ss_pred             Eec
Q 009944          253 VRR  255 (522)
Q Consensus       253 v~~  255 (522)
                      |..
T Consensus        83 v~l   85 (86)
T d2cqpa1          83 LVL   85 (86)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            974

>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=99.49  E-value=4.9e-14  Score=108.31  Aligned_cols=76  Identities=25%  Similarity=0.385  Sum_probs=63.1

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-------cCCCcEEEEEEeCHHHHHHHH-Hhc--C
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVEMRTVEEASNAM-ALD--G  243 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~-------~~~~g~afV~f~~~~~a~~a~-~~~--~  243 (522)
                      .++|||+|||..+|+++|+++|.+||+.           |..+.+       +.++|||||+|.+.++|..|+ .|+  +
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~-----------i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~   69 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEG-----------VLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGR   69 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTT-----------EEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCC
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCc-----------ceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCC
Confidence            3689999999999999999999999862           444544       456899999999999999999 565  4


Q ss_pred             ceecCceEEEecCCCCC
Q 009944          244 IIFEGVAVRVRRPTDYN  260 (522)
Q Consensus       244 ~~~~g~~~~v~~~~~~~  260 (522)
                      ..+.|+.|.|.|+++..
T Consensus        70 ~~~~g~~i~V~~A~p~~   86 (96)
T d2disa1          70 IQLWGHQIAVDWAEPEI   86 (96)
T ss_dssp             SCBTTBCCEEEESCSSC
T ss_pred             eEECCEEEEEEEcCCCC
Confidence            56689999999986543

>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=99.49  E-value=5.9e-14  Score=107.88  Aligned_cols=59  Identities=24%  Similarity=0.425  Sum_probs=54.6

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  514 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~  514 (522)
                      ++|+++|++||.|..|.|.+           |||||+|.+.++|.+||+.|||..|.|++|+|.|+.+..
T Consensus        31 ~~L~~~F~~~G~i~~~~i~r-----------g~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~   89 (98)
T d1wf2a_          31 SDVEAIFSKYGKIVGCSVHK-----------GFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK   89 (98)
T ss_dssp             HHHHHSSTTSSCEEEEEEET-----------EEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCC
T ss_pred             HHHHHHHhhcCCEEEEEEeC-----------CeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            38999999999999999943           899999999999999999999999999999999997654

>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=99.48  E-value=2.3e-14  Score=110.17  Aligned_cols=72  Identities=22%  Similarity=0.265  Sum_probs=63.9

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceecCceE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~~  251 (522)
                      ...+|||+|||+.+++++|+++|.+||.            |..+.+. .+|||||+|.+.++|++|| .||+..|.|+.|
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~------------v~~~~i~-~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i   80 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGD------------VCYADVQ-KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEG   80 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSC------------EEEEEEE-TTTEEEEEESSHHHHHHHHHHHSSEEEECTTS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcc------------ccccccc-ccceEEEEECCHHHHHHHHHHhCCCEeCCeEE
Confidence            4568999999999999999999999997            5566554 5799999999999999999 699999999999


Q ss_pred             EEecCC
Q 009944          252 RVRRPT  257 (522)
Q Consensus       252 ~v~~~~  257 (522)
                      +|.+..
T Consensus        81 ~v~~~~   86 (98)
T d1wg4a_          81 ETSYIR   86 (98)
T ss_dssp             CEEEEE
T ss_pred             EEEEEe
Confidence            998753

>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=99.46  E-value=3.5e-14  Score=107.04  Aligned_cols=78  Identities=22%  Similarity=0.217  Sum_probs=69.6

Q ss_pred             hhcccceeEEeCCCcc-CcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHH---hcCce
Q 009944          170 ATRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGII  245 (522)
Q Consensus       170 ~~~~~~~v~v~nlp~~-~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~---~~~~~  245 (522)
                      ..+.++.|||+|||.. +|++||.++|++||.            |..+.+...+++|||+|.+.++|..|+.   +++..
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~------------I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~   71 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGV------------ISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPAL   71 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSC------------EEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCE
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCC------------eEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCc
Confidence            3456789999999986 899999999999997            7888998999999999999999999993   47889


Q ss_pred             ecCceEEEecCCCC
Q 009944          246 FEGVAVRVRRPTDY  259 (522)
Q Consensus       246 ~~g~~~~v~~~~~~  259 (522)
                      +.|++|+|.+++.+
T Consensus        72 ~~gr~l~V~~s~~~   85 (89)
T d1x4da1          72 VFGKPVRVHLSQKY   85 (89)
T ss_dssp             ETTEECEEEEECCC
T ss_pred             cCCceEEEEECCCc
Confidence            99999999997644

>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=99.46  E-value=8.1e-15  Score=114.46  Aligned_cols=79  Identities=13%  Similarity=0.089  Sum_probs=65.4

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCceEE
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~~~  252 (522)
                      ...+|||+|||+++|+++|+++|..||.+...      ..+.....+.++|||||+|.+.++|++|+++++..|.|+.|.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~------~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~   80 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENA------VHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAF   80 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTT------EEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEE------EEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEE
Confidence            34679999999999999999999999875321      012222356789999999999999999999999999999999


Q ss_pred             EecCC
Q 009944          253 VRRPT  257 (522)
Q Consensus       253 v~~~~  257 (522)
                      |.++.
T Consensus        81 V~~~~   85 (103)
T d2cpya1          81 VHVVT   85 (103)
T ss_dssp             EEEEC
T ss_pred             EEECC
Confidence            98754

>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=99.45  E-value=2e-14  Score=110.82  Aligned_cols=77  Identities=23%  Similarity=0.332  Sum_probs=68.1

Q ss_pred             hcccceeEEeCCCcc-CcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHH---hcCcee
Q 009944          171 TRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIF  246 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~-~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~---~~~~~~  246 (522)
                      ....++|||+|||.. +|+++|.++|+.||.            |..+.+..++|||||+|.+.++|..|++   +++..|
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~------------V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~   82 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGK------------IKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWF   82 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSC------------CSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccc------------eeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceE
Confidence            345678999999985 899999999999997            6778888899999999999999999983   789999


Q ss_pred             cCceEEEecCCCC
Q 009944          247 EGVAVRVRRPTDY  259 (522)
Q Consensus       247 ~g~~~~v~~~~~~  259 (522)
                      .|+.|+|.+++.+
T Consensus        83 ~gr~l~V~~s~~~   95 (99)
T d1x4fa1          83 QGRCVKVDLSEKY   95 (99)
T ss_dssp             SSSCCEEEEECSC
T ss_pred             CCEEEEEEEcCCc
Confidence            9999999987544

>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=99.44  E-value=1e-14  Score=115.45  Aligned_cols=80  Identities=18%  Similarity=0.174  Sum_probs=66.6

Q ss_pred             hcccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCce
Q 009944          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (522)
Q Consensus       171 ~~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~  250 (522)
                      .....+|||+|||+++|+++|+++|..||.+...      ..+.....+..+|||||+|.+.++|.+|+++|+..|+|+.
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~------~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~   88 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDS------IYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRF   88 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTT------CEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSC
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccc------eeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEE
Confidence            3456689999999999999999999999875421      1233334567789999999999999999999999999999


Q ss_pred             EEEecC
Q 009944          251 VRVRRP  256 (522)
Q Consensus       251 ~~v~~~  256 (522)
                      |.|..+
T Consensus        89 i~V~~~   94 (112)
T d1wela1          89 IQVHPI   94 (112)
T ss_dssp             BEEEEE
T ss_pred             EEEEEc
Confidence            999764

>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=99.44  E-value=7.4e-15  Score=114.26  Aligned_cols=78  Identities=28%  Similarity=0.156  Sum_probs=64.2

Q ss_pred             cccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEE--EecCCCcEEEEEEeCHHHHHHHHHhcCceecCc
Q 009944          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV--YINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (522)
Q Consensus       172 ~~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~--~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~  249 (522)
                      ....+|||+|||+++|+++|+++|..||.+.          |..+  ..+..+|||||+|.+.++|++|+++|+..|.|+
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~~~----------v~~~~~~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR   82 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNPMR----------VHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHR   82 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCSE----------EEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSS
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCcce----------eeeEEecCCcceEEEEEEECCHHHHHHHHHcCCCEECCE
Confidence            4456899999999999999999999986421          2222  234568999999999999999999999999999


Q ss_pred             eEEEecCCCC
Q 009944          250 AVRVRRPTDY  259 (522)
Q Consensus       250 ~~~v~~~~~~  259 (522)
                      .|+|.++...
T Consensus        83 ~I~V~~s~~~   92 (102)
T d1weza_          83 YVELFLNSTA   92 (102)
T ss_dssp             CCEEEEECCC
T ss_pred             EEEEEEcCCC
Confidence            9999876543

>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=99.44  E-value=3.4e-14  Score=111.78  Aligned_cols=77  Identities=17%  Similarity=0.167  Sum_probs=63.8

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCcee--cCc
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF--EGV  249 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~--~g~  249 (522)
                      ...+|||+|||+.+|+++|+++|++||.|.          -+.+...+++|||||+|.+.++|+.|+ .|++..|  .+.
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~----------~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~   75 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVL----------KIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACC   75 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEE----------EEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEE----------EEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCc
Confidence            345799999999999999999999999843          122334567899999999999999999 7999988  468


Q ss_pred             eEEEecCCCC
Q 009944          250 AVRVRRPTDY  259 (522)
Q Consensus       250 ~~~v~~~~~~  259 (522)
                      +|+|.+++..
T Consensus        76 ~l~v~~s~~~   85 (108)
T d2adba1          76 TLRIDFSKLT   85 (108)
T ss_dssp             CCEEEECSSC
T ss_pred             EEEEEecCCc
Confidence            8999886543

>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=99.42  E-value=9.6e-14  Score=109.82  Aligned_cols=77  Identities=14%  Similarity=0.135  Sum_probs=66.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcCh-HHHHHHHHHHcCCccCCeEEEEE
Q 009944          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP-AVTDIACAALNGLKMGDKTLTVR  369 (522)
Q Consensus       291 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~-~~A~~Al~~l~g~~~~g~~l~v~  369 (522)
                      ..++-.+||+|||..+|+++|+++|++||+|..|.|+.+      +|||||.|.+. ++|..|+..|++..+.++.+.|.
T Consensus         8 ~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~   81 (113)
T d1owxa_           8 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   81 (113)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             CCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEE
Confidence            344456899999999999999999999999999999854      68999999996 78999999999988877777777


Q ss_pred             EccC
Q 009944          370 RATA  373 (522)
Q Consensus       370 ~~~~  373 (522)
                      +...
T Consensus        82 ~~~~   85 (113)
T d1owxa_          82 WEVL   85 (113)
T ss_dssp             EEEC
T ss_pred             Eeec
Confidence            7643

>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=99.42  E-value=1.9e-13  Score=105.49  Aligned_cols=64  Identities=23%  Similarity=0.370  Sum_probs=57.2

Q ss_pred             CCCCeEEEc--CCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCcc
Q 009944          292 EGPDRVFVG--GLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM  361 (522)
Q Consensus       292 ~~~~~l~v~--nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~  361 (522)
                      .+..+|+|.  |||..+|+++|+++|++||.|..|.+..+      +|||||+|.+.++|.+|+..|||..+
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            345678885  59999999999999999999999988764      57999999999999999999999877

>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=99.41  E-value=1.1e-13  Score=107.38  Aligned_cols=76  Identities=9%  Similarity=0.008  Sum_probs=66.5

Q ss_pred             ccceeEEeCCCccC-c----HHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCcee
Q 009944          173 HARRVYVGGLPPLA-N----EQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (522)
Q Consensus       173 ~~~~v~v~nlp~~~-t----~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~  246 (522)
                      ...+|||+||+..+ +    +++|.++|+.||.            |+++.+.++++||||+|.+.++|.+|+ .|||..|
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~------------i~~~~~~k~~~~afV~f~~~~~A~~Ai~~lng~~~   71 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDK------------DTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEF   71 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCS------------SCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhccccc------------ceEEEEecCCCEEEEEECCHHHHHHHHHHhccccc
Confidence            35689999999986 3    3568899999987            677888899999999999999999999 6999999


Q ss_pred             cCceEEEecCCCCC
Q 009944          247 EGVAVRVRRPTDYN  260 (522)
Q Consensus       247 ~g~~~~v~~~~~~~  260 (522)
                      .|++|+|.|++...
T Consensus        72 ~g~~l~v~~a~~~~   85 (104)
T d1weya_          72 LGKEMKLYFAQTLH   85 (104)
T ss_dssp             TTEECEEECCCCSS
T ss_pred             CCCEeEEeecccCC
Confidence            99999999986544

>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=99.40  E-value=3.9e-13  Score=103.31  Aligned_cols=80  Identities=18%  Similarity=0.359  Sum_probs=68.2

Q ss_pred             CCCCeEEEcCC--CCCC---------CHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCc
Q 009944          292 EGPDRVFVGGL--PYYF---------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK  360 (522)
Q Consensus       292 ~~~~~l~v~nL--p~~~---------t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~  360 (522)
                      ...++|+|.||  |.++         .+++|++.|++||.|..|.+..+    ..+|+|||+|.+.++|.+|+..|||..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            34578999999  5443         23689999999999999988754    467999999999999999999999999


Q ss_pred             cCCeEEEEEEccCCC
Q 009944          361 MGDKTLTVRRATASS  375 (522)
Q Consensus       361 ~~g~~l~v~~~~~~~  375 (522)
                      |+|++|.|.|+..+.
T Consensus        82 ~~gr~i~v~~~~g~~   96 (99)
T d2dita1          82 FGGRQITAQAWDGTT   96 (99)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCEEEEEEEeCCcC
Confidence            999999999987653

>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=99.39  E-value=6.7e-14  Score=101.29  Aligned_cols=59  Identities=17%  Similarity=0.272  Sum_probs=54.1

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEE
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVN  506 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~  506 (522)
                      ++|+++|++||.|..+.+..+..++..   +|+|||+|.+.++|.+|++.|||..|+|+.|+
T Consensus        13 ~~l~~~F~~~G~v~~~~~~~~~~~~~~---~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1          13 QDLVKLCQPYGKIVSTKAILDKTTNKC---KGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             HHHHTTSTTTSCEEEEEEECCSSSCSC---CSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             HHHHHHHhhhccccccccccccccccc---cceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            499999999999999999998877654   78999999999999999999999999999874

>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=99.35  E-value=4e-13  Score=104.41  Aligned_cols=80  Identities=11%  Similarity=0.206  Sum_probs=68.3

Q ss_pred             CCCeEEEcCC--CCCCC--------HHHHHHHHHhcCCceEEEEeeCCCCC--CcceEEEEEEcChHHHHHHHHHHcCCc
Q 009944          293 GPDRVFVGGL--PYYFT--------ETQIKELLESFGTLHGFDLVKDRDTG--NSKGYGFCVYQDPAVTDIACAALNGLK  360 (522)
Q Consensus       293 ~~~~l~v~nL--p~~~t--------~~~l~~~F~~~G~i~~v~~~~~~~~g--~~~g~afV~f~~~~~A~~Al~~l~g~~  360 (522)
                      ++++|.|.||  |..+.        .+||++.|++||.|..|.|+++..+.  ...|++||+|.+.++|.+|+..|||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            3568999999  44432        36799999999999999998865443  346899999999999999999999999


Q ss_pred             cCCeEEEEEEcc
Q 009944          361 MGDKTLTVRRAT  372 (522)
Q Consensus       361 ~~g~~l~v~~~~  372 (522)
                      |+|+.|.|.|+.
T Consensus        83 f~gR~v~v~f~~   94 (104)
T d1o0pa_          83 FANRVVVTKYCD   94 (104)
T ss_dssp             SSSSCCEEEEEC
T ss_pred             ECCeEEEEEEcC
Confidence            999999999984

>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=99.34  E-value=1.1e-12  Score=102.28  Aligned_cols=68  Identities=13%  Similarity=0.157  Sum_probs=59.3

Q ss_pred             HHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCCcccc
Q 009944          445 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYF  516 (522)
Q Consensus       445 ~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~~~~~  516 (522)
                      ++|+++|..||.|..+.++.+..++.+   +|+|||+|.++++|.+|++ ||+..|+||.|.|.++...+..
T Consensus        30 ~dI~~~F~~~g~v~~~v~~~~~~~~~~---kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~~~~~~   97 (104)
T d1wg5a_          30 EEIVQFFSGLEIVPNGMTLPVDFQGRS---TGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVR   97 (104)
T ss_dssp             HHHHHHTTTCCEEEEEEECCBCSSSCB---CSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEECTTTSC
T ss_pred             HHHHHHHHhcCCceEEEEEEeCCCCCc---ceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECCHHHhc
Confidence            599999999999998766666656654   7899999999999999996 8999999999999999887654

>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=99.34  E-value=1.4e-12  Score=95.66  Aligned_cols=70  Identities=19%  Similarity=0.275  Sum_probs=61.7

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHHhcCceecCce-EE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA-VR  252 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~-~~  252 (522)
                      .+.|+|.|+|++++++.| ++|.+||.            |.++.++..+|||||+|.+.++|++||++||..|.|+. |.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~------------I~~~~~~~~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vg   70 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGN------------ILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIG   70 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSC------------EEEEEECSSSSEEEEEESSHHHHHHHHTTTTCEETTTEECE
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhh------------hheEEecCCCCEEEEEEcccHHHHHHHhcCCCeECCcEEEE
Confidence            467999999999997555 68999997            78889999999999999999999999999999999985 56


Q ss_pred             EecC
Q 009944          253 VRRP  256 (522)
Q Consensus       253 v~~~  256 (522)
                      |...
T Consensus        71 V~~~   74 (81)
T d1wwha1          71 VKPC   74 (81)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            7754

>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=99.31  E-value=1.2e-12  Score=95.97  Aligned_cols=71  Identities=15%  Similarity=0.199  Sum_probs=60.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeE-EEEEEccC
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT-LTVRRATA  373 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~-l~v~~~~~  373 (522)
                      +.|+|.|||++++++.| .+|++||.|.++.+..      .+|||||+|.+.++|++||+ +||..|+|+. |.|..+..
T Consensus         5 ~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           5 TWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             cEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            47999999999986555 6899999999998643      46899999999999999996 9999999975 67888754

>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=99.28  E-value=3.5e-12  Score=98.17  Aligned_cols=64  Identities=19%  Similarity=0.254  Sum_probs=57.5

Q ss_pred             cccceeEEeC--CCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHH-HhcCceec
Q 009944          172 RHARRVYVGG--LPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (522)
Q Consensus       172 ~~~~~v~v~n--lp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~-~~~~~~~~  247 (522)
                      .+.++|+|.|  ||..+|+++|+++|.+||.            |..+.+..+++||||+|.+.++|..|+ +|||..+.
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~------------i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGL------------VDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSC------------EEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCc------------ccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            4457888855  9999999999999999997            788888899999999999999999999 79998873

>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=99.16  E-value=6.5e-12  Score=99.04  Aligned_cols=70  Identities=11%  Similarity=0.050  Sum_probs=60.8

Q ss_pred             cceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCH-HHHHHHH-HhcCceecCceE
Q 009944          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTV-EEASNAM-ALDGIIFEGVAV  251 (522)
Q Consensus       174 ~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~-~~a~~a~-~~~~~~~~g~~~  251 (522)
                      ...+||+|||+.+|+++|+++|.+||+            |..+.+...+|||||.|.+. ++|..|+ .+++..+.++.+
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~------------V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~   78 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGE------------IKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNK   78 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCC------------EEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCC------------hheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCce
Confidence            346799999999999999999999997            88899999999999999995 7788888 799988877766


Q ss_pred             EEec
Q 009944          252 RVRR  255 (522)
Q Consensus       252 ~v~~  255 (522)
                      .|.+
T Consensus        79 ~v~~   82 (113)
T d1owxa_          79 EVTW   82 (113)
T ss_dssp             SEEE
T ss_pred             EEEE
Confidence            6654

>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=98.34  E-value=1.6e-06  Score=58.27  Aligned_cols=67  Identities=15%  Similarity=0.144  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEeCC
Q 009944          440 YEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  512 (522)
Q Consensus       440 ~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~~~  512 (522)
                      ..++.+-|...|.++|.|.++.|.... +|.     -.|-|...+..+|..|+..|+-+.||+++|.|+|++-
T Consensus         6 ~kelqq~L~~~f~~h~~V~sv~l~~~~-dg~-----~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1           6 RKELQQLLQEAFARHGKVKSVELSPHT-DYQ-----LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHHHHHHSCEEEEEECSCC-STT-----CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHHHHHHhheeEEEEEEEecc-CCc-----EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            456778899999999999999986643 333     4789999999999999999999999999999999873

>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=97.92  E-value=1.1e-05  Score=57.04  Aligned_cols=57  Identities=23%  Similarity=0.421  Sum_probs=50.7

Q ss_pred             HHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccCCeEEEEEEe
Q 009944          442 EILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  510 (522)
Q Consensus       442 ~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~Gr~l~v~~~  510 (522)
                      .++.+|.+.|..||+|.-|++..           +..+|+|.+-+.|.+|+. |+|..+.|++|+|+.-
T Consensus        36 ~l~~~Llq~l~~~GeViLvRFv~-----------d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          36 DLRTELMQTLGSYGTIVLVRINQ-----------GQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHHHHSCCSEEEEET-----------TEEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             HHHHHHHHHHhhCCeEEEEEEeC-----------CeEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            35578999999999999999976           467999999999999998 8999999999999853

>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=97.70  E-value=0.00014  Score=48.72  Aligned_cols=61  Identities=18%  Similarity=0.192  Sum_probs=52.8

Q ss_pred             HHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          309 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       309 ~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      +.|.+.|.++|.|..+.+.... .|..  .|-|...+.++|..|+..||..+|+++.|.|.+++
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-STTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            4577889999999999887653 3443  59999999999999999999999999999999985

>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=97.39  E-value=0.00017  Score=50.87  Aligned_cols=55  Identities=15%  Similarity=0.294  Sum_probs=49.3

Q ss_pred             HHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHcCCccCCeEEEEEEcc
Q 009944          309 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (522)
Q Consensus       309 ~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (522)
                      .+|.+.|..||.|.-|+++.+        ...|+|.+-++|.+|+. ++|.++.|+.|+|....
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCC
Confidence            478899999999999999876        48999999999999988 99999999999998653

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.33  E-value=0.00058  Score=49.16  Aligned_cols=77  Identities=14%  Similarity=0.177  Sum_probs=62.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCC--cceEEEEEEcChHHHHHHHHHHcCCccC---C--eEEE
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTDIACAALNGLKMG---D--KTLT  367 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~--~~g~afV~f~~~~~A~~Al~~l~g~~~~---g--~~l~  367 (522)
                      ++|.|+.||+..||+++.+.+...|.+........+.+..  .-.-|||.|.+.++.....+.++|..|-   |  .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            4799999999999999999999999998888777654432  2356999999999999999999998872   2  2345


Q ss_pred             EEEc
Q 009944          368 VRRA  371 (522)
Q Consensus       368 v~~~  371 (522)
                      |.+|
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            6665

>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=96.19  E-value=0.013  Score=41.92  Aligned_cols=55  Identities=22%  Similarity=0.441  Sum_probs=45.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCceEEEEeeCCCCCCcceEEEEEEcChHHHHHHHHHHc
Q 009944          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  357 (522)
Q Consensus       295 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~~~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  357 (522)
                      ..||.-.+|..+...||.++|++||.|. |..+.+  |     -|||...+.++|..++..+.
T Consensus        16 dHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd--T-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          16 DHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD--T-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET--T-----EEEEECSCHHHHHHHHHHHH
T ss_pred             ceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC--c-----eEEEEecCHHHHHHHHHHhc
Confidence            3599999999999999999999999985 344443  2     59999999999999887654

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.46  E-value=0.16  Score=35.90  Aligned_cols=80  Identities=10%  Similarity=0.073  Sum_probs=57.4

Q ss_pred             EEEeeCCCCcCcCCChHHHHHHHHHHHHHhhccCCeEEEEecCCCCCCCCCCCccEEEEEecChHhHHHHHHHHhCCccC
Q 009944          422 VLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG  501 (522)
Q Consensus       422 v~~l~~~~~~~~l~~~~~~~~~~~~l~~~f~~~G~I~~v~i~~~~~~g~~~~g~G~afV~F~~~~~A~~Ai~~lng~~~~  501 (522)
                      |-.|+..++++             ++.+.+++.|.+........+....+ .....|||.|.+.++...-.+..+|+.|-
T Consensus         6 vRrLPP~Lte~-------------~F~~~l~~~~~~d~~~f~~Gk~s~~~-~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           6 IRRLPPTLTKE-------------QLQEHLQPMPEHDYFEFFSNDTSLYP-HMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             EEEECTTCCHH-------------HHHHHHCSCCCEEEEEEEESCCSSTT-CCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             EecCCCCCCHH-------------HHHHHhCCcCceEEEEEeCCCcCCCC-CcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            34477777765             66777788898888766554434332 33467999999999999999999999983


Q ss_pred             C-----eEEEEEEeCCccc
Q 009944          502 G-----NTVNAFYYPEDKY  515 (522)
Q Consensus       502 G-----r~l~v~~~~~~~~  515 (522)
                      +     -+-.|+|++-.+.
T Consensus        72 D~~g~~~~a~VE~AP~qkv   90 (91)
T d1uw4a_          72 DNKGQEYPAIVEFAPFQKA   90 (91)
T ss_dssp             CTTCCEEECEEEECSSCCC
T ss_pred             cCCCCEeeeEEEEcCcccc
Confidence            2     2446788876553

>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=87.94  E-value=0.39  Score=34.06  Aligned_cols=54  Identities=17%  Similarity=0.180  Sum_probs=43.7

Q ss_pred             ccceeEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEEeCHHHHHHHHH
Q 009944          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA  240 (522)
Q Consensus       173 ~~~~v~v~nlp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~a~~  240 (522)
                      ....||.-.+|......||.++|+.||.|.          |.=+    +.--|||...+.++|+.++.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~----------VswI----ddTSa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ----------ISWI----DDTSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCC----------CEEE----ETTEEEEECSCHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceE----------EEEe----cCceEEEEecCHHHHHHHHH
Confidence            345799999999999999999999998752          2222    22379999999999999884