Citrus Sinensis ID: 009954

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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
MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccEEEEEccccccHHHHHHHHHHHHHHHccccccccccEEEEEEEcccccEEEEEEccHHHHHHHHHccccEEccEEEEEccccccccccccccccccccccccHHHHccccccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEEccccccccEEEEEEEccHHHHHHHHHHHcccccccEEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEccccccccccccHHHHHHHHHHHHHHHccccEEEEEEcccccccccccccEEEEEEEccHHHHHHHHHHHcccEEcccEEEEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccHHcccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHHHHHcccccccccEEEEEEEcccccEEEEEEEcHHHHHHHHHcccEEEcccEEEEEcccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHHcccEEccEEcEEEEcccccHHcccccccccccccHHHHHHHHcccccccccccccccccccccEEEEEcccccHHHHccHHHHHHHHHHHHHHHHHcccEEEEEEcccccccccccccEEEEEEEccHHHHHHHHHHHccccccccEEEEEEEcHHHHccccccc
Coil and Loop (DISEMBL)
msgrdirydavgegsrhksswvsgrsrtgergrdrhhrdfksggddrrrdknykydregirdhdrtdrhrdynrdkerrhrhrsrshssdrfrnrskslspsrspskskrrsgfdmappaaamlpgaavpgqlpgvpsavpemaqnmlpfgatqlgafplmpvQVMTQQATRHARRvyvgglpplanEQAIATFFSQVMTaiggnsagpgdAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAvrvrrptdynptlaaalgpgqpspnlnLAAVGLasgaiggaegpdrvfvgglpyyfTETQIKELLESFgtlhgfdlvkdrdtgnskgygfcvyqdpavtDIACAALNglkmgdktLTVRRatasgqsktEQESILAQAQQHIAIQKMALQTsgmntlgggmslFGETLAKVLCLTEAITadaladdeEYEEILEDMREECgkygtlvnvviprpdqnggetpgvgKVFLEYYDAvgcataknalsgrkfggntvnafyypedkyfnkdysa
Flexible Loop (DISEMBL)
msgrdirydavgegsrhksswvsgrsrtgergrdrhhrdfksggddrrrdknykydregirdhdrtdrhrdynrdkerrhrhrsrshssdrfrnrskslspsrspskskrrsgFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNvviprpdqnggeTPGVGKVFLEYYDAVGCATAknalsgrkfggntvnafyypedkyfnkdysa
Low Complexity Region (SEG)
MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGddrrrdknykydrEGIrdhdrtdrhrdynrdKErrhrhrsrshssdrfrnrskslspsrspskskrrsGFDmappaaamlpgaavpgQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESilaqaqqhiaiqKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITadaladdeeyeeiledmreeCGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA
Disordered region (IsUnstruct)
**************************************************************************************************************************************************MLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM*************GIIFEGVAVRVRRPTDYNPTLAAAL********LNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT***********************HIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADAL*******************YGTLVNVVIP********TPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYF******
Disordered Region (DISOPRED)
*******************************************************************************************************************************************************************************RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVR******************************************VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR*****************************************SLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNK*Y**
Disordered Region (DISEMBL)
***********************************************RRDKNYKYDREGIRDHDRTDRHRDYN*****************************************DMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR****************AQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA
Disordered Region (DISPRO)
****************************************************************************************************************GFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLA**********NLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQ*****ESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFN*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA
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	521	2.2.26 [Sep-21-2011]
Q9ZR40	573	Splicing factor U2af larg	N/A	no	0.758	0.689	0.692	1e-166
Q9ZR39	555	Splicing factor U2af larg	N/A	no	0.761	0.715	0.689	1e-166
Q8L716	589	Splicing factor U2af larg	yes	no	0.756	0.668	0.686	1e-162
Q2QKB4	543	Splicing factor U2af larg	N/A	no	0.775	0.744	0.667	1e-153
O23212	573	Splicing factor U2af larg	no	no	0.767	0.698	0.660	1e-153
Q2QZL4	548	Splicing factor U2af larg	yes	no	0.756	0.718	0.666	1e-151
Q2R0Q1	574	Splicing factor U2af larg	no	no	0.721	0.655	0.637	1e-141
Q2QKB3	591	Splicing factor U2af larg	N/A	no	0.796	0.702	0.562	1e-124
Q24562	416	Splicing factor U2AF 50 k	yes	no	0.666	0.834	0.396	1e-70
P26368	475	Splicing factor U2AF 65 k	yes	no	0.756	0.829	0.4	3e-68

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

 Score =  584 bits (1505), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 284/410 (69%), Positives = 328/410 (80%), Gaps = 15/410 (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 IACAALNGLKMGDKTLTVRRAT-ASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 409
           IACAALNG+KMGDKTLTVRRA   + Q K EQES+L  AQQ IA+Q++ LQ + + T   
Sbjct: 415 IACAALNGIKMGDKTLTVRRANQGTTQPKPEQESVLLHAQQQIALQRLMLQPATLAT--- 471

Query: 410 GMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGG 469
                     KVL LTE I+AD L DDE+Y++ILEDMR ECGK+G+LVNVVIPRP  NG 
Sbjct: 472 ----------KVLSLTEVISADELNDDEDYQDILEDMRTECGKFGSLVNVVIPRPSPNGE 521

Query: 470 ETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
            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|Q9ZR39|U2A2A_NICPL Splicing factor U2af large subunit A OS=Nicotiana plumbaginifolia GN=U2AF65A PE=2 SV=1

 Score =  584 bits (1505), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 284/412 (68%), Positives = 325/412 (78%), Gaps = 15/412 (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 IACAALNGLKMGDKTLTVRRAT-ASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 409
           IACAALNG+KMGDKTLTVRRA   + Q   EQES+L  AQQ IA+Q+  LQ   + T   
Sbjct: 397 IACAALNGIKMGDKTLTVRRANQGTTQPNPEQESVLLHAQQQIALQRFMLQPGALAT--- 453

Query: 410 GMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGG 469
                     KVLCLTE +T D L DD++Y++ILEDMR EC K+G LVNVVIPRP+ NG 
Sbjct: 454 ----------KVLCLTEVVTVDELNDDDDYQDILEDMRTECEKFGALVNVVIPRPNPNGV 503

Query: 470 ETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 521
            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|Q8L716|U2A2B_ARATH Splicing factor U2af large subunit B OS=Arabidopsis thaliana GN=U2AF65B PE=2 SV=2

 Score =  573 bits (1477), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 282/411 (68%), Positives = 322/411 (78%), Gaps = 17/411 (4%)

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 DIACAALNGLKMGDKTLTVRRATASG-QSKTEQESILAQAQQHIAIQKMALQTSGMNTLG 408
           DIACAALNG+KMGDKTLTVRRA     Q K EQE +L  AQQ IA+Q++  Q  G     
Sbjct: 430 DIACAALNGIKMGDKTLTVRRAIQGAIQPKPEQEEVLLYAQQQIALQRLMFQPGG----- 484

Query: 409 GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG 468
                   T  K++CLT+ +TAD L DDEEY EI+EDMR+E GK+G LVNVVIPRP+ + 
Sbjct: 485 --------TPTKIVCLTQVVTADDLRDDEEYAEIMEDMRQEGGKFGNLVNVVIPRPNPDH 536

Query: 469 GETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
             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 =  543 bits (1400), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 283/424 (66%), Positives = 325/424 (76%), Gaps = 20/424 (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 GFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT-ASGQSKTEQESILAQAQQHIAIQKM 397
            FCVYQD  VTDIACAALNG+KMGDKTLTVRRA   S Q + EQE+IL QAQQ + +QK+
Sbjct: 371 AFCVYQDLNVTDIACAALNGIKMGDKTLTVRRANQGSAQPRPEQENILLQAQQQVQLQKL 430

Query: 398 ALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLV 457
             Q   + T             KV+CLT+ +TAD L DDEEYE+I+EDMR E GKYG LV
Sbjct: 431 VYQVGALPT-------------KVVCLTQVVTADELKDDEEYEDIMEDMRLEAGKYGNLV 477

Query: 458 NVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNK 517
            VVIPRP  +G    GVGKVFLEY D  G   AK A+ GRKFGGN V A +YPE+K+ ++
Sbjct: 478 KVVIPRPHPSGEPVSGVGKVFLEYADVDGSTKAKTAMHGRKFGGNPVVAVFYPENKFADE 537

Query: 518 DYSA 521
           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 =  541 bits (1394), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 276/418 (66%), Positives = 318/418 (76%), Gaps = 18/418 (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 DPAVTDIACAALNGLKMGDKTLTVRRAT-ASGQSKTEQESILAQAQQHIAIQKMALQTSG 403
           D +VTDIACAALNG+KMGDKTLTVRRA   +   K EQE++L  AQQ IA Q++ LQ   
Sbjct: 409 DLSVTDIACAALNGIKMGDKTLTVRRANQGTMLQKPEQENVLLHAQQQIAFQRVMLQPGA 468

Query: 404 MNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPR 463
           + T              V+CLT+ +T D L DDEEY +I+EDMR+E GK+G L NVVIPR
Sbjct: 469 VATT-------------VVCLTQVVTEDELRDDEEYGDIMEDMRQEGGKFGALTNVVIPR 515

Query: 464 PDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 521
           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 =  535 bits (1379), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 276/414 (66%), Positives = 318/414 (76%), Gaps = 20/414 (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 TDIACAALNGLKMGDKTLTVRRAT-ASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTL 407
           TDIACAALNG+KMGDKTLTVRRA   + Q + EQESIL QAQQ + +QK+  Q   + T 
Sbjct: 388 TDIACAALNGIKMGDKTLTVRRANQGAAQPRPEQESILLQAQQQVQLQKLVYQVGALPT- 446

Query: 408 GGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQN 467
                       KV+CLT+ ++AD L DDEEYE+I+EDMR E GKYG L+ VVIPRPD +
Sbjct: 447 ------------KVVCLTQVVSADELKDDEEYEDIMEDMRLEAGKYGNLIKVVIPRPDPS 494

Query: 468 GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 521
           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 =  503 bits (1296), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 248/389 (63%), Positives = 288/389 (74%), Gaps = 13/389 (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 T-ASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITA 430
              + Q + EQES+L   QQ   +QK+  Q  G           G    KV+CLT+ ++ 
Sbjct: 435 NQGASQPRPEQESMLLHVQQQAQMQKLMFQVGG-----------GALPTKVVCLTQVVSP 483

Query: 431 DALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATA 490
           D L DDEEYE+I++DMREE  +YG LV VVIPRPD +G    GVG+VFLE+ D      A
Sbjct: 484 DELRDDEEYEDIVQDMREEGCRYGNLVKVVIPRPDPSGAPVAGVGRVFLEFADVESSTKA 543

Query: 491 KNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
           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 =  444 bits (1143), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 249/443 (56%), Positives = 296/443 (66%), Gaps = 28/443 (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 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESIL 385
           +VKD++TGNSKGY FC+Y+D  VTDIACAALNG+++GD+TLTVRRA    + + EQE+IL
Sbjct: 423 IVKDKETGNSKGYAFCLYKDGTVTDIACAALNGIQLGDRTLTVRRANQGAEPRPEQENIL 482

Query: 386 AQAQQHIAIQKMALQTSGMNTLGGGMSLFGETL-AKVLCLTEAITADALADDEEYEEILE 444
            QAQQ   ++++  +              G TL  KV+CLT+ ++AD L DDEEY +ILE
Sbjct: 483 LQAQQEAQMKRLVYEV-------------GRTLTTKVVCLTQVVSADDLRDDEEYNDILE 529

Query: 445 DMREECGKY---GTLVNVVIPRP 464
           DM  E  KY    T+    I RP
Sbjct: 530 DMTLEGHKYVPHSTIAESFIIRP 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 =  267 bits (683), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 156/393 (39%), Positives = 220/393 (55%), Gaps = 46/393 (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 VRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGM-NTLGGGMSLFGETLAKVLCLTE 426
           V+RA+   ++     +           Q + LQ  G+ N +  G         +VLCL  
Sbjct: 280 VQRASVGAKNAQNAAN---------TTQSVMLQVPGLSNVVTSGPP------TEVLCLLN 324

Query: 427 AITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVG 486
            +T D L D+EEYE+ILED++EEC KYG + +V IPRP + G E PG GKVF+E+   + 
Sbjct: 325 MVTPDELRDEEEYEDILEDIKEECTKYGVVRSVEIPRPIE-GVEVPGCGKVFVEFNSVLD 383

Query: 487 CATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
           C  A+ AL+GRKF    V   Y+  DKY  +++
Sbjct: 384 CQKAQQALTGRKFSDRVVVTSYFDPDKYHRREF 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 =  259 bits (662), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 168/420 (40%), Positives = 234/420 (55%), Gaps = 26/420 (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 FCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMAL 399
           FC Y D  VTD A A LNG+++GDK L V+RA+   ++ T         Q  + +Q   L
Sbjct: 304 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATLVSPPSTINQTPVTLQVPGL 363

Query: 400 QTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNV 459
            +S +  +GG  +       +VLCL   +  + L DDEEYEEI+ED+R+EC KYG + ++
Sbjct: 364 MSSQVQ-MGGHPT-------EVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSI 415

Query: 460 VIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
            IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct: 416 EIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 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	521
388520789	527	unknown [Lotus japonicus]	0.932	0.922	0.654	1e-178
359497050	410	PREDICTED: splicing factor U2af large su	0.702	0.892	0.749	1e-172
156070760	553	unknown [Solanum melongena]	0.829	0.781	0.659	1e-165
188998293	554	U2 snRNP auxiliary factor large subunit	0.829	0.779	0.659	1e-165
75338884	573	RecName: Full=Splicing factor U2af large	0.758	0.689	0.692	1e-164
75338883	555	RecName: Full=Splicing factor U2af large	0.761	0.715	0.689	1e-164
156070776	551	unknown [Capsicum frutescens]	0.761	0.720	0.684	1e-164
156070797	558	unknown [Solanum bulbocastanum]	0.758	0.707	0.686	1e-162
297840477	589	hypothetical protein ARALYDRAFT_475241 [	0.756	0.668	0.690	1e-162
356509477	600	PREDICTED: splicing factor U2af large su	0.758	0.658	0.689	1e-162

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

 Score =  630 bits (1625), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 328/501 (65%), Positives = 389/501 (77%), Gaps = 15/501 (2%)

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 LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTE 380
           L  FDLV+D++TGNSKGYGFC+YQDPAVTD+ACA+LNGLK+GDKTLTVRRAT SG SKTE
Sbjct: 325 LRSFDLVRDKETGNSKGYGFCIYQDPAVTDMACASLNGLKVGDKTLTVRRATVSGHSKTE 384

Query: 381 QESILAQAQQHIAIQKMALQTSGMNTLGGGM--SLFGETLAKVLCLTEAITADALADDEE 438
           QE I AQAQQ+I +QK+AL+  G+N  G     +   E+  KVLCLTEAIT D L D+ E
Sbjct: 385 QEHIFAQAQQNITMQKVALEVVGLNIPGVERVPTTIDESATKVLCLTEAITTDELMDNGE 444

Query: 439 YEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRK 498
           YEEI+EDMR+ECGK+GTL+NVVIPRP+ +G +TPG+GKVFLEY D      AK+AL+GRK
Sbjct: 445 YEEIVEDMRDECGKFGTLMNVVIPRPNPSGEQTPGIGKVFLEYSDTAASFAAKSALNGRK 504

Query: 499 FGGNTVNAFYYPEDKYFNKDY 519
           FGGN V A+YYPE+K+ N ++
Sbjct: 505 FGGNMVTAYYYPEEKFHNMEF 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 =  612 bits (1579), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 308/411 (74%), Positives = 330/411 (80%), Gaps = 45/411 (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 ACAALNGLKMGDKTLTVRRATA-SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGG 410
           ACAALNGLKMGDKTLTVRRAT  SGQ+K+EQ++ILAQAQQHIAIQK+ALQ  G+N  G  
Sbjct: 284 ACAALNGLKMGDKTLTVRRATVGSGQAKSEQDNILAQAQQHIAIQKIALQAGGLNLPGA- 342

Query: 411 MSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGE 470
                                                      G LV+VVIPRP  NG  
Sbjct: 343 -------------------------------------------GALVHVVIPRPSPNGDL 359

Query: 471 TPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 521
            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 =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 302/458 (65%), Positives = 353/458 (77%), Gaps = 26/458 (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 TLTVRRATAS-GQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLC 423
           TLTVRRA     Q   EQES+L  AQQ IA+Q+  LQ   + T             K+LC
Sbjct: 407 TLTVRRANQGITQPNPEQESVLLHAQQQIALQRFMLQPGALAT-------------KILC 453

Query: 424 LTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYD 483
           LT+ ++ D L DD++Y++ILEDMR ECGK+G L+NVVIPRP+ NG  TPG+GKVFLEY D
Sbjct: 454 LTQVVSVDELKDDDDYQDILEDMRIECGKFGALLNVVIPRPNPNGEPTPGLGKVFLEYAD 513

Query: 484 AVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 521
               + 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 =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 302/458 (65%), Positives = 353/458 (77%), Gaps = 26/458 (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 TLTVRRATAS-GQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLC 423
           TLTVRRA     Q   EQES+L  AQQ IA+Q+  LQ   + T             K+LC
Sbjct: 408 TLTVRRANQGITQPNPEQESVLLHAQQQIALQRFMLQPGALAT-------------KILC 454

Query: 424 LTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYD 483
           LT+ ++ D L DD++Y++ILEDMR ECGK+G L+NVVIPRP+ NG  TPG+GKVFLEY D
Sbjct: 455 LTQVVSVDELKDDDDYQDILEDMRIECGKFGALLNVVIPRPNPNGEPTPGLGKVFLEYAD 514

Query: 484 AVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 521
               + 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|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 =  584 bits (1505), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 284/410 (69%), Positives = 328/410 (80%), Gaps = 15/410 (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 IACAALNGLKMGDKTLTVRRAT-ASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 409
           IACAALNG+KMGDKTLTVRRA   + Q K EQES+L  AQQ IA+Q++ LQ + + T   
Sbjct: 415 IACAALNGIKMGDKTLTVRRANQGTTQPKPEQESVLLHAQQQIALQRLMLQPATLAT--- 471

Query: 410 GMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGG 469
                     KVL LTE I+AD L DDE+Y++ILEDMR ECGK+G+LVNVVIPRP  NG 
Sbjct: 472 ----------KVLSLTEVISADELNDDEDYQDILEDMRTECGKFGSLVNVVIPRPSPNGE 521

Query: 470 ETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
            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|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 =  584 bits (1505), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 284/412 (68%), Positives = 325/412 (78%), Gaps = 15/412 (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 IACAALNGLKMGDKTLTVRRAT-ASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 409
           IACAALNG+KMGDKTLTVRRA   + Q   EQES+L  AQQ IA+Q+  LQ   + T   
Sbjct: 397 IACAALNGIKMGDKTLTVRRANQGTTQPNPEQESVLLHAQQQIALQRFMLQPGALAT--- 453

Query: 410 GMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGG 469
                     KVLCLTE +T D L DD++Y++ILEDMR EC K+G LVNVVIPRP+ NG 
Sbjct: 454 ----------KVLCLTEVVTVDELNDDDDYQDILEDMRTECEKFGALVNVVIPRPNPNGV 503

Query: 470 ETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 521
            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|156070776|gb|ABU45190.1| unknown [Capsicum frutescens]

 Score =  583 bits (1503), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 282/412 (68%), Positives = 328/412 (79%), Gaps = 15/412 (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 IACAALNGLKMGDKTLTVRRAT-ASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 409
           IACAALNG+KMGDKTLTVRRA   + Q   EQES+L  AQQ IA+Q+  LQ   + T   
Sbjct: 393 IACAALNGIKMGDKTLTVRRANQGTNQPNPEQESVLLHAQQQIALQRFMLQPGALAT--- 449

Query: 410 GMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGG 469
                     KVLCLT+ ++ D L DD++Y++ILEDMR ECGK+G+L+NVVIPRP+ +G 
Sbjct: 450 ----------KVLCLTQVVSVDELNDDDDYQDILEDMRVECGKFGSLLNVVIPRPNPSGE 499

Query: 470 ETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 521
            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 =  579 bits (1492), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 282/411 (68%), Positives = 326/411 (79%), Gaps = 16/411 (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 DIACAALNGLKMGDKTLTVRRAT-ASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG 408
           DIACAALNG+KMGDKTLTVRRA   + Q   EQES+L  AQQ IA+Q+  LQ   + T  
Sbjct: 399 DIACAALNGIKMGDKTLTVRRANQGTTQPNPEQESVLLHAQQQIALQRFMLQPGALAT-- 456

Query: 409 GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG 468
                      KVLCLTE ++ D L DD++Y++ILEDMR ECGK+G L+NVVIPRP+ NG
Sbjct: 457 -----------KVLCLTEVVSVDELKDDDDYQDILEDMRIECGKFGALLNVVIPRPNPNG 505

Query: 469 GETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
             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 =  578 bits (1489), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 284/411 (69%), Positives = 324/411 (78%), Gaps = 17/411 (4%)

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 DIACAALNGLKMGDKTLTVRRATASG-QSKTEQESILAQAQQHIAIQKMALQTSGMNTLG 408
           DIACAALNG+KMGDKTLTVRRA     Q K EQE +L  AQQ IA+Q++ LQ  G     
Sbjct: 430 DIACAALNGIKMGDKTLTVRRAIQGVIQPKPEQEEVLLHAQQQIALQRLMLQPGG----- 484

Query: 409 GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG 468
                   T  K++CLT+ +TAD L DDEEY +I+EDMR+E GK+G LVNVVIPRP+ + 
Sbjct: 485 --------TPTKIVCLTQVVTADDLRDDEEYADIMEDMRQEGGKFGNLVNVVIPRPNPDH 536

Query: 469 GETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
             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 =  577 bits (1486), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 286/415 (68%), Positives = 324/415 (78%), Gaps = 20/415 (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 VTDIACAALNGLKMGDKTLTVRRATASG---QSKTEQESILAQAQQHIAIQKMALQTSGM 404
           VTDIACAALNG+KMGDKTLTVRRA       Q K EQESIL  AQQ IA+QK+ LQ + +
Sbjct: 437 VTDIACAALNGIKMGDKTLTVRRANQGANPQQPKPEQESILMHAQQQIALQKLMLQPALV 496

Query: 405 NTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRP 464
            T             KV+CLT A+++D L DDE+YEEIL+DMR+EC K+GTLVNVVIPRP
Sbjct: 497 AT-------------KVVCLTHAVSSDELKDDEDYEEILDDMRQECSKFGTLVNVVIPRP 543

Query: 465 DQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
             +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	521
TAIR|locus:2206001	589	AT1G60900 [Arabidopsis thalian	0.756	0.668	0.618	2e-132
TAIR|locus:2115280	573	ATU2AF65A [Arabidopsis thalian	0.760	0.691	0.586	2.2e-122
UNIPROTKB|Q24JZ8	475	U2AF2 "Uncharacterized protein	0.650	0.713	0.385	3.3e-61
MGI|MGI:98886	475	U2af2 "U2 small nuclear ribonu	0.650	0.713	0.382	1.4e-60
RGD|1597319	475	LOC690372 "similar to U2 (RNU2	0.650	0.713	0.382	1.4e-60
UNIPROTKB|P26368	475	U2AF2 "Splicing factor U2AF 65	0.650	0.713	0.382	1.8e-60
UNIPROTKB|E2R0G3	471	U2AF2 "Uncharacterized protein	0.642	0.711	0.382	3.8e-60
FB|FBgn0005411	416	U2af50 "U2 small nuclear ribop	0.692	0.867	0.366	4.2e-59
ZFIN|ZDB-GENE-050706-131	470	u2af2a "U2 small nuclear RNA a	0.654	0.725	0.368	5.4e-59
ZFIN|ZDB-GENE-040426-1881	475	u2af2b "U2 small nuclear RNA a	0.644	0.707	0.368	3.4e-54

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

 Score = 1262 (449.3 bits), Expect = 2.0e-132, Sum P(2) = 2.0e-132
 Identities = 254/411 (61%), Positives = 290/411 (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 DIACAALNGLKMGDKTLTVRRATASG-QSKTEQESXXXXXXXXXXXXKMALQTSGMNTLG 408
             DIACAALNG+KMGDKTLTVRRA     Q K EQE             ++  Q  G  T  
Sbjct:   430 DIACAALNGIKMGDKTLTVRRAIQGAIQPKPEQEEVLLYAQQQIALQRLMFQPGGTPT-- 487

Query:   409 GGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVVIPRPDQNG 468
                        K++CLT+ +T                     GK+G LVNVVIPRP+ + 
Sbjct:   488 -----------KIVCLTQVVTADDLRDDEEYAEIMEDMRQEGGKFGNLVNVVIPRPNPDH 536

Query:   469 GETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
               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 = 1178 (419.7 bits), Expect = 2.2e-122, Sum P(2) = 2.2e-122
 Identities = 243/414 (58%), Positives = 278/414 (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 TDIACAALNGLKMGDKTLTVRRATASGQ-SKTEQESXXXXXXXXXXXXKMALQTSGMNTL 407
             TDIACAALNG+KMGDKTLTVRRA       K EQE+            ++ LQ   + T 
Sbjct:   413 TDIACAALNGIKMGDKTLTVRRANQGTMLQKPEQENVLLHAQQQIAFQRVMLQPGAVATT 472

Query:   408 GGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVVIPRPDQN 467
                          V+CLT+ +T                     GK+G L NVVIPRP  N
Sbjct:   473 -------------VVCLTQVVTEDELRDDEEYGDIMEDMRQEGGKFGALTNVVIPRPSPN 519

Query:   468 GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 521
             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 = 601 (216.6 bits), Expect = 3.3e-61, Sum P(2) = 3.3e-61
 Identities = 138/358 (38%), Positives = 193/358 (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 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESXXXXXXXXXXXXKMALQT 401
              Y D  VTD A A LNG+++GDK L V+RA+   ++ T                 + LQ 
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNAT-----LVSPLSTINQTPVTLQV 360

Query:   402 SGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVVI 461
              G+  +   + + G    +VLCL   +                     CGKYG + ++ I
Sbjct:   361 PGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECGKYGLVKSIEI 417

Query:   462 PRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
             PRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   418 PRP-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 = 595 (214.5 bits), Expect = 1.4e-60, Sum P(2) = 1.4e-60
 Identities = 137/358 (38%), Positives = 192/358 (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 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESXXXXXXXXXXXXKMALQT 401
              Y D  VTD A A LNG+++GDK L V+RA+   ++ T                 + LQ 
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNAT-----LVSLPSTINQTPVTLQV 360

Query:   402 SGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVVI 461
              G+  +   + + G    +VLCL   +                     C KYG + ++ I
Sbjct:   361 PGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEI 417

Query:   462 PRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
             PRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   418 PRP-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 = 595 (214.5 bits), Expect = 1.4e-60, Sum P(2) = 1.4e-60
 Identities = 137/358 (38%), Positives = 192/358 (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 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESXXXXXXXXXXXXKMALQT 401
              Y D  VTD A A LNG+++GDK L V+RA+   ++ T                 + LQ 
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNAT-----LVSLPSTINQTPVTLQV 360

Query:   402 SGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVVI 461
              G+  +   + + G    +VLCL   +                     C KYG + ++ I
Sbjct:   361 PGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEI 417

Query:   462 PRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
             PRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   418 PRP-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 = 594 (214.2 bits), Expect = 1.8e-60, Sum P(2) = 1.8e-60
 Identities = 137/358 (38%), Positives = 192/358 (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 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESXXXXXXXXXXXXKMALQT 401
              Y D  VTD A A LNG+++GDK L V+RA+   ++ T                 + LQ 
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNAT-----LVSPPSTINQTPVTLQV 360

Query:   402 SGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVVI 461
              G+  +   + + G    +VLCL   +                     C KYG + ++ I
Sbjct:   361 PGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEI 417

Query:   462 PRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
             PRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   418 PRP-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 = 591 (213.1 bits), Expect = 3.8e-60, Sum P(2) = 3.8e-60
 Identities = 137/358 (38%), Positives = 192/358 (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 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESXXXXXXXXXXXXKMALQT 401
              Y D  VTD A A LNG+++GDK L V+RA+   ++ T                 + LQ 
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNAT---------LSTINQTPVTLQV 356

Query:   402 SGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVVI 461
              G+  +   + + G    +VLCL   +                     C KYG + ++ I
Sbjct:   357 PGL--MSSQVQMGGHP-TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEI 413

Query:   462 PRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
             PRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y   D Y  +D+
Sbjct:   414 PRP-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 = 572 (206.4 bits), Expect = 4.2e-59, Sum P(2) = 4.2e-59
 Identities = 144/393 (36%), Positives = 201/393 (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 VRRATASGQSKTEQESXXXXXXXXXXXXKMALQTSGM-NTLGGGMSLFGETLAKVLCLTE 426
             V+RA+    +K  Q +             + LQ  G+ N +  G         +VLCL  
Sbjct:   280 VQRASVG--AKNAQNAANTTQS-------VMLQVPGLSNVVTSGPP------TEVLCLLN 324

Query:   427 AITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVG 486
              +T                    C KYG + +V IPRP + G E PG GKVF+E+   + 
Sbjct:   325 MVTPDELRDEEEYEDILEDIKEECTKYGVVRSVEIPRPIE-GVEVPGCGKVFVEFNSVLD 383

Query:   487 CATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
             C  A+ AL+GRKF    V   Y+  DKY  +++
Sbjct:   384 CQKAQQALTGRKFSDRVVVTSYFDPDKYHRREF 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 = 578 (208.5 bits), Expect = 5.4e-59, Sum P(2) = 5.4e-59
 Identities = 132/358 (36%), Positives = 191/358 (53%)

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 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESXXXXXXXXXXXXKMALQT 401
              Y D  ++D A A LNG+++GDK L V+RA+   ++ T                 + LQ 
Sbjct:   304 EYVDVNISDQAIAGLNGMQLGDKKLLVQRASVGSKNTT---------LTGINQTPVTLQV 354

Query:   402 SGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVVI 461
              G+  +   ++  G    +VLCL   +                     C KYG + ++ I
Sbjct:   355 PGL--MNSSVNQMGGIPTEVLCLMNMVAPEELLDDEEYEEIVEDVRDECSKYGQVKSIEI 412

Query:   462 PRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
             PRP  +G + PG GK+F+E+        A   L+GRKF    V   Y   D Y  +D+
Sbjct:   413 PRP-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

ZFIN|ZDB-GENE-040426-1881 u2af2b "U2 small nuclear RNA auxiliary factor 2b" [Danio rerio (taxid:7955)]

 Score = 560 (202.2 bits), Expect = 3.4e-54, P = 3.4e-54
 Identities = 132/358 (36%), Positives = 187/358 (52%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+++  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   139 PVPVVGSQMTRQARRLYVGNIPFGITEESMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 197

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+  ++++RRP DY P       PG  S N ++   
Sbjct:   198 KNFAFLEFRSVDETTQAMAFDGIIFQAQSLKIRRPHDYQPL------PGM-SENPSVYVP 250

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   251 GVVSTVV--PDSIHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 308

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESXXXXXXXXXXXXKMALQT 401
              Y D  V D A A LNG+++ DK L V+RA+   ++ T                 + LQ 
Sbjct:   309 EYVDVNVNDQAIAGLNGMQLADKKLLVQRASVGAKNAT---------MTSINETPVTLQV 359

Query:   402 SGMNTLGGGMSLFGETLAKVLCLTEAITXXXXXXXXXXXXXXXXXXXXCGKYGTLVNVVI 461
              G+ +    M   G    +VLCL   +                     C KYG + ++ I
Sbjct:   360 PGLTS--NPMIQMGGIPTEVLCLMNMVAPEELIDDEEYEEIVEDVKEECSKYGQVKSIEI 417

Query:   462 PRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
             PRP  +G + PG GK+F+E+        A   L+GRKF    V   Y   D Y  +D+
Sbjct:   418 PRP-VDGLDIPGTGKIFVEFTSVYDSQKAMQGLTGRKFANRVVVTKYCDPDAYHRRDF 474

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

---

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	0.7562	0.7189	yes	no
Q8L716	U2A2B_ARATH	No assigned EC number	0.6861	0.7562	0.6689	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	521
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-173
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	8e-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
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-13
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	3e-13
cd12648	98	cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 i	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
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-11
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	4e-11
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	7e-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
cd12647	96	cd12647, RRM_UHM_SPF45, RNA recognition motif in U	4e-10
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-10
smart00360	73	smart00360, RRM, RNA recognition motif	8e-10
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-09
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	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
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	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	3e-08
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	5e-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
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
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	1e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	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
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	4e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	5e-06
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	7e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	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
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-05
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	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
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-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
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
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	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
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	3e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	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
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	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
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	5e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	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
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	7e-05
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	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
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	8e-05
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	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
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-04
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	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
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-04
cd12329	75	cd12329, RRM2_hnRNPD_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
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	2e-04
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	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
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	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
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
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
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	7e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	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
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	9e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.001
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
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif 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
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	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
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	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
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 =  499 bits (1286), Expect = e-173
 Identities = 206/504 (40%), Positives = 259/504 (51%), Gaps = 30/504 (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 FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQS 377
           FG L  F+L+KD  TG SKGY FC Y+DP+VTD+A AALNG   GD  L V+RA      
Sbjct: 319 FGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQ 378

Query: 378 KT--EQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALAD 435
            T      +        A+ +  LQ              G    KV+ LT  +T D L D
Sbjct: 379 ATIDTSNGMAPVTLLAKALSQSILQI-------------GGKPTKVVQLTNLVTGDDLMD 425

Query: 436 DEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS 495
           DEEYEEI ED++ E  KYG L+N+VIPRP+ +   TPGVGKVFLEY D      A   ++
Sbjct: 426 DEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMN 485

Query: 496 GRKFGGNTVNAFYYPEDKYFNKDY 519
           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 =  130 bits (330), Expect = 7e-37
 Identities = 50/85 (58%), Positives = 64/85 (75%)

Query: 420 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFL 479
           +VLCL   +T + L DDEEYEEILED++EECGKYG +++VVIPRP+  G + PGVGKVF+
Sbjct: 2   RVLCLLNMVTPEELEDDEEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFV 61

Query: 480 EYYDAVGCATAKNALSGRKFGGNTV 504
           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 =  112 bits (282), Expect = 8e-27
 Identities = 122/551 (22%), Positives = 183/551 (33%), Gaps = 158/551 (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 SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV---RRATA 373
            FG +    L +D +TG SKG+GF  + D      A   +NG ++  + + V   + +T 
Sbjct: 209 PFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTY 268

Query: 374 SGQSKTEQESILAQAQQHIAI----------------QKMALQTSGMNTLGGGMSLFGE- 416
              +    E I  Q Q    +                    L   G  +    M      
Sbjct: 269 LLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRD 328

Query: 417 ----TLAKVLCLTEAITADAL------------------------ADDEE---YEEILED 445
                       T A+   A                         A +EE     EIL+D
Sbjct: 329 GIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDD 388

Query: 446 MREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVN 505
           ++EEC KYG +V++ +   +         GK++L++        A  AL+GR FGG  + 
Sbjct: 389 VKEECSKYGGVVHIYVDTKNSA-------GKIYLKFSSVDAALAAFQALNGRYFGGKMIT 441

Query: 506 AFYYPEDKYFN 516
           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: 421 VLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLE 480
           VL L   +    L ++EEYE+I+ED++EEC KYG +V+++IP+      E PG G+VF+E
Sbjct: 5   VLRLLNVLDDAHLQNEEEYEDIIEDIKEECQKYGPVVSLLIPK------ENPGKGQVFVE 58

Query: 481 YYDAVGCATAKNALSGRKFGGNTVNAFYYP 510
           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 = 71.9 bits (177), Expect = 9e-16
 Identities = 30/91 (32%), Positives = 48/91 (52%), Gaps = 7/91 (7%)

Query: 420 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFL 479
           K+L L   +T       E  E++ +++ EEC KYG ++NV++     +      V ++F+
Sbjct: 2   KILVLRNMVTPG-----EIDEDLKDEIEEECEKYGKVLNVIV-HEVASSEADDAV-RIFV 54

Query: 480 EYYDAVGCATAKNALSGRKFGGNTVNAFYYP 510
           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 = 66.9 bits (164), 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|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 71.5 bits (174), Expect = 1e-13
 Identities = 31/92 (33%), Positives = 52/92 (56%)

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

Query: 356 LNGLKMGDKTLTVRRATASGQSKTEQESILAQ 387
           LNG ++  + L V++A  + Q ++E  + L  
Sbjct: 177 LNGKELEGRPLRVQKAQPASQPRSELSNNLDA 208

Length = 306

>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 = 5e-13
 Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 440 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGV-GKVFLEYYDAVGCATAKNALSGRK 498
           +++  ++ EECGK+G +  V+I +  Q   E   +  K+F+E+        A  AL+GR 
Sbjct: 17  DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSLPSEAEKAIQALNGRW 76

Query: 499 FGGNTVNAFYYPEDKYFNKDYS 520
           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|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 = 61.0 bits (149), Expect = 6e-12
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 7/82 (8%)

Query: 429 TADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCA 488
                 +DE  +EI ED+ EEC K+G + ++ +        +    G V++++       
Sbjct: 11  DPAEETEDEWDDEIKEDVLEECSKFGPVEHIKVD-------KNSPEGVVYVKFKTVEAAQ 63

Query: 489 TAKNALSGRKFGGNTVNAFYYP 510
               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|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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 58.6 bits (141), Expect = 4e-11
 Identities = 33/78 (42%), Positives = 41/78 (52%)

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 NGLKMGDKTLTVRRATAS 374
           NGLK+  KT+ V  A  S
Sbjct: 66  NGLKLQTKTIKVSYARPS 83

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|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 = 7e-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|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 = 4e-10
 Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 4/83 (4%)

Query: 436 DEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS 495
           DE+ E    +++EEC KYG +  V+I        +   V ++F+E+        A   L+
Sbjct: 17  DEDLEP---EVKEECSKYGKVTKVLIFEIPGASPDDEAV-RIFVEFERVESAIKAVVDLN 72

Query: 496 GRKFGGNTVNAFYYPEDKYFNKD 518
           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 = 56.3 bits (135), 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|214636 smart00360, RRM, RNA recognition motif

 Score = 54.9 bits (133), Expect = 8e-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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 54.7 bits (131), Expect = 1e-09
 Identities = 30/78 (38%), Positives = 41/78 (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 NGLKMGDKTLTVRRATAS 374
           NGL++  KT+ V  A  S
Sbjct: 65  NGLRLQTKTIKVSYARPS 82

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|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: 433 LADDEEYEEILE-DMREECGKYGTLVNVVIPRPDQNGGETPG--VGKVFLEYYDAVGCAT 489
           +   ++ +E LE ++REECGK+G  V+ VI   ++ G E     + K+F+E+ D++    
Sbjct: 522 MVTPQDIDEFLEGEIREECGKFGV-VDRVIINFEKQGEEEDAEIIVKIFVEFSDSMEVDR 580

Query: 490 AKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA 521
           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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 58.4 bits (141), Expect = 3e-09
 Identities = 30/76 (39%), Positives = 42/76 (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 GDKTLTVRRATASGQS 377
            +KT+ V  A  S  S
Sbjct: 71  QNKTIKVSYARPSSDS 86

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|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 = 3e-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|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 50.1 bits (120), Expect = 5e-08
 Identities = 24/74 (32%), Positives = 37/74 (50%)

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

Query: 362 GDKTLTVRRATASG 375
            +K + V  A   G
Sbjct: 68  QNKRIKVAYARPGG 81

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|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|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 = 48.0 bits (115), Expect = 3e-07
 Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 13/82 (15%)

Query: 431 DALADDEEYEEILEDMREECGKYGTLVNVVI-PR-PDQNGGETPGVGKV-FLEYYDAVGC 487
           +   D     E+ +D+REEC K+G +  VV+  R PD       GV  V F E  +A   
Sbjct: 14  EFEEDPTLINELRDDLREECEKFGQVKKVVVFDRHPD-------GVASVKFKEPEEA--- 63

Query: 488 ATAKNALSGRKFGGNTVNAFYY 509
                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|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|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|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|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 44.7 bits (105), Expect = 4e-06
 Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 2/90 (2%)

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

Query: 350 DIACAALNGLKMGDKTLTVRRATASGQSKT 379
             A  A+NG ++G K L V+   +   SK 
Sbjct: 63  QAAIQAMNGFQIGMKRLKVQLKRSKNDSKP 92

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

>gnl|CDD|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|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 46.0 bits (109), 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|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|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: 447 REECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNA 506
            +    +G +  + + +              F+E+        A   L+G  FGG  +  
Sbjct: 2   YKLFSPFGNVEKIKLLKKKPG--------FAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53

Query: 507 FYY 509
            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: 444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 503
           E++RE   K+G + +V + R D+  G++ G    F+E+        A  AL+G++  G  
Sbjct: 14  EELRELFSKFGKVESVRLVR-DKETGKSKGFA--FVEFESEEDAEKALEALNGKELDGRP 70

Query: 504 VN 505
           + 
Sbjct: 71  LK 72

Length = 73

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

 Score = 47.0 bits (111), Expect = 2e-05
 Identities = 23/83 (27%), Positives = 41/83 (49%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           RV+VG + +   E  I+   + FG +   ++  D  TG  KG+ F  Y+ P    +A   
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168

Query: 356 LNGLKMGDKTLTVRRATASGQSK 378
           +NG  +G + + V R +   Q++
Sbjct: 169 MNGQMLGGRNIKVGRPSNMPQAQ 191

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

 Score = 42.8 bits (101), Expect = 2e-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|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|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|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: 425 TEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDA 484
              +T       E ++E  ED+  E  ++G + ++V+     N G+   +G V++++   
Sbjct: 21  QGVLTLSEEEIQEHFDEFYEDVFLELSRFGEIEDLVVC---DNLGDHL-LGNVYVKFETE 76

Query: 485 VGCATAKNALSGRKFGGNTVNAFYYP 510
                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|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 = 42.3 bits (100), 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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 42.4 bits (99), Expect = 3e-05
 Identities = 22/77 (28%), Positives = 39/77 (50%)

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

Query: 357 NGLKMGDKTLTVRRATA 373
           NG ++GD+ L V   T 
Sbjct: 66  NGYRLGDRVLQVSFKTN 82

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|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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 41.6 bits (97), Expect = 4e-05
 Identities = 22/76 (28%), Positives = 38/76 (50%)

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

Query: 357 NGLKMGDKTLTVRRAT 372
           NG ++GDK L V   T
Sbjct: 64  NGYRLGDKILQVSFKT 79

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|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: 444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 503
           ED+RE   K+G + +V I R      +    G  F+E+        A  AL+G++  G  
Sbjct: 13  EDLRELFSKFGEIESVRIVRDKDGKSK----GFAFVEFESPEDAEKALEALNGKELDGRK 68

Query: 504 VNA 506
           +  
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|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|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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 42.2 bits (99), 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 = 23/77 (29%), Positives = 39/77 (50%)

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

Query: 357 NGLKMGDKTLTVRRATA 373
           NG ++GD+ L V   T+
Sbjct: 64  NGYRLGDRVLQVSFKTS 80

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

 Score = 42.3 bits (99), Expect = 1e-04
 Identities = 19/77 (24%), Positives = 41/77 (53%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +   +  +++    FG +    ++ DR+TG S+G+GF  + D      A + 
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 356 LNGLKMGDKTLTVRRAT 372
           ++G ++  + + V  A 
Sbjct: 96  MDGKELNGRHIRVNPAN 112

Length = 144

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

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 9/93 (9%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++V  L     E +++EL   FG +    ++KD  +G S+G+ F  ++       A   +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 357 NGLKMGD----KTLTVRRATASGQSKTEQESIL 385
           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|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|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|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|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|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|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|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|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|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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 35/132 (26%), Positives = 58/132 (43%), Gaps = 8/132 (6%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +S +I GA     ++V GLP   T+ +++ +   FG +    ++ D  TG SKG GF  +
Sbjct: 83  SSDSIKGAN----LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRF 138

Query: 344 QDPAVTDIACAALNGLKMGDKT--LTVRRATASGQSKTEQESILAQAQQHIAIQKMALQT 401
                 D A   LNG      T  +TV+ A     S +  + +L+Q +     Q   +  
Sbjct: 139 DKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNS--KGLLSQLEAVQNPQTTRVPL 196

Query: 402 SGMNTLGGGMSL 413
           S + T  G   +
Sbjct: 197 STILTAAGIGPM 208

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|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|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 = 0.001
 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|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: 444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 503
           ED+++   K+G + ++ I R     G + G    F+E+ D      A  AL+G++ GG  
Sbjct: 13  EDLKDLFSKFGPIESIRIVR--DETGRSKGFA--FVEFEDEEDAEKALEALNGKELGGRE 68

Query: 504 V 504
           +
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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 49/233 (21%), Positives = 86/233 (36%), Gaps = 24/233 (10%)

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 ACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGM 404
           A   ++G  +G K L V  A    Q +   +    Q Q  +    M     G 
Sbjct: 342 AVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGGA 394

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|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: 435 DDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL 494
            DE++E  L++  E  G+ G +  + I        +    G V++ +  +   A A   L
Sbjct: 1   KDEDFERELKEEEEYFGEVGKINKIYIDDVGYENHK---RGNVYITFERSEDAARAIVDL 57

Query: 495 SGRKFGGNTVNA 506
           +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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 39.6 bits (92), Expect = 0.003
 Identities = 28/111 (25%), Positives = 49/111 (44%), Gaps = 1/111 (0%)

Query: 267 LGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL 326
           +     + +LN    G +        G + + V  LP   T+ ++  L  + G ++   +
Sbjct: 81  MANMASTNSLNSLGSGGSDDNDTNNSGTN-LIVNYLPQDMTDRELYALFRTIGPINTCRI 139

Query: 327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQS 377
           ++D  TG S GY F  +   A +  A   LNG+ + +K L V  A   G+S
Sbjct: 140 MRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGES 190

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

>gnl|CDD|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|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	521
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
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	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	99.96
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.96
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.95
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.95
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.95
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.93
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.92
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.92
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.91
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.9
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.9
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.9
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.9
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.9
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.88
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.87
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.87
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.85
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.84
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.83
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.83
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.83
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.82
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.81
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.79
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.78
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.78
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.77
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.76
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.75
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.73
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.7
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.68
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.67
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.65
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.62
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.6
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.6
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.6
KOG0122	270	consensus Translation initiation factor 3, subunit	99.57
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.57
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.56
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.53
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.53
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.53
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.52
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.51
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.5
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.5
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.49
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.49
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.49
PLN03120	260	nucleic acid binding protein; Provisional	99.48
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.48
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.48
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.47
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.45
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.43
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.4
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.4
smart00362	72	RRM_2 RNA recognition motif.	99.4
PLN03121	243	nucleic acid binding protein; Provisional	99.39
PLN03213	759	repressor of silencing 3; Provisional	99.39
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.37
smart00360	71	RRM RNA recognition motif.	99.37
PLN03120	260	nucleic acid binding protein; Provisional	99.32
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.32
smart00361	70	RRM_1 RNA recognition motif.	99.31
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.3
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.3
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.29
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.29
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.29
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.27
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.27
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.26
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.26
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.26
smart00361	70	RRM_1 RNA recognition motif.	99.24
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.24
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.23
KOG0122	270	consensus Translation initiation factor 3, subunit	99.2
PLN03121	243	nucleic acid binding protein; Provisional	99.19
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.17
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.14
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.07
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.06
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.06
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.05
KOG4660	549	consensus Protein Mei2, essential for commitment t	99.04
KOG0226	290	consensus RNA-binding proteins [General function p	99.04
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.03
smart00362	72	RRM_2 RNA recognition motif.	99.03
PLN03213	759	repressor of silencing 3; Provisional	99.02
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.01
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.01
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.0
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.99
smart00360	71	RRM RNA recognition motif.	98.99
KOG1996	378	consensus mRNA splicing factor [RNA processing and	98.92
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.91
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.87
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.87
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.85
KOG4210	285	consensus Nuclear localization sequence binding pr	98.84
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.84
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.82
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.82
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.81
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.78
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.71
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.7
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.69
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.67
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.67
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.61
KOG0151	877	consensus Predicted splicing regulator, contains R	98.55
KOG0226	290	consensus RNA-binding proteins [General function p	98.54
KOG4210	285	consensus Nuclear localization sequence binding pr	98.53
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.53
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.46
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	98.42
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.4
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.39
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.28
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.24
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.23
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.22
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.1
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.09
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.01
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.0
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.98
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.9
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.9
KOG0151	877	consensus Predicted splicing regulator, contains R	97.88
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.87
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.83
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.67
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.67
PF06495	182	Transformer: Fruit fly transformer protein; InterP	97.66
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.66
KOG2314	698	consensus Translation initiation factor 3, subunit	97.58
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.53
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.52
KOG2314	698	consensus Translation initiation factor 3, subunit	97.52
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.31
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.3
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.27
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.25
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.21
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.17
KOG3152	278	consensus TBP-binding protein, activator of basal	97.1
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.99
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.89
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.85
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.76
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.67
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.6
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.51
KOG2135	526	consensus Proteins containing the RNA recognition	96.44
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.38
KOG2548	653	consensus SWAP mRNA splicing regulator [RNA proces	96.36
KOG3263	196	consensus Nucleic acid binding protein [General fu	96.31
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.11
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.06
KOG3152	278	consensus TBP-binding protein, activator of basal	95.87
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.31
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	95.3
KOG2591	684	consensus c-Mpl binding protein, contains La domai	95.2
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	94.98
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.92
KOG2135	526	consensus Proteins containing the RNA recognition	94.82
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.63
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.53
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.46
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.45
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.32
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.19
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.08
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.01
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	93.34
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	92.74
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	92.52
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	91.16
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	91.0
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	90.64
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	90.59
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	89.61
KOG0670	752	consensus U4/U6-associated splicing factor PRP4 [R	88.97
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	88.36
KOG2891	445	consensus Surface glycoprotein [General function p	87.2
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	86.78
KOG4246	1194	consensus Predicted DNA-binding protein, contains	86.69
KOG2591	684	consensus c-Mpl binding protein, contains La domai	84.91
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	82.44
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	81.35

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

Probab=100.00  E-value=3.8e-61  Score=502.81  Aligned_cols=396  Identities=44%  Similarity=0.686  Sum_probs=292.0

Q ss_pred             CCCCCCCCCCccCCCCCCC----CCCCCCCCCCCCCccccCCCCcCCCcCCCCCCCCccccchhhhccCCeEEEeCCCcc
Q 009954          110 RRSGFDMAPPAAAMLPGAA----VPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPL  185 (521)
Q Consensus       110 ~~~~~d~~~~~~~~~~~~~----~~g~~p~~~p~~p~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~l~v~nlp~~  185 (521)
                      ....|+.+++++....+.+    ....+|+.++ .|++.+......  ....+..++.....++.....++|||+|||+.
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 222222221111  11111122222345567778899999999999


Q ss_pred             CcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEEEeCCCCCCccccc
Q 009954          186 ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAA  265 (521)
Q Consensus       186 ~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v~~~~~~~~~~~~  265 (521)
                      +|+++|.++|..++...+.....++.+|..+.+..++|||||+|.+.++|..||+|+|+.|.|+.|+|.++..+.+....
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            99999999999998877765555567799999999999999999999999999999999999999999988877643322


Q ss_pred             cCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcC
Q 009954          266 ALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD  345 (521)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~  345 (521)
                      ........+....................++|||+|||..+++++|.++|+.||.|..+.|+.+..+|.++|||||+|.+
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            21111111111111111111222234566899999999999999999999999999999999998899999999999999


Q ss_pred             hHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEee
Q 009954          346 PAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLT  425 (521)
Q Consensus       346 ~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~  425 (521)
                      .++|..||+.|+|..|+|+.|.|.++................     .   ....   ..............++.|++|.
T Consensus       347 ~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~-----~---~~~~---~~~~~~~~~~~~~~~s~v~~l~  415 (509)
T TIGR01642       347 PSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMA-----P---VTLL---AKALSQSILQIGGKPTKVVQLT  415 (509)
T ss_pred             HHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCcccccccc-----c---cccc---cccchhhhccccCCCceEEEec
Confidence            999999999999999999999999997533221110000000     0   0000   0000000111223678999999


Q ss_pred             CcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEE
Q 009954          426 EAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVN  505 (521)
Q Consensus       426 ~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~  505 (521)
                      |+++.++|.++.+|++|.++|+++|++||.|+.|.|+++..++....|+|+|||+|.++++|++||..|||+.|+|++|.
T Consensus       416 N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~  495 (509)
T TIGR01642       416 NLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVV  495 (509)
T ss_pred             cCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            99999999999999999999999999999999999998765555567889999999999999999999999999999999


Q ss_pred             EEEcCCCCcccccC
Q 009954          506 AFYYPEDKYFNKDY  519 (521)
Q Consensus       506 v~~~~~~~~~~~~~  519 (521)
                      |.|+++++|.+|.|
T Consensus       496 ~~~~~~~~~~~~~~  509 (509)
T TIGR01642       496 AAFYGEDCYKAGDY  509 (509)
T ss_pred             EEEeCHHHhhccCC
Confidence            99999999999988

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

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

Probab=100.00  E-value=5.3e-52  Score=427.80  Aligned_cols=316  Identities=26%  Similarity=0.423  Sum_probs=236.9

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      ....++|||+|||..+++++|+++|.+||.|....      .+.+..++.++|||||+|.+.++|.+||.|+|..+.|++
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 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQ------CIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRP  159 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE------EeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCee
Confidence            34567999999999999999999999999753321      133333466789999999999999999999999999999


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~  330 (521)
                      |.|.++...........                 ..........++|||+|||..+++++|.++|++||.|..|.|+.++
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                 0000011225789999999999999999999999999999999999


Q ss_pred             CCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHH------------HHHHHHHHHHHHh
Q 009954          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESIL------------AQAQQHIAIQKMA  398 (521)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~  398 (521)
                      .+|.++|||||+|.+.++|.+|+..|+|..|.|+.|.|.|+..............            .............
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            8999999999999999999999999999999999999999864211111000000            0000000000000


Q ss_pred             hhcc--CC-----------------------CCC-----CC--------CCCC-CCCCcceEEEeeCcCCcccCCChHHH
Q 009954          399 LQTS--GM-----------------------NTL-----GG--------GMSL-FGETLAKVLCLTEAITADALADDEEY  439 (521)
Q Consensus       399 ~~~~--~~-----------------------~~~-----~~--------~~~~-~~~~~~~v~~l~~~~~~~~~~~~~~~  439 (521)
                      ....  +.                       ..+     +.        .++. ....++.|++|.|+++..++.+..+|
T Consensus       303 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~  382 (457)
T TIGR01622       303 RDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFD  382 (457)
T ss_pred             cCCCCccccCCCccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHH
Confidence            0000  00                       000     00        0000 12367889999999999988889999


Q ss_pred             HHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCccc
Q 009954          440 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFN  516 (521)
Q Consensus       440 ~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~~  516 (521)
                      +++++||+++|++||.|+.|.|....       +.|+|||+|.++++|.+|++.|||+.|+|+.|.|.|+++++|.+
T Consensus       383 ~~~~~dv~~e~~k~G~v~~v~v~~~~-------~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~~~~~  452 (457)
T TIGR01622       383 NEILDDVKEECSKYGGVVHIYVDTKN-------SAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDVYDM  452 (457)
T ss_pred             HHHHHHHHHHHHhcCCeeEEEEeCCC-------CceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHHHHHh
Confidence            99999999999999999999997533       24889999999999999999999999999999999999999865

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=1.4e-47  Score=373.60  Aligned_cols=387  Identities=46%  Similarity=0.763  Sum_probs=313.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCccCCCCCC--------CCCCCCCCCCCCCCccccCCCCcCCCcCCCCCCCCccccchhhhc
Q 009954          101 PSRSPSKSKRRSGFDMAPPAAAMLPGA--------AVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATR  172 (521)
Q Consensus       101 rs~s~~r~r~~~~~d~~~~~~~~~~~~--------~~~g~~p~~~p~~p~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~  172 (521)
                      +++++...+....|+.++++++..++.        +..|+.|+........            ...+..|.+.+.++...
T Consensus       106 ~~~~~~~~r~~~~~~~~~~~fe~~~p~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~t~  173 (500)
T KOG0120|consen  106 RSRSRRYSRKRSLWDVPPEGFETITPDGAKLYKNFNATGQVPGDLSNPKKS------------LKLPQLPTPPMDSQATR  173 (500)
T ss_pred             cccccccccchhhhcCCCCCCcccCchhhhhhhhccccCCCCCCccccccc------------cccccCCCCccCcchhh
Confidence            344444466677899999988887762        1333333322111110            00334455566677888


Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~  252 (521)
                      ....++|+++|+.++++.+..+|..-..+.+++....+..++.+.++..+.|||++|.+.++|..|+.+++..+.|.+++
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            88999999999999999999999999888888887778899999999999999999999999999999999999999999


Q ss_pred             EeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 009954          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (521)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~  332 (521)
                      +..+..+...........+      .+..+...........++.+||++||..+++..+.++...||.+....++.+..+
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            9998888776655544433      2233444455556677889999999999999999999999999999999999999


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCC
Q 009954          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMS  412 (521)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (521)
                      |.++||||.+|.++.....|+..|||..+++..|.|+.+...........+  ..+.+...+.....+            
T Consensus       328 g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~--~~~~~~~~i~~~~~q------------  393 (500)
T KOG0120|consen  328 GNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFN--ISQSQVPGIPLLMTQ------------  393 (500)
T ss_pred             ccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCC--ccccccccchhhhcc------------
Confidence            999999999999999999999999999999999999998763221111111  000011122222111            


Q ss_pred             CCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHH
Q 009954          413 LFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKN  492 (521)
Q Consensus       413 ~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~  492 (521)
                       ....++.|++|.|++++++|.++++|++|.++|+..|.+||.|..|.|+++..++.+..|.|++||+|++.++|++|++
T Consensus       394 -~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~  472 (500)
T KOG0120|consen  394 -MAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAME  472 (500)
T ss_pred             -cCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHH
Confidence             2338899999999999999999999999999999999999999999999996688889999999999999999999999


Q ss_pred             HHhCCeeCCcEEEEEEcCCCCcccccCC
Q 009954          493 ALSGRKFGGNTVNAFYYPEDKYFNKDYS  520 (521)
Q Consensus       493 ~lng~~~~gr~l~v~~~~~~~~~~~~~~  520 (521)
                      .|+|++|+||+|.++||++++|++++|.
T Consensus       473 ~L~GrKF~nRtVvtsYydeDkY~~r~~~  500 (500)
T KOG0120|consen  473 ELTGRKFANRTVVASYYDEDKYHAREFE  500 (500)
T ss_pred             HccCceeCCcEEEEEecCHHHhhccccC
Confidence            9999999999999999999999999984

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

Probab=100.00  E-value=1.7e-42  Score=351.17  Aligned_cols=322  Identities=27%  Similarity=0.390  Sum_probs=237.4

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....++|||+|||+.+++++|+++|.+||.|..+.      .+.+..+++++|||||+|.+.++|..|+ .|||..|.|+
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            35678999999999999999999999999864422      1334446778999999999999999999 6999999999


Q ss_pred             eEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec
Q 009954          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (521)
Q Consensus       250 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~  329 (521)
                      .|+|.++.......        +.  ..        .........++|||+|||+.+++++|+++|+.||.|.+++|.++
T Consensus       178 ~IkV~rp~~~p~a~--------~~--~~--------~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D  239 (612)
T TIGR01645       178 NIKVGRPSNMPQAQ--------PI--ID--------MVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARA  239 (612)
T ss_pred             eeeecccccccccc--------cc--cc--------cccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEec
Confidence            99998654322110        00  00        00011223468999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCc---------hHHHHH---HHHH--HHHHHH-
Q 009954          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSK---------TEQESI---LAQA--QQHIAI-  394 (521)
Q Consensus       330 ~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~---------~~~~~~---~~~~--~~~~~~-  394 (521)
                      +.+|.++|||||+|.+.++|.+||+.|||+.|+|+.|+|.++.......         +.....   ...+  +..... 
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            9899999999999999999999999999999999999999987522221         000000   0000  000000 


Q ss_pred             HHHhhh---------------------------------------------------ccCCCCCCCC-----------CC
Q 009954          395 QKMALQ---------------------------------------------------TSGMNTLGGG-----------MS  412 (521)
Q Consensus       395 ~~~~~~---------------------------------------------------~~~~~~~~~~-----------~~  412 (521)
                      ......                                                   ..+...+|..           .|
T Consensus       320 ~~a~~g~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  399 (612)
T TIGR01645       320 GAAVLGPRAQSPATPSSSLPTDIGNKAVVSSAKKEAEEVPPLPQAAPAVVKPGPMEIPTPVPPPGLAIPSLVAPPGLVAP  399 (612)
T ss_pred             cccccccccCCCccccccccccccccccccccCCcccCCCCCccccccccCCCCcccccCCCCccccccccCCCccccCC
Confidence            000000                                                   0000000000           00


Q ss_pred             --------------------------------------------------------------------------------
Q 009954          413 --------------------------------------------------------------------------------  412 (521)
Q Consensus       413 --------------------------------------------------------------------------------  412 (521)
                                                                                                      
T Consensus       400 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  479 (612)
T TIGR01645       400 TEINPSFLASPRKKMKREKLPVTFGALDDTLAWKEPSKEDQTSEDGKMLAIMGEAAAALALEPKKKKKEKEGEELQPKLV  479 (612)
T ss_pred             CcCchhhhcCcccccccccccccccccccchhccccchhhhhhhhhhhcccchhhHHHHhhhhhHHhhhhhhhhhccccc
Confidence                                                                                            


Q ss_pred             ----------------------------CCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCC
Q 009954          413 ----------------------------LFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRP  464 (521)
Q Consensus       413 ----------------------------~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~  464 (521)
                                                  ...+.+++|++|.|+++.+++     .++|++||++.|++||.|.+|.|...
T Consensus       480 ~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~rp~~S~vVvL~NMv~~~el-----dedl~eDV~eEC~K~G~V~~v~I~~~  554 (612)
T TIGR01645       480 MNSEDASLASQEGMSIRGNSARHLVMQKLMRTNRSNVIVLRNMVTPQDI-----DEFLEGEIREECGKFGVVDRVIINFE  554 (612)
T ss_pred             ccccccccccccccccccchhhHHHHHhhcCCCCCCEEEEeCCCChHHh-----HHHHHHHHHHHhhcCceeEEEEEecC
Confidence                                        001235789999999998865     34588999999999999999999885


Q ss_pred             CCC-CCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCcccccCCC
Q 009954          465 DQN-GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA  521 (521)
Q Consensus       465 ~~~-~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~~~~~~~  521 (521)
                      ... .....+.|.+||+|.+.++|.+|+..|||++|+||.|.+.||++++|.+|+|+.
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 111123567899999999999999999999999999999999999999999984

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.

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

Probab=100.00  E-value=6.8e-43  Score=335.11  Aligned_cols=317  Identities=26%  Similarity=0.412  Sum_probs=239.6

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCc
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~  249 (521)
                      .+...++||+--|+..+++-+|.+||+.+|+|..      +.+|.+-+...++|.|||+|.+.+....|+.|.|+.+.|.
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrd------VriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~  248 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRD------VRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGV  248 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcce------eEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCc
Confidence            4566789999999999999999999999998643      3345566667789999999999999999999999999999


Q ss_pred             eEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCC-CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 009954          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGP-DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (521)
Q Consensus       250 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~  328 (521)
                      +|.|+........ .+...               ..........+ ..|||+||..++++++|+.+|++||.|..|.+..
T Consensus       249 pv~vq~sEaeknr-~a~~s---------------~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~  312 (549)
T KOG0147|consen  249 PVIVQLSEAEKNR-AANAS---------------PALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTK  312 (549)
T ss_pred             eeEecccHHHHHH-HHhcc---------------ccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeecc
Confidence            9999863322111 10000               00000111222 2399999999999999999999999999999999


Q ss_pred             cCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchH------HH----HHHH--HHHHHHHHHH
Q 009954          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTE------QE----SILA--QAQQHIAIQK  396 (521)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~------~~----~~~~--~~~~~~~~~~  396 (521)
                      +.+||.++||+||+|.+.++|.+|+..|||+.|.|+.|+|...+........      .+    ..+.  .......+.+
T Consensus       313 d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~k  392 (549)
T KOG0147|consen  313 DSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAK  392 (549)
T ss_pred             ccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHH
Confidence            9889999999999999999999999999999999999999876652111100      00    0000  0000000011


Q ss_pred             Hhhhc------------------------cCCCCC-----CCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHH
Q 009954          397 MALQT------------------------SGMNTL-----GGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMR  447 (521)
Q Consensus       397 ~~~~~------------------------~~~~~~-----~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~  447 (521)
                      ++...                        .+.+..     ..+.|.. ..++.|+.|.|++++.+.....|-.+|++||.
T Consensus       393 la~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~-~i~t~C~lL~nMFdpstete~n~d~eI~edV~  471 (549)
T KOG0147|consen  393 LAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAF-DIPTQCLLLSNMFDPSTETEPNWDQEIREDVI  471 (549)
T ss_pred             HhccCCccccchhhhHHHhccccchHHhhcCCcCccccCcccccccc-CCccHHHHHhhcCCcccccCcchhhHHHHHHH
Confidence            11000                        100000     0011111 27888999999999999888889999999999


Q ss_pred             HhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCcccc
Q 009954          448 EECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNK  517 (521)
Q Consensus       448 ~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~~~  517 (521)
                      +.|++||.|..|.|.++.        .||+||.|.+++.|..|+.+|||+.|.|+.|++.|++...|+..
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            999999999999998865        38999999999999999999999999999999999999888753

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=1.6e-41  Score=338.34  Aligned_cols=292  Identities=20%  Similarity=0.273  Sum_probs=212.8

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      ..+|||+|||..+|+++|+++|..||.|..+.      .+.+...+.++|||||+|.+.++|.+|+ .|||..|.|+.|+
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      1333344668899999999999999999 6999999999999


Q ss_pred             EeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 009954          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (521)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~  332 (521)
                      |.++.....                             .....+|||+|||..+++++|.++|++||.|..+.++.+..+
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            987543211                             112357999999999999999999999999999999998888


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCeeCC--eEEEEEEccCCCCCchHHHHHHHHHHHH-H-----------------
Q 009954          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASGQSKTEQESILAQAQQH-I-----------------  392 (521)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~~~~~~~~~~~~~~~~~~~~~-~-----------------  392 (521)
                      +.++|||||+|.+.++|+.||+.|||..+.|  ..|.|.|+....+............... .                 
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  6789999865332211100000000000 0                 


Q ss_pred             ---------------------HHHHH-hhhcc--CCCC------------CCCCCCCCCCCcceEEEeeCcCCcccCCCh
Q 009954          393 ---------------------AIQKM-ALQTS--GMNT------------LGGGMSLFGETLAKVLCLTEAITADALADD  436 (521)
Q Consensus       393 ---------------------~~~~~-~~~~~--~~~~------------~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~  436 (521)
                                           ..+.. .....  ....            .+...+.. .....+|.+.|+..       
T Consensus       208 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~lfV~NL~~-------  279 (352)
T TIGR01661       208 MHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAAS-DGAGYCIFVYNLSP-------  279 (352)
T ss_pred             ccCcccccccCcchhhhhhhhhhhhcccccccccccCCCccccccccccccCCCCCCC-CCCCcEEEEeCCCC-------
Confidence                                 00000 00000  0000            00000000 11111233333322       


Q ss_pred             HHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCc
Q 009954          437 EEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  514 (521)
Q Consensus       437 ~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~  514 (521)
                         .+.+++|+++|++||.|+.|+|+.+..++..   +|+|||+|.+.++|..||+.|||..|+|+.|+|.|++...+
T Consensus       280 ---~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~s---kG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       280 ---DTDETVLWQLFGPFGAVQNVKIIRDLTTNQC---KGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             ---CCCHHHHHHHHHhCCCeEEEEEeEcCCCCCc---cceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCCC
Confidence               2233699999999999999999999877664   67889999999999999999999999999999999987643

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

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

Probab=100.00  E-value=5.5e-36  Score=315.64  Aligned_cols=273  Identities=20%  Similarity=0.319  Sum_probs=209.7

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      ..+|||+|||.++++++|+++|+.||.|..+.       +.....+.++|||||+|.+.++|.+|+ .+||..+.|+.|.
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            45799999999999999999999999875432       222234567999999999999999999 7999999999999


Q ss_pred             EeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 009954          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (521)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~  332 (521)
                      |..........                        .......++|||+|||.++|+++|+++|+.||.|.++.++.+. +
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             CCcceEEEEEEcChHHHHHHHHHHcCCeeC----CeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCC
Q 009954          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMG----DKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG  408 (521)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~----g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  408 (521)
                      |.++|||||+|.+.++|.+|++.|+|..|.    |+.|.|.++..+..    ...................         
T Consensus       216 g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~e----r~~~~~~~~~~~~~~~~~~---------  282 (562)
T TIGR01628       216 GRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAE----REAELRRKFEELQQERKMK---------  282 (562)
T ss_pred             CCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChhh----hHHHHHhhHHhhhhhhhcc---------
Confidence            999999999999999999999999999999    99999999865322    1111111111100000000         


Q ss_pred             CCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHH
Q 009954          409 GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCA  488 (521)
Q Consensus       409 ~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~  488 (521)
                           ....+..|-+|...++.             ++|+++|+.||.|..|+|+.+. ++..   +|+|||+|.+.++|.
T Consensus       283 -----~~~~~l~V~nl~~~~~~-------------~~L~~~F~~~G~i~~~~i~~d~-~g~~---~g~gfV~f~~~~~A~  340 (562)
T TIGR01628       283 -----AQGVNLYVKNLDDTVTD-------------EKLRELFSECGEITSAKVMLDE-KGVS---RGFGFVCFSNPEEAN  340 (562)
T ss_pred             -----cCCCEEEEeCCCCccCH-------------HHHHHHHHhcCCeEEEEEEECC-CCCc---CCeEEEEeCCHHHHH
Confidence                 00122333333333332             5999999999999999999984 4443   578899999999999


Q ss_pred             HHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          489 TAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       489 ~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      +|+..|||..|+|++|.|.++..++
T Consensus       341 ~A~~~~~g~~~~gk~l~V~~a~~k~  365 (562)
T TIGR01628       341 RAVTEMHGRMLGGKPLYVALAQRKE  365 (562)
T ss_pred             HHHHHhcCCeeCCceeEEEeccCcH
Confidence            9999999999999999999987653

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

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

Probab=100.00  E-value=7.8e-36  Score=259.19  Aligned_cols=292  Identities=18%  Similarity=0.253  Sum_probs=221.1

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      +....|.|.-||..+|+++|+.+|...|+|.+|++      |.+..++.+.||+||.|.++++|++|+ .|||..+..+.
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKL------vRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KT  112 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKL------VRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKT  112 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeee------eeccccccccccceeeecChHHHHHHHhhhcceeeccce
Confidence            44557999999999999999999999999988766      888889999999999999999999999 79999999999


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~  330 (521)
                      |+|.++.+....                             ...-+|||.+||..+|..+|.++|++||.|..-+|..|.
T Consensus       113 IKVSyARPSs~~-----------------------------Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dq  163 (360)
T KOG0145|consen  113 IKVSYARPSSDS-----------------------------IKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQ  163 (360)
T ss_pred             EEEEeccCChhh-----------------------------hcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhc
Confidence            999986543321                             122479999999999999999999999999988888888


Q ss_pred             CCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC--eEEEEEEccCCCCCchHHHHHHHHHHH--------HHHHHHH---
Q 009954          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASGQSKTEQESILAQAQQ--------HIAIQKM---  397 (521)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~---  397 (521)
                      .+|.++|.+||.|...++|+.||+.|||..-.|  .+|.|.|+....+......-..-....        ..+.+..   
T Consensus       164 vtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~  243 (360)
T KOG0145|consen  164 VTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLD  243 (360)
T ss_pred             ccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccc
Confidence            899999999999999999999999999988766  579999998744433221111000000        0000000   


Q ss_pred             --------hhhccCCCC------CCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecC
Q 009954          398 --------ALQTSGMNT------LGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPR  463 (521)
Q Consensus       398 --------~~~~~~~~~------~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~  463 (521)
                              .....++..      .|...|..+.. .-|+.+.|+....+.          .-|-++|.+||.|.+|+|++
T Consensus       244 ~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~-g~ciFvYNLspd~de----------~~LWQlFgpFGAv~nVKvir  312 (360)
T KOG0145|consen  244 NLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGG-GWCIFVYNLSPDADE----------SILWQLFGPFGAVTNVKVIR  312 (360)
T ss_pred             cccchhhhhccCCCccccccceeeeeccCCCCCC-eeEEEEEecCCCchH----------hHHHHHhCcccceeeEEEEe
Confidence                    000011110      12222222222 234444444333321          37889999999999999999


Q ss_pred             CCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          464 PDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       464 ~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      |..+..   .+|++||.+.+-++|..||..|||..++++.|.|+|-+.+
T Consensus       313 D~ttnk---CKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  313 DFTTNK---CKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             cCCccc---ccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            985543   3566699999999999999999999999999999997654

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

Probab=100.00  E-value=3.1e-36  Score=305.47  Aligned_cols=243  Identities=19%  Similarity=0.299  Sum_probs=191.5

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceec-Cce
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE-GVA  250 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~-g~~  250 (521)
                      ..++|||+|||.++++++|+++|.+||.|..+.      .+.+ ..+.++|||||+|.+.++|++|| .||+..+. |+.
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            357899999999999999999999999865431      1333 55788999999999999999999 69998885 777


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEe-e
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLV-K  328 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~-i~~v~i~-~  328 (521)
                      |.|.++                                   ...++|||+|||..+++++|.++|++++. +..+.+. .
T Consensus       130 l~V~~S-----------------------------------~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~  174 (578)
T TIGR01648       130 LGVCIS-----------------------------------VDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHS  174 (578)
T ss_pred             cccccc-----------------------------------ccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEecc
Confidence            777542                                   11368999999999999999999999864 4444443 3


Q ss_pred             cCCCCCcceEEEEEEcChHHHHHHHHHHcC--CeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCC
Q 009954          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNT  406 (521)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  406 (521)
                      ...+++++|||||+|.+.++|.+|++.|+.  ..+.|+.|.|.|+.+......+                          
T Consensus       175 ~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~--------------------------  228 (578)
T TIGR01648       175 AADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDED--------------------------  228 (578)
T ss_pred             ccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeeccccccccc--------------------------
Confidence            334678899999999999999999998864  4688999999999763221100                          


Q ss_pred             CCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccc--cceeEEEecCCCCCCCCCCCccEEEEEecCH
Q 009954          407 LGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY--GTLVNVVIPRPDQNGGETPGVGKVFLEYYDA  484 (521)
Q Consensus       407 ~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~f--G~I~~v~i~~~~~~~~~~~g~g~afV~F~~~  484 (521)
                              .....++|.+.|+...          ..+++|+++|+.|  |.|+.|.+++           ++|||+|.+.
T Consensus       229 --------~~~~~k~LfVgNL~~~----------~tee~L~~~F~~f~~G~I~rV~~~r-----------gfAFVeF~s~  279 (578)
T TIGR01648       229 --------VMAKVKILYVRNLMTT----------TTEEIIEKSFSEFKPGKVERVKKIR-----------DYAFVHFEDR  279 (578)
T ss_pred             --------ccccccEEEEeCCCCC----------CCHHHHHHHHHhcCCCceEEEEeec-----------CeEEEEeCCH
Confidence                    0012234444444221          1225999999999  9999998865           5889999999


Q ss_pred             HHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          485 VGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       485 ~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      ++|++||+.|||..|+|+.|+|.|+...
T Consensus       280 e~A~kAi~~lnG~~i~Gr~I~V~~Akp~  307 (578)
T TIGR01648       280 EDAVKAMDELNGKELEGSEIEVTLAKPV  307 (578)
T ss_pred             HHHHHHHHHhCCCEECCEEEEEEEccCC
Confidence            9999999999999999999999998664

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

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

Probab=100.00  E-value=6.2e-36  Score=315.28  Aligned_cols=254  Identities=19%  Similarity=0.340  Sum_probs=201.0

Q ss_pred             eEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEEe
Q 009954          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR  254 (521)
Q Consensus       176 ~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v~  254 (521)
                      +|||+|||+++|+++|.++|++||.|..+      ..+.+..+.+++|||||+|.+.++|.+|+ .+|+..|.|+.|+|.
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            69999999999999999999999985331      11223334667899999999999999999 799999999999999


Q ss_pred             CCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCC
Q 009954          255 RPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN  334 (521)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~  334 (521)
                      |+......                           ......+|||+|||.++++++|+++|+.||.|.+|+|..+. +|.
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            85421100                           01123579999999999999999999999999999999884 889


Q ss_pred             cceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCC
Q 009954          335 SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLF  414 (521)
Q Consensus       335 ~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  414 (521)
                      ++|||||+|.+.++|.+|++.|+|..+.|+.|.|..........    .                           ....
T Consensus       128 skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~----~---------------------------~~~~  176 (562)
T TIGR01628       128 SRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHERE----A---------------------------APLK  176 (562)
T ss_pred             cccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccccccc----c---------------------------cccc
Confidence            99999999999999999999999999999999998764321110    0                           0000


Q ss_pred             CCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHH
Q 009954          415 GETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL  494 (521)
Q Consensus       415 ~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~l  494 (521)
                      ..++..|.+|...++             +++|+++|+.||.|..|.|+.+. ++.   .+|+|||+|.+.++|.+|++.|
T Consensus       177 ~~~~l~V~nl~~~~t-------------ee~L~~~F~~fG~i~~~~i~~~~-~g~---~~G~afV~F~~~e~A~~Av~~l  239 (562)
T TIGR01628       177 KFTNLYVKNLDPSVN-------------EDKLRELFAKFGEITSAAVMKDG-SGR---SRGFAFVNFEKHEDAAKAVEEM  239 (562)
T ss_pred             CCCeEEEeCCCCcCC-------------HHHHHHHHHhcCCEEEEEEEECC-CCC---cccEEEEEECCHHHHHHHHHHh
Confidence            002222223332222             25999999999999999999886 333   3578899999999999999999


Q ss_pred             hCCeeC----CcEEEEEEcCC
Q 009954          495 SGRKFG----GNTVNAFYYPE  511 (521)
Q Consensus       495 ng~~~~----gr~l~v~~~~~  511 (521)
                      ||..|.    |+.|.|.++..
T Consensus       240 ~g~~i~~~~~g~~l~v~~a~~  260 (562)
T TIGR01628       240 NGKKIGLAKEGKKLYVGRAQK  260 (562)
T ss_pred             CCcEecccccceeeEeecccC
Confidence            999999    99999988644

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

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

Probab=100.00  E-value=1.7e-35  Score=276.27  Aligned_cols=245  Identities=18%  Similarity=0.317  Sum_probs=204.1

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCcee-cCc
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF-EGV  249 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~-~g~  249 (521)
                      ..-+.||||.||.++.|++|.-+|.+.|+|...-      .+.+...+.++|||||+|.+.++|+.|+ .||+..| .|+
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            3457899999999999999999999999975432      2455566788999999999999999999 7999987 578


Q ss_pred             eEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEee
Q 009954          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVK  328 (521)
Q Consensus       250 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~-i~~v~i~~  328 (521)
                      .|.|.-+                                   ...++|||+|||.+.++++|.+.|++.++ |.+|.|..
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 88998887


Q ss_pred             cCC-CCCcceEEEEEEcChHHHHHHHHHHcC--CeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCC
Q 009954          329 DRD-TGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMN  405 (521)
Q Consensus       329 ~~~-~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  405 (521)
                      .+. ..+++|||||+|.+...|..|...|-.  +++.|..+.|.||.+...+..+  .                      
T Consensus       200 ~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded--~----------------------  255 (506)
T KOG0117|consen  200 SPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDED--T----------------------  255 (506)
T ss_pred             CccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChh--h----------------------
Confidence            664 567899999999999999999887753  6789999999999874333222  1                      


Q ss_pred             CCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHH
Q 009954          406 TLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAV  485 (521)
Q Consensus       406 ~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~  485 (521)
                                ....+|+.+.|+..          .++++.|+++|+.||.|+.|+.++|           +|||.|.+.+
T Consensus       256 ----------ms~VKvLYVRNL~~----------~tTeE~lk~~F~~~G~veRVkk~rD-----------YaFVHf~eR~  304 (506)
T KOG0117|consen  256 ----------MSKVKVLYVRNLME----------STTEETLKKLFNEFGKVERVKKPRD-----------YAFVHFAERE  304 (506)
T ss_pred             ----------hhheeeeeeeccch----------hhhHHHHHHHHHhccceEEeecccc-----------eeEEeecchH
Confidence                      13456666666532          3456799999999999999999986           7799999999


Q ss_pred             HHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          486 GCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       486 ~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      +|.+|++.|||..|+|..|.|+++.+-
T Consensus       305 davkAm~~~ngkeldG~~iEvtLAKP~  331 (506)
T KOG0117|consen  305 DAVKAMKETNGKELDGSPIEVTLAKPV  331 (506)
T ss_pred             HHHHHHHHhcCceecCceEEEEecCCh
Confidence            999999999999999999999997653

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

Probab=100.00  E-value=5.8e-35  Score=299.80  Aligned_cols=289  Identities=18%  Similarity=0.138  Sum_probs=203.3

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHH---ccCceecCce
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIFEGVA  250 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~---l~g~~~~g~~  250 (521)
                      ++.|||+|||+.+|+++|+++|++||.            |..+.+..+++||||+|.+.++|+.|+.   +++..+.|++
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            578999999999999999999999998            6667777789999999999999999994   5889999999


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~  330 (521)
                      |.|+++.........   ..    .          ..........+|+|.||+..+++++|+++|+.||.|..|.|+++.
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             CCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC--eEEEEEEccCCCCCc------h----------HHHHHHHH--HHH
Q 009954          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASGQSK------T----------EQESILAQ--AQQ  390 (521)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~~~~~~~~------~----------~~~~~~~~--~~~  390 (521)
                      .    +|+|||+|.+.++|.+|++.|||..|.|  +.|+|.|++......      .          +.+..+..  ...
T Consensus       133 ~----~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~  208 (481)
T TIGR01649       133 N----VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQR  208 (481)
T ss_pred             C----ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCcccccc
Confidence            2    4789999999999999999999999854  689999987622110      0          00000000  000


Q ss_pred             HHHHHH------Hhhhcc-----------CCCC---------CC-----CCCC-------CCCCCcceEEEeeCcCCccc
Q 009954          391 HIAIQK------MALQTS-----------GMNT---------LG-----GGMS-------LFGETLAKVLCLTEAITADA  432 (521)
Q Consensus       391 ~~~~~~------~~~~~~-----------~~~~---------~~-----~~~~-------~~~~~~~~v~~l~~~~~~~~  432 (521)
                      ......      ......           +..+         ..     .+.+       .....++.++.+.|+.... 
T Consensus       209 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~-  287 (481)
T TIGR01649       209 QPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEK-  287 (481)
T ss_pred             ccccccCCCccCCCcccccCCCCCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCC-
Confidence            000000      000000           0000         00     0000       0011244566666553210 


Q ss_pred             CCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          433 LADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       433 ~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                              .++++|+++|+.||.|..|+|+++.        .|+|||+|.++++|..||..|||..|.|++|+|.+....
T Consensus       288 --------vt~~~L~~lF~~yG~V~~vki~~~~--------~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       288 --------VNCDRLFNLFCVYGNVERVKFMKNK--------KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             --------CCHHHHHHHHHhcCCeEEEEEEeCC--------CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence                    1226999999999999999999864        378899999999999999999999999999999997543

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).

>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=257.79  Aligned_cols=236  Identities=23%  Similarity=0.361  Sum_probs=181.3

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      +...++|||+||...+||+-|..+|++.|.+..+            ++         .|.                   .
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~------------k~---------i~~-------------------e   42 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKT------------KV---------IFD-------------------E   42 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccc------------ee---------ehh-------------------h
Confidence            3457899999999999999999999999985432            21         121                   4


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~  330 (521)
                      |+|.|+....         .++.+.               ......|||+.|.+.++.++|++.|.+||.|.+++|++|.
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            5555543210         111111               1223469999999999999999999999999999999999


Q ss_pred             CCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCC
Q 009954          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGG  410 (521)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (521)
                      .|+++|||+||.|-+.++|+.||..|||.+|++|.|+-.|++.+....-...         .....+..+          
T Consensus        99 ~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~---------ltfdeV~NQ----------  159 (321)
T KOG0148|consen   99 NTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKP---------LTFDEVYNQ----------  159 (321)
T ss_pred             cCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccCCCC---------ccHHHHhcc----------
Confidence            9999999999999999999999999999999999999999987541111000         111112222          


Q ss_pred             CCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHH
Q 009954          411 MSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATA  490 (521)
Q Consensus       411 ~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~A  490 (521)
                         .++.++.|+|-....-+.           +++|++.|++||.|..|+|.++.         |+|||+|.+.|.|..|
T Consensus       160 ---ssp~NtsVY~G~I~~~lt-----------e~~mr~~Fs~fG~I~EVRvFk~q---------GYaFVrF~tkEaAahA  216 (321)
T KOG0148|consen  160 ---SSPDNTSVYVGNIASGLT-----------EDLMRQTFSPFGPIQEVRVFKDQ---------GYAFVRFETKEAAAHA  216 (321)
T ss_pred             ---CCCCCceEEeCCcCcccc-----------HHHHHHhcccCCcceEEEEeccc---------ceEEEEecchhhHHHH
Confidence               223666666643332111           15899999999999999999986         9999999999999999


Q ss_pred             HHHHhCCeeCCcEEEEEEcCCC
Q 009954          491 KNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       491 i~~lng~~~~gr~l~v~~~~~~  512 (521)
                      |..|||..|+|+.|+|+|-.+.
T Consensus       217 Iv~mNntei~G~~VkCsWGKe~  238 (321)
T KOG0148|consen  217 IVQMNNTEIGGQLVRCSWGKEG  238 (321)
T ss_pred             HHHhcCceeCceEEEEeccccC
Confidence            9999999999999999995543

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

Probab=100.00  E-value=1.8e-34  Score=275.26  Aligned_cols=323  Identities=16%  Similarity=0.241  Sum_probs=223.8

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEE
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v  253 (521)
                      .||||++||+.++.++|.++|+.+|.|.+|++      |.+.....++||+||+|.-.+++++|+ ++++..|.|+.|.|
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            58999999999999999999999999887643      444455678999999999999999999 79999999999999


Q ss_pred             eCCCCCCccccccCCCCCCC-CCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 009954          254 RRPTDYNPTLAAALGPGQPS-PNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (521)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~  332 (521)
                      ..+...........+..... .....    ..+...-......+|.|+|||+.|...+|..+|+.||.|..|.|++....
T Consensus        80 ~~A~~R~r~e~~~~~e~~~veK~~~q----~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dg  155 (678)
T KOG0127|consen   80 DPAKKRARSEEVEKGENKAVEKPIEQ----KRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDG  155 (678)
T ss_pred             ccccccccchhcccccchhhhccccc----CCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCC
Confidence            98776655432211111000 00000    00000000122468999999999999999999999999999999988755


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHH---HHHHHHH-HHHH-HHhhhc------
Q 009954          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESI---LAQAQQH-IAIQ-KMALQT------  401 (521)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~---~~~~~~~-~~~~-~~~~~~------  401 (521)
                      +.. |||||+|....+|.+||+.+||..|.|++|.|.||-++......+...   +..+... .... ......      
T Consensus       156 klc-GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed  234 (678)
T KOG0127|consen  156 KLC-GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEED  234 (678)
T ss_pred             Ccc-ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhc
Confidence            554 999999999999999999999999999999999998854433221110   0000000 0000 000000      


Q ss_pred             ----------cCCCCC----------------CC--CCCCCCCCcceEEEeeCcCC--cccCCChHHHHHHHHHHHHhhc
Q 009954          402 ----------SGMNTL----------------GG--GMSLFGETLAKVLCLTEAIT--ADALADDEEYEEILEDMREECG  451 (521)
Q Consensus       402 ----------~~~~~~----------------~~--~~~~~~~~~~~v~~l~~~~~--~~~~~~~~~~~~~~~dl~~~f~  451 (521)
                                ..+++-                ..  +....+........+....+  ..-+..|++|.++++.|.++|+
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                      000000                00  00000011111111111111  1223458889999999999999


Q ss_pred             cccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHH-----hC-CeeCCcEEEEEEcCC
Q 009954          452 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL-----SG-RKFGGNTVNAFYYPE  511 (521)
Q Consensus       452 ~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~l-----ng-~~~~gr~l~v~~~~~  511 (521)
                      +||+|..+.|+.++.++.+   .|+|||.|.+..+|..||+..     .| ..|.||.|+|..+-.
T Consensus       315 kFG~v~ya~iV~~k~T~~s---kGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~  377 (678)
T KOG0127|consen  315 KFGEVKYAIIVKDKDTGHS---KGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVT  377 (678)
T ss_pred             hhccceeEEEEeccCCCCc---ccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccc
Confidence            9999999999999988876   689999999999999999976     24 789999999998644

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

Probab=100.00  E-value=2.2e-34  Score=261.56  Aligned_cols=323  Identities=26%  Similarity=0.397  Sum_probs=241.7

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      +..-.|.||||.|.+.+.|+.|+..|.+||.|++.+.      ..+..+++++|||||+|+-+|.|+.|+ +|||.+++|
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            3456889999999999999999999999999865433      566668899999999999999999999 799999999


Q ss_pred             ceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 009954          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (521)
Q Consensus       249 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~  328 (521)
                      +.|+|.++..-...        +|....          ........++|||..+.++.+|+||+..|+.||+|..|.+.+
T Consensus       183 RNiKVgrPsNmpQA--------QpiID~----------vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr  244 (544)
T KOG0124|consen  183 RNIKVGRPSNMPQA--------QPIIDM----------VQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLAR  244 (544)
T ss_pred             ccccccCCCCCccc--------chHHHH----------HHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeec
Confidence            99999976543221        111000          001123457899999999999999999999999999999999


Q ss_pred             cCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCc--h------HHHHHHHHHHHHHHHHH--Hh
Q 009954          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSK--T------EQESILAQAQQHIAIQK--MA  398 (521)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~--~------~~~~~~~~~~~~~~~~~--~~  398 (521)
                      ++..+..+||+||+|.+..+...|+..||-+-++|..|+|..+.......  +      ........+.....+..  ..
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            99889999999999999999999999999999999999998775411110  0      00001111111111111  01


Q ss_pred             hhcc-----CCC-----------------------------------CC---------CCCCCC----------------
Q 009954          399 LQTS-----GMN-----------------------------------TL---------GGGMSL----------------  413 (521)
Q Consensus       399 ~~~~-----~~~-----------------------------------~~---------~~~~~~----------------  413 (521)
                      ....     +..                                   .|         |...|.                
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            0000     000                                   00         000000                


Q ss_pred             ------------------------------------CCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhcccccee
Q 009954          414 ------------------------------------FGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLV  457 (521)
Q Consensus       414 ------------------------------------~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~  457 (521)
                                                          .-...++|++|.|.++++++.+     +++.+|.+.|++||.|.
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                                                0145678999999999998754     56679999999999999


Q ss_pred             EEEecCCCCCCCCC-CCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCcccccCCC
Q 009954          458 NVVIPRPDQNGGET-PGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYSA  521 (521)
Q Consensus       458 ~v~i~~~~~~~~~~-~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~~~~~~~  521 (521)
                      .|.|......++.- .=.-..||+|....++.+|.+.|+|++|+|++|....|+...|.+++|+.
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            99998876443210 00234799999999999999999999999999999999999999999984

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

Probab=100.00  E-value=3.8e-33  Score=259.29  Aligned_cols=173  Identities=25%  Similarity=0.384  Sum_probs=146.1

Q ss_pred             hhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccC-cee
Q 009954          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG-IIF  246 (521)
Q Consensus       169 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g-~~~  246 (521)
                      +.+.+.-++||+-||..++|.||+++|++||.+..+++      ++|..++.++|||||.|.+.++|.+|+ .|+. +.|
T Consensus        29 ~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl------~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktl  102 (510)
T KOG0144|consen   29 NPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINL------IKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTL  102 (510)
T ss_pred             CCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEe------ecccccCcccceEEEEeccHHHHHHHHHHhhccccc
Confidence            34456678999999999999999999999999765443      788888899999999999999999999 6765 557


Q ss_pred             cC--ceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEE
Q 009954          247 EG--VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF  324 (521)
Q Consensus       247 ~g--~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v  324 (521)
                      .|  .+|.|+++......                            ....++|||+-|+..++|.+|+++|++||.|++|
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            77  67888875433221                            1123689999999999999999999999999999


Q ss_pred             EEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCC-eeCC--eEEEEEEccCCCC
Q 009954          325 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL-KMGD--KTLTVRRATASGQ  376 (521)
Q Consensus       325 ~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~-~~~g--~~l~v~~~~~~~~  376 (521)
                      .|.++. .+.++|||||.|.+.|.|..||+.|||. .+.|  .+|.|.|++.+..
T Consensus       155 ~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkd  208 (510)
T KOG0144|consen  155 YILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKD  208 (510)
T ss_pred             hheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCC
Confidence            999995 8999999999999999999999999994 4665  6799999988443

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

Probab=100.00  E-value=3.2e-32  Score=279.56  Aligned_cols=303  Identities=16%  Similarity=0.164  Sum_probs=197.7

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC--CCCeEEEEecCHHHHHHHH-HccCceecC--
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH--EKKFAFVEMRTVEEASNAM-ALDGIIFEG--  248 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~--~~g~afV~f~~~~~a~~A~-~l~g~~~~g--  248 (521)
                      ..+|||+||++.+|+++|+++|+.||.|            ..+.+..  ..++|||+|.+.++|.+|+ .|||..|.+  
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            4444333  3469999999999999999 699999965  


Q ss_pred             ceEEEeCCCCCCcc------cc-----ccC-CC-----------CCCCC---------Ccccccc---------------
Q 009954          249 VAVRVRRPTDYNPT------LA-----AAL-GP-----------GQPSP---------NLNLAAV---------------  281 (521)
Q Consensus       249 ~~i~v~~~~~~~~~------~~-----~~~-~~-----------~~~~~---------~~~~~~~---------------  281 (521)
                      +.|+|.|++...-.      ..     ..+ +.           ..+..         ....+..               
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            47888776531110      00     000 00           00000         0000000               


Q ss_pred             ----------cCC--C-------CCCCCCCCCCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEE
Q 009954          282 ----------GLA--S-------GAIGGAEGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC  341 (521)
Q Consensus       282 ----------~~~--~-------~~~~~~~~~~~l~v~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV  341 (521)
                                .+.  +       .........++|||+||+. .+++++|.++|+.||.|..|+|+.++     +|||||
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                      000  0       0000122456899999998 69999999999999999999999873     689999


Q ss_pred             EEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhh-ccCCCCCCCCCCCCCCCcce
Q 009954          342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQ-TSGMNTLGGGMSLFGETLAK  420 (521)
Q Consensus       342 ~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  420 (521)
                      +|.+.++|..||..|||..|.|+.|.|.+++......+..........   ........ ......++.........++.
T Consensus       319 ~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~---~~~d~~~~~~~r~~~~~~~~~~~~~~ps~  395 (481)
T TIGR01649       319 EMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLT---SYKDYSSSRNHRFKKPGSANKNNIQPPSA  395 (481)
T ss_pred             EECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCc---ccccccCCccccCCCcccccccccCCCCc
Confidence            999999999999999999999999999998653211111000000000   00000000 00000011000000112344


Q ss_pred             EEEeeCcCCcccCCChHHHHHHHHHHHHhhccccc--eeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCe
Q 009954          421 VLCLTEAITADALADDEEYEEILEDMREECGKYGT--LVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRK  498 (521)
Q Consensus       421 v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~--I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~  498 (521)
                      .|.+.|+...          .++++|+++|+.||.  |..|++.... ++    ..|+|||+|.+.++|..||..|||+.
T Consensus       396 ~L~v~NLp~~----------~tee~L~~lF~~~G~~~i~~ik~~~~~-~~----~~~~gfVeF~~~e~A~~Al~~ln~~~  460 (481)
T TIGR01649       396 TLHLSNIPLS----------VSEEDLKELFAENGVHKVKKFKFFPKD-NE----RSKMGLLEWESVEDAVEALIALNHHQ  460 (481)
T ss_pred             EEEEecCCCC----------CCHHHHHHHHHhcCCccceEEEEecCC-CC----cceeEEEEcCCHHHHHHHHHHhcCCc
Confidence            4555555321          122599999999998  8889886543 22    14788999999999999999999999


Q ss_pred             eCCcE------EEEEEcCC
Q 009954          499 FGGNT------VNAFYYPE  511 (521)
Q Consensus       499 ~~gr~------l~v~~~~~  511 (521)
                      |+|+.      |+|+|...
T Consensus       461 l~~~~~~~~~~lkv~fs~~  479 (481)
T TIGR01649       461 LNEPNGSAPYHLKVSFSTS  479 (481)
T ss_pred             cCCCCCCccceEEEEeccC
Confidence            99985      99999864

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=7.2e-30  Score=267.08  Aligned_cols=192  Identities=19%  Similarity=0.205  Sum_probs=141.5

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+|||..+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|..|+ .|||+.|.|+.|
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~------~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l  367 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNL------IKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKL  367 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE------EecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            4578999999999999999999999998654322      344456778999999999999999999 799999999999


Q ss_pred             EEeCCCCCCccccccCCC-CCCCCCcccccccCCC-CCCCCCCCCCeEEEcCCCCCC----------CHHHHHHHHHhcC
Q 009954          252 RVRRPTDYNPTLAAALGP-GQPSPNLNLAAVGLAS-GAIGGAEGPDRVFVGGLPYYF----------TETQIKELLESFG  319 (521)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~v~nLp~~~----------te~~l~~~F~~~G  319 (521)
                      .|.++............. ..+....   ...... .......+..+|+|.||...-          ..++|+++|++||
T Consensus       368 ~v~~a~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G  444 (509)
T TIGR01642       368 HVQRACVGANQATIDTSNGMAPVTLL---AKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYG  444 (509)
T ss_pred             EEEECccCCCCCCccccccccccccc---cccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcC
Confidence            999875432211110000 0000000   000000 001112345679999996421          1268999999999


Q ss_pred             CeeEEEEeecC---CCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          320 TLHGFDLVKDR---DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       320 ~i~~v~i~~~~---~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .|..|.|+++.   .++...|+|||+|.+.++|++||..|||.+|+|+.|.|.|...
T Consensus       445 ~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       445 PLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             CeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            99999998752   3456689999999999999999999999999999999999854

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

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

Probab=99.97  E-value=1.2e-29  Score=261.70  Aligned_cols=176  Identities=21%  Similarity=0.302  Sum_probs=139.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      ++|||+|||..+++++|+++|++||.|..|+|+.++.+|.++|||||+|.+.++|.+||. |+|..|.|++|.|.++...
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 8999999999999987431


Q ss_pred             CCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhcccc
Q 009954          375 GQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYG  454 (521)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG  454 (521)
                      .....                ...     ....+.     .+. ...|.+.|+...          .++++|+++|+.||
T Consensus       169 ~~~~~----------------~~~-----~~~~~~-----~p~-~~~l~v~nl~~~----------~te~~l~~~f~~~G  211 (457)
T TIGR01622       169 KNRAA----------------KAA-----THQPGD-----IPN-FLKLYVGNLHFN----------ITEQELRQIFEPFG  211 (457)
T ss_pred             hhhhh----------------hcc-----cccCCC-----CCC-CCEEEEcCCCCC----------CCHHHHHHHHHhcC
Confidence            11000                000     000000     011 233333333211          12259999999999


Q ss_pred             ceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCC
Q 009954          455 TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       455 ~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~  511 (521)
                      .|..|.|+.+..+|..   +|+|||+|.+.++|..|++.|||..|+|+.|+|.|+..
T Consensus       212 ~i~~v~~~~d~~~g~~---~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       212 DIEDVQLHRDPETGRS---KGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CeEEEEEEEcCCCCcc---ceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            9999999998766543   68899999999999999999999999999999999763

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=3.4e-30  Score=249.57  Aligned_cols=170  Identities=19%  Similarity=0.311  Sum_probs=146.8

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      .....++|||+|||+++|+++|+++|..||.|..+.      ++.+..++.++|||||+|.++++|.+|+ +|++..|.+
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 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCR------IMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRN  176 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE------EEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCC
Confidence            345678999999999999999999999999864422      1344456678899999999999999999 799999999


Q ss_pred             ceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 009954          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (521)
Q Consensus       249 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~  328 (521)
                      ++|+|.++.....                             ....++|||+|||..+++++|+++|++||.|..|.|+.
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            9999987543110                             01235799999999999999999999999999999999


Q ss_pred             cCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC--eEEEEEEccCC
Q 009954          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATAS  374 (521)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~~~~  374 (521)
                      ++.+|.++|||||+|.+.++|++||+.||+..|.|  +.|+|.++...
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  79999999763

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=2.8e-29  Score=243.16  Aligned_cols=172  Identities=26%  Similarity=0.352  Sum_probs=144.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||.++|+++|+++|+.||.|++|+|+.++.++.++|||||+|.++++|.+||+.|+|..|.++.|+|.|+
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            44578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhc
Q 009954          372 TASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  451 (521)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~  451 (521)
                      .+....                                    .....+.|-+|+..++             +++|+++|+
T Consensus       185 ~p~~~~------------------------------------~~~~~lfV~nLp~~vt-------------ee~L~~~F~  215 (346)
T TIGR01659       185 RPGGES------------------------------------IKDTNLYVTNLPRTIT-------------DDQLDTIFG  215 (346)
T ss_pred             cccccc------------------------------------cccceeEEeCCCCccc-------------HHHHHHHHH
Confidence            642100                                    0002222333333322             359999999


Q ss_pred             cccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCC--cEEEEEEcCCCCcc
Q 009954          452 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYYPEDKYF  515 (521)
Q Consensus       452 ~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~g--r~l~v~~~~~~~~~  515 (521)
                      +||+|+.|.|+++..++.+   +|+|||+|.+.++|++||+.||+..|.|  +.|+|.|+.+..-.
T Consensus       216 ~fG~V~~v~i~~d~~tg~~---kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~~  278 (346)
T TIGR01659       216 KYGQIVQKNILRDKLTGTP---RGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKA  278 (346)
T ss_pred             hcCCEEEEEEeecCCCCcc---ceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCccccc
Confidence            9999999999998877765   5899999999999999999999999866  79999998876443

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=99.96  E-value=5.4e-29  Score=242.20  Aligned_cols=242  Identities=19%  Similarity=0.335  Sum_probs=193.8

Q ss_pred             eEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEEe
Q 009954          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR  254 (521)
Q Consensus       176 ~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v~  254 (521)
                      .||||   +++|+..|.++|+++|.++..      ..+.+. +  +-|||||.|.++++|.+|| .+|...+.|++|+|.
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            58998   999999999999999997652      223444 3  8999999999999999999 799999999999999


Q ss_pred             CCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCC
Q 009954          255 RPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN  334 (521)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~  334 (521)
                      |....                                  +..|||.||+++++..+|.++|+.||.|++|+|..+. .| 
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            84311                                  1239999999999999999999999999999999995 56 


Q ss_pred             cceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCC
Q 009954          335 SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLF  414 (521)
Q Consensus       335 ~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  414 (521)
                      ++|| ||+|.++++|.+|+..|||..+.|+.|.|.....+......... ..                            
T Consensus       115 ~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~-~~----------------------------  164 (369)
T KOG0123|consen  115 SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLGE-YK----------------------------  164 (369)
T ss_pred             ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhcccccc-hh----------------------------
Confidence            9999 99999999999999999999999999999988653222111111 00                            


Q ss_pred             CCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHH
Q 009954          415 GETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL  494 (521)
Q Consensus       415 ~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~l  494 (521)
                       ..-+.+++.....+..+           ..|.++|..||.|..+.++.+....  +  .|++||.|.++++|..|+..|
T Consensus       165 -~~~t~v~vk~~~~~~~~-----------~~l~~~f~~~g~i~s~~v~~~~~g~--~--~~~gfv~f~~~e~a~~av~~l  228 (369)
T KOG0123|consen  165 -KRFTNVYVKNLEEDSTD-----------EELKDLFSAYGSITSVAVMRDSIGK--S--KGFGFVNFENPEDAKKAVETL  228 (369)
T ss_pred             -hhhhhhheeccccccch-----------HHHHHhhcccCcceEEEEeecCCCC--C--CCccceeecChhHHHHHHHhc
Confidence             01222333332222221           4899999999999999999987433  2  356699999999999999999


Q ss_pred             hCCeeCCcEEEEEEcCC
Q 009954          495 SGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       495 ng~~~~gr~l~v~~~~~  511 (521)
                      +|..++|..+-|.-+..
T Consensus       229 ~~~~~~~~~~~V~~aqk  245 (369)
T KOG0123|consen  229 NGKIFGDKELYVGRAQK  245 (369)
T ss_pred             cCCcCCccceeeccccc
Confidence            99999998888876544

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

Probab=99.96  E-value=2.6e-28  Score=237.46  Aligned_cols=290  Identities=22%  Similarity=0.353  Sum_probs=218.0

Q ss_pred             CCCCCCCCccccchhhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHH
Q 009954          155 LGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE  234 (521)
Q Consensus       155 ~~~~~~~p~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~  234 (521)
                      ...+.+.+..+|+.+.....  |||.||++.++..+|.++|+.||.|++|.        +...-..++|| ||+|.++++
T Consensus        59 ~~~~~~~~~rim~s~rd~~~--~~i~nl~~~~~~~~~~d~f~~~g~ilS~k--------v~~~~~g~kg~-FV~f~~e~~  127 (369)
T KOG0123|consen   59 FDVLKGKPIRIMWSQRDPSL--VFIKNLDESIDNKSLYDTFSEFGNILSCK--------VATDENGSKGY-FVQFESEES  127 (369)
T ss_pred             CcccCCcEEEeehhccCCce--eeecCCCcccCcHHHHHHHHhhcCeeEEE--------EEEcCCCceee-EEEeCCHHH
Confidence            34556677777777655444  99999999999999999999999987763        22222338999 999999999


Q ss_pred             HHHHH-HccCceecCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHH
Q 009954          235 ASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKE  313 (521)
Q Consensus       235 a~~A~-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~  313 (521)
                      |.+|+ .+||..+.|++|.|..............                    . .....+.++|.+++.+++++.|.+
T Consensus       128 a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~--------------------~-~~~~~t~v~vk~~~~~~~~~~l~~  186 (369)
T KOG0123|consen  128 AKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLG--------------------E-YKKRFTNVYVKNLEEDSTDEELKD  186 (369)
T ss_pred             HHHHHHHhcCcccCCCeeEEeeccchhhhccccc--------------------c-hhhhhhhhheeccccccchHHHHH
Confidence            99999 7999999999999976544332211000                    0 122235799999999999999999


Q ss_pred             HHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHH
Q 009954          314 LLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIA  393 (521)
Q Consensus       314 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~  393 (521)
                      +|..+|.|.++.++.+. .|.++||+||+|.+.++|..|+..|+|..+.+..+.|..+..    ..+....+........
T Consensus       187 ~f~~~g~i~s~~v~~~~-~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqk----k~e~~~~l~~~~~~~~  261 (369)
T KOG0123|consen  187 LFSAYGSITSVAVMRDS-IGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQK----KSEREAELKRKFEQEF  261 (369)
T ss_pred             hhcccCcceEEEEeecC-CCCCCCccceeecChhHHHHHHHhccCCcCCccceeeccccc----chhhHHHHhhhhHhhh
Confidence            99999999999999985 677999999999999999999999999999999999998865    2222222222211111


Q ss_pred             HHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCC
Q 009954          394 IQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPG  473 (521)
Q Consensus       394 ~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g  473 (521)
                      .+....              ....+..|-++...++.             +.|.++|+.||+|..++|+.+.. +.   .
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            111100              00122222222222222             48999999999999999999873 33   3


Q ss_pred             ccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          474 VGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       474 ~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      +|++||+|.+.++|..|+..+||..++|+.|.|.+.-..
T Consensus       311 kG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~  349 (369)
T KOG0123|consen  311 KGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRK  349 (369)
T ss_pred             cceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhh
Confidence            578899999999999999999999999999999886533

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.95  E-value=3.2e-27  Score=235.45  Aligned_cols=197  Identities=23%  Similarity=0.374  Sum_probs=144.8

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC--c
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--V  249 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g--~  249 (521)
                      ..++|||+|||..+++++|.++|.+||.+..+.      .+.+...+.++|||||+|.+.++|..|+ .|||..+.|  .
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~------~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~  161 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSR------ILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTE  161 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEE------EEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCce
Confidence            356899999999999999999999999853211      0112223457899999999999999999 799999887  5


Q ss_pred             eEEEeCCCCCCccccccCC--------CCCCC-------------------------CCc--------------------
Q 009954          250 AVRVRRPTDYNPTLAAALG--------PGQPS-------------------------PNL--------------------  276 (521)
Q Consensus       250 ~i~v~~~~~~~~~~~~~~~--------~~~~~-------------------------~~~--------------------  276 (521)
                      +|.|.++............        +....                         ...                    
T Consensus       162 ~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  241 (352)
T TIGR01661       162 PITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAA  241 (352)
T ss_pred             eEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhccccccccc
Confidence            7888876533211000000        00000                         000                    


Q ss_pred             c--------cccccCCCC--CCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCh
Q 009954          277 N--------LAAVGLASG--AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP  346 (521)
Q Consensus       277 ~--------~~~~~~~~~--~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~  346 (521)
                      .        ........+  .........+|||+|||..+++++|.++|++||.|.+|+|+.++.+|.++|||||+|.+.
T Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~  321 (352)
T TIGR01661       242 QRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNY  321 (352)
T ss_pred             ccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCH
Confidence            0        000000000  000112234799999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCeeCCeEEEEEEccCCC
Q 009954          347 AVTDIACAALNGLKMGDKTLTVRRATASG  375 (521)
Q Consensus       347 ~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (521)
                      ++|.+||+.|||..|+|+.|+|.|...+.
T Consensus       322 ~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       322 DEAAMAILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             HHHHHHHHHhCCCEECCeEEEEEEccCCC
Confidence            99999999999999999999999997654

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

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

Probab=99.95  E-value=3.3e-27  Score=240.02  Aligned_cols=175  Identities=20%  Similarity=0.411  Sum_probs=141.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||+.+++++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.+...
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            46899999999999999999999999999999999999999999999999999999999999999999999999997654


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEE--eeCcCCcccCCChHHHHHHHHHHHHhhc
Q 009954          374 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLC--LTEAITADALADDEEYEEILEDMREECG  451 (521)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~--l~~~~~~~~~~~~~~~~~~~~dl~~~f~  451 (521)
                      ..+..+.....                           ........+|++  |+..++.             ++|+++|+
T Consensus       187 ~p~a~~~~~~~---------------------------~~~~~~~~rLfVgnLp~~vte-------------edLk~lFs  226 (612)
T TIGR01645       187 MPQAQPIIDMV---------------------------QEEAKKFNRIYVASVHPDLSE-------------TDIKSVFE  226 (612)
T ss_pred             ccccccccccc---------------------------cccccccceEEeecCCCCCCH-------------HHHHHHHh
Confidence            22211100000                           000011223333  3333233             59999999


Q ss_pred             cccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCC
Q 009954          452 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       452 ~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~  511 (521)
                      .||.|+.|.|+++..++..   +|||||+|.+.++|..||..|||+.|+|+.|+|.++..
T Consensus       227 ~FG~I~svrl~~D~~tgks---KGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       227 AFGEIVKCQLARAPTGRGH---KGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             hcCCeeEEEEEecCCCCCc---CCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCC
Confidence            9999999999998866543   57889999999999999999999999999999998653

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=2.2e-27  Score=208.25  Aligned_cols=178  Identities=18%  Similarity=0.342  Sum_probs=150.4

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      .--|||+.|.+.++.++|++.|.+||+|..+.      +|.|..+.+++||+||.|...++|+.|| +|||+=|++|.|+
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~ak------virD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IR  135 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAK------VIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIR  135 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccce------EeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceee
Confidence            45699999999999999999999999986554      5899999999999999999999999999 7999999999999


Q ss_pred             EeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 009954          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (521)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~  332 (521)
                      -+|+.-+....             +.................++|||+|++..++|++|++.|++||.|..|+|.++   
T Consensus       136 TNWATRKp~e~-------------n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~---  199 (321)
T KOG0148|consen  136 TNWATRKPSEM-------------NGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD---  199 (321)
T ss_pred             ccccccCcccc-------------CCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc---
Confidence            99976544110             00001111111222345578999999999999999999999999999999998   


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCC
Q 009954          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQ  376 (521)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~  376 (521)
                         +|||||.|.+.|.|.+||..|||..|+|..|++.|.+....
T Consensus       200 ---qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  200 ---QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             ---cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCC
Confidence               78999999999999999999999999999999999977443

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

Probab=99.93  E-value=4.7e-25  Score=218.28  Aligned_cols=290  Identities=20%  Similarity=0.254  Sum_probs=206.5

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      ......-|+|+|||..+..++|..+|..||.            |..+.+....--|+|+|.++.+|.+|+ .|....+..
T Consensus       381 ~~rs~~vil~kNlpa~t~~~elt~~F~~fG~------------i~rvllp~~G~~aiv~fl~p~eAr~Afrklaysr~k~  448 (725)
T KOG0110|consen  381 AERSDTVILVKNLPAGTLSEELTEAFLRFGE------------IGRVLLPPGGTGAIVEFLNPLEARKAFRKLAYSRFKS  448 (725)
T ss_pred             hhhhcceeeeccCccccccHHHHHHhhcccc------------cceeecCcccceeeeeecCccchHHHHHHhchhhhcc
Confidence            3344577999999999999999999999998            444444434445999999999999999 699988888


Q ss_pred             ceEEEeCCCCCCcccc---ccC--CCCCC---CCCcccccc----c--CC--CCC-----CCCCCCCCeEEEcCCCCCCC
Q 009954          249 VAVRVRRPTDYNPTLA---AAL--GPGQP---SPNLNLAAV----G--LA--SGA-----IGGAEGPDRVFVGGLPYYFT  307 (521)
Q Consensus       249 ~~i~v~~~~~~~~~~~---~~~--~~~~~---~~~~~~~~~----~--~~--~~~-----~~~~~~~~~l~v~nLp~~~t  307 (521)
                      .++.+.|+........   ...  .+..+   .+.......    .  ..  -+.     .......++|||.||+++++
T Consensus       449 ~plyle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt  528 (725)
T KOG0110|consen  449 APLYLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTT  528 (725)
T ss_pred             CccccccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccc
Confidence            8888877553222200   000  00000   000000000    0  00  000     01112234499999999999


Q ss_pred             HHHHHHHHHhcCCeeEEEEeecCCC---CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHH
Q 009954          308 ETQIKELLESFGTLHGFDLVKDRDT---GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESI  384 (521)
Q Consensus       308 e~~l~~~F~~~G~i~~v~i~~~~~~---g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~  384 (521)
                      .++|..+|.+.|.|.++.|...+..   -.|.|||||+|.++++|+.|++.|+|+.|.|..|.|.++..+....-.    
T Consensus       529 ~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  529 LEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVG----  604 (725)
T ss_pred             hhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccccc----
Confidence            9999999999999999988776421   135599999999999999999999999999999999999631111000    


Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCC
Q 009954          385 LAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRP  464 (521)
Q Consensus       385 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~  464 (521)
                                    .+          .+. ....++|           |+.|.+|+.+..+|+++|+.||.|..|.|++.
T Consensus       605 --------------K~----------~~~-kk~~tKI-----------lVRNipFeAt~rEVr~LF~aFGqlksvRlPKK  648 (725)
T KOG0110|consen  605 --------------KK----------KSK-KKKGTKI-----------LVRNIPFEATKREVRKLFTAFGQLKSVRLPKK  648 (725)
T ss_pred             --------------cc----------ccc-cccccee-----------eeeccchHHHHHHHHHHHhcccceeeeccchh
Confidence                          00          000 0011222           33455777888999999999999999999997


Q ss_pred             CCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCc
Q 009954          465 DQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  514 (521)
Q Consensus       465 ~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~  514 (521)
                      ...+   -+.|++||+|-++.+|.+|+..|....|-||.|.+.|+..+..
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            3222   2356779999999999999999999999999999999988764

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

Probab=99.92  E-value=5.7e-25  Score=205.02  Aligned_cols=173  Identities=26%  Similarity=0.398  Sum_probs=140.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCe-eC--CeEEEEE
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK-MG--DKTLTVR  369 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~-~~--g~~l~v~  369 (521)
                      ..-+|||+-+|..++|.||+++|++||.|..|.|++|+.||.++|||||.|.+.++|.+|+.+||+.+ |-  ..+|.|.
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk  112 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVK  112 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeec
Confidence            33479999999999999999999999999999999999999999999999999999999999999854 44  4788999


Q ss_pred             EccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHh
Q 009954          370 RATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREE  449 (521)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~  449 (521)
                      |++.......+                                   +...+|-.|+.-.+.             .+|+++
T Consensus       113 ~Ad~E~er~~~-----------------------------------e~KLFvg~lsK~~te-------------~evr~i  144 (510)
T KOG0144|consen  113 YADGERERIVE-----------------------------------ERKLFVGMLSKQCTE-------------NEVREI  144 (510)
T ss_pred             ccchhhhcccc-----------------------------------chhhhhhhccccccH-------------HHHHHH
Confidence            98642111100                                   022233334433333             499999


Q ss_pred             hccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCe-eCC--cEEEEEEcCCCCcccc
Q 009954          450 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRK-FGG--NTVNAFYYPEDKYFNK  517 (521)
Q Consensus       450 f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~-~~g--r~l~v~~~~~~~~~~~  517 (521)
                      |++||.|++|.|+++. .+.   .+|||||+|.+.|.|..||+.|||.. +.|  .+|.|.|++..+-..+
T Consensus       145 Fs~fG~Ied~~ilrd~-~~~---sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~  211 (510)
T KOG0144|consen  145 FSRFGHIEDCYILRDP-DGL---SRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDG  211 (510)
T ss_pred             HHhhCccchhhheecc-ccc---ccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCchH
Confidence            9999999999999987 433   36999999999999999999999987 666  6899999998775443

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

Probab=99.92  E-value=2.9e-25  Score=183.91  Aligned_cols=172  Identities=25%  Similarity=0.405  Sum_probs=143.3

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ....+|||+||+..++++.|.++|-+.|.++..+.      ..+..+...+|||||+|.++++|+.|+ -||...+.|++
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~i------PkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrp   80 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHI------PKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRP   80 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeec------chhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCce
Confidence            34568999999999999999999999997432211      222333457899999999999999999 59999999999


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeec
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVKD  329 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~-v~i~~~  329 (521)
                      |+|..+......                            .....+|||+||.+.++|..|.+.|+.||.|.. -+|+++
T Consensus        81 Irv~kas~~~~n----------------------------l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd  132 (203)
T KOG0131|consen   81 IRVNKASAHQKN----------------------------LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRD  132 (203)
T ss_pred             eEEEeccccccc----------------------------ccccccccccccCcchhHHHHHHHHHhccccccCCccccc
Confidence            999875421111                            112248999999999999999999999999765 478999


Q ss_pred             CCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCC
Q 009954          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQS  377 (521)
Q Consensus       330 ~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~  377 (521)
                      +.||.++|||||.|.+.|.+.+|+..|+|..+.+++|+|.|+..+...
T Consensus       133 ~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  133 PDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTK  180 (203)
T ss_pred             ccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCC
Confidence            999999999999999999999999999999999999999999875443

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

Probab=99.91  E-value=7.6e-24  Score=184.66  Aligned_cols=170  Identities=26%  Similarity=0.433  Sum_probs=146.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEE
Q 009954          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       290 ~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      ..+..++|.|.-||..+|+++|+.+|...|+|+++++++|+.+|.+-||+||.|.++++|++|++.|||..+..+.|+|+
T Consensus        37 t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   37 TDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             cCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            34566789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHh
Q 009954          370 RATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREE  449 (521)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~  449 (521)
                      |+.+....                                    .-..+..|-.|+...++.             +|..+
T Consensus       117 yARPSs~~------------------------------------Ik~aNLYvSGlPktMtqk-------------elE~i  147 (360)
T KOG0145|consen  117 YARPSSDS------------------------------------IKDANLYVSGLPKTMTQK-------------ELEQI  147 (360)
T ss_pred             eccCChhh------------------------------------hcccceEEecCCccchHH-------------HHHHH
Confidence            99762111                                    011455555666665554             89999


Q ss_pred             hccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCC--cEEEEEEcCC
Q 009954          450 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYYPE  511 (521)
Q Consensus       450 f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~g--r~l~v~~~~~  511 (521)
                      |++||.|..-+|..|..+|. ++  |.+||.|+..++|+.||+.|||..--|  .+|.|.|++.
T Consensus       148 Fs~fGrIItSRiL~dqvtg~-sr--GVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFann  208 (360)
T KOG0145|consen  148 FSPFGRIITSRILVDQVTGL-SR--GVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANN  208 (360)
T ss_pred             HHHhhhhhhhhhhhhcccce-ec--ceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCC
Confidence            99999999999999998876 34  555999999999999999999999877  4688888754

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

Probab=99.90  E-value=8.5e-24  Score=175.23  Aligned_cols=171  Identities=22%  Similarity=0.318  Sum_probs=143.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ....+|||+||+..++++-|.++|-+.|+|..|.++++..+...+|||||+|.++|+|+-|++.||+..|.|++|+|..+
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            34469999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             cCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhc
Q 009954          372 TASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  451 (521)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~  451 (521)
                      .. .+....                                  ...+.+|-+|...++.             ..|.+.|+
T Consensus        87 s~-~~~nl~----------------------------------vganlfvgNLd~~vDe-------------~~L~dtFs  118 (203)
T KOG0131|consen   87 SA-HQKNLD----------------------------------VGANLFVGNLDPEVDE-------------KLLYDTFS  118 (203)
T ss_pred             cc-cccccc----------------------------------ccccccccccCcchhH-------------HHHHHHHH
Confidence            52 111000                                  0134445555443333             37899999


Q ss_pred             cccceeEE-EecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          452 KYGTLVNV-VIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       452 ~fG~I~~v-~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      .||.|... .|+++..+|++   .|++||.|++.+.+.+||..|||..+++++++|+++-.+.
T Consensus       119 afG~l~~~P~i~rd~~tg~~---~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~  178 (203)
T KOG0131|consen  119 AFGVLISPPKIMRDPDTGNP---KGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKD  178 (203)
T ss_pred             hccccccCCcccccccCCCC---CCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecC
Confidence            99998775 88898877775   4677999999999999999999999999999999975543

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

Probab=99.90  E-value=1e-23  Score=192.20  Aligned_cols=173  Identities=21%  Similarity=0.424  Sum_probs=147.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      ++|||+.+.+.+-|+.|+..|.+||+|++|.+..|+.|++.+|||||+|+-+|.|+.|++.|||..++|+.|+|....+-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999988765


Q ss_pred             CCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhcccc
Q 009954          375 GQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYG  454 (521)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG  454 (521)
                      .|..+-.+.....+.                           ...+|++-....++.+           +||+..|+.||
T Consensus       194 pQAQpiID~vqeeAk---------------------------~fnRiYVaSvHpDLSe-----------~DiKSVFEAFG  235 (544)
T KOG0124|consen  194 PQAQPIIDMVQEEAK---------------------------KFNRIYVASVHPDLSE-----------TDIKSVFEAFG  235 (544)
T ss_pred             cccchHHHHHHHHHH---------------------------hhheEEeeecCCCccH-----------HHHHHHHHhhc
Confidence            555544433322211                           4556676655555543           59999999999


Q ss_pred             ceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEE
Q 009954          455 TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFY  508 (521)
Q Consensus       455 ~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~  508 (521)
                      +|++|.+.+....+.+ +  |++|++|.+...-..||..||-+.|||+-|+|--
T Consensus       236 ~I~~C~LAr~pt~~~H-k--GyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk  286 (544)
T KOG0124|consen  236 EIVKCQLARAPTGRGH-K--GYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGK  286 (544)
T ss_pred             ceeeEEeeccCCCCCc-c--ceeeEEeccccchHHHhhhcchhhcccceEeccc
Confidence            9999999999855553 4  5559999999999999999999999999999864

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

Probab=99.90  E-value=1.3e-22  Score=206.62  Aligned_cols=200  Identities=20%  Similarity=0.242  Sum_probs=147.8

Q ss_pred             HHHHHHHH-HccCceecCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHH
Q 009954          232 VEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQ  310 (521)
Q Consensus       232 ~~~a~~A~-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~  310 (521)
                      .++|.+|| +++|..+........+..+-              +.+.          .......++|||+|||.+++|++
T Consensus        19 ~~~a~~a~~~~~gy~~~~~~g~r~~g~Pp--------------~~~~----------~~~p~~~~~lFVgnLp~~~tEd~   74 (578)
T TIGR01648        19 DEAALKALLERTGYTLVQENGQRKYGGPP--------------PGWS----------GVQPGRGCEVFVGKIPRDLYEDE   74 (578)
T ss_pred             cHHHHHHHHHhhCccccccCCcccCCCCC--------------Cccc----------CCCCCCCCEEEeCCCCCCCCHHH
Confidence            57788888 79998887766666553211              1000          00123347899999999999999


Q ss_pred             HHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC-CeEEEEEEccCCCCCchHHHHHHHHHH
Q 009954          311 IKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRATASGQSKTEQESILAQAQ  389 (521)
Q Consensus       311 l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~~~~~~~~~~~~~~~~~~~~  389 (521)
                      |+++|++||.|..|+|+.| .+|.++|||||+|.+.++|++||+.||+..|. |+.|.|.++..                
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 79999999999999999999999999998885 77777765521                


Q ss_pred             HHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccc-eeEEEecCCCCCC
Q 009954          390 QHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGT-LVNVVIPRPDQNG  468 (521)
Q Consensus       390 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~-I~~v~i~~~~~~~  468 (521)
                                                .....|-+|+...+             +++|.++|++|+. |+.+.+.....+.
T Consensus       138 --------------------------~~rLFVgNLP~~~T-------------eeeL~eeFskv~egvv~vIv~~~~~~k  178 (578)
T TIGR01648       138 --------------------------NCRLFVGGIPKNKK-------------REEILEEFSKVTEGVVDVIVYHSAADK  178 (578)
T ss_pred             --------------------------CceeEeecCCcchh-------------hHHHHHHhhcccCCceEEEEecccccc
Confidence                                      02222223333222             2589999999874 5555554322111


Q ss_pred             CCCCCccEEEEEecCHHHHHHHHHHHhC--CeeCCcEEEEEEcCCCC
Q 009954          469 GETPGVGKVFLEYYDAVGCATAKNALSG--RKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       469 ~~~~g~g~afV~F~~~~~A~~Ai~~lng--~~~~gr~l~v~~~~~~~  513 (521)
                        .+..|+|||+|.++++|..|+..|+.  ..+.|+.|.|.|+..+.
T Consensus       179 --gKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~  223 (578)
T TIGR01648       179 --KKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEE  223 (578)
T ss_pred             --CccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccc
Confidence              23468889999999999999998864  35899999999987654

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.

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

Probab=99.90  E-value=5.5e-23  Score=198.46  Aligned_cols=177  Identities=20%  Similarity=0.305  Sum_probs=135.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCC
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASG  375 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (521)
                      +||+--|...+++-+|.++|+.+|.|..|.|+.|..++.++|.|||+|.+.+....||. |.|..+.|.+|.|.....  
T Consensus       181 tvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~sEa--  257 (549)
T KOG0147|consen  181 TVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLSEA--  257 (549)
T ss_pred             HHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecccHH--
Confidence            45555666667788999999999999999999999999999999999999999999995 999999999999997632  


Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhhhccCCCC-CCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhcccc
Q 009954          376 QSKTEQESILAQAQQHIAIQKMALQTSGMNT-LGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYG  454 (521)
Q Consensus       376 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG  454 (521)
                            +.            +......++.. .+...|.   ..+.|-+|             .++.++++|+.+|++||
T Consensus       258 ------ek------------nr~a~~s~a~~~k~~~~p~---~rl~vgnL-------------HfNite~~lr~ifepfg  303 (549)
T KOG0147|consen  258 ------EK------------NRAANASPALQGKGFTGPM---RRLYVGNL-------------HFNITEDMLRGIFEPFG  303 (549)
T ss_pred             ------HH------------HHHHhccccccccccccch---hhhhhccc-------------ccCchHHHHhhhccCcc
Confidence                  10            00111111111 1111111   11222222             22233369999999999


Q ss_pred             ceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          455 TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       455 ~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      .|+.|.++++..+|. ++|+|  ||+|.+.++|.+|+..|||+.|.|+.|+|..+++.
T Consensus       304 ~Ie~v~l~~d~~tG~-skgfG--fi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  304 KIENVQLTKDSETGR-SKGFG--FITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             cceeeeecccccccc-ccCcc--eEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            999999999988887 45555  99999999999999999999999999999988764

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

Probab=99.90  E-value=1.1e-22  Score=190.86  Aligned_cols=164  Identities=22%  Similarity=0.330  Sum_probs=138.2

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-------cCCCCeEEEEecCHHHHHHHH-H-c
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVEMRTVEEASNAM-A-L  241 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~-------~~~~g~afV~f~~~~~a~~A~-~-l  241 (521)
                      +...+.|||||||.+.++++|.+.|++.++           -|+++.+       .+++|||||+|.+...|..|- . +
T Consensus       161 Svan~RLFiG~IPK~k~keeIlee~~kVte-----------GVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~  229 (506)
T KOG0117|consen  161 SVANCRLFIGNIPKTKKKEEILEEMKKVTE-----------GVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLM  229 (506)
T ss_pred             eeecceeEeccCCccccHHHHHHHHHhhCC-----------CeeEEEEecCccccccccceEEEEeecchhHHHHHhhcc
Confidence            356789999999999999999999999865           2555544       356899999999999999988 4 4


Q ss_pred             cC-ceecCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCC
Q 009954          242 DG-IIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT  320 (521)
Q Consensus       242 ~g-~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~  320 (521)
                      ++ ..+.|..+.|.|+.+......                        ........|||+||+.+||++.|+++|+.||.
T Consensus       230 ~g~~klwgn~~tVdWAep~~e~de------------------------d~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~  285 (506)
T KOG0117|consen  230 PGKIKLWGNAITVDWAEPEEEPDE------------------------DTMSKVKVLYVRNLMESTTEETLKKLFNEFGK  285 (506)
T ss_pred             CCceeecCCcceeeccCcccCCCh------------------------hhhhheeeeeeeccchhhhHHHHHHHHHhccc
Confidence            54 668999999999876543211                        11233467999999999999999999999999


Q ss_pred             eeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCC
Q 009954          321 LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQS  377 (521)
Q Consensus       321 i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~  377 (521)
                      |+.|+.++|        ||||.|.+.++|.+||+.|||..|.|..|.|..|++....
T Consensus       286 veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~  334 (506)
T KOG0117|consen  286 VERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKK  334 (506)
T ss_pred             eEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhh
Confidence            999998877        9999999999999999999999999999999999884433

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

Probab=99.88  E-value=4.4e-22  Score=190.95  Aligned_cols=195  Identities=18%  Similarity=0.311  Sum_probs=144.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      .||||++||+.++.++|.++|+.+|+|..+.++.++.++.++||+||.|.-.++++.|++.+.+..|.|+.|.|.++...
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            59999999999999999999999999999999999999999999999999999999999999999999999999999774


Q ss_pred             CCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhcccc
Q 009954          375 GQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYG  454 (521)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG  454 (521)
                      .-........ ..     +......+..+    -- .-...+..-.|            +.|++|..-..||+.+|+.||
T Consensus        86 ~r~e~~~~~e-~~-----~veK~~~q~~~----~k-~~v~~~k~rLI------------IRNLPf~~k~~dLk~vFs~~G  142 (678)
T KOG0127|consen   86 ARSEEVEKGE-NK-----AVEKPIEQKRP----TK-AKVDLPKWRLI------------IRNLPFKCKKPDLKNVFSNFG  142 (678)
T ss_pred             ccchhccccc-ch-----hhhcccccCCc----ch-hhccCccceEE------------eecCCcccCcHHHHHHHhhcc
Confidence            3322100000 00     00000000000    00 00000011112            223333333369999999999


Q ss_pred             ceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCccc
Q 009954          455 TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFN  516 (521)
Q Consensus       455 ~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~~  516 (521)
                      .|..|.|++......    .|+|||+|....+|..||+.|||..|+||+|-|.|+-..+-+.
T Consensus       143 ~V~Ei~IP~k~dgkl----cGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye  200 (678)
T KOG0127|consen  143 KVVEIVIPRKKDGKL----CGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYE  200 (678)
T ss_pred             eEEEEEcccCCCCCc----cceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccccccc
Confidence            999999998774444    2888999999999999999999999999999999976554443

>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=2.3e-22  Score=178.59  Aligned_cols=146  Identities=25%  Similarity=0.457  Sum_probs=131.9

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEE
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v  253 (521)
                      -+|||||||..+++.+|+.+|++||+            |+.+.+.  |.||||..++...|..|+ .|+|..|.|..|.|
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygk------------VlECDIv--KNYgFVHiEdktaaedairNLhgYtLhg~nInV   68 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGK------------VLECDIV--KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINV   68 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCc------------eEeeeee--cccceEEeecccccHHHHhhcccceecceEEEE
Confidence            36999999999999999999999998            5555553  579999999999999999 69999999999999


Q ss_pred             eCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCC
Q 009954          254 RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG  333 (521)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g  333 (521)
                      +.++.+.                               ...++|+|+||.+.++.++|+..|++||+|..+.|+++    
T Consensus        69 eaSksKs-------------------------------k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd----  113 (346)
T KOG0109|consen   69 EASKSKS-------------------------------KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD----  113 (346)
T ss_pred             EeccccC-------------------------------CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc----
Confidence            9765442                               22358999999999999999999999999999999987    


Q ss_pred             CcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          334 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       334 ~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                          |+||.|.-.++|..|+..|+|..|.|+.++|+.++.
T Consensus       114 ----y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~sts  149 (346)
T KOG0109|consen  114 ----YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTS  149 (346)
T ss_pred             ----eeEEEEeeccchHHHHhcccccccccceeeeeeecc
Confidence                999999999999999999999999999999998876

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

Probab=99.87  E-value=5.8e-21  Score=173.90  Aligned_cols=208  Identities=20%  Similarity=0.366  Sum_probs=157.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeE
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT  365 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~--------~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~  365 (521)
                      .+.|||.|||.++|.+++.++|++||.|.        .|+|.++. .|.-+|=|+|.|...++...|++.|++..|.|+.
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            35699999999999999999999999886        48888885 6999999999999999999999999999999999


Q ss_pred             EEEEEccC--CCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCCh-HHHHHH
Q 009954          366 LTVRRATA--SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADD-EEYEEI  442 (521)
Q Consensus       366 l~v~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~-~~~~~~  442 (521)
                      |+|..|+-  ++...+..... .........+........+. +.- ....-....+++++.|+++++++..+ ....+|
T Consensus       213 ~rVerAkfq~Kge~~~~~k~k-~k~~~~kk~~k~q~k~~dw~-pd~-~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dl  289 (382)
T KOG1548|consen  213 LRVERAKFQMKGEYDASKKEK-GKCKDKKKLKKQQQKLLDWR-PDR-DDPSKARADRTVILKNMFTPEDFEKNPDLLNDL  289 (382)
T ss_pred             EEEehhhhhhccCcCcccccc-cccccHHHHHHHHHhhcccC-CCc-cccccccCCcEEEeeecCCHHHhccCHHHHHHH
Confidence            99999876  11111100000 00000001111111111111 000 01111245668899999999999887 668999


Q ss_pred             HHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          443 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       443 ~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      ++||++.|++||.|.+|.|.-.++.       |.|-|.|.+.++|..||+.|+|+.|+||+|.++..+-.
T Consensus       290 kedl~eec~K~G~v~~vvv~d~hPd-------GvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  290 KEDLTEECEKFGQVRKVVVYDRHPD-------GVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHHHhCCcceEEEeccCCC-------ceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            9999999999999999999865543       78899999999999999999999999999999987654

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

Probab=99.85  E-value=4.3e-21  Score=170.55  Aligned_cols=149  Identities=22%  Similarity=0.408  Sum_probs=127.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      .+|||+|||..+++.+|+.+|++||+|+.+.|+++        ||||..++...|..||..|||..|.|..|.|.-++.+
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            47999999999999999999999999999999987        8999999999999999999999999999999988753


Q ss_pred             CCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhcccc
Q 009954          375 GQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYG  454 (521)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG  454 (521)
                      ..                                        ..+++.+-+...+...           ++|+..|++||
T Consensus        75 sk----------------------------------------~stkl~vgNis~tctn-----------~ElRa~fe~yg  103 (346)
T KOG0109|consen   75 SK----------------------------------------ASTKLHVGNISPTCTN-----------QELRAKFEKYG  103 (346)
T ss_pred             CC----------------------------------------CccccccCCCCccccC-----------HHHhhhhcccC
Confidence            11                                        2222222222222221           58999999999


Q ss_pred             ceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          455 TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       455 ~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      +|+.|.|.+           +++||.|.-.++|..||..|+|..|.|+.++|+..+...
T Consensus       104 pviecdivk-----------dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrl  151 (346)
T KOG0109|consen  104 PVIECDIVK-----------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL  151 (346)
T ss_pred             Cceeeeeec-----------ceeEEEEeeccchHHHHhcccccccccceeeeeeecccc
Confidence            999999988           478999999999999999999999999999999876543

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

Probab=99.84  E-value=1.4e-20  Score=174.73  Aligned_cols=304  Identities=15%  Similarity=0.174  Sum_probs=190.5

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHH---ccCceecCc
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIFEGV  249 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~---l~g~~~~g~  249 (521)
                      .++-|+++|||.+++|++|.+++.+||.            |..+...+.+..||++|.+.+.|...+.   .-.-.+.|+
T Consensus        27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~------------vtn~~~lkGknQAflem~d~~sAvtmv~~y~~~~p~lr~~   94 (492)
T KOG1190|consen   27 PSKVVHLRNLPWEVTEEELISLGLPFGK------------VTNLLMLKGKNQAFLEMADEESAVTMVNYYTSVTPVLRGQ   94 (492)
T ss_pred             CcceeEeccCCccccHHHHHHhcccccc------------eeeeeeeccchhhhhhhcchhhhhheeecccccCccccCc
Confidence            4678999999999999999999999998            6777777788899999999999988552   222446788


Q ss_pred             eEEEeCCCCCCccccccC----C-----CCCCCC--CcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhc
Q 009954          250 AVRVRRPTDYNPTLAAAL----G-----PGQPSP--NLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESF  318 (521)
Q Consensus       250 ~i~v~~~~~~~~~~~~~~----~-----~~~~~~--~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~  318 (521)
                      +|.|+++....-......    +     ......  ...........|...+....-+++|.++-+.++-+-|..+|++|
T Consensus        95 ~~yiq~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~f  174 (492)
T KOG1190|consen   95 PIYIQYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKF  174 (492)
T ss_pred             ceeehhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhc
Confidence            888887442111100000    0     000000  11111111122222233334467899999999999999999999


Q ss_pred             CCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee--CCeEEEEEEccCCCCCchHHH------HH---HHH
Q 009954          319 GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVRRATASGQSKTEQE------SI---LAQ  387 (521)
Q Consensus       319 G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--~g~~l~v~~~~~~~~~~~~~~------~~---~~~  387 (521)
                      |.|..|.-....  ..  --|+|+|.+.+.|+.|..+|+|..|  +-|+|+|.|++.......-..      ..   ...
T Consensus       175 G~VlKIiTF~Kn--n~--FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~g  250 (492)
T KOG1190|consen  175 GFVLKIITFTKN--NG--FQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVG  250 (492)
T ss_pred             ceeEEEEEEecc--cc--hhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCC
Confidence            999888655542  11  1389999999999999999999876  447888888765110000000      00   000


Q ss_pred             ----HHHHHHHHHHhhhc----cCCCCCCCCC------CCC-CCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhcc
Q 009954          388 ----AQQHIAIQKMALQT----SGMNTLGGGM------SLF-GETLAKVLCLTEAITADALADDEEYEEILEDMREECGK  452 (521)
Q Consensus       388 ----~~~~~~~~~~~~~~----~~~~~~~~~~------~~~-~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~  452 (521)
                          ..+...........    .+...+....      +.. .+.-..++.+.|. .+        +..+.+-|..+|+.
T Consensus       251 d~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnl-n~--------~~VT~d~LftlFgv  321 (492)
T KOG1190|consen  251 DGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNL-NE--------EAVTPDVLFTLFGV  321 (492)
T ss_pred             ccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecC-ch--------hccchhHHHHHHhh
Confidence                00000000000000    0000000000      000 0111233333332 11        22233589999999


Q ss_pred             ccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEc
Q 009954          453 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  509 (521)
Q Consensus       453 fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~  509 (521)
                      ||.|..|+|..++.        -.|.|+|.+...|+-|++.|+|..+-|++|+|++.
T Consensus       322 YGdVqRVkil~nkk--------d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~S  370 (492)
T KOG1190|consen  322 YGDVQRVKILYNKK--------DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLS  370 (492)
T ss_pred             hcceEEEEeeecCC--------cceeeeecchhHHHHHHHHhhcceecCceEEEeec
Confidence            99999999999763        35799999999999999999999999999999984

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

Probab=99.83  E-value=6.3e-20  Score=160.93  Aligned_cols=202  Identities=20%  Similarity=0.268  Sum_probs=144.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCe-eC--CeEEEEEE
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK-MG--DKTLTVRR  370 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~-~~--g~~l~v~~  370 (521)
                      .++|||+-|...-.|+|++.+|..||.|.++.+.+.+ .|.+||+|||.|.+..+|+.||..|||.. +-  ...|.|.|
T Consensus        19 drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   19 DRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             chhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            3689999999999999999999999999999999986 89999999999999999999999999943 43  47789999


Q ss_pred             ccCCCCCchHHHHH------------------HHHHHHH------------------------HHHHHHhhhcc-----C
Q 009954          371 ATASGQSKTEQESI------------------LAQAQQH------------------------IAIQKMALQTS-----G  403 (521)
Q Consensus       371 ~~~~~~~~~~~~~~------------------~~~~~~~------------------------~~~~~~~~~~~-----~  403 (521)
                      ++.........-..                  ....+..                        ..++....-..     .
T Consensus        98 ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A~  177 (371)
T KOG0146|consen   98 ADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAAA  177 (371)
T ss_pred             ccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhcccccC
Confidence            87622111000000                  0000000                        01111000000     0


Q ss_pred             -------CCC---------CCCCC--------------------------------------------------------
Q 009954          404 -------MNT---------LGGGM--------------------------------------------------------  411 (521)
Q Consensus       404 -------~~~---------~~~~~--------------------------------------------------------  411 (521)
                             .+.         ++...                                                        
T Consensus       178 Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aay  257 (371)
T KOG0146|consen  178 PVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAAY  257 (371)
T ss_pred             CcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhhc
Confidence                   000         00000                                                        


Q ss_pred             -----------CC------------CCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCC
Q 009954          412 -----------SL------------FGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG  468 (521)
Q Consensus       412 -----------~~------------~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~  468 (521)
                                 |.            +..++.+|+.|+..+...             +|..+|-+||.|++.++..|..+.
T Consensus       258 paays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDa-------------EliQmF~PFGhivSaKVFvDRATN  324 (371)
T KOG0146|consen  258 PAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDA-------------ELIQMFLPFGHIVSAKVFVDRATN  324 (371)
T ss_pred             chhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccH-------------HHHHHhccccceeeeeeeehhccc
Confidence                       00            125667777777776665             899999999999999999998776


Q ss_pred             CCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          469 GETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       469 ~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      . ++.+|  ||.|+|+.+|+.||..|||+.||-+.|+|.+--++
T Consensus       325 Q-SKCFG--FVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPk  365 (371)
T KOG0146|consen  325 Q-SKCFG--FVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPK  365 (371)
T ss_pred             c-cccee--eEecCCchhHHHHHHHhcchhhhhhhhhhhhcCcc
Confidence            6 44445  99999999999999999999999999999885544

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

Probab=99.83  E-value=2.2e-20  Score=185.48  Aligned_cols=167  Identities=22%  Similarity=0.427  Sum_probs=139.6

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC---------CCCeEEEEecCHHHHHHHH-HccCc
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH---------EKKFAFVEMRTVEEASNAM-ALDGI  244 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~---------~~g~afV~f~~~~~a~~A~-~l~g~  244 (521)
                      ++|||.||++.+|.++|..+|...|.|            +++.+..         +.|||||+|.+.++|+.|+ .|+|.
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~V------------lS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgt  583 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTV------------LSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGT  583 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeE------------EEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCc
Confidence            349999999999999999999999884            4443332         3499999999999999999 79999


Q ss_pred             eecCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEE
Q 009954          245 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF  324 (521)
Q Consensus       245 ~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v  324 (521)
                      .|.|..|.|+++.....   .+.+...+                 .....+.|+|+|||+.++..+|+++|..||.|.+|
T Consensus       584 vldGH~l~lk~S~~k~~---~~~gK~~~-----------------~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksv  643 (725)
T KOG0110|consen  584 VLDGHKLELKISENKPA---STVGKKKS-----------------KKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSV  643 (725)
T ss_pred             eecCceEEEEeccCccc---cccccccc-----------------cccccceeeeeccchHHHHHHHHHHHhcccceeee
Confidence            99999999998651111   11110000                 01224689999999999999999999999999999


Q ss_pred             EEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          325 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       325 ~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      +|+.....+.++|||||+|-++.+|..|+.+|.++.|.|+.|.+.|+..
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            9998866777899999999999999999999999999999999999976

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

Probab=99.83  E-value=1.5e-19  Score=177.58  Aligned_cols=188  Identities=16%  Similarity=0.244  Sum_probs=140.0

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....++++|++||..+++.++.+++..||.+.++.+      +++..++.++||||.+|.+...+..|+ .|||+.++++
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      777788899999999999999999999 6999999999


Q ss_pred             eEEEeCCCCCCccccccCCCCCCCCCccc---ccccCCCC-CCCCCCCCCeEEEcCCCC--CC-CH-------HHHHHHH
Q 009954          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNL---AAVGLASG-AIGGAEGPDRVFVGGLPY--YF-TE-------TQIKELL  315 (521)
Q Consensus       250 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~-~~~~~~~~~~l~v~nLp~--~~-te-------~~l~~~F  315 (521)
                      ++.|+.+..-...         +....+.   ...+.... ..........|.+.|+-.  +. .+       ++|+..|
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            9999875432221         1111110   01111111 111223334455656521  11 11       5678888


Q ss_pred             HhcCCeeEEEEeecCC---CCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          316 ESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       316 ~~~G~i~~v~i~~~~~---~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ++||.|.+|.|.++-.   ..-..|..||+|.+.+++++|+++|+|.+|+|+.|...|...
T Consensus       431 ~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  431 AKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             cccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            9999999999988721   223456789999999999999999999999999999999854

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

Probab=99.82  E-value=8.5e-19  Score=162.90  Aligned_cols=297  Identities=16%  Similarity=0.142  Sum_probs=192.8

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCe-EEEEecCHHHHHHHH-HccCceecC--c
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKF-AFVEMRTVEEASNAM-ALDGIIFEG--V  249 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~-afV~f~~~~~a~~A~-~l~g~~~~g--~  249 (521)
                      --.++|+++-+-+|-+-|..+|++||.+           .+-+.+.+..+| |.|+|.+.+.|+.|. .|+|..|..  +
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            3468899999999999999999999984           344455667775 999999999999999 799988764  5


Q ss_pred             eEEEeCCCC----------CCccccc---cCCCCCCCC---------------Cccccccc---CCC---CCCCCCCCCC
Q 009954          250 AVRVRRPTD----------YNPTLAA---ALGPGQPSP---------------NLNLAAVG---LAS---GAIGGAEGPD  295 (521)
Q Consensus       250 ~i~v~~~~~----------~~~~~~~---~~~~~~~~~---------------~~~~~~~~---~~~---~~~~~~~~~~  295 (521)
                      .|+|.+++.          +...-..   ..+..+|.-               ....+...   ...   +..+......
T Consensus       219 tLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~  298 (492)
T KOG1190|consen  219 TLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANV  298 (492)
T ss_pred             EEEeehhhcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCce
Confidence            566654331          1111000   001000000               00000000   000   0011111245


Q ss_pred             eEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          296 RVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       296 ~l~v~nLp~~-~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      .|.|.||... +|.+.|..+|..||.|..|+|..++.     --|+|+|.+...|+.|++.|+|..+.|+.|+|.+++..
T Consensus       299 vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~  373 (492)
T KOG1190|consen  299 VLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHT  373 (492)
T ss_pred             EEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCc
Confidence            6889999765 89999999999999999999988753     35999999999999999999999999999999999763


Q ss_pred             CCCchHHH-H--HHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhc
Q 009954          375 GQSKTEQE-S--ILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  451 (521)
Q Consensus       375 ~~~~~~~~-~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~  451 (521)
                      ....+... .  .+........+       .....||.-.....-.++..+.|.++.+.-          .+++|+++|.
T Consensus       374 ~vqlp~egq~d~glT~dy~~spL-------hrfkkpgsKN~~ni~PpsatlHlsnip~sv----------see~lk~~f~  436 (492)
T KOG1190|consen  374 NVQLPREGQEDQGLTKDYGNSPL-------HRFKKPGSKNYQNIFPPSATLHLSNIPPSV----------SEEDLKNLFQ  436 (492)
T ss_pred             cccCCCCCCccccccccCCCCch-------hhccCcccccccccCCchhheeeccCCccc----------chhHHHHhhh
Confidence            22221100 0  00000000000       000112221111222345566777665432          1269999999


Q ss_pred             cccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCc-EEEEEEcC
Q 009954          452 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGN-TVNAFYYP  510 (521)
Q Consensus       452 ~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr-~l~v~~~~  510 (521)
                      .-|-.++....-.+       +.-+|++++.++|+|..|+..|+++.+++. .|+|+|..
T Consensus       437 ~~g~~vkafkff~k-------d~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSk  489 (492)
T KOG1190|consen  437 EPGGQVKAFKFFQK-------DRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSK  489 (492)
T ss_pred             cCCceEEeeeecCC-------CcceeecccCChhHhhhhccccccccCCCCceEEEEeec
Confidence            99987665443321       125899999999999999999999999876 99999964

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

Probab=99.81  E-value=6.5e-18  Score=158.13  Aligned_cols=190  Identities=22%  Similarity=0.288  Sum_probs=133.9

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHH-HHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQV-MTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~-G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ..+.+||.|||+++.+++|+++|... |+|..+       .......++.+|+|.|+|+++|.+++|+ .||...+.|++
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yv-------eLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~  115 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYV-------ELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRE  115 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEee-------eeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCce
Confidence            35679999999999999999999964 442211       0122234678999999999999999999 69999999999


Q ss_pred             EEEeCCCCCCccccccC---CC------------------------------CC-----CCC--Cc-----------ccc
Q 009954          251 VRVRRPTDYNPTLAAAL---GP------------------------------GQ-----PSP--NL-----------NLA  279 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~---~~------------------------------~~-----~~~--~~-----------~~~  279 (521)
                      |.|+...+.+...-...   +.                              ..     +..  ..           +..
T Consensus       116 l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~  195 (608)
T KOG4212|consen  116 LVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYN  195 (608)
T ss_pred             EEEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhh
Confidence            99985443221110000   00                              00     000  00           000


Q ss_pred             cccCC-----CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHH
Q 009954          280 AVGLA-----SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA  354 (521)
Q Consensus       280 ~~~~~-----~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~  354 (521)
                      ..+.+     +--.-.+....++||.||...+....|++.|.-.|.|..|.+-.++ -|.++|||.|+|..+-+|..||.
T Consensus       196 lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idK-eG~s~G~~vi~y~hpveavqaIs  274 (608)
T KOG4212|consen  196 LFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDK-EGNSRGFAVIEYDHPVEAVQAIS  274 (608)
T ss_pred             cccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeecc-ccccCCeeEEEecchHHHHHHHH
Confidence            00000     0000112334579999999999999999999999999999999997 57999999999999999999999


Q ss_pred             HHcCCeeCCeEEEEEE
Q 009954          355 ALNGLKMGDKTLTVRR  370 (521)
Q Consensus       355 ~l~g~~~~g~~l~v~~  370 (521)
                      .|++.-+..++..+..
T Consensus       275 ml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  275 MLDRQGLFDRRMTVRL  290 (608)
T ss_pred             hhccCCCccccceeec
Confidence            9997666666666665

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

Probab=99.79  E-value=2.6e-18  Score=164.16  Aligned_cols=171  Identities=22%  Similarity=0.283  Sum_probs=130.8

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  253 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v  253 (521)
                      ..-|.+.+||+.+|+++|.+||+.++.-         ..++....++..|-|||+|.+.+++++||+.+-..+..+-|.|
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            3468899999999999999999988531         1133334477789999999999999999999999999999999


Q ss_pred             eCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeecCCC
Q 009954          254 RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDRDT  332 (521)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~-v~i~~~~~~  332 (521)
                      -.+........-.                  +...........|.|++||+.||++||.+||+..-.|.. |.++.+ ..
T Consensus        81 f~~~~~e~d~~~~------------------~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d-~r  141 (510)
T KOG4211|consen   81 FTAGGAEADWVMR------------------PGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD-QR  141 (510)
T ss_pred             EccCCcccccccc------------------CCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc-CC
Confidence            7543322211100                  000001123457999999999999999999998766666 445555 46


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      +.+.|-|||+|++.+.|++||.. |...|+-+-|.|-.+..
T Consensus       142 gR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss~  181 (510)
T KOG4211|consen  142 GRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSSR  181 (510)
T ss_pred             CCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhHH
Confidence            78999999999999999999985 77889999999987643

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

Probab=99.78  E-value=5.2e-18  Score=140.90  Aligned_cols=172  Identities=26%  Similarity=0.369  Sum_probs=129.2

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC---CCeEEEEecCHHHHHHHH-HccCceec
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE---KKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~---~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      ...++|||+|||.++.+.+|.++|.+||.            |.++.+...   ..||||+|+++.+|+.|+ .-+|..+.
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            555554432   579999999999999999 79999999


Q ss_pred             CceEEEeCCCCCCccccccCCCCCCCCCcccccc-cCCCC-C--CCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE
Q 009954          248 GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV-GLASG-A--IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG  323 (521)
Q Consensus       248 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~-~--~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~  323 (521)
                      |..|+|+++...-.......       ..+-... +...+ .  .....+..+|.|.+||++.+++||+++....|.|..
T Consensus        72 g~rLRVEfprggr~s~~~~G-------~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCf  144 (241)
T KOG0105|consen   72 GCRLRVEFPRGGRSSSDRRG-------SYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCF  144 (241)
T ss_pred             cceEEEEeccCCCccccccc-------ccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeee
Confidence            99999998776542211000       0000000 00000 0  111223457999999999999999999999999999


Q ss_pred             EEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee--CCeEEEEE
Q 009954          324 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVR  369 (521)
Q Consensus       324 v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--~g~~l~v~  369 (521)
                      ..+.+|       |++.|+|...|+.+-|+..|+...+  .|....+.
T Consensus       145 adv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yir  185 (241)
T KOG0105|consen  145 ADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIR  185 (241)
T ss_pred             eeeecc-------cceeeeeeehhhHHHHHHhhccccccCcCcEeeEE
Confidence            999887       3799999999999999999988665  34444433

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

Probab=99.78  E-value=2.6e-19  Score=168.06  Aligned_cols=173  Identities=21%  Similarity=0.378  Sum_probs=147.4

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~  252 (521)
                      +.++|||++|++.++++.|+++|.+||++..|.+      +.+..+++++||+||+|.+++....+|......|.|+.|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~v------m~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve   78 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVV------MRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVE   78 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEE------eccCCCCCcccccceecCCCcchheeecccccccCCcccc
Confidence            6789999999999999999999999999776543      4555567889999999999999999998778889999999


Q ss_pred             EeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 009954          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (521)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~  332 (521)
                      +..+..........                       ......+|||++||.++++++++++|++||.|..+.++.|..+
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            98765544321100                       0112357999999999999999999999999999999999999


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCC
Q 009954          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASG  375 (521)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (521)
                      ..++||+||.|.+.+.+.+++. ..-+.|.|+.|.|..|.++.
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            9999999999999999999987 47899999999999997743

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

Probab=99.77  E-value=2e-18  Score=151.56  Aligned_cols=83  Identities=28%  Similarity=0.502  Sum_probs=78.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..|+|||-.||.+..+.+|...|-+||.|.+.+|..|..|+.+|+|+||.|.++.+|+.||.+|||+.|+-+.|+|..-.
T Consensus       284 eGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKR  363 (371)
T KOG0146|consen  284 EGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKR  363 (371)
T ss_pred             CcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcC
Confidence            34789999999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             CCC
Q 009954          373 ASG  375 (521)
Q Consensus       373 ~~~  375 (521)
                      ++.
T Consensus       364 Pkd  366 (371)
T KOG0146|consen  364 PKD  366 (371)
T ss_pred             ccc
Confidence            654

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

Probab=99.76  E-value=5.8e-17  Score=148.94  Aligned_cols=282  Identities=18%  Similarity=0.188  Sum_probs=188.3

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHH---ccCceecCce
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIFEGVA  250 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~---l~g~~~~g~~  250 (521)
                      +--|+|.+|-..++|.+|.+.++.||.            +.-+.....+..|.|+|++.+.|..++.   -+...+.|++
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            446999999999999999999999998            5556666778899999999999999983   4667788888


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCe-EE--EcCCCCCCCHHHHHHHHHhcCCeeEEEEe
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDR-VF--VGGLPYYFTETQIKELLESFGTLHGFDLV  327 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-l~--v~nLp~~~te~~l~~~F~~~G~i~~v~i~  327 (521)
                      ..++++....-..        +             +  .....++. |.  |-|--+.+|-+-|..++...|+|..|.|+
T Consensus        99 Al~NyStsq~i~R--------~-------------g--~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIf  155 (494)
T KOG1456|consen   99 ALFNYSTSQCIER--------P-------------G--DESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIF  155 (494)
T ss_pred             hhcccchhhhhcc--------C-------------C--CCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEE
Confidence            8887753221110        0             0  01122233 33  55656779999999999999999999888


Q ss_pred             ecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee--CCeEEEEEEccCCCCCchHHHHH-H------------------H
Q 009954          328 KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVRRATASGQSKTEQESI-L------------------A  386 (521)
Q Consensus       328 ~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--~g~~l~v~~~~~~~~~~~~~~~~-~------------------~  386 (521)
                      +.  +|.   -|.|||.+.+.|++|..+|||.-|  +-++|+|.||++........+.. .                  .
T Consensus       156 kk--ngV---QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~  230 (494)
T KOG1456|consen  156 KK--NGV---QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYD  230 (494)
T ss_pred             ec--cce---eeEEeechhHHHHHHHhhcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCc
Confidence            76  454   599999999999999999999665  56899999998821111100000 0                  0


Q ss_pred             HHHHHHHHHHHhhhccC-C--------CCCCCCC--------------CCC-CCCcceEEEeeCcCCcccCCChHHHHHH
Q 009954          387 QAQQHIAIQKMALQTSG-M--------NTLGGGM--------------SLF-GETLAKVLCLTEAITADALADDEEYEEI  442 (521)
Q Consensus       387 ~~~~~~~~~~~~~~~~~-~--------~~~~~~~--------------~~~-~~~~~~v~~l~~~~~~~~~~~~~~~~~~  442 (521)
                      ...+..........-.+ .        ..++.+.              +.. ...+..|+.+..+ +...+..       
T Consensus       231 r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGL-dh~k~N~-------  302 (494)
T KOG1456|consen  231 RQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGL-DHGKMNC-------  302 (494)
T ss_pred             cccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEec-cccccch-------
Confidence            00000000000000000 0        0000000              111 1122223222222 1222221       


Q ss_pred             HHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          443 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       443 ~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                       +.|..+|+.||+|+.|++++.++        |.|+|++.+..+.++|+..|||..+-|.+|.|-+....
T Consensus       303 -drlFNl~ClYGNV~rvkFmkTk~--------gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~  363 (494)
T KOG1456|consen  303 -DRLFNLFCLYGNVERVKFMKTKP--------GTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQN  363 (494)
T ss_pred             -hhhhhhhhhcCceeeEEEeeccc--------ceeEEEcCcHHHHHHHHHHhccCccccceEEEeecccc
Confidence             58999999999999999999762        67899999999999999999999999999999875543

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

Probab=99.75  E-value=4e-17  Score=141.73  Aligned_cols=185  Identities=21%  Similarity=0.317  Sum_probs=141.2

Q ss_pred             CCeEEEeCCCccCcHHHHHH----HHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          174 ARRVYVGGLPPLANEQAIAT----FFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~----~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      ..||||.||+..+..++|+.    +|++||.|+.         |....+.+-+|-|||.|.+.+.|..|+ +|+|..+.|
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            34999999999999999887    9999998543         556667788999999999999999999 899999999


Q ss_pred             ceEEEeCCCCCCccccccCC---CCCC----------------CCCccc-ccccCCCC-CCCCCCCCCeEEEcCCCCCCC
Q 009954          249 VAVRVRRPTDYNPTLAAALG---PGQP----------------SPNLNL-AAVGLASG-AIGGAEGPDRVFVGGLPYYFT  307 (521)
Q Consensus       249 ~~i~v~~~~~~~~~~~~~~~---~~~~----------------~~~~~~-~~~~~~~~-~~~~~~~~~~l~v~nLp~~~t  307 (521)
                      +.|+|+|+...........+   ...+                ...... ......+. ......+...||+.|||..++
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            99999998876554332111   0000                000000 00000000 011233445699999999999


Q ss_pred             HHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC-CeEEEEEEcc
Q 009954          308 ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRAT  372 (521)
Q Consensus       308 e~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~~~  372 (521)
                      .+.|..+|.+|.....|+++...     .+.|||+|.+...|..|...|.|..|. ...+.|.++.
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            99999999999999999988753     568999999999999999999998886 8888888874

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

Probab=99.73  E-value=4.2e-17  Score=138.30  Aligned_cols=83  Identities=23%  Similarity=0.554  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.|+|..|.|+.|+|.|+
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            44578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      ...
T Consensus       112 ~~~  114 (144)
T PLN03134        112 NDR  114 (144)
T ss_pred             CcC
Confidence            763

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

Probab=99.70  E-value=3.3e-16  Score=136.10  Aligned_cols=195  Identities=17%  Similarity=0.274  Sum_probs=135.1

Q ss_pred             CeEEEcCCCCCCCHHHHHH----HHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          295 DRVFVGGLPYYFTETQIKE----LLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~----~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      .||||.||+..+..++|+.    +|++||.|.+|...+   +...+|-|||.|.+.+.|..|+.+|+|+.|.|+.++|.|
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    999999999998765   567799999999999999999999999999999999999


Q ss_pred             ccCCCCCchHHHHHHHHHHH-----HHH--HHHHhhhccCCCCCCCCC--C--CCCCCcceEEEeeCcCCcccCCChHHH
Q 009954          371 ATASGQSKTEQESILAQAQQ-----HIA--IQKMALQTSGMNTLGGGM--S--LFGETLAKVLCLTEAITADALADDEEY  439 (521)
Q Consensus       371 ~~~~~~~~~~~~~~~~~~~~-----~~~--~~~~~~~~~~~~~~~~~~--~--~~~~~~~~v~~l~~~~~~~~~~~~~~~  439 (521)
                      |+.+..........+.....     ...  .+.........+++....  |  .....+..++.+.++....        
T Consensus        87 A~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es--------  158 (221)
T KOG4206|consen   87 AKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSES--------  158 (221)
T ss_pred             ccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcch--------
Confidence            98732221111100000000     000  000000000001111111  1  1223445555555554443        


Q ss_pred             HHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeC-CcEEEEEEcC
Q 009954          440 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG-GNTVNAFYYP  510 (521)
Q Consensus       440 ~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~-gr~l~v~~~~  510 (521)
                        ..+.|..+|+.|.-...|.++...        .++|||+|.+...|..|.+.|+|..|- ..++.+.|+.
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              225778888888888888887754        279999999999999999999999997 8888888764

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.68  E-value=4.7e-16  Score=143.48  Aligned_cols=290  Identities=19%  Similarity=0.212  Sum_probs=189.4

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE-ecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY-INHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~-~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ...-|...+||+..++.+|..||+..-..       .+...++.. .+...|.|.|.|.+.|.-+.|++-+...+.++.|
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            34456788999999999999999876332       122233333 3556799999999999999999988888999999


Q ss_pred             EEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcC----CeeEEEEe
Q 009954          252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG----TLHGFDLV  327 (521)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G----~i~~v~i~  327 (521)
                      .|-.+.....-.-+..+...+.+-.             ..+..-.|.+++||+++++.++.++|.+.-    ..+.|-++
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            9965443222111110000000000             001122477999999999999999997432    34455555


Q ss_pred             ecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhc------
Q 009954          328 KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQT------  401 (521)
Q Consensus       328 ~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------  401 (521)
                      +.+ +|+.+|-|||.|..+++|+.||.. |...|+.+.|.+-.++.                 .+..+-+....      
T Consensus       199 ~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFRSTa-----------------aEvqqvlnr~~s~pLi~  259 (508)
T KOG1365|consen  199 TRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFRSTA-----------------AEVQQVLNREVSEPLIP  259 (508)
T ss_pred             ECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHHHhH-----------------HHHHHHHHhhccccccC
Confidence            553 799999999999999999999985 55555555544443321                 01111111111      


Q ss_pred             --cCCCCCCCCCCCCCCCc-ceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccc-eeE--EEecCCCCCCCCCCCcc
Q 009954          402 --SGMNTLGGGMSLFGETL-AKVLCLTEAITADALADDEEYEEILEDMREECGKYGT-LVN--VVIPRPDQNGGETPGVG  475 (521)
Q Consensus       402 --~~~~~~~~~~~~~~~~~-~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~-I~~--v~i~~~~~~~~~~~g~g  475 (521)
                        ...-.++.+....++.. ..|+.|..+          +|+.+++||-.||..|-. |..  |.+..+. .|.+   .|
T Consensus       260 ~~~sp~~p~~p~~~~p~~~~kdcvRLRGL----------Py~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrP---SG  325 (508)
T KOG1365|consen  260 GLTSPLLPGGPARLVPPTRSKDCVRLRGL----------PYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRP---SG  325 (508)
T ss_pred             CCCCCCCCCCccccCCCCCCCCeeEecCC----------ChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCc---Ch
Confidence              11111122222222222 446665544          677788999999999885 333  6666655 6666   49


Q ss_pred             EEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCcc
Q 009954          476 KVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYF  515 (521)
Q Consensus       476 ~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~  515 (521)
                      .|||+|.+.++|..|...-+......|.|.|-.+.-++..
T Consensus       326 eAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~eeln  365 (508)
T KOG1365|consen  326 EAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVEELN  365 (508)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHHHHH
Confidence            9999999999999999999998888999999887766554

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

Probab=99.67  E-value=3.3e-15  Score=128.24  Aligned_cols=180  Identities=22%  Similarity=0.316  Sum_probs=121.5

Q ss_pred             hhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC----CCCeEEEEecCHHHHHHHH-HccC
Q 009954          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH----EKKFAFVEMRTVEEASNAM-ALDG  243 (521)
Q Consensus       169 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~----~~g~afV~f~~~~~a~~A~-~l~g  243 (521)
                      +.....++|||.|||.++...+|..+|..|--..++        .+. .+.+    .+.+|||.|.+...|..|+ .|||
T Consensus        29 ~~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgs--------lLK-~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNG   99 (284)
T KOG1457|consen   29 DEPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGS--------LLK-YTSKGDQVCKPVAFATFTSHQFALAAMNALNG   99 (284)
T ss_pred             ccccccceeeeccCCcccCHHHHHHHhccCCCccce--------eee-eccCCCccccceEEEEecchHHHHHHHHHhcC
Confidence            445568999999999999999999999988321111        111 1222    3479999999999999999 7999


Q ss_pred             ceec---CceEEEeCCCCCCccccccCCC-CCCCCCccc-----------------------------------------
Q 009954          244 IIFE---GVAVRVRRPTDYNPTLAAALGP-GQPSPNLNL-----------------------------------------  278 (521)
Q Consensus       244 ~~~~---g~~i~v~~~~~~~~~~~~~~~~-~~~~~~~~~-----------------------------------------  278 (521)
                      +.|+   +..|+|..++............ +.+.+....                                         
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   5778887655422211110000 000000000                                         


Q ss_pred             -----ccccC----------CCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEE
Q 009954          279 -----AAVGL----------ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY  343 (521)
Q Consensus       279 -----~~~~~----------~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f  343 (521)
                           +....          +.....+...+.+|||.||.++++|++|+.+|+.|-....++|-..  .|.  .+|||+|
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--GGM--PVAFADF  255 (284)
T ss_pred             hhhhhhhhhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CCc--ceEeecH
Confidence                 00000          0011122334568999999999999999999999988877776543  333  4799999


Q ss_pred             cChHHHHHHHHHHcCCee
Q 009954          344 QDPAVTDIACAALNGLKM  361 (521)
Q Consensus       344 ~~~~~A~~Al~~l~g~~~  361 (521)
                      ++.+.|..||..|.|..|
T Consensus       256 ~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  256 EEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             HHHHHHHHHHHHhhccee
Confidence            999999999999999776

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

Probab=99.65  E-value=4.5e-15  Score=123.59  Aligned_cols=182  Identities=19%  Similarity=0.265  Sum_probs=127.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||.++-+.+|.++|.+||.|..|.|...+   ...+||||+|+++.+|+.||..-+|..+.|+.|.|.++.
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            34789999999999999999999999999999987653   235799999999999999999999999999999999997


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCC-----CCCCCCCCcceEEE--eeCcCCcccCCChHHHHHHHHH
Q 009954          373 ASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG-----GMSLFGETLAKVLC--LTEAITADALADDEEYEEILED  445 (521)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~v~~--l~~~~~~~~~~~~~~~~~~~~d  445 (521)
                      -........                 -...+....|.     ..|..--..-.|++  |+..-+.             +|
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            522110000                 00000000010     11111112233333  3333222             58


Q ss_pred             HHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCee--CCcEEEEEEcCCCCcccc
Q 009954          446 MREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF--GGNTVNAFYYPEDKYFNK  517 (521)
Q Consensus       446 l~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~--~gr~l~v~~~~~~~~~~~  517 (521)
                      |+++.-+-|.|-...+.++.          ...|+|.+.|+.+.|+..|....+  .|-+.-+.........++
T Consensus       132 LKDHmReaGdvCfadv~rDg----------~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yirv~~~~~~~~~  195 (241)
T KOG0105|consen  132 LKDHMREAGDVCFADVQRDG----------VGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIRVRGDENRDQG  195 (241)
T ss_pred             HHHHHHhhCCeeeeeeeccc----------ceeeeeeehhhHHHHHHhhccccccCcCcEeeEEecccCCCccc
Confidence            99999999999999998873          449999999999999999998776  455554444444433433

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

Probab=99.62  E-value=1.2e-13  Score=127.30  Aligned_cols=299  Identities=15%  Similarity=0.138  Sum_probs=187.3

Q ss_pred             EeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCCeEEEEecCHHHHHHHH-HccCceecC--ceEEEe
Q 009954          179 VGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAM-ALDGIIFEG--VAVRVR  254 (521)
Q Consensus       179 v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~-~~~g~afV~f~~~~~a~~A~-~l~g~~~~g--~~i~v~  254 (521)
                      |-|--+.+|-+-|..+....|+            |..+.+- +..-.|.|+|.+.+.|++|. .|||..|..  ..|+|.
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            4454456899999999999887            4444444 34447999999999999999 799988754  678888


Q ss_pred             CCCCCCcc--------c----cccCCCCCCCCC---------------cccc--ccc-----------------------
Q 009954          255 RPTDYNPT--------L----AAALGPGQPSPN---------------LNLA--AVG-----------------------  282 (521)
Q Consensus       255 ~~~~~~~~--------~----~~~~~~~~~~~~---------------~~~~--~~~-----------------------  282 (521)
                      ++++..-.        +    ....++-.+..+               .++.  ..+                       
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            76631100        0    000000000000               0000  000                       


Q ss_pred             -CCCCCCCCCCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCe
Q 009954          283 -LASGAIGGAEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK  360 (521)
Q Consensus       283 -~~~~~~~~~~~~~~l~v~nLp~~-~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~  360 (521)
                       .....+++......+.|.+|... +.-+.|..+|-.||.|+.|++++.+     .|.|.||+.+..+.++|+..||+..
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             00111123344567899999877 5678899999999999999999875     4679999999999999999999999


Q ss_pred             eCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHH-hhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHH
Q 009954          361 MGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKM-ALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEY  439 (521)
Q Consensus       361 ~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~  439 (521)
                      +.|.+|.|.+++......-+.....+..   ...... ...+.....++.+.-.-...+++|+..-|..-.-        
T Consensus       350 lfG~kl~v~~SkQ~~v~~~~pflLpDgS---pSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~v--------  418 (494)
T KOG1456|consen  350 LFGGKLNVCVSKQNFVSPVQPFLLPDGS---PSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGV--------  418 (494)
T ss_pred             cccceEEEeeccccccccCCceecCCCC---cchhhcccccccccCChhHhhcccccCCcceeEEecCCCcc--------
Confidence            9999999999875222211000000000   000000 1111112233333333344667777766543221        


Q ss_pred             HHHHHHHHHhhccccc-eeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCc------EEEEEEcCCC
Q 009954          440 EEILEDMREECGKYGT-LVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGN------TVNAFYYPED  512 (521)
Q Consensus       440 ~~~~~dl~~~f~~fG~-I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr------~l~v~~~~~~  512 (521)
                        +++.|.++|..-+. -.+|+|...+.....   .|  .++|++.++|..||..+|-..|.+.      +|++-|.+..
T Consensus       419 --tEe~l~~i~nek~v~~~svkvFp~kserSs---sG--llEfe~~s~Aveal~~~NH~pi~~p~gs~PfilKlcfsts~  491 (494)
T KOG1456|consen  419 --TEEQLIGICNEKDVPPTSVKVFPLKSERSS---SG--LLEFENKSDAVEALMKLNHYPIEGPNGSFPFILKLCFSTSK  491 (494)
T ss_pred             --CHHHHHHHhhhcCCCcceEEeecccccccc---cc--eeeeehHHHHHHHHHHhccccccCCCCCCCeeeeeeecccc
Confidence              22577788776553 566777665533332   36  9999999999999999999998774      5666665543

>PF00076 RRM_1: RNA recognition motif

Probab=99.60  E-value=5.6e-15  Score=110.06  Aligned_cols=70  Identities=27%  Similarity=0.644  Sum_probs=67.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       297 l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      |||+|||..+++++|+++|++||.|..+.+..+ .++..+|+|||+|.+.++|.+|++.|+|..++|+.|+
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            799999999999999999999999999999997 5899999999999999999999999999999999885

(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 ....

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

Probab=99.60  E-value=1.3e-15  Score=143.12  Aligned_cols=175  Identities=19%  Similarity=0.322  Sum_probs=137.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||++|+..++++.|++.|.+||.|..+.+++++.++.++||+||+|++++....+|.. .-+.|.|+.|.+..+.
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            447899999999999999999999999999999999999999999999999999999988874 5688999999999886


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhcc
Q 009954          373 ASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGK  452 (521)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~  452 (521)
                      +.......    ..                            -...-+|++-....+.           .++++++.|++
T Consensus        84 ~r~~~~~~----~~----------------------------~~~tkkiFvGG~~~~~-----------~e~~~r~yfe~  120 (311)
T KOG4205|consen   84 SREDQTKV----GR----------------------------HLRTKKIFVGGLPPDT-----------TEEDFKDYFEQ  120 (311)
T ss_pred             Cccccccc----cc----------------------------ccceeEEEecCcCCCC-----------chHHHhhhhhc
Confidence            52211000    00                            0011223332222222           22599999999


Q ss_pred             ccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCcc
Q 009954          453 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYF  515 (521)
Q Consensus       453 fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~  515 (521)
                      ||.|..+.++.|..+..+   .|++||.|.+.+.+.+++. ...+.|+|+.|.|--+.+++..
T Consensus       121 ~g~v~~~~~~~d~~~~~~---rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  121 FGKVADVVIMYDKTTSRP---RGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             cceeEeeEEeeccccccc---ccceeeEeccccccceecc-cceeeecCceeeEeeccchhhc
Confidence            999999999999876554   4566999999999999988 5899999999999887766544

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

Probab=99.60  E-value=2.1e-15  Score=132.80  Aligned_cols=165  Identities=21%  Similarity=0.312  Sum_probs=126.3

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEE
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v  253 (521)
                      ..|||++||+.+.+.+|..||..||.+.            ++.+  ..||+||+|.+..+|.-|+ .+|+..|.|..+.|
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  3578899999999999999 89999999988888


Q ss_pred             eCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCC
Q 009954          254 RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG  333 (521)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g  333 (521)
                      .++.......    +.+.......     ...-...+....+.|+|.+++..+.+.+|.+.|.++|.+....+       
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            8876433221    0011000000     00001112344567999999999999999999999999965544       


Q ss_pred             CcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          334 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       334 ~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                       ..+++||+|.+.++|.+||..|+|..+.|+.|.+..
T Consensus       132 -~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  132 -RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             -hccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence             245799999999999999999999999999999943

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

Probab=99.57  E-value=9e-15  Score=127.65  Aligned_cols=81  Identities=28%  Similarity=0.437  Sum_probs=78.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ...+|.|.||+.+++|++|.++|.+||.|..|.|.++++||.++|||||.|.+.++|++||+.|||+-+..-.|.|.|++
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            45679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      +
T Consensus       268 P  268 (270)
T KOG0122|consen  268 P  268 (270)
T ss_pred             C
Confidence            6

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

Probab=99.57  E-value=4.1e-14  Score=129.56  Aligned_cols=194  Identities=17%  Similarity=0.154  Sum_probs=133.3

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE---ecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~---~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ...|||.|||.++|-+++.++|++||.|......  +++-+.+.   -+.-+|-|.+.|.-.+++..|+ -|++..|.|+
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t--~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQT--GEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCC--CCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            4569999999999999999999999987543211  11222222   2345799999999999999999 5999999999


Q ss_pred             eEEEeCCCCCCccccccCC----CCCCCCC---cccccccCCCCC--CCCCCCCCeEEEcCCCCC----CC-------HH
Q 009954          250 AVRVRRPTDYNPTLAAALG----PGQPSPN---LNLAAVGLASGA--IGGAEGPDRVFVGGLPYY----FT-------ET  309 (521)
Q Consensus       250 ~i~v~~~~~~~~~~~~~~~----~~~~~~~---~~~~~~~~~~~~--~~~~~~~~~l~v~nLp~~----~t-------e~  309 (521)
                      .|+|+.++-.....-....    ...+...   ...-..+..+..  ..-....++|.|.||-..    .+       .+
T Consensus       212 ~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlke  291 (382)
T KOG1548|consen  212 KLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKE  291 (382)
T ss_pred             EEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHH
Confidence            9999876522111000000    0000000   000000111111  122345578999998432    22       36


Q ss_pred             HHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          310 QIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       310 ~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      +|.+.+++||.|..|.|.-.    .+.|.+-|.|.+.++|..||+.|+|.+|+|++|......-
T Consensus       292 dl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  292 DLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDG  351 (382)
T ss_pred             HHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCC
Confidence            78889999999999988743    3578899999999999999999999999999999987644

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

Probab=99.56  E-value=7.5e-15  Score=129.27  Aligned_cols=161  Identities=22%  Similarity=0.375  Sum_probs=121.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCC
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASG  375 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (521)
                      .|||++||+.+.+.+|..+|..||.|..|.+..        ||+||+|.+..+|.-|+..|+|..|.|..+.|.|+....
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            699999999999999999999999999998764        489999999999999999999999999889999987521


Q ss_pred             CCchHHHHHHHHHHHHHHHHHHhhhccCCCCCC-----CCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhh
Q 009954          376 QSKTEQESILAQAQQHIAIQKMALQTSGMNTLG-----GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREEC  450 (521)
Q Consensus       376 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f  450 (521)
                      -..                        +..++|     ...-..+....+.+++.+..+.          .-+++|.+.|
T Consensus        75 ~~~------------------------g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r----------~~~qdl~d~~  120 (216)
T KOG0106|consen   75 RGR------------------------GRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLR----------VSWQDLKDHF  120 (216)
T ss_pred             ccc------------------------CCCCCCCccchhhccCCcccccceeeeccchhh----------hhHHHHhhhh
Confidence            110                        011111     0011111123334444333222          1236999999


Q ss_pred             ccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEc
Q 009954          451 GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  509 (521)
Q Consensus       451 ~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~  509 (521)
                      +.+|.+....++.           +.+||+|.+.++|.+||..|+|..+.|+.|++...
T Consensus       121 ~~~g~~~~~~~~~-----------~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  121 RPAGEVTYVDARR-----------NFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             cccCCCchhhhhc-----------cccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            9999996665533           56699999999999999999999999999999443

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.53  E-value=4.8e-14  Score=104.90  Aligned_cols=70  Identities=27%  Similarity=0.580  Sum_probs=65.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       297 l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      |+|+|||+.+++++|+++|+.||.|..+.+..++. |..+|+|||+|.+.++|.+|++.++|..|+|+.|.
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=99.53  E-value=2.4e-14  Score=111.97  Aligned_cols=80  Identities=25%  Similarity=0.402  Sum_probs=76.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+||...++|++|.++|+++|.|..|.+-.|+.+..+.|||||+|.+.++|..||+-++|..+..++|.|.|..
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            34799999999999999999999999999999999999999999999999999999999999999999999999999974

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

Probab=99.53  E-value=1.9e-14  Score=122.14  Aligned_cols=83  Identities=24%  Similarity=0.434  Sum_probs=78.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      .++...|.|-||-+-|+.++|+.+|++||.|-+|.|+.|+-|+.++|||||.|....+|+.|+++|+|.+|.|+.|.|++
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            34557899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccC
Q 009954          371 ATA  373 (521)
Q Consensus       371 ~~~  373 (521)
                      |.-
T Consensus        90 ary   92 (256)
T KOG4207|consen   90 ARY   92 (256)
T ss_pred             hhc
Confidence            865

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

Probab=99.52  E-value=9.5e-14  Score=139.53  Aligned_cols=76  Identities=20%  Similarity=0.420  Sum_probs=70.5

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ...++|||||+|+..+++.+|.++|+.||.            |..+.+...+|||||.+.+..+|.+|| +|+...+.++
T Consensus       418 sV~SrTLwvG~i~k~v~e~dL~~~feefGe------------iqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k  485 (894)
T KOG0132|consen  418 SVCSRTLWVGGIPKNVTEQDLANLFEEFGE------------IQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVADK  485 (894)
T ss_pred             eEeeeeeeeccccchhhHHHHHHHHHhccc------------ceeEeeccCCceeEEEEeehhHHHHHHHHHhcccccce
Confidence            455789999999999999999999999998            788888999999999999999999999 7999999999


Q ss_pred             eEEEeCCCC
Q 009954          250 AVRVRRPTD  258 (521)
Q Consensus       250 ~i~v~~~~~  258 (521)
                      .|+|.|+..
T Consensus       486 ~Iki~Wa~g  494 (894)
T KOG0132|consen  486 TIKIAWAVG  494 (894)
T ss_pred             eeEEeeecc
Confidence            999999643

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

Probab=99.51  E-value=5.1e-13  Score=125.65  Aligned_cols=198  Identities=17%  Similarity=0.277  Sum_probs=132.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLE-SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      +.+||.|||+++-|++|+++|. +.|.|+.|.|..| .+|+++|+|.|||+++|.+++|++.||.+.+.|++|.|.-...
T Consensus        45 R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   45 RSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             ceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            4599999999999999999999 8999999999999 5899999999999999999999999999999999999987654


Q ss_pred             CCCCchHHHH-----HH-----------------------------------HHHHHHHHHHHHhhhccCCCCCCCCC--
Q 009954          374 SGQSKTEQES-----IL-----------------------------------AQAQQHIAIQKMALQTSGMNTLGGGM--  411 (521)
Q Consensus       374 ~~~~~~~~~~-----~~-----------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~--  411 (521)
                      .......+..     .+                                   ........+.+.-....+.+..+...  
T Consensus       124 ~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~F  203 (608)
T KOG4212|consen  124 EQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASF  203 (608)
T ss_pred             hhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhh
Confidence            1100000000     00                                   00000000000000000000000000  


Q ss_pred             -----CCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHH
Q 009954          412 -----SLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVG  486 (521)
Q Consensus       412 -----~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~  486 (521)
                           -..++...++++           .++-|..=-..|++.|.--|.|+.|.+--++ .+..   .|+|.++|.++-+
T Consensus       204 lr~~h~f~pPl~~k~fv-----------anl~~~vg~~kL~qvfgmAGkv~~vdf~idK-eG~s---~G~~vi~y~hpve  268 (608)
T KOG4212|consen  204 LRSLHIFSPPLHNKVFV-----------ANLDYKVGNKKLKQVFGMAGKVQSVDFSIDK-EGNS---RGFAVIEYDHPVE  268 (608)
T ss_pred             hhhccCCCCCccceeee-----------eccccccchHHHHHHhccceeeeeeceeecc-cccc---CCeeEEEecchHH
Confidence                 001122222222           2222222225899999999999999887777 3443   4789999999999


Q ss_pred             HHHHHHHHhCCeeCCcEEEEEE
Q 009954          487 CATAKNALSGRKFGGNTVNAFY  508 (521)
Q Consensus       487 A~~Ai~~lng~~~~gr~l~v~~  508 (521)
                      |..||..|++.-+..++..+.+
T Consensus       269 avqaIsml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  269 AVQAISMLDRQGLFDRRMTVRL  290 (608)
T ss_pred             HHHHHHhhccCCCccccceeec
Confidence            9999999998777888877776

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

Probab=99.50  E-value=1e-13  Score=125.96  Aligned_cols=84  Identities=29%  Similarity=0.601  Sum_probs=77.8

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          288 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       288 ~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      ......+++|+|.|||+..-+-||+.+|.+||.|.+|.|+.+  ...||||+||.|+++++|++|.++|||..+.|++|.
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            334567789999999999999999999999999999999987  466899999999999999999999999999999999


Q ss_pred             EEEccC
Q 009954          368 VRRATA  373 (521)
Q Consensus       368 v~~~~~  373 (521)
                      |.-++.
T Consensus       168 Vn~ATa  173 (376)
T KOG0125|consen  168 VNNATA  173 (376)
T ss_pred             Eeccch
Confidence            999876

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

Probab=99.50  E-value=4.7e-13  Score=128.52  Aligned_cols=171  Identities=16%  Similarity=0.281  Sum_probs=123.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ...|.+++||.++|++||.+||+.+ .|.++.+.+.  +|+..|-|||+|.+.|++++||+ ++-..++.+-|.|--+..
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRR--NGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGG   85 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcC-ceeEEEEecc--CCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCC
Confidence            3568899999999999999999998 4777766665  89999999999999999999999 588889999999988755


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccc
Q 009954          374 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  453 (521)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~f  453 (521)
                      +...                   ......+.+        . ..+-.|+.|-.+          +|.-+++||.+||+.-
T Consensus        86 ~e~d-------------------~~~~~~g~~--------s-~~~d~vVRLRGL----------Pfscte~dI~~FFaGL  127 (510)
T KOG4211|consen   86 AEAD-------------------WVMRPGGPN--------S-SANDGVVRLRGL----------PFSCTEEDIVEFFAGL  127 (510)
T ss_pred             cccc-------------------ccccCCCCC--------C-CCCCceEEecCC----------CccCcHHHHHHHhcCC
Confidence            2210                   000000000        0 023334444333          1112235999999976


Q ss_pred             cceeE-EEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCC
Q 009954          454 GTLVN-VVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       454 G~I~~-v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~  511 (521)
                      =.|.. |.++.+. .+.+   .|-|||+|++.+.|++|+.. |...|+-|-|.|--...
T Consensus       128 ~Iv~~gi~l~~d~-rgR~---tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss~  181 (510)
T KOG4211|consen  128 EIVPDGILLPMDQ-RGRP---TGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSSR  181 (510)
T ss_pred             cccccceeeeccC-CCCc---ccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhHH
Confidence            55555 4455544 4444   58999999999999999996 88889999988865443

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

Probab=99.49  E-value=1.5e-13  Score=123.45  Aligned_cols=82  Identities=27%  Similarity=0.506  Sum_probs=78.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ++.+||||+-|+++++|..|+..|+.||+|+.|.|+.+..||.++|||||+|+++-+..+|.+..+|.+|+|+.|.|.+-
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            56689999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      ..
T Consensus       179 Rg  180 (335)
T KOG0113|consen  179 RG  180 (335)
T ss_pred             cc
Confidence            54

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

Probab=99.49  E-value=9.5e-14  Score=117.83  Aligned_cols=85  Identities=19%  Similarity=0.377  Sum_probs=71.0

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      .....++|||+|||+.+|+++|+++|.+||.|..+.      ++.+..++.++|||||+|.+.++|+.|+ .||+..|.|
T Consensus        30 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~------i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~G  103 (144)
T PLN03134         30 LRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAK------VIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNG  103 (144)
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEE------EEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            345567899999999999999999999999864421      1334445678999999999999999999 699999999


Q ss_pred             ceEEEeCCCCCC
Q 009954          249 VAVRVRRPTDYN  260 (521)
Q Consensus       249 ~~i~v~~~~~~~  260 (521)
                      +.|+|.++....
T Consensus       104 r~l~V~~a~~~~  115 (144)
T PLN03134        104 RHIRVNPANDRP  115 (144)
T ss_pred             EEEEEEeCCcCC
Confidence            999999876543

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

Probab=99.49  E-value=8.8e-14  Score=115.31  Aligned_cols=75  Identities=21%  Similarity=0.431  Sum_probs=71.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+||+..+++.||..+|..||+|.+|+|...+     .|||||||+++.+|..|+..|+|..|.|..|+|+.++-
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     78999999999999999999999999999999999865

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.48  E-value=2.2e-13  Score=123.29  Aligned_cols=75  Identities=21%  Similarity=0.360  Sum_probs=70.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ++|||+|||+.+++++|+++|+.||.|.+|.|+.+..   .+|||||+|.+.++|..||. |+|..|.|+.|.|.++..
T Consensus         5 rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          5 RTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            6899999999999999999999999999999998753   47899999999999999996 999999999999999875

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

Probab=99.48  E-value=5.5e-15  Score=122.86  Aligned_cols=82  Identities=33%  Similarity=0.662  Sum_probs=77.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCC
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASG  375 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (521)
                      -|||+|||+.+||.||...|++||.|++|.|++|+.||.++||||+.|++.-+...|+..|||..|.|+.|+|.......
T Consensus        37 ~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~Yk  116 (219)
T KOG0126|consen   37 YIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSNYK  116 (219)
T ss_pred             EEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeeccccc
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999886644


Q ss_pred             CC
Q 009954          376 QS  377 (521)
Q Consensus       376 ~~  377 (521)
                      .+
T Consensus       117 ~p  118 (219)
T KOG0126|consen  117 KP  118 (219)
T ss_pred             CC
Confidence            33

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

Probab=99.48  E-value=2.9e-13  Score=101.81  Aligned_cols=79  Identities=23%  Similarity=0.481  Sum_probs=72.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      +...-|||.|||..+|.++..++|.+||.|..|+|-..++   .+|.|||.|++..+|.+|+..|+|..+.++.+.|.|.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            4446799999999999999999999999999999987654   4889999999999999999999999999999999998


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      ++
T Consensus        93 q~   94 (124)
T KOG0114|consen   93 QP   94 (124)
T ss_pred             CH
Confidence            65

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

Probab=99.47  E-value=5e-12  Score=125.56  Aligned_cols=193  Identities=12%  Similarity=0.047  Sum_probs=136.6

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC-CCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-KKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~-~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      .+.+.+-+.+++++..+.++++||...-.       .... +.......+ .|-++|+|.....+++|+.-|...+-.+.
T Consensus       309 ~d~~y~~~~gm~fn~~~nd~rkfF~g~~~-------~~~~-l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~  380 (944)
T KOG4307|consen  309 SDKYYNNYKGMEFNNDFNDGRKFFPGRNA-------QSTD-LSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRP  380 (944)
T ss_pred             chhheeeecccccccccchhhhhcCcccc-------cccc-hhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcc
Confidence            45667888899999999999999885421       1111 222233334 79999999999999999999999999999


Q ss_pred             EEEeCCCCCCccccccCCCCCC--CCCcccccc------cCCCCCC--CCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCC
Q 009954          251 VRVRRPTDYNPTLAAALGPGQP--SPNLNLAAV------GLASGAI--GGAEGPDRVFVGGLPYYFTETQIKELLESFGT  320 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~--~~~~~~~~~------~~~~~~~--~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~  320 (521)
                      +.|..+.......+.......+  ....+.+..      ...++..  .......+|||..||..+++.++.++|...-.
T Consensus       381 ~q~~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~  460 (944)
T KOG4307|consen  381 FQTGPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAA  460 (944)
T ss_pred             eeecCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhh
Confidence            9998766544432221111111  000000000      0001111  22334568999999999999999999998777


Q ss_pred             eeE-EEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          321 LHG-FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       321 i~~-v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      |++ |.|...+ ++..++.|||+|..++++.+|+..-+.++++.+.|+|.-...
T Consensus       461 Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~  513 (944)
T KOG4307|consen  461 VEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIAD  513 (944)
T ss_pred             hhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeechhh
Confidence            776 6666664 788899999999999999999988888999999999997765

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

Probab=99.45  E-value=1.2e-13  Score=109.07  Aligned_cols=82  Identities=28%  Similarity=0.420  Sum_probs=78.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      ..|||.++...++|++|.+.|..||.|+.|.|..|..||-.+|||+|+|++.++|++|+..|||..|.|..|.|.|+-.+
T Consensus        73 wIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~  152 (170)
T KOG0130|consen   73 WIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVK  152 (170)
T ss_pred             EEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEec
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999764


Q ss_pred             CC
Q 009954          375 GQ  376 (521)
Q Consensus       375 ~~  376 (521)
                      +.
T Consensus       153 gp  154 (170)
T KOG0130|consen  153 GP  154 (170)
T ss_pred             CC
Confidence            43

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

Probab=99.43  E-value=2.4e-13  Score=118.54  Aligned_cols=80  Identities=26%  Similarity=0.542  Sum_probs=73.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+||+..+..+.|+++|++||.|+.+.|+.|+.+|+++||+||.|.+.+.|.+|++. ..-.|+||...|..|.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            346799999999999999999999999999999999999999999999999999999999985 3467899998888876


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      .
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            5

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

Probab=99.40  E-value=2.5e-12  Score=124.26  Aligned_cols=80  Identities=35%  Similarity=0.710  Sum_probs=76.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ..+|||+|||..+++++|.++|..||.|..|.+..+..+|.++|||||+|.+.++|..|+..|+|..|.|+.|.|.++..
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            47899999999999999999999999999999999988999999999999999999999999999999999999999753

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

Probab=99.40  E-value=3.3e-12  Score=109.96  Aligned_cols=82  Identities=24%  Similarity=0.339  Sum_probs=68.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec-CCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC---CeEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG---DKTLT  367 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~---g~~l~  367 (521)
                      ...+||||.+||.++...+|+.+|..|-..+...|... +.....+-+|||.|.+..+|..|+++|||..|+   +..|+
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            34689999999999999999999999877777665443 222334579999999999999999999999984   88999


Q ss_pred             EEEccC
Q 009954          368 VRRATA  373 (521)
Q Consensus       368 v~~~~~  373 (521)
                      |.+++.
T Consensus       112 iElAKS  117 (284)
T KOG1457|consen  112 IELAKS  117 (284)
T ss_pred             eeehhc
Confidence            999876

>smart00362 RRM_2 RNA recognition motif

Probab=99.40  E-value=2.3e-12  Score=96.11  Aligned_cols=72  Identities=39%  Similarity=0.691  Sum_probs=67.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEE
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      +|+|+|||..+++++|.++|.+||.|..+.+..++  +.++|+|||+|.+.++|..|++.|+|..+.|+.|.|.
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=99.39  E-value=2.5e-12  Score=114.48  Aligned_cols=75  Identities=15%  Similarity=0.260  Sum_probs=69.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .+|||+||++.+|+++|+++|+.||.|.+|.|+.+.   ...|||||+|.++++|..|+. |+|..|.++.|.|.....
T Consensus         6 ~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          6 YTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             eEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            689999999999999999999999999999999884   446899999999999999996 999999999999998764

>PLN03213 repressor of silencing 3; Provisional

Probab=99.39  E-value=1.6e-12  Score=124.25  Aligned_cols=76  Identities=17%  Similarity=0.351  Sum_probs=71.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCh--HHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~--~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ..+|||+||++.++++||..+|+.||.|..|.|++  .+|  +|||||+|.+.  .++.+||..|||..+.|+.|+|..|
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA   85 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA   85 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence            35899999999999999999999999999999995  477  99999999988  7899999999999999999999999


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      ++
T Consensus        86 KP   87 (759)
T PLN03213         86 KE   87 (759)
T ss_pred             cH
Confidence            76

>PF13893 RRM_5: RNA recognition motif

Probab=99.37  E-value=3.2e-12  Score=90.17  Aligned_cols=56  Identities=23%  Similarity=0.438  Sum_probs=51.0

Q ss_pred             HHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEc
Q 009954          446 MREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  509 (521)
Q Consensus       446 l~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~  509 (521)
                      |.++|++||+|.+|.+....        .++|||+|.+.++|..|++.|||..|+|++|+|.|+
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            67899999999999998864        278999999999999999999999999999999985

(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 ....

>smart00360 RRM RNA recognition motif

Probab=99.37  E-value=3.2e-12  Score=94.90  Aligned_cols=71  Identities=38%  Similarity=0.700  Sum_probs=67.0

Q ss_pred             EcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEE
Q 009954          299 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       299 v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      |+|||..+++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|..|++.|++..+.|+.|.|.
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            57999999999999999999999999999987789999999999999999999999999999999998873

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.32  E-value=5.8e-12  Score=114.18  Aligned_cols=76  Identities=25%  Similarity=0.358  Sum_probs=66.9

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec---CCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN---HEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~---~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      .++|||+|||+.+|+++|+++|+.||.            |.++.+.   ..+|||||+|.+.++|..||.|+|..|.|+.
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   2479999999999999999999999999999


Q ss_pred             EEEeCCCCCCc
Q 009954          251 VRVRRPTDYNP  261 (521)
Q Consensus       251 i~v~~~~~~~~  261 (521)
                      |.|.++..+..
T Consensus        72 V~Vt~a~~~~~   82 (260)
T PLN03120         72 VTITPAEDYQL   82 (260)
T ss_pred             EEEEeccCCCC
Confidence            99998776654

>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=99.32  E-value=1.9e-11  Score=91.63  Aligned_cols=74  Identities=38%  Similarity=0.689  Sum_probs=68.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      +|+|+|||..+++++|.++|..||.|..+.+..++.+ ..+|+|||+|.+.++|..|++.+++..+.|+.|.|.+
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            4899999999999999999999999999999987644 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).

>smart00361 RRM_1 RNA recognition motif

Probab=99.31  E-value=1.2e-11  Score=91.53  Aligned_cols=62  Identities=15%  Similarity=0.287  Sum_probs=55.6

Q ss_pred             HHHHHHHHH----hcCCeeEEE-EeecCCC--CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEE
Q 009954          308 ETQIKELLE----SFGTLHGFD-LVKDRDT--GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       308 e~~l~~~F~----~~G~i~~v~-i~~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      +++|.++|+    +||.|..|. |+.++.+  +.++|+|||+|.+.++|.+|++.|||..+.|+.|.+.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            577888888    999999995 7776666  9999999999999999999999999999999999863

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

Probab=99.30  E-value=4.2e-12  Score=108.05  Aligned_cols=74  Identities=23%  Similarity=0.359  Sum_probs=65.7

Q ss_pred             hHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          436 DEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       436 ~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      |+.|.|+-++|+.+|++||.|-+|.|+.+..+...   .|||||.|....||+.|+.+|.|..|+|+.|+|+++-..
T Consensus        20 NLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~s---RgFaFVrf~~k~daedA~damDG~~ldgRelrVq~aryg   93 (256)
T KOG4207|consen   20 NLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQS---RGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARYG   93 (256)
T ss_pred             ceeccCCHHHHHHHHHHhCcccceecccccccccc---cceeEEEeeecchHHHHHHhhcceeeccceeeehhhhcC
Confidence            44455555799999999999999999999988876   688899999999999999999999999999999997543

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

Probab=99.30  E-value=5.8e-12  Score=124.03  Aligned_cols=79  Identities=37%  Similarity=0.693  Sum_probs=77.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      +.|||+|+|+++++++|.++|+..|.|.+++++.|++||.++|||||+|.+.++|..|+..|||..+.|+.|+|.|+..
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASN   97 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccc
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999999999976

>PF13893 RRM_5: RNA recognition motif

Probab=99.29  E-value=1.5e-11  Score=86.66  Aligned_cols=56  Identities=23%  Similarity=0.486  Sum_probs=51.1

Q ss_pred             HHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          311 IKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       311 l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      |.++|++||.|..|.+....     +++|||+|.+.++|.+|++.|||..+.|++|+|.|+
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            68999999999999997763     579999999999999999999999999999999986

(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 ....

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

Probab=99.29  E-value=2e-12  Score=110.92  Aligned_cols=81  Identities=21%  Similarity=0.410  Sum_probs=78.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||++|...++|.-|...|-+||.|++|+++.|-++++.+|||||+|.-.|+|..||..||+..|.|+.|+|.++.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            34789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      +
T Consensus        89 P   89 (298)
T KOG0111|consen   89 P   89 (298)
T ss_pred             C
Confidence            8

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

Probab=99.29  E-value=1.4e-11  Score=112.36  Aligned_cols=79  Identities=24%  Similarity=0.398  Sum_probs=68.8

Q ss_pred             hhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCCeEEEEecCHHHHHHHH-HccC
Q 009954          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-ALDG  243 (521)
Q Consensus       169 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~----~~~~g~afV~f~~~~~a~~A~-~l~g  243 (521)
                      ......+.|+|.|||+..-+.||+.+|.+||.|            .++.|    ..+||||||+|++.++|++|- +|||
T Consensus        91 ~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~V------------ldVEIIfNERGSKGFGFVTmen~~dadRARa~LHg  158 (376)
T KOG0125|consen   91 SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKV------------LDVEIIFNERGSKGFGFVTMENPADADRARAELHG  158 (376)
T ss_pred             CCCCCCceeEeecCCccccCccHHHHHHhhCce------------eeEEEEeccCCCCccceEEecChhhHHHHHHHhhc
Confidence            344567899999999999999999999999984            44443    247999999999999999999 7999


Q ss_pred             ceecCceEEEeCCCCC
Q 009954          244 IIFEGVAVRVRRPTDY  259 (521)
Q Consensus       244 ~~~~g~~i~v~~~~~~  259 (521)
                      ..|.|++|.|+.+...
T Consensus       159 t~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  159 TVVEGRKIEVNNATAR  174 (376)
T ss_pred             ceeeceEEEEeccchh
Confidence            9999999999987654

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

Probab=99.27  E-value=6.9e-12  Score=104.19  Aligned_cols=74  Identities=31%  Similarity=0.463  Sum_probs=65.7

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~-~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ..++|||+||+..+++.+|...|..||.            +..+++.. ..|||||+|+++.+|..|+ .|+|..|.|..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~------------lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r   76 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGP------------LRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSR   76 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCc------------ceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCce
Confidence            3678999999999999999999999997            56666654 5699999999999999999 79999999999


Q ss_pred             EEEeCCCC
Q 009954          251 VRVRRPTD  258 (521)
Q Consensus       251 i~v~~~~~  258 (521)
                      |+|+....
T Consensus        77 ~rVE~S~G   84 (195)
T KOG0107|consen   77 IRVELSTG   84 (195)
T ss_pred             EEEEeecC
Confidence            99986543

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

Probab=99.27  E-value=2.3e-11  Score=117.47  Aligned_cols=169  Identities=23%  Similarity=0.290  Sum_probs=114.5

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      .++|||+|||..+|+++|.++|..||.+....      ...+..++..+|||||+|.+.++|..|+ .+++..|.|+.|.
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      1233346778999999999999999999 6999999999999


Q ss_pred             EeCCCC-CCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC
Q 009954          253 VRRPTD-YNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD  331 (521)
Q Consensus       253 v~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~  331 (521)
                      |.+... .........     . ......................+++.+++..++..++..+|..+|.+..+.+.....
T Consensus       189 v~~~~~~~~~~~~~~~-----~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (306)
T COG0724         189 VQKAQPASQPRSELSN-----N-LDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKD  262 (306)
T ss_pred             eecccccccccccccc-----c-cchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCC
Confidence            998543 110000000     0 000000001111222334456799999999999999999999999997777766543


Q ss_pred             CCCcceEEEEEEcChHHHHHHHH
Q 009954          332 TGNSKGYGFCVYQDPAVTDIACA  354 (521)
Q Consensus       332 ~g~~~g~afV~f~~~~~A~~Al~  354 (521)
                      ........++.+.....+..++.
T Consensus       263 ~~~~~~~~~~~~~~~~~~~~~~~  285 (306)
T COG0724         263 GKIPKSRSFVGNEASKDALESNS  285 (306)
T ss_pred             CcccccccccchhHHHhhhhhhc
Confidence            33344444444444444444443

>PF00076 RRM_1: RNA recognition motif

Probab=99.26  E-value=8.6e-12  Score=92.68  Aligned_cols=68  Identities=35%  Similarity=0.535  Sum_probs=56.1

Q ss_pred             EEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEE-EecCCCCeEEEEecCHHHHHHHH-HccCceecCceEE
Q 009954          177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV-YINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       177 l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~-~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      |||+|||.++|+++|+++|.+||.+..+        .+.. ..+..++||||+|.+.++|.+|+ .|+|..+.|+.|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESI--------KVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEE--------EEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccc--------cccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            7999999999999999999999985321        1111 12345799999999999999999 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 ....

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

Probab=99.26  E-value=1e-11  Score=97.38  Aligned_cols=78  Identities=24%  Similarity=0.402  Sum_probs=66.9

Q ss_pred             hhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC------CCCeEEEEecCHHHHHHHH-Hc
Q 009954          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAM-AL  241 (521)
Q Consensus       169 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~a~~A~-~l  241 (521)
                      .+...+++|||+||++.+||++|.++|+++|.|            ..+.++.      .-|||||+|.+.++|..|| -+
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            456779999999999999999999999999985            3333333      3499999999999999999 59


Q ss_pred             cCceecCceEEEeCCCC
Q 009954          242 DGIIFEGVAVRVRRPTD  258 (521)
Q Consensus       242 ~g~~~~g~~i~v~~~~~  258 (521)
                      +|..+..++|.|.|...
T Consensus        99 sgtrLddr~ir~D~D~G  115 (153)
T KOG0121|consen   99 SGTRLDDRPIRIDWDAG  115 (153)
T ss_pred             ccCcccccceeeecccc
Confidence            99999999999987543

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

Probab=99.26  E-value=1.1e-10  Score=117.89  Aligned_cols=78  Identities=27%  Similarity=0.491  Sum_probs=72.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      +||||++|+..++|.||.++|+.||.|.+|.++..      +|||||.+....+|.+||.+|+...+.++.|+|.|+..+
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            58999999999999999999999999999998765      789999999999999999999999999999999999876


Q ss_pred             CCCc
Q 009954          375 GQSK  378 (521)
Q Consensus       375 ~~~~  378 (521)
                      +...
T Consensus       496 G~ks  499 (894)
T KOG0132|consen  496 GPKS  499 (894)
T ss_pred             Ccch
Confidence            6543

>smart00361 RRM_1 RNA recognition motif

Probab=99.24  E-value=3.3e-11  Score=89.09  Aligned_cols=63  Identities=25%  Similarity=0.354  Sum_probs=49.8

Q ss_pred             HHHHHHHhhccccceeEEE-ecCCCCC--CCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEE
Q 009954          442 ILEDMREECGKYGTLVNVV-IPRPDQN--GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF  507 (521)
Q Consensus       442 ~~~dl~~~f~~fG~I~~v~-i~~~~~~--~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~  507 (521)
                      |.+.+.++|+.||.|.+|. |..+..+  +..   +|+|||+|.+.++|.+|++.|||..|+|+.|+++
T Consensus         5 l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~---rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        5 FEREFSEEEEYFGEVGKINKIYIDNVGYENHK---RGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             HHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCC---cEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            3345555555999999995 5555434  432   5788999999999999999999999999999874

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.24  E-value=6.8e-12  Score=116.33  Aligned_cols=191  Identities=20%  Similarity=0.192  Sum_probs=127.5

Q ss_pred             eEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE--ecCCCCeEEEEecCHHHHHHHHHccCceecCceEEE
Q 009954          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY--INHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  253 (521)
Q Consensus       176 ~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v  253 (521)
                      .|.+.|||++.|+.++.+||.+--.+.+     ..+.|.-+.  -++..|-|||.|..+++|+.||.-|...|+.+-|.+
T Consensus       163 ivRmRGLPfdat~~dVv~FF~~~cpv~~-----g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIEl  237 (508)
T KOG1365|consen  163 IVRMRGLPFDATALDVVEFFGPPCPVTG-----GTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIEL  237 (508)
T ss_pred             EEEecCCCCCcchHHHHHhcCCCCcccC-----CccceEEEECCCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHH
Confidence            5788999999999999999974333221     122344443  355679999999999999999977777777766666


Q ss_pred             eCCCCCCccccccCCCCCCCCC-cccccccCCCC-CCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCC-eeE--EEEee
Q 009954          254 RRPTDYNPTLAAALGPGQPSPN-LNLAAVGLASG-AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHG--FDLVK  328 (521)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~-i~~--v~i~~  328 (521)
                      -++....-..........+... .........+. -........+|.+++||+..+.+||.++|..|.. |..  |.++.
T Consensus       238 FRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~  317 (508)
T KOG1365|consen  238 FRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVL  317 (508)
T ss_pred             HHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEE
Confidence            4322111000000000000000 00000000000 0111223568999999999999999999998876 443  77777


Q ss_pred             cCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      + ..|.+.|-|||+|.+.|.|..|....+.+....+.|.|-.+.
T Consensus       318 N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S  360 (508)
T KOG1365|consen  318 N-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCS  360 (508)
T ss_pred             c-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeecc
Confidence            6 479999999999999999999999999888889999998764

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

Probab=99.23  E-value=7.2e-12  Score=109.39  Aligned_cols=80  Identities=19%  Similarity=0.335  Sum_probs=69.1

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ..-.+||||||++.++.++|+++|++||+|+..++      |.|..+++++|||||+|.+.+.|.+|++--.-.|+||+.
T Consensus        10 T~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavv------itd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~a   83 (247)
T KOG0149|consen   10 TTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVV------ITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKA   83 (247)
T ss_pred             ceEEEEEEcCcccccchHHHHHHHHHhCceEEEEE------EeccCCccccceeeEEeecHHHHHHHhcCCCCccccccc
Confidence            34568999999999999999999999999876543      778889999999999999999999999666667899887


Q ss_pred             EEeCCC
Q 009954          252 RVRRPT  257 (521)
Q Consensus       252 ~v~~~~  257 (521)
                      .++.+.
T Consensus        84 NcnlA~   89 (247)
T KOG0149|consen   84 NCNLAS   89 (247)
T ss_pred             ccchhh
Confidence            777543

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

Probab=99.20  E-value=2.1e-11  Score=106.76  Aligned_cols=83  Identities=19%  Similarity=0.252  Sum_probs=74.4

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      ...+.++|-|.||+.++++.+|.++|.+||.|...++      .++..++.++|||||.|.+.++|.+|+ .|||.-+..
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvyl------ardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~  258 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYL------ARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDN  258 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEE------EEccccCcccceEEEEEecHHHHHHHHHHccCcccce
Confidence            3447789999999999999999999999999866544      778889999999999999999999999 799999999


Q ss_pred             ceEEEeCCCC
Q 009954          249 VAVRVRRPTD  258 (521)
Q Consensus       249 ~~i~v~~~~~  258 (521)
                      --|.|.|+++
T Consensus       259 LILrvEwskP  268 (270)
T KOG0122|consen  259 LILRVEWSKP  268 (270)
T ss_pred             EEEEEEecCC
Confidence            9999999764

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.19  E-value=7.5e-11  Score=105.12  Aligned_cols=76  Identities=24%  Similarity=0.268  Sum_probs=66.0

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe---cCCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~---~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      ..+|+|+||++.+|+++|++||+.||.|            .++.+   +..++||||+|.++++|..|+.|+|..|.++.
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   34568999999999999999999999999999


Q ss_pred             EEEeCCCCCCc
Q 009954          251 VRVRRPTDYNP  261 (521)
Q Consensus       251 i~v~~~~~~~~  261 (521)
                      |.|.....+..
T Consensus        73 I~It~~~~y~~   83 (243)
T PLN03121         73 VCITRWGQYED   83 (243)
T ss_pred             EEEEeCccccc
Confidence            99987666554

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

Probab=99.17  E-value=1.4e-12  Score=108.62  Aligned_cols=91  Identities=26%  Similarity=0.362  Sum_probs=80.6

Q ss_pred             cchhhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCc
Q 009954          166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI  244 (521)
Q Consensus       166 ~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~  244 (521)
                      .+.+....+.-|||||||+.+||.+|.-.|++||+++..++      |.+..+++++||||+.|++......|+ .|||.
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            44456677889999999999999999999999999877655      788889999999999999999999999 79999


Q ss_pred             eecCceEEEeCCCCCCcc
Q 009954          245 IFEGVAVRVRRPTDYNPT  262 (521)
Q Consensus       245 ~~~g~~i~v~~~~~~~~~  262 (521)
                      .|.|+.|+|.....|..+
T Consensus       101 ki~gRtirVDHv~~Yk~p  118 (219)
T KOG0126|consen  101 KILGRTIRVDHVSNYKKP  118 (219)
T ss_pred             eecceeEEeeecccccCC
Confidence            999999999877666543

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.14  E-value=5.6e-10  Score=108.48  Aligned_cols=172  Identities=22%  Similarity=0.229  Sum_probs=114.5

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCC---eEEEEecCHHHHHHHH-HccCcee
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTVEEASNAM-ALDGIIF  246 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g---~afV~f~~~~~a~~A~-~l~g~~~  246 (521)
                      ..-+++||||+||++++|++|...|..||.+.-...   + ..........+|   |+|+.|+++......+ +..- .-
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP---~-k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~-~~  330 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWP---G-KANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE-GE  330 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceEeecC---C-CccccccCCCCCcccEEEEEecchHHHHHHHHHHhh-cc
Confidence            355789999999999999999999999998532111   0 001111122356   9999999999888777 2110 00


Q ss_pred             cCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHH-hcCCeeEEE
Q 009954          247 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLE-SFGTLHGFD  325 (521)
Q Consensus       247 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~-~~G~i~~v~  325 (521)
                      ..--++|.-+......        -....+.++.....-......++.+||||++||-.++-++|..+|+ .||.|..+-
T Consensus       331 ~~~yf~vss~~~k~k~--------VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaG  402 (520)
T KOG0129|consen  331 GNYYFKVSSPTIKDKE--------VQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVG  402 (520)
T ss_pred             cceEEEEecCcccccc--------eeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEE
Confidence            0111222211111000        0000011111111111333456778999999999999999999999 899999999


Q ss_pred             EeecCCCCCcceEEEEEEcChHHHHHHHHH
Q 009954          326 LVKDRDTGNSKGYGFCVYQDPAVTDIACAA  355 (521)
Q Consensus       326 i~~~~~~g~~~g~afV~f~~~~~A~~Al~~  355 (521)
                      |-+|++-+-++|-|=|.|.+...-.+||.+
T Consensus       403 IDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  403 IDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             eccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            999988999999999999999999999875

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

Probab=99.07  E-value=1.1e-10  Score=92.50  Aligned_cols=82  Identities=24%  Similarity=0.230  Sum_probs=70.3

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ..+--.|||.++...+|+++|.+.|..||+|+..++      -.+..++.-+|||+|+|.+.++|+.|+ ++||..+.|+
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            344557999999999999999999999999765433      355566777999999999999999999 7999999999


Q ss_pred             eEEEeCCCC
Q 009954          250 AVRVRRPTD  258 (521)
Q Consensus       250 ~i~v~~~~~  258 (521)
                      +|.|.|+-.
T Consensus       143 ~v~VDw~Fv  151 (170)
T KOG0130|consen  143 NVSVDWCFV  151 (170)
T ss_pred             ceeEEEEEe
Confidence            999998643

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

Probab=99.06  E-value=2.2e-10  Score=86.49  Aligned_cols=69  Identities=26%  Similarity=0.466  Sum_probs=59.3

Q ss_pred             HHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          439 YEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       439 ~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      |..+.+++.++|.+||.|..|.|=....+      .|.|||.|+++.+|.+|+..|+|..+.++.|.|-|+...+
T Consensus        28 ~~ITseemydlFGkyg~IrQIRiG~~k~T------rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~   96 (124)
T KOG0114|consen   28 FKITSEEMYDLFGKYGTIRQIRIGNTKET------RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPED   96 (124)
T ss_pred             ccccHHHHHHHhhcccceEEEEecCccCc------CceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHH
Confidence            33445799999999999999999665433      5889999999999999999999999999999999976543

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

Probab=99.06  E-value=5.1e-10  Score=111.54  Aligned_cols=196  Identities=9%  Similarity=0.017  Sum_probs=125.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      +.+-+.+++.++.+.|++++|... .|-.+.|..+...+..+|.++|+|....++++|+.. +...+-.+.|.|..+...
T Consensus       312 ~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~g~~  389 (944)
T KOG4307|consen  312 YYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPPGNL  389 (944)
T ss_pred             heeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCCCcc
Confidence            446689999999999999998842 244445555554556688999999999999999885 666777888888876551


Q ss_pred             CCCchHHHHHHHHHHHHHHHHHHhhhcc--------CCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHH
Q 009954          375 GQSKTEQESILAQAQQHIAIQKMALQTS--------GMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDM  446 (521)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl  446 (521)
                      .-.....-...  .    .. ......+        +...+|..++..- -...|+.|..+.-...          +.++
T Consensus       390 ~~~~a~~~~~~--~----~~-~~~~~~hg~p~~~pr~~~~~gq~vp~P~-~ag~~lyv~~lP~~t~----------~~~~  451 (944)
T KOG4307|consen  390 GRNGAPPFQAG--V----PP-PVIQNNHGRPIAPPRAMVRPGQNVPFPG-GAGGALYVFQLPVMTP----------IVPP  451 (944)
T ss_pred             ccccCcccccc--C----CC-CcccccCCCCCCCcccccCCCCCCCCCC-CccceEEeccCCcccc----------ccch
Confidence            11100000000  0    00 0000000        1111232222222 2234555444322222          2488


Q ss_pred             HHhhccccceeE-EEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCc
Q 009954          447 REECGKYGTLVN-VVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  514 (521)
Q Consensus       447 ~~~f~~fG~I~~-v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~  514 (521)
                      .++|..--.|++ |.|.+.. ++.-   .+.|||.|.+++++.+|+..-+-+++|.+.|+|.-+.++.+
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            999998778888 6665554 4332   36789999999999999999999999999999999887766

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.05  E-value=3.4e-10  Score=84.01  Aligned_cols=61  Identities=21%  Similarity=0.421  Sum_probs=53.2

Q ss_pred             HHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEE
Q 009954          441 EILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVN  505 (521)
Q Consensus       441 ~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~  505 (521)
                      +.+++|+++|+.||.|..|.+..+.. +   .++|+|||+|.++++|..|++.++|..|+|+.|+
T Consensus        10 ~~~~~l~~~f~~~g~v~~v~~~~~~~-~---~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen   10 TTEEDLRNFFSRFGPVEKVRLIKNKD-G---QSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             --HHHHHHHCTTSSBEEEEEEEESTT-S---SEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCHHHHHHHHHhcCCcceEEEEeeec-c---ccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            34479999999999999999998753 3   3468999999999999999999999999999985

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 ....

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

Probab=99.04  E-value=1.7e-09  Score=106.18  Aligned_cols=178  Identities=17%  Similarity=0.191  Sum_probs=114.9

Q ss_pred             hhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE-ecCCCCeEEEEecCHHHHHHHH-HccCcee
Q 009954          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY-INHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (521)
Q Consensus       169 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~-~~~~~g~afV~f~~~~~a~~A~-~l~g~~~  246 (521)
                      ......++|+|-|||..+++++|..+|..||+|.            .+. +....|.+||+|.+..+|++|+ +|++..|
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            4456788999999999999999999999999954            333 3446799999999999999999 7999999


Q ss_pred             cCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 009954          247 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (521)
Q Consensus       247 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i  326 (521)
                      .|+.|+  .+......    .+......-++.....+.....++-. ...+|. .|++..+..-+...|.-+|.+.. ..
T Consensus       138 ~~~~~k--~~~~~~~~----~~~~~~~~~~~~~~~p~a~s~pgg~~-~~~~~g-~l~P~~s~~~~~~~~~~~~~~~~-~~  208 (549)
T KOG4660|consen  138 AGKRIK--RPGGARRA----MGLQSGTSFLNHFGSPLANSPPGGWP-RGQLFG-MLSPTRSSILLEHISSVDGSSPG-RE  208 (549)
T ss_pred             hhhhhc--CCCccccc----chhcccchhhhhccchhhcCCCCCCc-CCccee-eeccchhhhhhhcchhccCcccc-cc
Confidence            999988  21111111    11111111111000000001111111 122333 38888888777777778887765 32


Q ss_pred             eecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       327 ~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                           ++.-.-.-|++|.+..++..++..+ |..+.+....++++.+
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                 2221224689999999987776644 7777887777777765

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

Probab=99.04  E-value=6.3e-10  Score=98.15  Aligned_cols=131  Identities=23%  Similarity=0.367  Sum_probs=107.2

Q ss_pred             cCCCCeEEEEecCHHHHHHHH-HccCceecCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeE
Q 009954          219 NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRV  297 (521)
Q Consensus       219 ~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  297 (521)
                      +.-.+++|+.|.....-.++. +-+++++.-.+|++.....+......                       .-.+...+|
T Consensus       137 ~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedPsl~-----------------------ew~~~DfRI  193 (290)
T KOG0226|consen  137 QPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDPSLA-----------------------EWDEDDFRI  193 (290)
T ss_pred             CccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCcccc-----------------------cCcccccee
Confidence            445689999999887777777 56777777777777655444332111                       112334689


Q ss_pred             EEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       298 ~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      |++.|..+++.+.|...|.+|-.....++++++.||+++||+||-|.++.++..|+.+|+|.+++.+.|++..+.
T Consensus       194 fcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~  268 (290)
T KOG0226|consen  194 FCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSE  268 (290)
T ss_pred             ecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhh
Confidence            999999999999999999999999999999999999999999999999999999999999999999999988653

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

Probab=99.03  E-value=1e-09  Score=94.28  Aligned_cols=81  Identities=31%  Similarity=0.515  Sum_probs=75.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhc-CCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESF-GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~-G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ....++|..+|..+.+..|..+|.+| |.|..+++.+++.||.++|||||+|++.+.|.-|-+.||+..|.|+-|.|.+.
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            34568999999999999999999988 77888899899999999999999999999999999999999999999999998


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      .+
T Consensus       128 pp  129 (214)
T KOG4208|consen  128 PP  129 (214)
T ss_pred             Cc
Confidence            65

>smart00362 RRM_2 RNA recognition motif

Probab=99.03  E-value=1.1e-09  Score=81.25  Aligned_cols=67  Identities=37%  Similarity=0.635  Sum_probs=57.7

Q ss_pred             eEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC----CCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH----EKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       176 ~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~----~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      +|+|+|||..+++++|+++|.+||.            +..+.+..    .+++|||+|.+.++|..|+ .+++..+.|+.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~------------v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~   68 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGP------------IESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRP   68 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCC------------EEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEE
Confidence            5899999999999999999999997            34444333    4599999999999999999 69999999999


Q ss_pred             EEEe
Q 009954          251 VRVR  254 (521)
Q Consensus       251 i~v~  254 (521)
                      |.|+
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=99.02  E-value=6.3e-10  Score=106.73  Aligned_cols=73  Identities=19%  Similarity=0.406  Sum_probs=62.3

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec--CCCCeEEEEecCH--HHHHHHH-HccCceecC
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--HEKKFAFVEMRTV--EEASNAM-ALDGIIFEG  248 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~--~~~g~afV~f~~~--~~a~~A~-~l~g~~~~g  248 (521)
                      .-+||||||++.+|+++|..+|..||.|..            +.+.  ..+|||||+|.+.  .++.+|+ .|||..|.|
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkd------------VEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKG   77 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDA------------VEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKG   77 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeE------------EEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecC
Confidence            458999999999999999999999998543            3222  2389999999987  6899999 799999999


Q ss_pred             ceEEEeCCCC
Q 009954          249 VAVRVRRPTD  258 (521)
Q Consensus       249 ~~i~v~~~~~  258 (521)
                      +.|+|+.++.
T Consensus        78 R~LKVNKAKP   87 (759)
T PLN03213         78 GRLRLEKAKE   87 (759)
T ss_pred             ceeEEeeccH
Confidence            9999987663

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

Probab=99.01  E-value=6.4e-10  Score=102.39  Aligned_cols=82  Identities=20%  Similarity=0.403  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      .+.+.|||-.|.+-++.+||.-+|+.||.|.++.|++|..||.+-.||||+|.+.+++++|.-.|++..|..+.|+|.|+
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            45578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      +.
T Consensus       317 QS  318 (479)
T KOG0415|consen  317 QS  318 (479)
T ss_pred             hh
Confidence            65

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

Probab=99.01  E-value=1.7e-10  Score=99.19  Aligned_cols=83  Identities=22%  Similarity=0.325  Sum_probs=72.4

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....++||||+|...+|+.-|...|-+||.|...      ....+....+++|||||+|...|+|..|| .||+..+.|+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dI------qiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~Gr   80 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDI------QIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGR   80 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhc------ccccchhcccccceeEEEeeccchhHHHhhcCchhhhcce
Confidence            3456899999999999999999999999997543      23566677889999999999999999999 7999999999


Q ss_pred             eEEEeCCCCC
Q 009954          250 AVRVRRPTDY  259 (521)
Q Consensus       250 ~i~v~~~~~~  259 (521)
                      .|+|+++.+.
T Consensus        81 tirVN~AkP~   90 (298)
T KOG0111|consen   81 TIRVNLAKPE   90 (298)
T ss_pred             eEEEeecCCc
Confidence            9999987653

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

Probab=99.00  E-value=2.3e-10  Score=112.88  Aligned_cols=81  Identities=27%  Similarity=0.414  Sum_probs=74.4

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEE
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v  253 (521)
                      +.|||||+|+++++++|.++|...|.|+.+.+      +.|..+++.+||||++|.+.++|..|+ .|||..+.|++|+|
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            78999999999999999999999999877654      778888999999999999999999999 79999999999999


Q ss_pred             eCCCCCCc
Q 009954          254 RRPTDYNP  261 (521)
Q Consensus       254 ~~~~~~~~  261 (521)
                      .|+.....
T Consensus        93 ~~~~~~~~  100 (435)
T KOG0108|consen   93 NYASNRKN  100 (435)
T ss_pred             ecccccch
Confidence            99886554

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

Probab=98.99  E-value=7.8e-10  Score=99.84  Aligned_cols=78  Identities=19%  Similarity=0.220  Sum_probs=70.4

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      .+-+||||+-|+.+++|..|+..|..||.|....      .|.+..+++++|||||+|+++.+...|. +.+|.+|.|+.
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~Ikrir------lV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrr  172 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIR------LVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRR  172 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEE------EeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcE
Confidence            4678999999999999999999999999986533      3777788999999999999999999999 79999999999


Q ss_pred             EEEeC
Q 009954          251 VRVRR  255 (521)
Q Consensus       251 i~v~~  255 (521)
                      |.|.+
T Consensus       173 i~VDv  177 (335)
T KOG0113|consen  173 ILVDV  177 (335)
T ss_pred             EEEEe
Confidence            99974

>smart00360 RRM RNA recognition motif

Probab=98.99  E-value=1e-09  Score=81.27  Aligned_cols=62  Identities=26%  Similarity=0.461  Sum_probs=55.0

Q ss_pred             HHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEE
Q 009954          443 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF  507 (521)
Q Consensus       443 ~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~  507 (521)
                      .++|+++|+.||.|..|.+..+..++..   .|+|||+|.+.++|..|+..|++..++|+.|.|.
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            3699999999999999999987654433   5889999999999999999999999999999873

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

Probab=98.92  E-value=1e-09  Score=98.58  Aligned_cols=97  Identities=31%  Similarity=0.519  Sum_probs=79.6

Q ss_pred             CcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhC
Q 009954          417 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  496 (521)
Q Consensus       417 ~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng  496 (521)
                      ++++|+.|.|.+...+..     +++++.+++.|++||.|.+|.|.-.+.....  -.-..||+|.++++|.+|+-.|||
T Consensus       279 ~ptkvlllrnmVg~gevd-----~elede~keEceKyg~V~~viifeip~~p~d--eavRiFveF~r~e~aiKA~VdlnG  351 (378)
T KOG1996|consen  279 CPTKVLLLRNMVGAGEVD-----EELEDETKEECEKYGKVGNVIIFEIPSQPED--EAVRIFVEFERVESAIKAVVDLNG  351 (378)
T ss_pred             cchHHHHhhhhcCccccc-----HHHHHHHHHHHHhhcceeeEEEEecCCCccc--hhheeeeeeccHHHHHHHHHhcCC
Confidence            788888888888776543     3466789999999999999998776422211  123479999999999999999999


Q ss_pred             CeeCCcEEEEEEcCCCCcccccCC
Q 009954          497 RKFGGNTVNAFYYPEDKYFNKDYS  520 (521)
Q Consensus       497 ~~~~gr~l~v~~~~~~~~~~~~~~  520 (521)
                      ++||||.+++.|++.++|.+.+++
T Consensus       352 RyFGGr~v~A~Fyn~ekfs~~ela  375 (378)
T KOG1996|consen  352 RYFGGRVVSACFYNLEKFSNLELA  375 (378)
T ss_pred             ceecceeeeheeccHHhhhhhhhh
Confidence            999999999999999999987653

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

Probab=98.91  E-value=7.8e-09  Score=100.91  Aligned_cols=81  Identities=20%  Similarity=0.371  Sum_probs=76.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||.+|...+-..||+.+|++||.|+..+|+++..+...++|+||++.+.++|.+||+.||...|.|+.|.|..++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            34689999999999999999999999999999999987787889999999999999999999999999999999999997


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      +
T Consensus       484 N  484 (940)
T KOG4661|consen  484 N  484 (940)
T ss_pred             c
Confidence            7

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

Probab=98.87  E-value=8.3e-09  Score=95.31  Aligned_cols=76  Identities=16%  Similarity=0.344  Sum_probs=67.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHc-CCeeCCeEEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN-GLKMGDKTLTVRR  370 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~-g~~~~g~~l~v~~  370 (521)
                      ..-.+|||++|-..++|.+|+++|.+||.|.+|.+...      +++|||+|.+.+.|+.|.+.+- ...|+|..|.|.|
T Consensus       226 ~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~W  299 (377)
T KOG0153|consen  226 TSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKW  299 (377)
T ss_pred             cceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEe
Confidence            34468999999999999999999999999999998875      5699999999999999886654 4678999999999


Q ss_pred             ccC
Q 009954          371 ATA  373 (521)
Q Consensus       371 ~~~  373 (521)
                      ..+
T Consensus       300 g~~  302 (377)
T KOG0153|consen  300 GRP  302 (377)
T ss_pred             CCC
Confidence            976

>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=98.87  E-value=1.2e-08  Score=76.14  Aligned_cols=68  Identities=37%  Similarity=0.573  Sum_probs=58.3

Q ss_pred             eEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-----CCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-----EKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       176 ~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~-----~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      +|+|+|||..+++++|+++|..+|.+            ..+.+..     ..++|||+|.+.++|..|+ .+++..+.|+
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            48999999999999999999999873            3333332     3799999999999999999 7999999999


Q ss_pred             eEEEeC
Q 009954          250 AVRVRR  255 (521)
Q Consensus       250 ~i~v~~  255 (521)
                      .+.|.+
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).

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

Probab=98.85  E-value=3.8e-10  Score=97.17  Aligned_cols=138  Identities=23%  Similarity=0.295  Sum_probs=113.4

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC----CCeEEEEecCHHHHHHHHH-ccCcee
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEMRTVEEASNAMA-LDGIIF  246 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~----~g~afV~f~~~~~a~~A~~-l~g~~~  246 (521)
                      +..++|||+|+-..++|+-|.++|-+.|.            |+.+.+...    ..||||.|.++-....|++ +||..+
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGP------------V~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l   74 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGP------------VYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDL   74 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCc------------eEEEeCCCCccCCCceeeeecccccchhhhhhhcccchh
Confidence            45689999999999999999999999987            666665432    3599999999999999995 899999


Q ss_pred             cCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcC----CCCCCCHHHHHHHHHhcCCee
Q 009954          247 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGG----LPYYFTETQIKELLESFGTLH  322 (521)
Q Consensus       247 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~n----Lp~~~te~~l~~~F~~~G~i~  322 (521)
                      .+..++|+.                                          +.++    |...++++.+...|+.-|++.
T Consensus        75 ~~~e~q~~~------------------------------------------r~G~shapld~r~~~ei~~~v~s~a~p~~  112 (267)
T KOG4454|consen   75 EEDEEQRTL------------------------------------------RCGNSHAPLDERVTEEILYEVFSQAGPIE  112 (267)
T ss_pred             ccchhhccc------------------------------------------ccCCCcchhhhhcchhhheeeecccCCCC
Confidence            999988853                                          3344    566788999999999999999


Q ss_pred             EEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCe
Q 009954          323 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK  364 (521)
Q Consensus       323 ~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~  364 (521)
                      .+++..+. +|..+.++|+.+...-..-.|+....+..+.-+
T Consensus       113 ~~R~~~~~-d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~  153 (267)
T KOG4454|consen  113 GVRIPTDN-DGRNRNFGFVTYQRLCAVPFALDLYQGLELFQK  153 (267)
T ss_pred             Cccccccc-cCCccCccchhhhhhhcCcHHhhhhcccCcCCC
Confidence            99999885 588888999998887777778877666544333

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.84  E-value=2.5e-09  Score=100.93  Aligned_cols=176  Identities=18%  Similarity=0.212  Sum_probs=132.1

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCc-eecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGI-IFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~-~~~g~~  250 (521)
                      ....++|++++...+.+.++..++..+|.....-      ....-....++++++|.|...+.+..|+++.+. .+.+..
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~------~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~  159 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDAR------SSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNK  159 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccch------hhhhccccccccceeeccccHHHHHHHHHhhhcccccccc
Confidence            3467899999999999998999999998743221      112223455789999999999999999987775 444444


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEE-EcCCCCCCCHHHHHHHHHhcCCeeEEEEeec
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVF-VGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~  329 (521)
                      +..-........        .           .............++| |.+|+..+++++|+.+|..+|.|+.+++..+
T Consensus       160 ~~~dl~~~~~~~--------~-----------~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~  220 (285)
T KOG4210|consen  160 GEKDLNTRRGLR--------P-----------KNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTD  220 (285)
T ss_pred             ccCccccccccc--------c-----------cchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCC
Confidence            433221111100        0           0000011122334555 9999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       330 ~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      +.++..+|||||+|.....+..|+.. ....+.++++.+.+..+
T Consensus       221 ~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  263 (285)
T KOG4210|consen  221 EESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEP  263 (285)
T ss_pred             CCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCC
Confidence            99999999999999999999999987 78999999999999876

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

Probab=98.84  E-value=8.4e-09  Score=88.66  Aligned_cols=65  Identities=14%  Similarity=0.296  Sum_probs=59.5

Q ss_pred             HHHHhhccc-cceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          445 DMREECGKY-GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       445 dl~~~f~~f-G~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      .|..+|.+| |.|..+.+.++..||+.   +|+|||+|.+.+.|..|.+.||+..|+|+-|.|.+++++
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            677777777 78888899899999986   688899999999999999999999999999999999998

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

Probab=98.82  E-value=1.7e-09  Score=111.24  Aligned_cols=158  Identities=15%  Similarity=0.242  Sum_probs=123.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      .+.+||++||+..+++.+|+..|..+|.|..|.|...+ -+.---||||.|.+...+..|+..+.+..|..-.+++.+..
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            44689999999999999999999999999999987764 23334489999999999999999999988876677666664


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhcc
Q 009954          373 ASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGK  452 (521)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~  452 (521)
                      ++.+..                                      +...+-.|..+.+.             ..|..+|..
T Consensus       450 ~kst~t--------------------------------------tr~~sgglg~w~p~-------------~~l~r~fd~  478 (975)
T KOG0112|consen  450 PKSTPT--------------------------------------TRLQSGGLGPWSPV-------------SRLNREFDR  478 (975)
T ss_pred             cccccc--------------------------------------eeeccCCCCCCChH-------------HHHHHHhhc
Confidence            311110                                      11112223333333             389999999


Q ss_pred             ccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCC--cEEEEEEcCC
Q 009954          453 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYYPE  511 (521)
Q Consensus       453 fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~g--r~l~v~~~~~  511 (521)
                      ||.|..|.+..-         .-+|||.|.+...|+.|++.|-|..|||  +.|.|.|+.+
T Consensus       479 fGpir~Idy~hg---------q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~  530 (975)
T KOG0112|consen  479 FGPIRIIDYRHG---------QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASP  530 (975)
T ss_pred             cCcceeeecccC---------CcceeeecccCccchhhHHHHhcCcCCCCCcccccccccC
Confidence            999999887542         2589999999999999999999999988  7799988754

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.82  E-value=1.9e-10  Score=117.75  Aligned_cols=236  Identities=14%  Similarity=0.132  Sum_probs=167.7

Q ss_pred             CCeEEEeCCCccCcHH-HHHHHHHHHHHhhcCCCCCCCCceEEEEecC------CCCeEEEEecCHHHHHHHHHccCcee
Q 009954          174 ARRVYVGGLPPLANEQ-AIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAMALDGIIF  246 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~-~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~a~~A~~l~g~~~  246 (521)
                      .....+.++.+..... .++..|..+|.            +..++...      ...++++.+.....++.|....+..+
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            3456677777776555 56778888876            33333332      23488999999999999998888888


Q ss_pred             cCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 009954          247 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (521)
Q Consensus       247 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i  326 (521)
                      .++.+.|..+.........   ...+                .......++||+||++.+.+.+|...|..+|.+..+++
T Consensus       639 a~~~~av~~ad~~~~~~~~---kvs~----------------n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi  699 (881)
T KOG0128|consen  639 ANRSAAVGLADAEEKEENF---KVSP----------------NEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQI  699 (881)
T ss_pred             CCccccCCCCCchhhhhcc---CcCc----------------hHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHH
Confidence            8877777543322211000   0000                00011246899999999999999999999999988887


Q ss_pred             eecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCC
Q 009954          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNT  406 (521)
Q Consensus       327 ~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  406 (521)
                      ......+..+|+|||+|..+++|.+|+....+..++...|.|.                                     
T Consensus       700 ~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~~v~i~-------------------------------------  742 (881)
T KOG0128|consen  700 VIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKISVAIS-------------------------------------  742 (881)
T ss_pred             HHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhhhhhee-------------------------------------
Confidence            7666688999999999999999999998655554442111111                                     


Q ss_pred             CCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHH
Q 009954          407 LGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVG  486 (521)
Q Consensus       407 ~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~  486 (521)
                                        .+.           +.-+.+.++.+|..+|++.++.++... .|.+   +|.|||.|.+..+
T Consensus       743 ------------------g~p-----------f~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkp---kg~a~v~y~~ea~  789 (881)
T KOG0128|consen  743 ------------------GPP-----------FQGTKEELKSLASKTGNVTSLRLVTVR-AGKP---KGKARVDYNTEAD  789 (881)
T ss_pred             ------------------CCC-----------CCCchHHHHhhccccCCccccchhhhh-cccc---ccceeccCCCcch
Confidence                              001           111225899999999999999876654 5555   7999999999999


Q ss_pred             HHHHHHHHhCCeeCCcEEEEEEcC
Q 009954          487 CATAKNALSGRKFGGNTVNAFYYP  510 (521)
Q Consensus       487 A~~Ai~~lng~~~~gr~l~v~~~~  510 (521)
                      |..++..+.+..+.-+.+.|..-+
T Consensus       790 ~s~~~~s~d~~~~rE~~~~v~vsn  813 (881)
T KOG0128|consen  790 ASRKVASVDVAGKRENNGEVQVSN  813 (881)
T ss_pred             hhhhcccchhhhhhhcCccccccC
Confidence            999999999988888877777633

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

Probab=98.81  E-value=3.1e-09  Score=109.41  Aligned_cols=162  Identities=20%  Similarity=0.335  Sum_probs=127.2

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      ....+++||++||+..+++.+|+..|..+|.+...       -|....++....||||.|.+...+-.|. ++.+..|..
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~V-------DiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~  440 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEV-------DIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGN  440 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhcccccc-------ccccCCCCcccchhhhhhhccccCcccchhhcCCcccc
Confidence            34568899999999999999999999999984210       0111123445679999999999999999 788877765


Q ss_pred             ceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 009954          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (521)
Q Consensus       249 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~  328 (521)
                      -.+++.+...                               -....+.+++++|.+.+....|...|..||.|..|.+-.
T Consensus       441 g~~r~glG~~-------------------------------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h  489 (975)
T KOG0112|consen  441 GTHRIGLGQP-------------------------------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH  489 (975)
T ss_pred             Cccccccccc-------------------------------ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc
Confidence            5555543211                               112335799999999999999999999999999887643


Q ss_pred             cCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC--eEEEEEEccCCC
Q 009954          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASG  375 (521)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~~~~~  375 (521)
                      .      .-||||+|.+...|+.|+..|-|..|+|  +.+.|.|+....
T Consensus       490 g------q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~  532 (975)
T KOG0112|consen  490 G------QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPG  532 (975)
T ss_pred             C------CcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCC
Confidence            3      3489999999999999999999999986  779999998743

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.78  E-value=3.1e-10  Score=116.23  Aligned_cols=151  Identities=23%  Similarity=0.270  Sum_probs=123.7

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      .....++||.||++.+.+.+|...|..+|.+...      .+.+....+.-+|+|||+|..++++.+|+.++-..+.|+ 
T Consensus       664 ~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~v------qi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK-  736 (881)
T KOG0128|consen  664 IRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVV------QIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGK-  736 (881)
T ss_pred             HHHHHHHHHhhcchhhcCchhhhhcCccchhhhH------HHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhh-
Confidence            3456789999999999999999999999874321      112222334457999999999999999998776666551 


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~  330 (521)
                                                                  ..|+|.|+|+..|.++|+.+|.++|.++++.++...
T Consensus       737 --------------------------------------------~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r  772 (881)
T KOG0128|consen  737 --------------------------------------------ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR  772 (881)
T ss_pred             --------------------------------------------hhhheeCCCCCCchHHHHhhccccCCccccchhhhh
Confidence                                                        268899999999999999999999999999988774


Q ss_pred             CCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                       .|+++|.|||.|.++.+|.++...+++..+.-..+.|..+.+
T Consensus       773 -~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  773 -AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             -ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence             899999999999999999999998888877777777776544

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

Probab=98.71  E-value=1.2e-08  Score=100.34  Aligned_cols=174  Identities=14%  Similarity=0.098  Sum_probs=108.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ..+|+|-|||..+++++|..+|+.||.|..|+.     +-...|.+||+|.++-+|+.|+++|++..|.|+.|+......
T Consensus        75 ~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~  149 (549)
T KOG4660|consen   75 QGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGAR  149 (549)
T ss_pred             cceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCccc
Confidence            358999999999999999999999999999764     444578999999999999999999999999999988221111


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccc
Q 009954          374 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  453 (521)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~f  453 (521)
                        ...--+..       ..-....... ...+.+|.     .+....+..|.+..+..             -+.-.|.-+
T Consensus       150 --~~~~~~~~-------~~~~~~~~~p-~a~s~pgg-----~~~~~~~g~l~P~~s~~-------------~~~~~~~~~  201 (549)
T KOG4660|consen  150 --RAMGLQSG-------TSFLNHFGSP-LANSPPGG-----WPRGQLFGMLSPTRSSI-------------LLEHISSVD  201 (549)
T ss_pred             --ccchhccc-------chhhhhccch-hhcCCCCC-----CcCCcceeeeccchhhh-------------hhhcchhcc
Confidence              00000000       0000000000 00111111     11222233344333331             344556667


Q ss_pred             cceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcC
Q 009954          454 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  510 (521)
Q Consensus       454 G~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~  510 (521)
                      |.+.. ......        ....|++|.+..++..++..+ |+.+.|.....+|-.
T Consensus       202 ~~~~~-~~~~~~--------~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~  248 (549)
T KOG4660|consen  202 GSSPG-RETPLL--------NHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSG  248 (549)
T ss_pred             Ccccc-ccccch--------hhhhhhhhccccchhhcccCC-ceecCCCCceEEecC
Confidence            76665 222211        125699999999998888765 888888877666643

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

Probab=98.70  E-value=2.9e-08  Score=91.69  Aligned_cols=78  Identities=17%  Similarity=0.361  Sum_probs=69.7

Q ss_pred             CCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHh
Q 009954          416 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  495 (521)
Q Consensus       416 ~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~ln  495 (521)
                      +-+...+|-.|++|.+            +||--+|+.||+|..|.|+++..+|..   .-+|||+|.+.+++++|.-+|.
T Consensus       238 PeNVLFVCKLNPVTtD------------eDLeiIFSrFG~i~sceVIRD~ktgds---LqyaFiEFen~escE~AyFKMd  302 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTD------------EDLEIIFSRFGKIVSCEVIRDRKTGDS---LQYAFIEFENKESCEQAYFKMD  302 (479)
T ss_pred             CcceEEEEecCCcccc------------cchhhHHhhcccceeeeEEecccccch---hheeeeeecchhhHHHHHhhhc
Confidence            4556666777788777            499999999999999999999988875   5789999999999999999999


Q ss_pred             CCeeCCcEEEEEE
Q 009954          496 GRKFGGNTVNAFY  508 (521)
Q Consensus       496 g~~~~gr~l~v~~  508 (521)
                      +..|..+.|.|.|
T Consensus       303 NvLIDDrRIHVDF  315 (479)
T KOG0415|consen  303 NVLIDDRRIHVDF  315 (479)
T ss_pred             ceeeccceEEeeh
Confidence            9999999999998

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

Probab=98.69  E-value=8.2e-08  Score=87.15  Aligned_cols=81  Identities=23%  Similarity=0.413  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ....+|+|.|||+.++++||+++|+.||.+..+.|..++ +|.+.|.|-|.|...++|..|++.++|..+.|+.+++...
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            334689999999999999999999999999999998885 8999999999999999999999999999999999999987


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      ..
T Consensus       160 ~~  161 (243)
T KOG0533|consen  160 SS  161 (243)
T ss_pred             cC
Confidence            65

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

Probab=98.67  E-value=7.5e-09  Score=89.35  Aligned_cols=159  Identities=17%  Similarity=0.268  Sum_probs=114.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      +...+|||.||...++|+-|.++|-+.|+|..|.|..+. .++.+ ||||.|.++-...-|++.|||..+.+..+.|.+-
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            334789999999999999999999999999999998885 56666 9999999999999999999999999999999876


Q ss_pred             cCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhc
Q 009954          372 TASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  451 (521)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~  451 (521)
                      .-..+.+.                                             ..-++.             +.+...|+
T Consensus        85 ~G~shapl---------------------------------------------d~r~~~-------------ei~~~v~s  106 (267)
T KOG4454|consen   85 CGNSHAPL---------------------------------------------DERVTE-------------EILYEVFS  106 (267)
T ss_pred             cCCCcchh---------------------------------------------hhhcch-------------hhheeeec
Confidence            43111110                                             001111             36677788


Q ss_pred             cccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCe-----------eCCcEEEEEEcCCCCc
Q 009954          452 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRK-----------FGGNTVNAFYYPEDKY  514 (521)
Q Consensus       452 ~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~-----------~~gr~l~v~~~~~~~~  514 (521)
                      .-|+|..+.+..+.. +.. ...|  ||.+...-..-.|+....+..           .||..|--+..++..|
T Consensus       107 ~a~p~~~~R~~~~~d-~rn-rn~~--~~~~qr~~~~P~~~~~y~~l~~~~~~~~~ggk~Gg~~lpqsgfsPs~~  176 (267)
T KOG4454|consen  107 QAGPIEGVRIPTDND-GRN-RNFG--FVTYQRLCAVPFALDLYQGLELFQKKVTIGGKQGGKQLPQSGFSPSAY  176 (267)
T ss_pred             ccCCCCCcccccccc-CCc-cCcc--chhhhhhhcCcHHhhhhcccCcCCCCcccccccCCCcCCcccCCcccc
Confidence            888999999988764 221 2234  777776666666666555443           4555555444444433

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

Probab=98.67  E-value=4.3e-08  Score=90.70  Aligned_cols=79  Identities=24%  Similarity=0.374  Sum_probs=70.8

Q ss_pred             hhhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH--HccCce
Q 009954          168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM--ALDGII  245 (521)
Q Consensus       168 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~--~l~g~~  245 (521)
                      +.......+|||+||-..+++.+|+++|.+||.            +..+.+...+++|||+|.+.+.|+.|.  .+|...
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGe------------irsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lv  289 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGE------------IRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLV  289 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCC------------eeeEEeecccccceeeehhhHHHHHHHHhhcceee
Confidence            345566789999999999999999999999998            777888888999999999999999999  388888


Q ss_pred             ecCceEEEeCCCC
Q 009954          246 FEGVAVRVRRPTD  258 (521)
Q Consensus       246 ~~g~~i~v~~~~~  258 (521)
                      |.|+.|+|.|...
T Consensus       290 I~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  290 INGFRLKIKWGRP  302 (377)
T ss_pred             ecceEEEEEeCCC
Confidence            9999999999776

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

Probab=98.61  E-value=1e-07  Score=93.25  Aligned_cols=82  Identities=22%  Similarity=0.400  Sum_probs=72.2

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....+.|||.+|...+...+|+++|++||.+++..+      |.+..+...+.|+||++.+.++|.++| .|+...|.|+
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKV------VTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGr  475 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKV------VTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGR  475 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceee------eecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcce
Confidence            345678999999999999999999999999887543      666677777899999999999999999 6999999999


Q ss_pred             eEEEeCCCC
Q 009954          250 AVRVRRPTD  258 (521)
Q Consensus       250 ~i~v~~~~~  258 (521)
                      .|.|..++.
T Consensus       476 mISVEkaKN  484 (940)
T KOG4661|consen  476 MISVEKAKN  484 (940)
T ss_pred             eeeeeeccc
Confidence            999987664

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

Probab=98.55  E-value=2.1e-07  Score=93.67  Aligned_cols=83  Identities=18%  Similarity=0.311  Sum_probs=73.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC---CCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~---~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      ...+++|||+||++.++++.|...|..||+|.+|+|+....   ....+-++||-|.+..+|+.|++.|+|..+.+..++
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            34456799999999999999999999999999999987542   334556899999999999999999999999999999


Q ss_pred             EEEccC
Q 009954          368 VRRATA  373 (521)
Q Consensus       368 v~~~~~  373 (521)
                      +.|++.
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999966

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

Probab=98.54  E-value=3.7e-08  Score=87.16  Aligned_cols=147  Identities=16%  Similarity=0.298  Sum_probs=106.5

Q ss_pred             HHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHH
Q 009954          312 KELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQH  391 (521)
Q Consensus       312 ~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~  391 (521)
                      ...|+-|-.+...+++++. -+.-.+++|+.|.....-.++-..-++.+++-.+|++.-.+....+..            
T Consensus       117 ~~~f~~~p~L~ktk~v~~~-p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedPsl------------  183 (290)
T KOG0226|consen  117 PVVFSEYPSLVKTKLVRDR-PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDPSL------------  183 (290)
T ss_pred             hhhhccchhhhhhhhhhcC-CCccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCccc------------
Confidence            5666666666666666664 466688999999988777777666667777777766665433111100            


Q ss_pred             HHHHHHhhhccCCCCCCCCCCCCCCCcceEEE--eeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCC
Q 009954          392 IAIQKMALQTSGMNTLGGGMSLFGETLAKVLC--LTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGG  469 (521)
Q Consensus       392 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~--l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~  469 (521)
                                          .+-.....+|+|  |.|.++++             -|...|.+|-.....+++++.-++.
T Consensus       184 --------------------~ew~~~DfRIfcgdlgNevnd~-------------vl~raf~Kfpsf~~akviRdkRTgK  230 (290)
T KOG0226|consen  184 --------------------AEWDEDDFRIFCGDLGNEVNDD-------------VLARAFKKFPSFQKAKVIRDKRTGK  230 (290)
T ss_pred             --------------------ccCccccceeecccccccccHH-------------HHHHHHHhccchhhccccccccccc
Confidence                                001123444444  66666665             7899999999999999999998887


Q ss_pred             CCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEE
Q 009954          470 ETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF  507 (521)
Q Consensus       470 ~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~  507 (521)
                       ++|+|  ||.|.++.++..|+..|+|.++|.+.|++.
T Consensus       231 -Skgyg--fVSf~~pad~~rAmrem~gkyVgsrpiklR  265 (290)
T KOG0226|consen  231 -SKGYG--FVSFRDPADYVRAMREMNGKYVGSRPIKLR  265 (290)
T ss_pred             -cccce--eeeecCHHHHHHHHHhhcccccccchhHhh
Confidence             45555  999999999999999999999999998864

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.53  E-value=6.1e-08  Score=91.57  Aligned_cols=176  Identities=15%  Similarity=0.132  Sum_probs=128.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ...++|++++...+.+.++..++..+|.+....+........++|+++|.|...+.+..||...-...+.++.+.....+
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            34679999999999999999999999988777777666688899999999999999999998533346666666555544


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEE---EeeCcCCcccCCChHHHHHHHHHHHHh
Q 009954          373 ASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVL---CLTEAITADALADDEEYEEILEDMREE  449 (521)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~---~l~~~~~~~~~~~~~~~~~~~~dl~~~  449 (521)
                      ...+......               ..           ...  .....++   .+...             +.+++|+.+
T Consensus       167 ~~~~~~~n~~---------------~~-----------~~~--~~s~~~~~~~~~~f~-------------~~~d~~~~~  205 (285)
T KOG4210|consen  167 RRGLRPKNKL---------------SR-----------LSS--GPSDTIFFVGELDFS-------------LTRDDLKEH  205 (285)
T ss_pred             cccccccchh---------------cc-----------ccc--Cccccceeecccccc-------------cchHHHhhh
Confidence            3221000000               00           000  0122222   22222             233588999


Q ss_pred             hccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          450 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       450 f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      |..+|.|+.+.++.+..++..   .|+|||.|.+...+..|+.. +...++|+++.+.+-....
T Consensus       206 ~~~~~~i~~~r~~~~~~s~~~---kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  206 FVSSGEITSVRLPTDEESGDS---KGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             ccCcCcceeeccCCCCCccch---hhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCc
Confidence            999999999999999988775   57779999999999999998 9999999999998866553

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

Probab=98.53  E-value=9.6e-07  Score=68.38  Aligned_cols=79  Identities=23%  Similarity=0.329  Sum_probs=70.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHh--cCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC----CeEEEE
Q 009954          295 DRVFVGGLPYYFTETQIKELLES--FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG----DKTLTV  368 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~--~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~----g~~l~v  368 (521)
                      +||.|+|||...|.++|.+++..  .|....+.++.|..++.+.|||||-|.+++.|.+-.+.++|..+.    .+.+.|
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            58999999999999999999984  466778899999889999999999999999999999999998764    678899


Q ss_pred             EEccC
Q 009954          369 RRATA  373 (521)
Q Consensus       369 ~~~~~  373 (521)
                      .||..
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            99864

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

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

Probab=98.46  E-value=2.2e-07  Score=84.82  Aligned_cols=80  Identities=23%  Similarity=0.411  Sum_probs=75.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ....+||+|+...+|.++|..+|+.||.|..|.|..+..+|.++|||||+|.+.+.+..|+. |+|..|.|+.+.|.+..
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            34679999999999999999999999999999999999999999999999999999999999 99999999999999875


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      .
T Consensus       179 ~  179 (231)
T KOG4209|consen  179 T  179 (231)
T ss_pred             e
Confidence            3

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

Probab=98.42  E-value=1.2e-07  Score=84.60  Aligned_cols=76  Identities=21%  Similarity=0.342  Sum_probs=66.7

Q ss_pred             HHHHHHHHHHHHhhc-cccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCcc
Q 009954          437 EEYEEILEDMREECG-KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYF  515 (521)
Q Consensus       437 ~~~~~~~~dl~~~f~-~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~  515 (521)
                      ..|++..+||..+|+ +||+|+.+.|..+.....    .|-+||+|...++|++|++.|||+.|+|++|.+.|.+...|.
T Consensus        76 ~~~defyEd~f~E~~~kygEiee~~Vc~Nl~~hl----~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~~r  151 (260)
T KOG2202|consen   76 RHEDEFYEDVFTELEDKYGEIEELNVCDNLGDHL----VGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTDFR  151 (260)
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhhhhhhcccchhh----hhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCchh
Confidence            457788889999999 999999999988765554    378899999999999999999999999999999999887765


Q ss_pred             c
Q 009954          516 N  516 (521)
Q Consensus       516 ~  516 (521)
                      .
T Consensus       152 e  152 (260)
T KOG2202|consen  152 E  152 (260)
T ss_pred             h
Confidence            4

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

Probab=98.40  E-value=6.3e-07  Score=88.26  Aligned_cols=79  Identities=23%  Similarity=0.407  Sum_probs=66.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ..+|||.|||.++++.+|.++|..||.|+...|....-.+...+||||+|.+.++++.||++ +-..|+++.|.|.--..
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            34599999999999999999999999999887765432344449999999999999999996 68889999999996543

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.39  E-value=3.2e-07  Score=86.10  Aligned_cols=179  Identities=16%  Similarity=0.075  Sum_probs=119.8

Q ss_pred             eEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEEEeC
Q 009954          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (521)
Q Consensus       176 ~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v~~  255 (521)
                      .|.|.||.+.+|.++++.+|..+|.|-...+.+.   +-++.+..-...|||.|.+...+..|..|..++|-++.|.|..
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            6899999999999999999999999765433221   2333344445789999999999999999999999998888864


Q ss_pred             CCCCC-ccc--cccCCCCCCCCC-------------------ccccccc---CCCC--CCCCCCCCCeEEEcCCCCCCCH
Q 009954          256 PTDYN-PTL--AAALGPGQPSPN-------------------LNLAAVG---LASG--AIGGAEGPDRVFVGGLPYYFTE  308 (521)
Q Consensus       256 ~~~~~-~~~--~~~~~~~~~~~~-------------------~~~~~~~---~~~~--~~~~~~~~~~l~v~nLp~~~te  308 (521)
                      ..... +..  ...+++....+.                   .+.+.+.   +.+.  +....+...+|+|.+|+..+..
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            33221 111  001111100000                   0000000   0000  0011122367999999999999


Q ss_pred             HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC
Q 009954          309 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (521)
Q Consensus       309 ~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  362 (521)
                      .++.+.|..+|.|....+.-.    ...-+|-|+|........|+. ++|..+.
T Consensus       166 ~e~~e~f~r~Gev~ya~~ask----~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  166 PESGESFERKGEVSYAHTASK----SRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             hhhhhhhhhcchhhhhhhhcc----CCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            999999999999987766433    334578899999999999988 5787776

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.28  E-value=9e-06  Score=79.75  Aligned_cols=162  Identities=23%  Similarity=0.298  Sum_probs=99.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC---CCCcce---EEEEEEcChHHHHHHHHHHcCCeeCCeEE
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKG---YGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~---~g~~~g---~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (521)
                      -.++|||++||.+++|+.|...|..||.+. |.+....+   --.++|   |+|+.|+++...+..|.+..- .-.+--+
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~-~~~~~yf  335 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE-GEGNYYF  335 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh-cccceEE
Confidence            346899999999999999999999999874 33332111   112456   999999999988877765431 1122223


Q ss_pred             EEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCC------CCCCCCCCCCCcceEEEeeCcCCcccCCChHHHH
Q 009954          367 TVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNT------LGGGMSLFGETLAKVLCLTEAITADALADDEEYE  440 (521)
Q Consensus       367 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~  440 (521)
                      +|.-.+.+...                     .+..++..      -....+..+-...+|-.|+-+++-+         
T Consensus       336 ~vss~~~k~k~---------------------VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~---------  385 (520)
T KOG0129|consen  336 KVSSPTIKDKE---------------------VQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAE---------  385 (520)
T ss_pred             EEecCcccccc---------------------eeEEeeEeccchhhhccCcccCccceEEecCCCCcchHH---------
Confidence            33322221110                     00000100      0112222222333344455555544         


Q ss_pred             HHHHHHHHhhc-cccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHH
Q 009954          441 EILEDMREECG-KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA  493 (521)
Q Consensus       441 ~~~~dl~~~f~-~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~  493 (521)
                          +|..+|+ .||.|..|-|..|+.- +.-+|.|  =|.|.+...=-+||.+
T Consensus       386 ----eLA~imd~lyGgV~yaGIDtD~k~-KYPkGaG--RVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  386 ----ELAMIMEDLFGGVLYVGIDTDPKL-KYPKGAG--RVTFSNQQAYIKAISA  432 (520)
T ss_pred             ----HHHHHHHHhcCceEEEEeccCccc-CCCCCcc--eeeecccHHHHHHHhh
Confidence                8888888 7999999999998633 3334444  9999999999999874

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.24  E-value=3.9e-06  Score=79.00  Aligned_cols=197  Identities=13%  Similarity=0.093  Sum_probs=120.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC---CCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~---~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ..|.|.||.+.+|.++++.+|...|.|..+.|+....   -....-.|||.|.+...+..|-. |.++.|=++.|.|..+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEec
Confidence            4799999999999999999999999999999887432   22334589999999999988865 7778888888877766


Q ss_pred             cCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCC--CCCCCCCCC------CCCcceEEEeeCcCCcc------cC----
Q 009954          372 TASGQSKTEQESILAQAQQHIAIQKMALQTSGMN--TLGGGMSLF------GETLAKVLCLTEAITAD------AL----  433 (521)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~------~~~~~~v~~l~~~~~~~------~~----  433 (521)
                      -...++...  .+..          +..++..+.  .+++..|..      ...++.||.-+.+....      ++    
T Consensus        87 ~~~~~p~r~--af~~----------l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~  154 (479)
T KOG4676|consen   87 GDEVIPDRF--AFVE----------LADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTR  154 (479)
T ss_pred             CCCCCccHH--HHHh----------cCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhh
Confidence            443322221  1111          111111110  011111111      11222222222221111      11    


Q ss_pred             -CChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          434 -ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       434 -~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                       +.++.-..+..++.+.|+.+|.|....+.-.. .      .-.+.|+|........|+. ++|+.+.-+...+..+.+.
T Consensus       155 ~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask~-~------s~~c~~sf~~qts~~halr-~~gre~k~qhsr~ai~kP~  226 (479)
T KOG4676|consen  155 EVQSLISAAILPESGESFERKGEVSYAHTASKS-R------SSSCSHSFRKQTSSKHALR-SHGRERKRQHSRRAIIKPH  226 (479)
T ss_pred             hhhcchhhhcchhhhhhhhhcchhhhhhhhccC-C------CcchhhhHhhhhhHHHHHH-hcchhhhhhhhhhhhcCcc
Confidence             11233344557899999999999887765432 1      1234599999999999988 5888877555555554443

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.23  E-value=6.8e-08  Score=91.28  Aligned_cols=152  Identities=18%  Similarity=0.293  Sum_probs=118.3

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCc-eecCceEE
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI-IFEGVAVR  252 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~-~~~g~~i~  252 (521)
                      ..+|++||.+.++..+|..+|...-.            -..-.+.-..||+||.+.+...|.+|+ .++|+ .+.|+.+.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~------------~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e   69 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKI------------PGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQE   69 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccC------------CCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceee
Confidence            46899999999999999999986511            111122234689999999999999999 57775 48899998


Q ss_pred             EeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEE-eecCC
Q 009954          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL-VKDRD  331 (521)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i-~~~~~  331 (521)
                      |.+.-....                               ..+.+-|.|+|+...++.|-.++..||.+..+.. ..+++
T Consensus        70 ~~~sv~kkq-------------------------------rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e  118 (584)
T KOG2193|consen   70 VEHSVPKKQ-------------------------------RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE  118 (584)
T ss_pred             ccchhhHHH-------------------------------HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH
Confidence            875322211                               1245889999999999999999999999998865 33433


Q ss_pred             CCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          332 TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       332 ~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      +    -..-|+|.+.+.+..||..|+|..|.+..++|.|...
T Consensus       119 t----avvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPd  156 (584)
T KOG2193|consen  119 T----AVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPD  156 (584)
T ss_pred             H----HHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCch
Confidence            2    2345789999999999999999999999999998744

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.22  E-value=6.4e-06  Score=60.39  Aligned_cols=68  Identities=13%  Similarity=0.259  Sum_probs=47.5

Q ss_pred             eEEEcCCCCCCCHHH----HHHHHHhcCC-eeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          296 RVFVGGLPYYFTETQ----IKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       296 ~l~v~nLp~~~te~~----l~~~F~~~G~-i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      .|+|.|||.+.+...    |+.++..+|. |..|.          .+.|+|.|.+.+.|.+|.+.|+|..+.|..|.|.|
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            599999999998765    5667777765 66652          24699999999999999999999999999999999


Q ss_pred             ccC
Q 009954          371 ATA  373 (521)
Q Consensus       371 ~~~  373 (521)
                      ...
T Consensus        74 ~~~   76 (90)
T PF11608_consen   74 SPK   76 (90)
T ss_dssp             S--
T ss_pred             cCC
Confidence            843

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

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

Probab=98.10  E-value=9.9e-06  Score=79.96  Aligned_cols=76  Identities=22%  Similarity=0.343  Sum_probs=62.4

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe--cCCCCeEEEEecCHHHHHHHHHccCceecCc
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~--~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~  249 (521)
                      ....+|||.|||+++++.+|.++|..||.|...        -+.+..  +....||||+|.+.++++.|+.-+...++++
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            344569999999999999999999999997532        233333  3334899999999999999998889999999


Q ss_pred             eEEEeC
Q 009954          250 AVRVRR  255 (521)
Q Consensus       250 ~i~v~~  255 (521)
                      ++.|+.
T Consensus       358 kl~Vee  363 (419)
T KOG0116|consen  358 KLNVEE  363 (419)
T ss_pred             eEEEEe
Confidence            999974

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.09  E-value=2.5e-07  Score=87.61  Aligned_cols=159  Identities=16%  Similarity=0.261  Sum_probs=114.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcC-CeeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG-LKMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g-~~~~g~~l~v~~~~~  373 (521)
                      +.||++||.+.++..||..+|...-.-.+-.++.      ..|||||.+.+..-|.+|++.|+| ..+.|..+.|.+.-+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            3689999999999999999998542111111111      247999999999999999999999 468999999988754


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccc
Q 009954          374 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  453 (521)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~f  453 (521)
                      +.+....                                         +.+-++...          .-++-|-.+...|
T Consensus        76 kkqrsrk-----------------------------------------~Qirnippq----------l~wevld~Ll~qy  104 (584)
T KOG2193|consen   76 KKQRSRK-----------------------------------------IQIRNIPPQ----------LQWEVLDSLLAQY  104 (584)
T ss_pred             HHHHhhh-----------------------------------------hhHhcCCHH----------HHHHHHHHHHhcc
Confidence            2221111                                         001111000          1124677888999


Q ss_pred             cceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCccc
Q 009954          454 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFN  516 (521)
Q Consensus       454 G~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~~  516 (521)
                      |+|+.|........      ....-|+|.+.+.++.||..|||..|.+..+++.|++.+....
T Consensus       105 g~ve~~eqvnt~~e------tavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiPdeq~~q  161 (584)
T KOG2193|consen  105 GTVENCEQVNTDSE------TAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIPDEQNAQ  161 (584)
T ss_pred             CCHhHhhhhccchH------HHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCchhhhhc
Confidence            99999977554321      1345789999999999999999999999999999998765543

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

Probab=98.01  E-value=2e-05  Score=61.13  Aligned_cols=79  Identities=11%  Similarity=0.172  Sum_probs=60.4

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC----c
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG----V  249 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g----~  249 (521)
                      .||+|.|||...|.++|.+++.....  +.+  +=.-..+|.....+.|||||.|.+++.|.+.. .++|..+..    +
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            58999999999999999999987521  110  00112466667788999999999999999999 699998863    5


Q ss_pred             eEEEeCCC
Q 009954          250 AVRVRRPT  257 (521)
Q Consensus       250 ~i~v~~~~  257 (521)
                      .+.|.+|.
T Consensus        78 vc~i~yAr   85 (97)
T PF04059_consen   78 VCEISYAR   85 (97)
T ss_pred             EEEEehhH
Confidence            66777653

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

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.00  E-value=1.8e-05  Score=73.00  Aligned_cols=84  Identities=18%  Similarity=0.314  Sum_probs=62.6

Q ss_pred             eEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCee
Q 009954          420 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF  499 (521)
Q Consensus       420 ~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~  499 (521)
                      .|++++..+..++....+       .--++|++||.|.+|.|-+..+..+.+.+..-+||.|.+.+||.+||....|..+
T Consensus       118 YVigi~pkva~Ee~~~vL-------k~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~  190 (480)
T COG5175         118 YVIGIPPKVADEEVAPVL-------KRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLL  190 (480)
T ss_pred             EEecCCCCCCcccccccc-------cchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccc
Confidence            345555555555432211       2358899999999999987764444444433369999999999999999999999


Q ss_pred             CCcEEEEEEcC
Q 009954          500 GGNTVNAFYYP  510 (521)
Q Consensus       500 ~gr~l~v~~~~  510 (521)
                      +|+-|+++|-+
T Consensus       191 DGr~lkatYGT  201 (480)
T COG5175         191 DGRVLKATYGT  201 (480)
T ss_pred             cCceEeeecCc
Confidence            99999999854

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

Probab=97.98  E-value=7.3e-06  Score=76.93  Aligned_cols=82  Identities=23%  Similarity=0.389  Sum_probs=75.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~--------~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  363 (521)
                      ....+|||.+||..+++.+|.++|.++|.|.        .|.|.++++|+.++|-|.|.|.+...|+.|+.-+++..|.|
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            3445899999999999999999999999885        47888999999999999999999999999999999999999


Q ss_pred             eEEEEEEccC
Q 009954          364 KTLTVRRATA  373 (521)
Q Consensus       364 ~~l~v~~~~~  373 (521)
                      ..|+|..|..
T Consensus       144 n~ikvs~a~~  153 (351)
T KOG1995|consen  144 NTIKVSLAER  153 (351)
T ss_pred             CCchhhhhhh
Confidence            9999998865

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

Probab=97.90  E-value=3.3e-05  Score=70.43  Aligned_cols=68  Identities=15%  Similarity=0.236  Sum_probs=59.9

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCcc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYF  515 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~  515 (521)
                      +||+++|+.||.+..+.|-.+. .|..   .|+|-|.|...+||..|++.+||..++|+.+++..+......
T Consensus        98 ~Dl~eLF~~~~~~~r~~vhy~~-~G~s---~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~~~~  165 (243)
T KOG0533|consen   98 ADLKELFAEFGELKRVAVHYDR-AGRS---LGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSPSQS  165 (243)
T ss_pred             HHHHHHHHHhccceEEeeccCC-CCCC---CccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCcccc
Confidence            5999999999999999998877 4443   588999999999999999999999999999999987765554

>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=97.90  E-value=2.2e-05  Score=62.52  Aligned_cols=71  Identities=23%  Similarity=0.322  Sum_probs=45.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcC-----CeeCCeEEEEE
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG-----LKMGDKTLTVR  369 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g-----~~~~g~~l~v~  369 (521)
                      ..|+|.+++..++.++|+++|+.||.|..|.+.....      .|||.|.+++.|+.|+..+.-     ..+.+..+++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            3688999999999999999999999999999877532      699999999999999987753     45677776666


Q ss_pred             Ec
Q 009954          370 RA  371 (521)
Q Consensus       370 ~~  371 (521)
                      ..
T Consensus        76 vL   77 (105)
T PF08777_consen   76 VL   77 (105)
T ss_dssp             --
T ss_pred             EC
Confidence            54

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

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

Probab=97.88  E-value=1.9e-05  Score=80.03  Aligned_cols=81  Identities=20%  Similarity=0.315  Sum_probs=65.3

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCCeEEEEecCHHHHHHHH-HccCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-ALDGII  245 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~----~~~~g~afV~f~~~~~a~~A~-~l~g~~  245 (521)
                      ......|||+||++.++++.|...|..||+|.+..       |.-..+    ...+.++||-|.+..+|++|+ .|+|+.
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvK-------imwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~i  243 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVK-------IMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGII  243 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCccccee-------eecccchhhhccccccceeeehhhhhHHHHHHHhccee
Confidence            34467899999999999999999999999865421       111111    234679999999999999999 799999


Q ss_pred             ecCceEEEeCCCC
Q 009954          246 FEGVAVRVRRPTD  258 (521)
Q Consensus       246 ~~g~~i~v~~~~~  258 (521)
                      +.+..+++.|.+.
T Consensus       244 v~~~e~K~gWgk~  256 (877)
T KOG0151|consen  244 VMEYEMKLGWGKA  256 (877)
T ss_pred             eeeeeeeeccccc
Confidence            9999999999754

>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=97.87  E-value=0.00014  Score=53.51  Aligned_cols=70  Identities=23%  Similarity=0.265  Sum_probs=48.2

Q ss_pred             eEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEEe
Q 009954          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR  254 (521)
Q Consensus       176 ~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v~  254 (521)
                      .|+|.|||.+.+...|+.-+.+.-.       ..+..|+.+    ..+.|+|.|.+.+.|.+|+ .|+|..+.|.+|.|.
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsd-------NCGGkVl~v----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSD-------NCGGKVLSV----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHH-------TTT--EEE------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhh-------ccCCEEEEE----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            5999999999998888877776544       123346666    3589999999999999999 699999999999999


Q ss_pred             CC
Q 009954          255 RP  256 (521)
Q Consensus       255 ~~  256 (521)
                      +.
T Consensus        73 ~~   74 (90)
T PF11608_consen   73 FS   74 (90)
T ss_dssp             SS
T ss_pred             Ec
Confidence            75

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

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

Probab=97.83  E-value=1e-05  Score=73.94  Aligned_cols=83  Identities=27%  Similarity=0.295  Sum_probs=69.2

Q ss_pred             hhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecC
Q 009954          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (521)
Q Consensus       169 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g  248 (521)
                      +.......+||+|+.+.+|.+++...|+.||.+..      +.+..+...+..+|||||+|.+.+.+..|+.|++..|.|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~------~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~  169 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINR------VTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPG  169 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccc------eeeeccccCCCcceeEEEecccHhhhHHHhhcCCccccc
Confidence            45567789999999999999999999999998532      123444455568999999999999999999999999999


Q ss_pred             ceEEEeCCC
Q 009954          249 VAVRVRRPT  257 (521)
Q Consensus       249 ~~i~v~~~~  257 (521)
                      +.+.|.+-.
T Consensus       170 ~~i~vt~~r  178 (231)
T KOG4209|consen  170 PAIEVTLKR  178 (231)
T ss_pred             ccceeeeee
Confidence            999997643

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

Probab=97.67  E-value=0.00012  Score=66.52  Aligned_cols=77  Identities=14%  Similarity=0.135  Sum_probs=59.4

Q ss_pred             EEEcCCC--CCCC---HHHHHHHHHhcCCeeEEEEeecCCCCCc-ceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          297 VFVGGLP--YYFT---ETQIKELLESFGTLHGFDLVKDRDTGNS-KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       297 l~v~nLp--~~~t---e~~l~~~F~~~G~i~~v~i~~~~~~g~~-~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      |.+.|+-  -.++   ++++.+.|++||.|..|.|.-.+..-.. .--.||+|..+++|.+|+-.|||.+|+|+.|...|
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            5555652  2333   3679999999999999988776532211 12379999999999999999999999999999998


Q ss_pred             ccC
Q 009954          371 ATA  373 (521)
Q Consensus       371 ~~~  373 (521)
                      ...
T Consensus       364 yn~  366 (378)
T KOG1996|consen  364 YNL  366 (378)
T ss_pred             ccH
Confidence            753

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.67  E-value=5.1e-05  Score=70.44  Aligned_cols=79  Identities=24%  Similarity=0.380  Sum_probs=70.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCC--eeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGT--LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~--i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      .++||+||-+.+|.+||.+.+...|.  +.++++..+..+|.++|||+|...+....++.|+.|-.+.|.|..-.|..+.
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            36999999999999999999987764  7788888888899999999999999999999999999999999887777665


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      .
T Consensus       161 K  161 (498)
T KOG4849|consen  161 K  161 (498)
T ss_pred             h
Confidence            4

>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=97.66  E-value=0.0002  Score=59.94  Aligned_cols=16  Identities=25%  Similarity=0.378  Sum_probs=12.1

Q ss_pred             CCCCCCCCCccCCCCC
Q 009954          111 RSGFDMAPPAAAMLPG  126 (521)
Q Consensus       111 ~~~~d~~~~~~~~~~~  126 (521)
                      ...|+.++++|+...+
T Consensus       116 ~~yv~VPp~gf~~~y~  131 (182)
T PF06495_consen  116 TKYVDVPPPGFEYAYG  131 (182)
T ss_pred             eeeccCCCcccccccC
Confidence            3479999999976654

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

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.66  E-value=0.00012  Score=67.79  Aligned_cols=79  Identities=15%  Similarity=0.328  Sum_probs=63.8

Q ss_pred             CeEEEcCCCCCCCHHHH------HHHHHhcCCeeEEEEeecCCC-CCcceEE--EEEEcChHHHHHHHHHHcCCeeCCeE
Q 009954          295 DRVFVGGLPYYFTETQI------KELLESFGTLHGFDLVKDRDT-GNSKGYG--FCVYQDPAVTDIACAALNGLKMGDKT  365 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l------~~~F~~~G~i~~v~i~~~~~~-g~~~g~a--fV~f~~~~~A~~Al~~l~g~~~~g~~  365 (521)
                      +-+||-+||+.+..+++      .++|.+||.|..|.|-+...+ +...+.+  ||.|.+.|+|..||.+.+|..++|+.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            45899999999877662      578999999998877664322 2222323  99999999999999999999999999


Q ss_pred             EEEEEccC
Q 009954          366 LTVRRATA  373 (521)
Q Consensus       366 l~v~~~~~  373 (521)
                      |+..|.+.
T Consensus       195 lkatYGTT  202 (480)
T COG5175         195 LKATYGTT  202 (480)
T ss_pred             EeeecCch
Confidence            99999865

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

Probab=97.58  E-value=0.00034  Score=69.40  Aligned_cols=85  Identities=20%  Similarity=0.353  Sum_probs=65.5

Q ss_pred             CcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhC
Q 009954          417 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  496 (521)
Q Consensus       417 ~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng  496 (521)
                      ..-.|+++.+.+-..    ..-.+-++.-|.++|+++|+|+++.++.++.+|.    +|++|++|++..+|+.|++.|||
T Consensus        56 g~D~vVvv~g~PvV~----~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggt----kG~lf~E~~~~~~A~~aVK~l~G  127 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVG----PARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGT----KGYLFVEYASMRDAKKAVKSLNG  127 (698)
T ss_pred             CcceEEEECCCcccC----hhHHHHHHHHHHHHHHhhccccceeeccCccCCe----eeEEEEEecChhhHHHHHHhccc
Confidence            334456665553332    1234556678899999999999999999987775    59999999999999999999999


Q ss_pred             CeeC-CcEEEEEEc
Q 009954          497 RKFG-GNTVNAFYY  509 (521)
Q Consensus       497 ~~~~-gr~l~v~~~  509 (521)
                      ..|. ++++.|...
T Consensus       128 ~~ldknHtf~v~~f  141 (698)
T KOG2314|consen  128 KRLDKNHTFFVRLF  141 (698)
T ss_pred             ceecccceEEeehh
Confidence            9985 566766554

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

Probab=97.53  E-value=0.00084  Score=55.70  Aligned_cols=61  Identities=18%  Similarity=0.394  Sum_probs=49.9

Q ss_pred             HHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          440 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       440 ~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      +.+..+|.+.|..||+|+-|++.-           +..+|.|.+-..|.+|+. |+|..++|+.|+|.+-+++
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            456678999999999999888866           456999999999999988 8999999999999987765

; PDB: 1UFW_A 2DNR_A.

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

Probab=97.52  E-value=0.00025  Score=48.63  Aligned_cols=52  Identities=19%  Similarity=0.327  Sum_probs=42.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHH
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC  353 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al  353 (521)
                      +.|.|.|.++...+. |..+|..||.|..+.+...      .-+.||.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            468899999876654 6669999999999887732      337999999999999985

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

Probab=97.52  E-value=0.00035  Score=69.27  Aligned_cols=77  Identities=25%  Similarity=0.359  Sum_probs=63.3

Q ss_pred             CeEEEcCCCCCCCH------HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC-CeEEE
Q 009954          295 DRVFVGGLPYYFTE------TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLT  367 (521)
Q Consensus       295 ~~l~v~nLp~~~te------~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~  367 (521)
                      ..|+|.|+|.--..      .-|..+|+++|+|..+.++.+.++| .+||.|++|++..+|+.|++.|||..|. +.++.
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            47899999864322      3478899999999999999886555 8999999999999999999999998874 66777


Q ss_pred             EEEcc
Q 009954          368 VRRAT  372 (521)
Q Consensus       368 v~~~~  372 (521)
                      |..-+
T Consensus       138 v~~f~  142 (698)
T KOG2314|consen  138 VRLFK  142 (698)
T ss_pred             eehhh
Confidence            76543

>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=97.31  E-value=0.00093  Score=52.28  Aligned_cols=77  Identities=19%  Similarity=0.264  Sum_probs=51.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEE-EeecC------CCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCe-EE
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFD-LVKDR------DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK-TL  366 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~-i~~~~------~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~-~l  366 (521)
                      +-|.|-|.|+. ....|.++|++||.|.+.. +.++.      .......+..|+|.++.+|.+||. -||..|+|. .+
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mv   84 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLMV   84 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEEE
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEEE
Confidence            46889899988 5567899999999997764 11100      001123479999999999999999 499999885 55


Q ss_pred             EEEEccC
Q 009954          367 TVRRATA  373 (521)
Q Consensus       367 ~v~~~~~  373 (521)
                      -|.|+++
T Consensus        85 GV~~~~~   91 (100)
T PF05172_consen   85 GVKPCDP   91 (100)
T ss_dssp             EEEE-HH
T ss_pred             EEEEcHH
Confidence            6777743

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.

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

Probab=97.30  E-value=0.00012  Score=65.76  Aligned_cols=64  Identities=11%  Similarity=0.221  Sum_probs=54.2

Q ss_pred             HHHHHHHH-hcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          309 TQIKELLE-SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       309 ~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ++|..+|+ +||.|+.+.|-.+. .-.-.|-+||.|...++|++|++.|||.+|.|++|...++..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            67888888 99999998665542 334467899999999999999999999999999999998854

>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=97.27  E-value=0.00077  Score=53.66  Aligned_cols=58  Identities=21%  Similarity=0.332  Sum_probs=38.1

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCC-----eeCCcEEEEEEcC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGR-----KFGGNTVNAFYYP  510 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~-----~~~gr~l~v~~~~  510 (521)
                      ++|+++|+.||.|..|.+.+-.         -.|||.|.+.+.|+.|+..+.-.     .|.+..+++....
T Consensus        16 e~iK~~f~~~g~V~yVD~~~G~---------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vLe   78 (105)
T PF08777_consen   16 EDIKEAFSQFGEVAYVDFSRGD---------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVLE   78 (105)
T ss_dssp             HHHHHHT-SS--EEEEE--TT----------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE---
T ss_pred             HHHHHHHHhcCCcceEEecCCC---------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEECC
Confidence            6999999999999999986633         45699999999999999988866     5677777766543

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

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

Probab=97.25  E-value=0.00085  Score=45.96  Aligned_cols=52  Identities=19%  Similarity=0.527  Sum_probs=43.7

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM  239 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~  239 (521)
                      +.|-|.|.+++..+. +..+|..||.            |.++.......+.||.|.+..+|++||
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            468899998887754 5558889998            777777778899999999999999986

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.21  E-value=0.00083  Score=60.31  Aligned_cols=100  Identities=21%  Similarity=0.264  Sum_probs=81.4

Q ss_pred             HHHHH-HccCceecCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHH
Q 009954          235 ASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKE  313 (521)
Q Consensus       235 a~~A~-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~  313 (521)
                      |..|- +|++....|+.+.|.++..                                    ..|+|.||..-++.+.|..
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 6899999999999998532                                    2699999999999999999


Q ss_pred             HHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHc--C--CeeCCeEEEEEEc
Q 009954          314 LLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--G--LKMGDKTLTVRRA  371 (521)
Q Consensus       314 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~--g--~~~~g~~l~v~~~  371 (521)
                      .|+.||+|....++.| ..++..+-++|+|...-.|.+|+..+.  |  ....++++.|...
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            9999999998777766 478888999999999999999998873  2  2345666666554

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

Probab=97.17  E-value=0.00043  Score=65.30  Aligned_cols=90  Identities=19%  Similarity=0.138  Sum_probs=72.2

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCC--CCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceec
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSA--GPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~--~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      .....+|||.+||..+++.+|.++|.++|.|.-..-.  ..+.+-++..+...++-|.|.|.+...|+.|+ -+++..+.
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            3446689999999999999999999999988654332  12233455667788999999999999999999 59999999


Q ss_pred             CceEEEeCCCCCC
Q 009954          248 GVAVRVRRPTDYN  260 (521)
Q Consensus       248 g~~i~v~~~~~~~  260 (521)
                      +..|+|..+....
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999997655433

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

Probab=97.10  E-value=0.00036  Score=62.51  Aligned_cols=71  Identities=21%  Similarity=0.443  Sum_probs=61.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC--------CCcce----EEEEEEcChHHHHHHHHHHcCCeeC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT--------GNSKG----YGFCVYQDPAVTDIACAALNGLKMG  362 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~--------g~~~g----~afV~f~~~~~A~~Al~~l~g~~~~  362 (521)
                      -.||+++||+.+...-|+++|+.||.|-.|.|.....+        |...+    -|+|+|.+...|..+...|||..|+
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            47999999999999999999999999999998876544        22232    3789999999999999999999999


Q ss_pred             CeE
Q 009954          363 DKT  365 (521)
Q Consensus       363 g~~  365 (521)
                      |+.
T Consensus       155 gkk  157 (278)
T KOG3152|consen  155 GKK  157 (278)
T ss_pred             CCC
Confidence            865

>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=96.99  E-value=0.0039  Score=48.78  Aligned_cols=83  Identities=20%  Similarity=0.247  Sum_probs=51.2

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCC-CCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCc-e
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSA-GPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV-A  250 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~-~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~-~  250 (521)
                      ....|.|-|.|+. ....|.++|++||.|+..... .....+.............|+|.++.+|.+||..||..|.|. .
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~m   83 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLM   83 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEE
Confidence            4567999999998 456788999999985321000 000000000244566799999999999999999999999985 4


Q ss_pred             EEEeCC
Q 009954          251 VRVRRP  256 (521)
Q Consensus       251 i~v~~~  256 (521)
                      +-|.+.
T Consensus        84 vGV~~~   89 (100)
T PF05172_consen   84 VGVKPC   89 (100)
T ss_dssp             EEEEE-
T ss_pred             EEEEEc
Confidence            556553

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.

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

Probab=96.89  E-value=0.00076  Score=64.87  Aligned_cols=67  Identities=13%  Similarity=0.232  Sum_probs=56.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec---CCCC--Cc--------ceEEEEEEcChHHHHHHHHHHcCC
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD---RDTG--NS--------KGYGFCVYQDPAVTDIACAALNGL  359 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~---~~~g--~~--------~g~afV~f~~~~~A~~Al~~l~g~  359 (521)
                      ..++|.+.|||.+-..+.|.++|..+|.|..|+|...   ++++  .+        +-+|+|+|...+.|.+|.+.|+..
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~e  309 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNPE  309 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhchh
Confidence            4478999999999999999999999999999999876   3322  22        347999999999999999988653

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

Probab=96.85  E-value=0.001  Score=63.94  Aligned_cols=72  Identities=15%  Similarity=0.283  Sum_probs=52.9

Q ss_pred             CcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCC---CCCCCCCC-------CccEEEEEecCHHH
Q 009954          417 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRP---DQNGGETP-------GVGKVFLEYYDAVG  486 (521)
Q Consensus       417 ~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~---~~~~~~~~-------g~g~afV~F~~~~~  486 (521)
                      .++++|+..|+...-      .|    +.|.++|+.+|.|..|.|+..   +.+.....       -+-||+|+|...+.
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            567777766553332      22    689999999999999999988   33322111       14579999999999


Q ss_pred             HHHHHHHHhCCe
Q 009954          487 CATAKNALSGRK  498 (521)
Q Consensus       487 A~~Ai~~lng~~  498 (521)
                      |.+|.+.||...
T Consensus       299 A~KA~e~~~~e~  310 (484)
T KOG1855|consen  299 ARKARELLNPEQ  310 (484)
T ss_pred             HHHHHHhhchhh
Confidence            999999886544

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.76  E-value=0.0078  Score=44.50  Aligned_cols=53  Identities=19%  Similarity=0.387  Sum_probs=40.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHc
Q 009954          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  357 (521)
Q Consensus       297 l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  357 (521)
                      ||--..|..+...||.++|+.||.|. |..+.+.       -|||.....+.|..|+..+.
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 5556553       59999999999999999875

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.67  E-value=0.011  Score=41.49  Aligned_cols=55  Identities=20%  Similarity=0.349  Sum_probs=45.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhc---CCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHH
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL  356 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~---G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l  356 (521)
                      +..|+|.|+.. ++.+||+.+|..|   .....|.++.|.       -|-|.|.+.+.|.+||.+|
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            35799999855 7778899999988   235688888885       3999999999999999864

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

Probab=96.60  E-value=0.012  Score=49.04  Aligned_cols=56  Identities=20%  Similarity=0.364  Sum_probs=46.6

Q ss_pred             HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          309 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       309 ~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .+|.+.|..||.+.-|++..+        .-+|.|.+-+.|.+|+. |+|.+++|+.|+|..-++
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            478889999999888887765        38999999999999998 899999999999998765

; PDB: 1UFW_A 2DNR_A.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.51  E-value=0.0051  Score=55.39  Aligned_cols=93  Identities=19%  Similarity=0.247  Sum_probs=71.2

Q ss_pred             HHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeC
Q 009954          347 AVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTE  426 (521)
Q Consensus       347 ~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~  426 (521)
                      .-|..|-.+|++....|+.+.|.|+..                                           ....|++|+.
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~-------------------------------------------a~l~V~nl~~   41 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH-------------------------------------------AELYVVNLMQ   41 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc-------------------------------------------ceEEEEecch
Confidence            346677788999999999999999953                                           3455666665


Q ss_pred             cCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCee
Q 009954          427 AITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF  499 (521)
Q Consensus       427 ~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~  499 (521)
                      .+..+             .|.+.|..||+|....+..|. .+.+   .+-.+|+|...-.|.+|+...+-.-|
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            55554             788999999999999888875 3333   24449999999999999998754333

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

Probab=96.44  E-value=0.019  Score=56.25  Aligned_cols=75  Identities=16%  Similarity=0.166  Sum_probs=63.1

Q ss_pred             ccCCeEEEeCCCccC-cHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          172 RHARRVYVGGLPPLA-NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~-t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      ...+.|-+.-.|+.+ |-++|...|.+||.            |.++.+..+.-.|.|+|.+..+|-.|....+..|.++.
T Consensus       370 ~dhs~l~lek~~~glnt~a~ln~hfA~fG~------------i~n~qv~~~~~~a~vTF~t~aeag~a~~s~~avlnnr~  437 (526)
T KOG2135|consen  370 VDHSPLALEKSPFGLNTIADLNPHFAQFGE------------IENIQVDYSSLHAVVTFKTRAEAGEAYASHGAVLNNRF  437 (526)
T ss_pred             cccchhhhhccCCCCchHhhhhhhhhhcCc------------cccccccCchhhheeeeeccccccchhccccceecCce
Confidence            445667777778876 78899999999998            56666666677899999999999999989999999999


Q ss_pred             EEEeCCCC
Q 009954          251 VRVRRPTD  258 (521)
Q Consensus       251 i~v~~~~~  258 (521)
                      |+|-|.+.
T Consensus       438 iKl~whnp  445 (526)
T KOG2135|consen  438 IKLFWHNP  445 (526)
T ss_pred             eEEEEecC
Confidence            99998654

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

Probab=96.38  E-value=0.0034  Score=62.95  Aligned_cols=76  Identities=25%  Similarity=0.254  Sum_probs=62.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee---CCeEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLE-SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM---GDKTLT  367 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~-~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~---~g~~l~  367 (521)
                      ...+.|+|.||--..|.-+|+.++. ..|.|+..+|-+-      +..|||.|.+.++|...+.+|||..+   +++.|.
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkI------KShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~  515 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKI------KSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLI  515 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHHHHh------hcceeEecccHHHHHHHHHHHhccccCCCCCceeE
Confidence            3456799999999999999999999 6666777643222      34699999999999999999999765   678999


Q ss_pred             EEEccC
Q 009954          368 VRRATA  373 (521)
Q Consensus       368 v~~~~~  373 (521)
                      +.|...
T Consensus       516 adf~~~  521 (718)
T KOG2416|consen  516 ADFVRA  521 (718)
T ss_pred             eeecch
Confidence            999854

>KOG2548 consensus SWAP mRNA splicing regulator [RNA processing and modification]

Probab=96.36  E-value=0.007  Score=59.81  Aligned_cols=16  Identities=13%  Similarity=-0.120  Sum_probs=7.5

Q ss_pred             eCCCccCcHHHHHHHH
Q 009954          180 GGLPPLANEQAIATFF  195 (521)
Q Consensus       180 ~nlp~~~t~~~l~~~f  195 (521)
                      ||--+..|.......|
T Consensus       555 G~~r~klt~~~~lk~r  570 (653)
T KOG2548|consen  555 GNSRPKLTFFECLKSR  570 (653)
T ss_pred             CCCCCcccHHHHHHHH
Confidence            4444555654444333

>KOG3263 consensus Nucleic acid binding protein [General function prediction only]

Probab=96.31  E-value=0.00057  Score=56.96  Aligned_cols=11  Identities=0%  Similarity=-0.070  Sum_probs=5.2

Q ss_pred             HHHHHHHHHHH
Q 009954          189 QAIATFFSQVM  199 (521)
Q Consensus       189 ~~l~~~f~~~G  199 (521)
                      ++..+++...|
T Consensus       141 eEeiEMmk~MG  151 (196)
T KOG3263|consen  141 EEEIEMMKIMG  151 (196)
T ss_pred             HHHHHHHHHhC
Confidence            34455555443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.11  E-value=0.019  Score=47.01  Aligned_cols=55  Identities=11%  Similarity=0.219  Sum_probs=45.7

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  509 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~  509 (521)
                      ..|....+.||+|.+|.+.-.          --|.|.|.+..+|.+|+.+++. ..-|..+.|+|-
T Consensus       105 ~sV~~~Ls~fGpI~SVT~cGr----------qsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWq  159 (166)
T PF15023_consen  105 KSVIQRLSVFGPIQSVTLCGR----------QSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQ  159 (166)
T ss_pred             HHHHHHHHhcCCcceeeecCC----------ceEEEEehhhHHHHHHHHhhcC-CCCCceEEeecc
Confidence            356667789999999998542          3689999999999999999877 677888999884

>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=96.06  E-value=0.016  Score=51.13  Aligned_cols=63  Identities=14%  Similarity=0.291  Sum_probs=48.5

Q ss_pred             HHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHh--CCeeCCcEEEEEEcCCCC
Q 009954          442 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS--GRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       442 ~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~ln--g~~~~gr~l~v~~~~~~~  513 (521)
                      .++.|.++|..|+.+..+.+.+.         ++-+.|.|.+.++|..|...|+  +..|.|..|+|.|.....
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s---------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS---------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT---------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC---------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            44689999999999988888774         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.

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

Probab=95.87  E-value=0.0043  Score=55.80  Aligned_cols=76  Identities=17%  Similarity=0.221  Sum_probs=60.7

Q ss_pred             cceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCC---------CCCCCCccEEEEEecCHHHHH
Q 009954          418 LAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQN---------GGETPGVGKVFLEYYDAVGCA  488 (521)
Q Consensus       418 ~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~---------~~~~~g~g~afV~F~~~~~A~  488 (521)
                      .+-|+.|.++++-.+-          ..|+++|+.||.|=.|.+.+....         ++...-+--++|+|.+.-.|.
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            5668888888766543          389999999999999999876544         333333333699999999999


Q ss_pred             HHHHHHhCCeeCCcE
Q 009954          489 TAKNALSGRKFGGNT  503 (521)
Q Consensus       489 ~Ai~~lng~~~~gr~  503 (521)
                      .+...|||..|||++
T Consensus       143 ~iAe~Lnn~~Iggkk  157 (278)
T KOG3152|consen  143 RIAELLNNTPIGGKK  157 (278)
T ss_pred             HHHHHhCCCccCCCC
Confidence            999999999999986

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

Probab=95.31  E-value=0.012  Score=59.21  Aligned_cols=77  Identities=13%  Similarity=0.152  Sum_probs=64.0

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceec-
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE-  247 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~-  247 (521)
                      ....++.|+|.||-.-+|..+|+.++..-|.+           |.+.|+.+=+..|||.|.+.++|.... .|||..|. 
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~-----------Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~  508 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGN-----------VEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPP  508 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCc-----------hHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCC
Confidence            34567789999999999999999999976553           666788888999999999999999988 79999884 


Q ss_pred             --CceEEEeCCC
Q 009954          248 --GVAVRVRRPT  257 (521)
Q Consensus       248 --g~~i~v~~~~  257 (521)
                        ++.|.+.|..
T Consensus       509 sNPK~L~adf~~  520 (718)
T KOG2416|consen  509 SNPKHLIADFVR  520 (718)
T ss_pred             CCCceeEeeecc
Confidence              4667776544

>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=95.30  E-value=0.43  Score=44.38  Aligned_cols=194  Identities=10%  Similarity=0.107  Sum_probs=113.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC-------CCCCcceEEEEEEcChHHHHH----HHHHHcC--Cee
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-------DTGNSKGYGFCVYQDPAVTDI----ACAALNG--LKM  361 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-------~~g~~~g~afV~f~~~~~A~~----Al~~l~g--~~~  361 (521)
                      +.|...|+..+++-..+...|-+||+|++|.++.+.       +.........+-|-+.+.+..    .|+.|+-  ..+
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            458899999999999999999999999999999874       112334568899999887654    3444443  457


Q ss_pred             CCeEEEEEEccCCCCCchH-HHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHH
Q 009954          362 GDKTLTVRRATASGQSKTE-QESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYE  440 (521)
Q Consensus       362 ~g~~l~v~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~  440 (521)
                      ....|.|.|..-+-+.... +......  +......+...          +....-+.+-++.+...+..++        
T Consensus        96 ~S~~L~lsFV~l~y~~~~~~~~~~~~~--~~~~~~~L~~~----------i~~~gATRSl~IeF~~~~~~~d--------  155 (309)
T PF10567_consen   96 KSESLTLSFVSLNYQKKTDPNDEEADF--SDYLVASLQYN----------IINRGATRSLAIEFKDPVDKDD--------  155 (309)
T ss_pred             CCcceeEEEEEEeccccccccccccch--hhHHhhhhhhe----------eecCCcceEEEEEecCccchhH--------
Confidence            7888888887653322211 1100000  00000111000          0000113333444444433221        


Q ss_pred             HHHHHHHHhhcccc----ceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcC
Q 009954          441 EILEDMREECGKYG----TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  510 (521)
Q Consensus       441 ~~~~dl~~~f~~fG----~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~  510 (521)
                      .+++.| .+...=+    .|+.|.|+....... .-|..+|.+.|-++..|...+.-|.-....-..-+|.|++
T Consensus       156 l~~~kL-~fL~~~~n~RYVlEsIDlVna~~~~~-~Fp~~YaILtFlnIsMAiEV~dYlk~~~~~~~Iskc~fVs  227 (309)
T PF10567_consen  156 LIEKKL-PFLKNSNNKRYVLESIDLVNADEPSK-HFPKNYAILTFLNISMAIEVLDYLKSNSKKLGISKCFFVS  227 (309)
T ss_pred             HHHHhh-hhhccCCCceEEEEEEEEeccCcccc-cCCcceEEEeehhHHhHHHHHHHHHhcccccCcceEEEEe
Confidence            233344 3333333    478888877553322 3466889999999999999998877443333344566654

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=95.20  E-value=0.059  Score=53.96  Aligned_cols=68  Identities=12%  Similarity=0.172  Sum_probs=55.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHH--hcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcC--CeeCCeEEEEE
Q 009954          295 DRVFVGGLPYYFTETQIKELLE--SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVR  369 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~--~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v~  369 (521)
                      +.|.|+.||..+-+++|+.+|.  .+-.+.+|.+..+..       =||.|++..||+.|.+.|.-  ..|.|++|...
T Consensus       176 cIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-------WyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-------WYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-------eEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            4578999999999999999999  477788887765531       59999999999999988854  45777777654

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=94.98  E-value=0.03  Score=52.56  Aligned_cols=80  Identities=15%  Similarity=0.108  Sum_probs=59.0

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHH-ccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~  250 (521)
                      ...-++|||||-+.+|.++|.+.+...|...    +...+-+.+..-+.++|||+|...+....++.|+ |-...|.|+.
T Consensus        78 Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~----~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~  153 (498)
T KOG4849|consen   78 GRKYCCYVGNLLWYTTDADLLKALQSTGLAQ----FADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQS  153 (498)
T ss_pred             CceEEEEecceeEEeccHHHHHHHHhhhHHH----HhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCC
Confidence            3345799999999999999999988877521    0011112333346789999999999999999995 7778899987


Q ss_pred             EEEeC
Q 009954          251 VRVRR  255 (521)
Q Consensus       251 i~v~~  255 (521)
                      -.|..
T Consensus       154 P~V~~  158 (498)
T KOG4849|consen  154 PTVLS  158 (498)
T ss_pred             Ceeec
Confidence            66643

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.92  E-value=0.079  Score=43.46  Aligned_cols=71  Identities=14%  Similarity=0.183  Sum_probs=53.4

Q ss_pred             CeEEEcCCCCCC----CHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          295 DRVFVGGLPYYF----TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       295 ~~l~v~nLp~~~----te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      .+|.|+=|..++    +...|...++.||+|.+|.+...       -.|.|.|.+..+|.+|+.+++. ..-|..+.+.|
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            467776655543    33456677789999999976432       2599999999999999999865 56778888888


Q ss_pred             ccC
Q 009954          371 ATA  373 (521)
Q Consensus       371 ~~~  373 (521)
                      -..
T Consensus       159 qqr  161 (166)
T PF15023_consen  159 QQR  161 (166)
T ss_pred             ccc
Confidence            643

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

Probab=94.82  E-value=0.017  Score=56.64  Aligned_cols=58  Identities=10%  Similarity=0.244  Sum_probs=50.8

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~  511 (521)
                      .+|-.+|.+||+|+.|.|....         =-|.|+|.+..+|-.|.. .++..|+||-|+|.|.+.
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            5899999999999999997652         135999999999988876 599999999999999876

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.63  E-value=0.014  Score=55.14  Aligned_cols=78  Identities=18%  Similarity=0.329  Sum_probs=62.0

Q ss_pred             eEEEcCCCCCCCHHHHH---HHHHhcCCeeEEEEeecCC--CCC-cceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEE
Q 009954          296 RVFVGGLPYYFTETQIK---ELLESFGTLHGFDLVKDRD--TGN-SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~---~~F~~~G~i~~v~i~~~~~--~g~-~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      -+||-+|+..+..+.+.   +.|.+||.|..|.+..++.  .+. ...-+||.|...++|..||...+|+.+.|+.|+..
T Consensus        79 lvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka~  158 (327)
T KOG2068|consen   79 LVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKAS  158 (327)
T ss_pred             hhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHHh
Confidence            47888999887666554   4788999999998888752  111 12238999999999999999999999999998888


Q ss_pred             EccC
Q 009954          370 RATA  373 (521)
Q Consensus       370 ~~~~  373 (521)
                      +...
T Consensus       159 ~gtt  162 (327)
T KOG2068|consen  159 LGTT  162 (327)
T ss_pred             hCCC
Confidence            8776

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.53  E-value=0.018  Score=54.31  Aligned_cols=65  Identities=17%  Similarity=0.300  Sum_probs=51.3

Q ss_pred             HHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCC
Q 009954          447 REECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       447 ~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~  511 (521)
                      .+.|.+||.|.+|.+.++...-....+..-+||.|...++|..||...+|+.+.|+.|++.+.+.
T Consensus        98 ~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka~~gtt  162 (327)
T KOG2068|consen   98 TEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKASLGTT  162 (327)
T ss_pred             cccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHHhhCCC
Confidence            46799999999999988763111111222279999999999999999999999999998887553

>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=94.46  E-value=0.27  Score=39.36  Aligned_cols=53  Identities=13%  Similarity=0.216  Sum_probs=42.0

Q ss_pred             HHHHHhhcccc-ceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCC
Q 009954          444 EDMREECGKYG-TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG  501 (521)
Q Consensus       444 ~dl~~~f~~fG-~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~g  501 (521)
                      ++|..+.+.+- .|..++|.++..     ++.-.+.++|.+.++|..=...+||+.|+-
T Consensus        28 d~l~~f~~~~~~~i~~~riird~~-----pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   28 DFLLFFGAPFREDIEHIRIIRDGT-----PNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             HHHHHhhhcccccEEEEEEeeCCC-----CceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            46666666655 478889999773     234679999999999999999999999764

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

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

Probab=94.45  E-value=0.17  Score=46.89  Aligned_cols=76  Identities=24%  Similarity=0.331  Sum_probs=61.1

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecC-ceEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG-VAVR  252 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g-~~i~  252 (521)
                      ...|-|-|+|+..+ .-|..+|.+||.            |++........+-+|.|.+.-+|.+||..||+.|.| ..|-
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            55688889988755 467789999998            666666667779999999999999999999999988 4577


Q ss_pred             EeCCCCCCcc
Q 009954          253 VRRPTDYNPT  262 (521)
Q Consensus       253 v~~~~~~~~~  262 (521)
                      |..+.+....
T Consensus       264 VkpCtDksvi  273 (350)
T KOG4285|consen  264 VKPCTDKSVI  273 (350)
T ss_pred             eeecCCHHHh
Confidence            7776655443

>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=94.32  E-value=0.56  Score=37.55  Aligned_cols=66  Identities=12%  Similarity=0.180  Sum_probs=48.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~-i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  363 (521)
                      .+.+...|..++-++|..+.+.+-. |..++|+++.  ...+-.+++.|.+.+.|..-...+||+.|+.
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            3445455555666677766665544 7788999873  3356689999999999999999999988753

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

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

Probab=94.19  E-value=0.086  Score=48.81  Aligned_cols=57  Identities=18%  Similarity=0.276  Sum_probs=46.0

Q ss_pred             HHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEE-EEEEcCC
Q 009954          445 DMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTV-NAFYYPE  511 (521)
Q Consensus       445 dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l-~v~~~~~  511 (521)
                      .|-.+|+.||+|++.....   +|      ...+|.|.+.-+|.+||.. ||+.|+|..+ -|.-++.
T Consensus       212 ~vL~~F~~cG~Vvkhv~~~---ng------NwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  212 IVLNLFSRCGEVVKHVTPS---NG------NWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             HHHHHHHhhCeeeeeecCC---CC------ceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecCC
Confidence            7889999999999988874   33      3679999999999999995 9999988654 3555443

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=94.08  E-value=0.059  Score=47.41  Aligned_cols=79  Identities=14%  Similarity=0.090  Sum_probs=50.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHh-cCCe---eEEEEeecC-CCC-CcceEEEEEEcChHHHHHHHHHHcCCeeC---C--
Q 009954          295 DRVFVGGLPYYFTETQIKELLES-FGTL---HGFDLVKDR-DTG-NSKGYGFCVYQDPAVTDIACAALNGLKMG---D--  363 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~-~G~i---~~v~i~~~~-~~g-~~~g~afV~f~~~~~A~~Al~~l~g~~~~---g--  363 (521)
                      .+|.|++||+.+|++++.+.++. ++..   ..+.-.... ... ..-.-|||.|.+.+++..-+..++|+.|-   |  
T Consensus         8 ~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~~   87 (176)
T PF03467_consen    8 TKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGNE   87 (176)
T ss_dssp             -EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-E
T ss_pred             ceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCCC
Confidence            58999999999999999987776 6655   333311211 111 12345999999999999999999997762   2  


Q ss_pred             eEEEEEEccC
Q 009954          364 KTLTVRRATA  373 (521)
Q Consensus       364 ~~l~v~~~~~  373 (521)
                      ....|.+|--
T Consensus        88 ~~~~VE~Apy   97 (176)
T PF03467_consen   88 YPAVVEFAPY   97 (176)
T ss_dssp             EEEEEEE-SS
T ss_pred             cceeEEEcch
Confidence            4456777644

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.

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

Probab=94.01  E-value=0.036  Score=58.24  Aligned_cols=71  Identities=14%  Similarity=0.177  Sum_probs=61.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee--CCeEEEEEEccC
Q 009954          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVRRATA  373 (521)
Q Consensus       297 l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--~g~~l~v~~~~~  373 (521)
                      ..+.|.+...+-.-|..+|++||.|.+++..++-.      .|.|+|.+.+.|..|+++|+|+.+  -|.+.+|.+++.
T Consensus       301 ~~~~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  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            44566667778888999999999999999888743      699999999999999999999764  688999999987

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=93.34  E-value=0.22  Score=43.95  Aligned_cols=61  Identities=20%  Similarity=0.254  Sum_probs=45.4

Q ss_pred             CHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHc--CCeeCCeEEEEEEccC
Q 009954          307 TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTVRRATA  373 (521)
Q Consensus       307 te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~v~~~~~  373 (521)
                      ..+.|.++|..|+.+..+.+.+.      -+-..|.|.+.++|..|...|+  +..+.|..++|.|+..
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            34789999999999888776654      2248999999999999999999  9999999999999954

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.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=92.74  E-value=0.12  Score=53.11  Aligned_cols=69  Identities=14%  Similarity=0.130  Sum_probs=55.0

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....-+|||+|+...+..+-++..+..+|.+..+            ...   .|||..|..+..+..|+ .++...+.|.
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~------------kr~---~fgf~~f~~~~~~~ra~r~~t~~~~~~~  101 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSW------------KRD---KFGFCEFLKHIGDLRASRLLTELNIDDQ  101 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhCCcchhh------------hhh---hhcccchhhHHHHHHHHHHhcccCCCcc
Confidence            3445689999999999999999999999875332            111   29999999999999999 5777888887


Q ss_pred             eEEEe
Q 009954          250 AVRVR  254 (521)
Q Consensus       250 ~i~v~  254 (521)
                      .+.++
T Consensus       102 kl~~~  106 (668)
T KOG2253|consen  102 KLIEN  106 (668)
T ss_pred             hhhcc
Confidence            77665

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=92.52  E-value=0.72  Score=32.46  Aligned_cols=54  Identities=19%  Similarity=0.250  Sum_probs=37.9

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM  239 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~  239 (521)
                      ..|+|.|+ .+++.++|+.+|..|....      .  +..--++.  -.-|-|.|.+.+.|.+||
T Consensus         6 eavhirGv-d~lsT~dI~~y~~~y~~~~------~--~~~IEWId--DtScNvvf~d~~~A~~AL   59 (62)
T PF10309_consen    6 EAVHIRGV-DELSTDDIKAYFSEYFDEE------G--PFRIEWID--DTSCNVVFKDEETAARAL   59 (62)
T ss_pred             ceEEEEcC-CCCCHHHHHHHHHHhcccC------C--CceEEEec--CCcEEEEECCHHHHHHHH
Confidence            47999999 4588899999999992110      0  12112222  235789999999999999

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=91.16  E-value=1.6  Score=32.56  Aligned_cols=41  Identities=15%  Similarity=0.202  Sum_probs=34.4

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHh
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  495 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~ln  495 (521)
                      .||.++|++||.|.=--|.-           .-|||...+.+.|..|+..++
T Consensus        23 ~DI~qlFspfG~I~VsWi~d-----------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   23 SDIYQLFSPFGQIYVSWIND-----------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             HHHHHHCCCCCCEEEEEECT-----------TEEEEEECCCHHHHHHHHHHT
T ss_pred             hhHHHHhccCCcEEEEEEcC-----------CcEEEEeecHHHHHHHHHHhc
Confidence            59999999999987555522           368999999999999999875

; 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.

>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=91.00  E-value=1.2  Score=32.89  Aligned_cols=59  Identities=24%  Similarity=0.318  Sum_probs=36.3

Q ss_pred             CCCCHHHHHHHHHhcCC-----eeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          304 YYFTETQIKELLESFGT-----LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       304 ~~~te~~l~~~F~~~G~-----i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ..++..+|..++...+.     |-.|.|...        |+||+-... .|..++..|++..+.|+.|.|..|
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            34778889998887654     446776654        799998755 688899999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=90.64  E-value=0.37  Score=47.42  Aligned_cols=67  Identities=18%  Similarity=0.351  Sum_probs=52.0

Q ss_pred             CcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhcccc-ceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHh
Q 009954          417 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYG-TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  495 (521)
Q Consensus       417 ~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG-~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~ln  495 (521)
                      .-..|+.+++.++.-             ||..|+..|- .|.+|+|+++....     .-.+.|+|.+.++|..-.+.+|
T Consensus        75 ~mLcilaVP~~mt~~-------------Dll~F~~~~~~~I~~irivRd~~pn-----rymvLIkFr~q~da~~Fy~efN  136 (493)
T KOG0804|consen   75 TMLCILAVPAYMTSH-------------DLLRFCASFIKQISDIRIVRDGMPN-----RYMVLIKFRDQADADTFYEEFN  136 (493)
T ss_pred             cEEEEEeccccccHH-------------HHHHHHHHHhhhhheeEEeecCCCc-----eEEEEEEeccchhHHHHHHHcC
Confidence            334455566665554             8888888776 49999999976333     3578999999999999999999


Q ss_pred             CCeeCC
Q 009954          496 GRKFGG  501 (521)
Q Consensus       496 g~~~~g  501 (521)
                      |..|+-
T Consensus       137 Gk~Fn~  142 (493)
T KOG0804|consen  137 GKQFNS  142 (493)
T ss_pred             CCcCCC
Confidence            999875

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=90.59  E-value=0.99  Score=44.52  Aligned_cols=68  Identities=18%  Similarity=0.293  Sum_probs=58.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~-i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  363 (521)
                      .+.|+|-.+|..++..||..|+..|-. |..|+|++|..  ..+=.++|.|.+.++|..-.+.+||..|+.
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            467999999999999999999997665 88999999642  224468999999999999999999988753

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

Probab=89.61  E-value=0.41  Score=50.72  Aligned_cols=72  Identities=13%  Similarity=0.242  Sum_probs=60.3

Q ss_pred             hHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCee--CCcEEEEEEcCCCC
Q 009954          436 DEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF--GGNTVNAFYYPEDK  513 (521)
Q Consensus       436 ~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~--~gr~l~v~~~~~~~  513 (521)
                      +.....+-.-|..+|.+||.|.++...++.         ..|.|+|.+.+.|-.|+.+|+|..+  -|-+.+|.|+....
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            334445556899999999999999998864         5789999999999999999999984  67889999988776


Q ss_pred             ccc
Q 009954          514 YFN  516 (521)
Q Consensus       514 ~~~  516 (521)
                      |++
T Consensus       376 ~~e  378 (1007)
T KOG4574|consen  376 MYE  378 (1007)
T ss_pred             ccc
Confidence            654

>KOG0670 consensus U4/U6-associated splicing factor PRP4 [RNA processing and modification]

Probab=88.97  E-value=0.45  Score=48.15  Aligned_cols=16  Identities=25%  Similarity=0.719  Sum_probs=9.1

Q ss_pred             HHHHHHhcCCeeEEEE
Q 009954          311 IKELLESFGTLHGFDL  326 (521)
Q Consensus       311 l~~~F~~~G~i~~v~i  326 (521)
                      |++++.+||.-..+.|
T Consensus       520 LRevLKKyG~nvGL~i  535 (752)
T KOG0670|consen  520 LREVLKKYGRNVGLHI  535 (752)
T ss_pred             HHHHHHHhCcccceee
Confidence            6666666665444433

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=88.36  E-value=0.58  Score=48.39  Aligned_cols=71  Identities=25%  Similarity=0.403  Sum_probs=61.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ....++||+|+...+..+-++.+...+|-|.++....         |+|++|....-+..|+..|+-..++|..+.+..-
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            3446899999999999999999999999998776543         8999999999999999999988888888776653

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=87.20  E-value=0.29  Score=44.67  Aligned_cols=82  Identities=23%  Similarity=0.501  Sum_probs=54.8

Q ss_pred             CCCCeEEEcCCCCCC------------CHHHHHHHHHhcCCeeEEEEee-cC----CCCCcc-----eE---------EE
Q 009954          292 EGPDRVFVGGLPYYF------------TETQIKELLESFGTLHGFDLVK-DR----DTGNSK-----GY---------GF  340 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~------------te~~l~~~F~~~G~i~~v~i~~-~~----~~g~~~-----g~---------af  340 (521)
                      +.+.+|++.+||..+            +++-|+..|+.||.|..|.|+. |+    .+|...     ||         ||
T Consensus       147 erpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipicdplr~~mn~kisgiq~~gfg~g~dlffeay  226 (445)
T KOG2891|consen  147 ERPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPICDPLREEMNGKISGIQFHGFGFGGDLFFEAY  226 (445)
T ss_pred             CCCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcccchhHHHhcCccccceeeccccCcchhHHHH
Confidence            456788888888643            5678999999999999988764 22    244432     33         45


Q ss_pred             EEEcChHHHHHHHHHHcCCee----C----CeEEEEEEccC
Q 009954          341 CVYQDPAVTDIACAALNGLKM----G----DKTLTVRRATA  373 (521)
Q Consensus       341 V~f~~~~~A~~Al~~l~g~~~----~----g~~l~v~~~~~  373 (521)
                      |+|..-..-..|+.+|-|..+    .    .-.|+|.|...
T Consensus       227 vqfmeykgfa~amdalr~~k~akk~d~~ffqanvkvdfdrs  267 (445)
T KOG2891|consen  227 VQFMEYKGFAQAMDALRGMKLAKKGDDGFFQANVKVDFDRS  267 (445)
T ss_pred             HHHHHHHhHHHHHHHHhcchHHhhcCCcccccccccccchh
Confidence            677666666778888877543    2    23566666544

>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=86.78  E-value=0.53  Score=35.82  Aligned_cols=72  Identities=19%  Similarity=0.284  Sum_probs=44.1

Q ss_pred             EEEEecCHHHHHHHHHc--cCceecCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCC
Q 009954          225 AFVEMRTVEEASNAMAL--DGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGL  302 (521)
Q Consensus       225 afV~f~~~~~a~~A~~l--~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL  302 (521)
                      |+|+|....-|+..+.+  +...+.+..+.|.-.. +...         ....+.   .       -.....++|.|.||
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P-~~~~---------~~~k~q---v-------~~~vs~rtVlvsgi   60 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSP-VTLG---------HLQKFQ---V-------FSGVSKRTVLVSGI   60 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEe-EecC---------CceEEE---E-------EEcccCCEEEEeCC
Confidence            68999999999999954  4455666666554210 0000         000000   0       00133478999999


Q ss_pred             CCCCCHHHHHHHHH
Q 009954          303 PYYFTETQIKELLE  316 (521)
Q Consensus       303 p~~~te~~l~~~F~  316 (521)
                      |...++++|++.++
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 [].

>KOG4246 consensus Predicted DNA-binding protein, contains SAP domain [General function prediction only]

Probab=86.69  E-value=0.35  Score=50.94  Aligned_cols=6  Identities=0%  Similarity=-0.430  Sum_probs=3.0

Q ss_pred             EEEEec
Q 009954          477 VFLEYY  482 (521)
Q Consensus       477 afV~F~  482 (521)
                      +||.|.
T Consensus       972 ~~v~~d  977 (1194)
T KOG4246|consen  972 EAVVID  977 (1194)
T ss_pred             ceeeec
Confidence            455554

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=84.91  E-value=2.4  Score=43.02  Aligned_cols=53  Identities=13%  Similarity=0.211  Sum_probs=38.3

Q ss_pred             HHHHHhhcc--ccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCe--eCCcEEEE
Q 009954          444 EDMREECGK--YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRK--FGGNTVNA  506 (521)
Q Consensus       444 ~dl~~~f~~--fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~--~~gr~l~v  506 (521)
                      ++|+.+|..  +-.+++|.+.-+.          -=||.|++..||+.|.+-|.-..  |-|+.|.+
T Consensus       190 e~Vk~lf~~encPk~iscefa~N~----------nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  190 EVVKALFKGENCPKVISCEFAHND----------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             HHHHHHhccCCCCCceeeeeeecC----------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            689999985  4468888876653          23999999999999987765433  55555443

>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=82.44  E-value=4.6  Score=28.93  Aligned_cols=51  Identities=20%  Similarity=0.263  Sum_probs=39.4

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEE
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNA  506 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v  506 (521)
                      +||+..+..|+- ..|..-+   +       | -||-|.+..+|+++....+|..+.+..|.+
T Consensus        15 ~d~K~~Lr~y~~-~~I~~d~---t-------G-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   15 EDFKKRLRKYRW-DRIRDDR---T-------G-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             HHHHHHHhcCCc-ceEEecC---C-------E-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            588888888853 3444433   2       3 399999999999999999999998877654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>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=81.35  E-value=0.64  Score=40.94  Aligned_cols=67  Identities=16%  Similarity=0.223  Sum_probs=41.3

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHH-HHHhhcCCCCCCCCceEEEE--ecC------CCCeEEEEecCHHHHHHHH-Hcc
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQ-VMTAIGGNSAGPGDAVVNVY--INH------EKKFAFVEMRTVEEASNAM-ALD  242 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~-~G~~~~~~~~~~~~~v~~~~--~~~------~~g~afV~f~~~~~a~~A~-~l~  242 (521)
                      ...+|.|++||+++|++++.+.+.. ++....         ...+.  ...      .-.-|||.|.+.+++.... .++
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         01111  111      1247999999999988888 699


Q ss_pred             CceecC
Q 009954          243 GIIFEG  248 (521)
Q Consensus       243 g~~~~g  248 (521)
                      |..|.+
T Consensus        77 g~~F~D   82 (176)
T PF03467_consen   77 GHVFVD   82 (176)
T ss_dssp             TEEEE-
T ss_pred             CcEEEC
Confidence            988754

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	521
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 =		3e-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		7e-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		2e-12
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		6e-10
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		8e-10
3v4m_A	105	Crystal Structure Of A Rna Binding Domain Of A U2 S		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
4fxw_A	106	Structure Of Phosphorylated Sf1 Complex With U2af65		2e-09
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		2e-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-06
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		6e-09
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		8e-09
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		8e-09
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-06
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		7e-08
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		1e-07
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-07
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		9e-06
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-06
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-06
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		1e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		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		3e-06
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		3e-06
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
2khc_A	118	Bruno Rrm3+ Length = 118		2e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		2e-05
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		2e-05
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		3e-05
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		4e-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
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		4e-05
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		5e-05
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		5e-05
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		5e-05
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		6e-05
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		6e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		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
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
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		1e-04
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		2e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-04
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		2e-04
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		2e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		3e-04
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		3e-04
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		3e-04
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		4e-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
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 = 94/204 (46%), Positives = 131/204 (64%), Gaps = 10/204 (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       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 AALNGLKMGDKTLTVRRATASGQS 377
           A LNG+++GDK L V+RA+   ++
Sbjct: 174 AGLNGMQLGDKKLLVQRASVGAKN 197

>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 = 3e-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 = 94.0 bits (232), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 45/82 (54%), Positives = 58/82 (70%)
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 LNGLKMGDKTLTVRRATASGQS 377
           LNG+++GDK L V+RA+   ++
Sbjct: 63  LNGMQLGDKKLLVQRASVGAKN 84

>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of Hu2af65 Length = 90

Iteration: 1
 Score = 92.0 bits (227), Expect = 7e-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 = 70.5 bits (171), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 39/87 (44%), Positives = 50/87 (57%), Gaps = 1/87 (1%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC YQD      A   L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 357 NGLKMGDKTLTVRRATASGQSKTEQES 383
           NG +   + L V  A AS ++K E +S
Sbjct: 71  NGREFSGRALRVDNA-ASEKNKEELKS 96

>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|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 62.0 bits (149), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 34/81 (41%), Positives = 42/81 (51%)
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 NGLKMGDKTLTVRRATASGQS 377
           NGLK+  KT+ V  A  S  S
Sbjct: 67  NGLKLQTKTIKVSYARPSSAS 87

>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: 450 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 509
           C KYG + ++ IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y 
Sbjct: 36  CSKYGLVKSIEIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVVVTKYC 94
Query: 510 PEDKYFNKDY 519
             D Y  +D+
Sbjct: 95  DPDSYHRRDF 104

>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: 450 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 509
           C KYG + ++ IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y 
Sbjct: 35  CSKYGLVKSIEIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYC 93
Query: 510 PEDKYFNKDY 519
             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: 450 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 509
           C KYG + ++ IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y 
Sbjct: 35  CSKYGLVKSIEIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYC 93
Query: 510 PEDKYFNKDY 519
             D Y  +D+
Sbjct: 94  DPDSYHRRDF 103

>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm Domain Length = 106

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 450 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 509
           C KYG + ++ IPRP  +G E PG GK+F+E+     C  A   L+GRKF    V   Y 
Sbjct: 37  CSKYGLVKSIEIPRP-VDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVVVTKYC 95
Query: 510 PEDKYFNKDY 519
             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 = 60.5 bits (145), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/81 (41%), Positives = 42/81 (51%)
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 NGLKMGDKTLTVRRATASGQS 377
           NGLK+  KT+ V  A  S  S
Sbjct: 67  NGLKLQTKTIKVSYARPSSAS 87

>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 = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 41/83 (49%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           RV+VG + Y   E  I++    FG +   D+  D  T   KG+ F  Y+ P    +A   
Sbjct: 30  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 356 LNGLKMGDKTLTVRRATASGQSK 378
           +N + +G + + V R +  GQ++
Sbjct: 90  MNSVMLGGRNIKVGRPSNIGQAQ 112

>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 = 58.5 bits (140), Expect = 8e-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 = 8e-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|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 41/83 (49%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           RV+VG + Y   E  I++    FG +   D+  D  T   KG+ F  Y+ P    +A   
Sbjct: 15  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 356 LNGLKMGDKTLTVRRATASGQSK 378
           +N + +G + + V R +  GQ++
Sbjct: 75  MNSVMLGGRNIKVGRPSNIGQAQ 97

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 55.5 bits (132), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 31/81 (38%), Positives = 42/81 (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 NGLKMGDKTLTVRRATASGQS 377
           NGL++  KT+ V  A  S  S
Sbjct: 65  NGLRLQTKTIKVSYARPSSAS 85

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 29/82 (35%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
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 NGLKMGDKTLTVRRATASGQSK 378
           NG  + +K L V  A ASG  +
Sbjct: 105 NGFNILNKRLKVALA-ASGHQR 125

>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|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 = 48.5 bits (114), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 39/83 (46%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           RV+VG + Y   E  I++    FG +   D   D  T   KG+ F  Y+ P    +A   
Sbjct: 14  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 356 LNGLKMGDKTLTVRRATASGQSK 378
            N + +G + + V R +  GQ++
Sbjct: 74  XNSVXLGGRNIKVGRPSNIGQAQ 96

>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|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 42/84 (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 CAALNGLKMGDKTLTVRRATASGQ 376
              LNGL++  KT+ V  A  S +
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSE 84

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 42/84 (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 CAALNGLKMGDKTLTVRRATASGQ 376
              LNGL++  KT+ V  A  S +
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSE 84

>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 = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 51/104 (49%), Gaps = 6/104 (5%)
Query: 282 GLASGAIGGA----EGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNS 335
           GL   +IG A    EGP+   +F+  LP  F +  + ++   FG +    +  D+ T  S
Sbjct: 7   GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS 66
Query: 336 KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKT 379
           K +GF  Y +P     A  ++NG ++G K L V+   +   SK+
Sbjct: 67  KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKS 110

>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 = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/84 (27%), Positives = 47/84 (55%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +++      A  A
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 356 LNGLKMGDKTLTVRRATASGQSKT 379
           +NG  +  + + V +A  S  +++
Sbjct: 74  MNGKSVDGRQIRVDQAGKSSDNRS 97

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-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|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/90 (33%), Positives = 46/90 (51%), Gaps = 1/90 (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 CAALNGLKMGDKTLTVRRATASGQSKTEQE 382
              LNG ++G + L    ++ S  S    E
Sbjct: 61  VRNLNGYQLGSRFLKCGYSSNSDISGVSLE 90

>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|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|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 34/55 (61%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           ++F+GGL +  TE  ++E    +GT+    ++KD  TG S+G+GF  ++ P+  D
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVD 59

>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|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 29/89 (32%), Positives = 46/89 (51%), Gaps = 3/89 (3%)
Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G  ++FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V 
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVA 61
Query: 350 DIACAALNGLKMGDKTLTVR-RATASGQS 377
           + AC  +NG+K+  + + VR    ASG S
Sbjct: 62  ERACRMMNGMKLSGREIDVRIDRNASGPS 90

>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 = 46.6 bits (109), 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|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 46.2 bits (108), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 29/89 (32%), Positives = 45/89 (50%), Gaps = 3/89 (3%)
Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   +FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V 
Sbjct: 1   GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVA 58
Query: 350 DIACAALNGLKMGDKTLTVR-RATASGQS 377
           + AC  +NG+K+  + + VR    ASG S
Sbjct: 59  ERACRMMNGMKLSGREIDVRIDRNASGPS 87

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ Q +EL+  FG+L    LV    TG SKGYGF  Y        A + L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 357 NGLKMGDKTLTVRRATASGQ 376
            G  +G +TL V   T +GQ
Sbjct: 158 LGKPLGPRTLYV-HWTDAGQ 176

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ Q +EL+  FG+L    LV    TG SKGYGF  Y        A + L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 357 NGLKMGDKTLTVRRATASGQ 376
            G  +G +TL V   T +GQ
Sbjct: 158 LGKPLGPRTLYV-HWTDAGQ 176

>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 = 5e-05,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ Q +EL+  FG+L    LV    TG SKGYGF  Y        A + L
Sbjct: 96  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 357 NGLKMGDKTLTVRRATASGQ 376
            G  +G +TL V   T +GQ
Sbjct: 156 LGKPLGPRTLYV-HWTDAGQ 174

>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|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|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|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: 450 CGKYGTLVNVVIPRPDQNGGETPG--VGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF 507
           CGK+G  VN VI   ++ G E     + K+F+E+  A     A  AL+GR F G  V A 
Sbjct: 150 CGKFGA-VNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAE 208
Query: 508 YYPEDKYFNKDYSA 521
            Y ++++ N D SA
Sbjct: 209 VYDQERFDNSDLSA 222

>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|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL +  T+  ++     +G +    ++KD+ T  S+G+GF  ++DP       A+
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 356 ----LNGLKMGDKTLTVRRATASGQS 377
               L+G  +  K  T R    SG S
Sbjct: 78  RPHTLDGRNIDPKPCTPRGMQPSGPS 103

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 41/81 (50%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V+VGGL    +E  + EL    G +    + KDR TG  +GYGF  +      D A   +
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 357 NGLKMGDKTLTVRRATASGQS 377
           + +K+  K + V +A+A  ++
Sbjct: 78  DMIKLYGKPIRVNKASAHNKN 98

>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|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 1/81 (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 IACAALNGLKMGDKTLTVRRA 371
            A   +NG  +  K + V +A
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQA 83

>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|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-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  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 356 LNGLKMGDKTLTVRRAT 372
           + G  +G + +    AT
Sbjct: 77  MGGQWLGGRQIRTNWAT 93

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           +++FVGG+P+   ET+++E  + FG +    ++ D +    +G+GF  ++D    D A  
Sbjct: 11  NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 355 ALNGLKMGDKTLTVRRA 371
                 MG K + V+RA
Sbjct: 71  MHFHDIMG-KKVEVKRA 86

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  TE  ++   E +G L    +++D  +  S+G+GF  +   A  D A AA
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 356 ----LNGLKMGDKTLTVRRATASGQS 377
               ++G  +  K    R  + SG S
Sbjct: 89  RPHSIDGRVVEPKRAVAREESGSGPS 114

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE ++++L E +G      + KD      KG+GF   +   + +IA   
Sbjct: 24  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 356 LNGLKMGDKTLTVRRATASG 375
           L+ + +  K L VR A  S 
Sbjct: 78  LDNMPLRGKQLRVRFACHSA 97

>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 = 42.7 bits (99), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 450 CGKYGTLVNVVIPRPDQNGGETPG--VGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAF 507
           CGK+G  VN VI   ++ G E     + K+F+E+  A     A  AL+GR F G  V A 
Sbjct: 46  CGKFGA-VNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAE 104
Query: 508 YYPEDKYFNKDYSA 521
            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|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	521
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-71
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	4e-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;	3e-33
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-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	1e-18
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	5e-27
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	3e-24
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-24
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	9e-10
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	2e-17
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-04
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-23
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-14
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	6e-19
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	9e-22
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-21
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-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
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-19
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-19
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-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	5e-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
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	9e-08
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-17
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-08
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-17
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-07
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
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-16
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-08
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
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-16
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-16
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-06
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
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-16
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-16
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-05
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	7e-16
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	7e-16
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-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
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-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
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-15
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-07
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-15
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	8e-06
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
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-15
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-07
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	4e-15
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	6e-15
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	7e-15
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-06
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	9e-15
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	4e-05
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
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-14
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-07
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-14
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-04
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-14
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-07
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	8e-07
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-06
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-04
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-14
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	7e-09
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-14
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-08
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-14
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	7e-07
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-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
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-14
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-04
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	4e-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
2div_A	99	TRNA selenocysteine associated protein; structural	5e-14
2div_A	99	TRNA selenocysteine associated protein; structural	2e-05
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
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	5e-14
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	8e-14
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-05
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-13
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	7e-07
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
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-13
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	5e-04
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
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-13
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-06
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-05
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-13
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	7e-05
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	3e-13
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-13
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-07
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
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
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	5e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-05
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-13
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-07
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
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	7e-13
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	7e-13
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	7e-13
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
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-12
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-12
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-08
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	3e-12
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-12
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	8e-07
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-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
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-11
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-05
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-11
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	6e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-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
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
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-04
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-08
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
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-06
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
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-10
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	6e-05
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	4e-10
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-04
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	5e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	6e-10
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	5e-10
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-07
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-10
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	8e-09
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-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	8e-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	2e-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
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	8e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-05
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	8e-07
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	5e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	7e-08
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	7e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-08
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	9e-09
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-06
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	3e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	6e-07
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-08
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-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
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-07
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-06
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	4e-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	5e-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-07
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	4e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-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
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
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	7e-07
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	7e-07
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	8e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-06
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	8e-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
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	6e-05
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-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
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-04
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
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,	4e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-05
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-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 =  225 bits (575), Expect = 2e-71
 Identities = 91/204 (44%), Positives = 126/204 (61%), Gaps = 10/204 (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 AALNGLKMGDKTLTVRRATASGQS 377
           A LNG+++GDK L V+RA+   ++
Sbjct: 174 AGLNGMQLGDKKLLVQRASVGAKN 197

>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 = 83.5 bits (207), Expect = 1e-18
 Identities = 36/215 (16%), Positives = 70/215 (32%), Gaps = 40/215 (18%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHG-----FDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           R++VG +P+  TE  + +   +   L G      + V        K + F  ++    T 
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 351 IACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG-G 409
            A A  +G+    ++L +RR             +      ++      +     + L  G
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRP----HDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIG 120

Query: 410 GMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGG 469
           G+  +         L +                 + ++E    +G L    + + D   G
Sbjct: 121 GLPNY---------LND-----------------DQVKELLTSFGPLKAFNLVK-DSATG 153

Query: 470 ETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTV 504
            + G    F EY D      A   L+G + G   +
Sbjct: 154 LSKGYA--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 = 69.6 bits (171), Expect = 4e-14
 Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 6/87 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHG-----FDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           R++VG +P+  TE  + +   +   L G      + V        K + F  ++    T 
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 351 IACAALNGLKMGDKTLTVRRATASGQS 377
            A  A +G+    ++L +RR       
Sbjct: 66  QAM-AFDGIIFQGQSLKIRRPHDYQPL 91

>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 (319), Expect = 3e-33
 Identities = 59/347 (17%), Positives = 97/347 (27%), Gaps = 101/347 (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 YGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKM 397
           YGF  Y        A + L G  +G +TL V        +     ++L      +     
Sbjct: 139 YGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT----DAGQLTPALLHSRCLCVD---- 190

Query: 398 ALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLV 457
                                     L          D +        +        +  
Sbjct: 191 -------R------------------LPPGFN-----DVDA-------LCRALSAVHSPT 213

Query: 458 NVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTV 504
              +    Q+G    G     LEY  A     A+    G   GG+ +
Sbjct: 214 FCQLAC-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 = 91.2 bits (227), Expect = 1e-20
 Identities = 39/234 (16%), Positives = 65/234 (27%), Gaps = 44/234 (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 GYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQ 390
           G+    Y+   + + A    +GL +G   L V         ++   +++A    
Sbjct: 227 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQAT 280

>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: 415 GETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGV 474
           G    +VLCL   +  + L DDEEYEEI+ED+R+EC KYG + ++ IPRP  +G E PG 
Sbjct: 1   GGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRP-VDGVEVPGC 59

Query: 475 GKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
           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: 387 QAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDM 446
            + +H+ +QK+  +                  + V+ L   +        +  +++  ++
Sbjct: 4   SSARHMVMQKLLRKQE----------------STVMVLRNMVDPK-----DIDDDLEGEV 42

Query: 447 REECGKYGTLVNVVIPRPDQNGGET-PGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVN 505
            EECGK+G +  V+I +  Q   E    + K+F+E+  A     A  AL+GR F G  V 
Sbjct: 43  TEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVV 102

Query: 506 AFYYPEDKYFNKDYSA 521
           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: 420 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFL 479
           +   L+         +     EI +D+ EEC K+G ++++ + +           G V++
Sbjct: 8   QCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN-------SAQGNVYV 60

Query: 480 EYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNK 517
           +         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 = 83.9 bits (208), Expect = 1e-18
 Identities = 41/213 (19%), Positives = 80/213 (37%), Gaps = 41/213 (19%)

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           G      RV+VG + Y   E  I++    FG +   D+  D  T   KG+ F  Y+ P  
Sbjct: 23  GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEA 82

Query: 349 TDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG 408
             +A   +N + +G + + V R +  GQ++   + +  +A+                   
Sbjct: 83  AQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF----------------- 125

Query: 409 GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG 468
               ++      V  + + ++ D +             +     +G + +  + R D   
Sbjct: 126 --NRIY------VASVHQDLSDDDI-------------KSVFEAFGKIKSATLAR-DPTT 163

Query: 469 GETPGVGKVFLEYYDAVGCATAKNALSGRKFGG 501
           G+  G G  F+EY  A     A ++++    GG
Sbjct: 164 GKHKGYG--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 =  109 bits (275), Expect = 5e-27
 Identities = 46/334 (13%), Positives = 94/334 (28%), Gaps = 100/334 (29%)

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 CAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMS 412
              LNGLK+   TL  + +    +SK       A  +                    G  
Sbjct: 176 VEKLNGLKIEGYTLVTKVSNPLEKSKRTDS---ATLE--------------------GRE 212

Query: 413 LFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETP 472
           +       +  L+  +       DE        +RE    +G++  + IP   +      
Sbjct: 213 IM------IRNLSTELL------DE------NLLRESFEGFGSIEKINIPAGQKEHSFNN 254

Query: 473 GVGKVFLEYYDAVGCATAKNALS--GRKFGGNTV 504
                F+ + +     +A+ AL       G   +
Sbjct: 255 CCA--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: 414 FGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPG 473
            G+   KV+ L   + A      E  E++  + +EEC KYG +   VI      G     
Sbjct: 3   MGKCPTKVVLLRNMVGAG-----EVDEDLEVETKEECEKYGKVGKCVIFEIP--GAPDDE 55

Query: 474 VGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYS 520
             ++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 (252), Expect = 3e-24
 Identities = 40/259 (15%), Positives = 75/259 (28%), Gaps = 53/259 (20%)

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----LKMGDKTLTVRRATASGQSKTEQESILAQAQQHIA 393
            GF  +        A          L    + + V             E ++ + QQ+  
Sbjct: 139 KGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHK 198

Query: 394 IQKMALQTSGMNTLGGGMS 412
            ++   + +   T     +
Sbjct: 199 EREQPPRFAQPGTFEFEYA 217

>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 = 95.4 bits (238), Expect = 5e-24
 Identities = 29/96 (30%), Positives = 45/96 (46%), Gaps = 4/96 (4%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V++G +PY  TE QI +L  + G +    ++ D  TG SKGY F  ++D   +  A   
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 356 LNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQH 391
           LNG ++G + L    ++ S  S    E        H
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVSLE----HHHHH 95

>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

>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: 420 KVLCLTEAIT-ADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVF 478
           +V+ +       D   D     EI ED+R EC K+G +  +++     +G          
Sbjct: 16  RVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDG-------VAS 68

Query: 479 LEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNK-DYSA 521
           + + 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 = 79.2 bits (196), Expect = 2e-17
 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 NGLKMGDKTLTVRRATASGQSKTE 380
           NGL++  KT+ V  A  S  S  +
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

>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 = 68.7 bits (169), Expect = 6e-14
 Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 1/86 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++VG L    TE  +K+  +  G +    ++ D+    +  Y F  Y      +IA   L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 357 NGLKMGDKTLTVRRATASGQSKTEQE 382
           NG ++ +  + +  A  S QS ++  
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDT 87

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 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 = 83.0 bits (206), Expect = 6e-19
 Identities = 47/207 (22%), Positives = 72/207 (34%), Gaps = 52/207 (25%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ ++  L  + G ++   +++D  TG S GY F  +     +  A   L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 357 NGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGE 416
           NG+ + +K L V  A   G+S                                  +L+  
Sbjct: 66  NGITVRNKRLKVSYARPGGESI------------------------------KDTNLY-- 93

Query: 417 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGK 476
               V  L   IT D L                 GKYG++V   I R D+  G   GV  
Sbjct: 94  ----VTNLPRTITDDQL-------------DTIFGKYGSIVQKNILR-DKLTGRPRGVA- 134

Query: 477 VFLEYYDAVGCATAKNALSGRKFGGNT 503
            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 = 46/227 (20%), Positives = 76/227 (33%), Gaps = 52/227 (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 QDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQ 390
            D    D          +      VR+A     SK E  S  +  + 
Sbjct: 154 DDHDSVDKIVIQ-KYHTVNGHNCEVRKA----LSKQEMASASSSQRG 195

>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 = 65.8 bits (161), Expect = 1e-12
 Identities = 39/194 (20%), Positives = 75/194 (38%), Gaps = 45/194 (23%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           E   ++F+GGL +  T+  ++   E +GTL    +++D +T  S+G+GF  Y      D 
Sbjct: 11  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70

Query: 352 ACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGM 411
           A  A    K+  + +  +RA +   S         +   H+ ++K+         +GG  
Sbjct: 71  AMNA-RPHKVDGRVVEPKRAVSREDS--------QRPGAHLTVKKI--------FVGG-- 111

Query: 412 SLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGET 471
                       + E                   +R+   +YG +  + I   D+  G+ 
Sbjct: 112 ------------IKEDTEEH-------------HLRDYFEQYGKIEVIEIMT-DRGSGKK 145

Query: 472 PGVGKVFLEYYDAV 485
            G   V  + +D+V
Sbjct: 146 RGFAFVTFDDHDSV 159

>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 = 66.4 bits (163), Expect = 4e-13
 Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 2/82 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  TE  ++E    +GT+    ++KD  TG S+G+GF  ++ P+  D     
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64

Query: 356 LNGLKMGDKTLTVRRATASGQS 377
            +   +  K +  +RA    + 
Sbjct: 65  QH--ILDGKVIDPKRAIPRDEQ 84

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 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

>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 = 86.6 bits (215), Expect = 1e-19
 Identities = 41/216 (18%), Positives = 79/216 (36%), Gaps = 48/216 (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 VTDIACAALNGLKMGDKTLTVRRATASGQSKTEQES 383
             + A   +NG+ + D+ + V R  +  + + E  +
Sbjct: 155 AAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGA 190

>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 = 68.8 bits (169), Expect = 6e-14
 Identities = 20/91 (21%), Positives = 40/91 (43%), Gaps = 2/91 (2%)

Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTD 350
              ++FVG +P  ++E  ++EL E +G ++  ++++DR      SKG  F  +       
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 351 IACAALNGLKMGDKTLTVRRATASGQSKTEQ 381
            A  AL+ +K+        +   +   K   
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKNNA 92

>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 = 80.9 bits (200), Expect = 2e-18
 Identities = 30/123 (24%), Positives = 47/123 (38%), Gaps = 2/123 (1%)

Query: 264 AAALGPGQPSPNLNLAAVGLASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTL 321
               G       L               E      + V  +P    E Q+++L E +G +
Sbjct: 10  YDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI 69

Query: 322 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQ 381
               +V DR+T  S+GYGF  +Q  +    A A LNG  + +K L V  A +  Q     
Sbjct: 70  ESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIA 129

Query: 382 ESI 384
            ++
Sbjct: 130 GAV 132

>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 = 78.4 bits (194), Expect = 5e-18
 Identities = 26/89 (29%), Positives = 49/89 (55%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG+ G A    ++FVGGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +
Sbjct: 2   SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           ++      A  A+NG  +  + + V +A 
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRVDQAG 90

>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

>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 = 9e-08
 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

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

 Score = 76.5 bits (189), Expect = 2e-17
 Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 2/83 (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 TDIACAALNGLKMGDKTLTVRRA 371
            + AC  +NG+K+  + + VR  
Sbjct: 61  AERACRMMNGMKLSGREIDVRID 83

>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

>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 = 28/90 (31%), Positives = 43/90 (47%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG I        V+VGGL    +E  + EL    G +    + KDR TG  +GYGF  +
Sbjct: 5   SSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATA 373
                 D A   ++ +K+  K + V +A+A
Sbjct: 65  LSEEDADYAIKIMDMIKLYGKPIRVNKASA 94

>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

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

 Score = 74.4 bits (183), Expect = 2e-16
 Identities = 14/99 (14%), Positives = 29/99 (29%)

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           GG      V    L     ET +K++   +G +   +++    T    G    ++     
Sbjct: 1   GGQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRG 60

Query: 349 TDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQ 387
                  L+   +    +  +      Q     E I+  
Sbjct: 61  AKETVKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNG 99

>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

>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

>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 = 75.6 bits (186), Expect = 3e-16
 Identities = 24/88 (27%), Positives = 38/88 (43%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FV  +     E +I+E    +G +    L  DR TG SKGY    Y+       A  A
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 356 LNGLKMGDKTLTVRRATASGQSKTEQES 383
           LNG ++  +T+ V      G  + ++  
Sbjct: 134 LNGAEIMGQTIQVDWCFVKGPKRVKKSE 161

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 49.4 bits (118), 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

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 75.0 bits (184), Expect = 3e-16
 Identities = 27/115 (23%), Positives = 46/115 (40%), Gaps = 2/115 (1%)

Query: 271 QPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD--LVK 328
           +PSP  N     +     G       V+VG   ++ T+ Q+ +++ S G     +    +
Sbjct: 32  EPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAE 91

Query: 329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQES 383
           +R  G SKGY   V             L G  +  + + VR AT    S+ E ++
Sbjct: 92  NRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQA 146

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 47.6 bits (113), 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

>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

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 73.1 bits (180), Expect = 5e-16
 Identities = 27/106 (25%), Positives = 42/106 (39%), 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------GLKMGDKTLTVRRATASGQSKTEQES 383
                     AA +      GLK+  + L V  A    ++ +   S
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 = 3e-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

>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

>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 = 72.7 bits (179), Expect = 7e-16
 Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 1/111 (0%)

Query: 273 SPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT 332
           S  L   ++G A     G EG   +F+  LP  F +  + ++   FG +    +  D+ T
Sbjct: 5   SSGLTQQSIGAAGSQKEGPEGA-NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 63

Query: 333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQES 383
             SK +GF  Y +P     A  ++NG ++G K L V+   +   SK+   S
Sbjct: 64  NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPSS 114

>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 = 7e-16
 Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 7/97 (7%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN---SKGYGFCVYQDP 346
           G+ G   +F+  L +  TE  +K +    G +    + K ++      S G+GF  Y+ P
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 347 AVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQES 383
                A   L G  +    L VR +    +  T+  S
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRIS----ERATKPAS 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 = 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

>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 = 45.0 bits (107), 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

>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 = 1e-15
 Identities = 29/98 (29%), Positives = 41/98 (41%), Gaps = 3/98 (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 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSK 378
             +        A A ++G       L V  A  S  S 
Sbjct: 62  ISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSG 99

>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

>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

>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 = 70.4 bits (173), Expect = 3e-15
 Identities = 17/89 (19%), Positives = 35/89 (39%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SGA  G  GP  + V  +P+  +  +I +    +  + G   +K  + G   G     +
Sbjct: 5   SSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           +       A   LN   +G + + +   +
Sbjct: 65  ESRDEATAAVIDLNDRPIGSRKVKLVLGS 93

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 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

>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 = 27/101 (26%), Positives = 39/101 (38%), Gaps = 6/101 (5%)

Query: 289 GGAEGPDR------VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 342
           G   GP R      +FV G+    TE  I +    +G +    L  DR TG  KGY    
Sbjct: 11  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70

Query: 343 YQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQES 383
           Y+       A   LNG  +  + ++V      G  K ++  
Sbjct: 71  YETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRG 111

>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

>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 = 70.8 bits (174), Expect = 3e-15
 Identities = 23/108 (21%), Positives = 44/108 (40%), Gaps = 5/108 (4%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SGA+        VFV  L Y     ++KE+    G +   D+++D+D G S+G G   +
Sbjct: 5   SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTF 63

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQH 391
           +       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

>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: 436 DEEYEEILEDM-REECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL 494
            E Y+E  E++  E   KYG +  + +            VG V++++        A   L
Sbjct: 33  QEHYDEFFEEVFTEMEEKYGEVEEMNVCDN----LGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 495 SGRKFGGNTVNAFYYP 510
           + R F G  ++A   P
Sbjct: 89  NNRWFNGQPIHAELSP 104

>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 = 70.0 bits (172), Expect = 6e-15
 Identities = 31/101 (30%), Positives = 50/101 (49%), Gaps = 4/101 (3%)

Query: 284 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
            S  + G++       +FVGGLPY+ T+  +++  E FG +    ++ DR TG S+GYGF
Sbjct: 4   GSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGF 63

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQ 381
               D A  + AC   N +  G +   V  A    + ++ Q
Sbjct: 64  VTMADRAAAERACKDPNPIIDG-RKANVNLAYLGAKPRSLQ 103

>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 = 70.0 bits (172), Expect = 7e-15
 Identities = 26/93 (27%), Positives = 45/93 (48%), Gaps = 5/93 (5%)

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 IACAALNGLKMGDKTLTVRRATASGQSKTEQES 383
            A   +NG  +  K + V +A    +  + Q  
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQA----KKPSFQSG 91

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 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

>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 = 69.2 bits (170), Expect = 9e-15
 Identities = 26/102 (25%), Positives = 42/102 (41%), Gaps = 7/102 (6%)

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
            G   P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF  + +   
Sbjct: 4   EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVD 62

Query: 349 TDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQ 390
                   + +    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

>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

>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

>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 = 69.2 bits (170), Expect = 1e-14
 Identities = 24/102 (23%), Positives = 44/102 (43%), Gaps = 6/102 (5%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G  G   +F+  L        + +   +FG +    +V   D   SKGYGF  ++     
Sbjct: 1   GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQEAA 58

Query: 350 DIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQH 391
           + 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

>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 = 51.1 bits (122), Expect = 1e-07
 Identities = 23/207 (11%), Positives = 51/207 (24%), Gaps = 27/207 (13%)

Query: 297 VFVGGL-PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           + V  L P   T   +  L   +G +    ++ +      K        D     +A + 
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60

Query: 356 LNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFG 415
           LNG K+  K + +  +         +        +      +       +     +    
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120

Query: 416 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVG 475
            TL  +  +  +++ + L             +      G +V                  
Sbjct: 121 ATLH-LSNIPPSVSEEDL-------------KVLFSSNGGVVKGFKFFQKDRKM------ 160

Query: 476 KVFLEYYDAVGCATAKNALSGRKFGGN 502
              ++         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 = 8e-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

>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 = 68.4 bits (168), Expect = 2e-14
 Identities = 13/88 (14%), Positives = 33/88 (37%), Gaps = 5/88 (5%)

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
                 +    L +  TE ++KE+ E        ++      G SKG  +  ++  A  +
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSEADAE 67

Query: 351 IACAALNGLKMGDKTLTVRRATASGQSK 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

>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 = 57.4 bits (138), Expect = 1e-09
 Identities = 27/222 (12%), Positives = 54/222 (24%), Gaps = 24/222 (10%)

Query: 290 GAEGPDRVFVGGL-PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           GA+ P  + V GL        ++  +   +G +     +K +      G       D   
Sbjct: 1   GADSP-VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYA 54

Query: 349 TDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG 408
            D A   LN   M  + + V  +        +   +   +  +    +            
Sbjct: 55  VDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQA 114

Query: 409 GGMSLFGETLAKVLC-LTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQN 467
               +   +           +T              E+  E C + G      + +    
Sbjct: 115 AKNRIQHPSNVLHFFNAPLEVTE-------------ENFFEICDELGVKRPTSV-KVFSG 160

Query: 468 GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY 509
             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

>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 = 68.4 bits (168), Expect = 2e-14
 Identities = 25/100 (25%), Positives = 40/100 (40%), Gaps = 2/100 (2%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG +     P  ++VG L    TE  I +L    G      ++ +  +     Y F  +
Sbjct: 5   SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEF 62

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQES 383
            +      A AA+NG K+  K + V  AT     K+   S
Sbjct: 63  YEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGPSS 102

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 52.6 bits (127), 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

>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 = 68.0 bits (167), Expect = 2e-14
 Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 7/95 (7%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G +++++G L    T   +++L           L          GY F  Y D    
Sbjct: 4   GSSGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWA 57

Query: 350 DIACAALNG-LKMGDKTLTVRRATASGQSKTEQES 383
             A   L+G +++  K + V  + +     +   S
Sbjct: 58  IRAIETLSGKVELHGKIMEVDYSVSKKLRSSGPSS 92

>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

>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

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 68.5 bits (168), Expect = 2e-14
 Identities = 18/88 (20%), Positives = 31/88 (35%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +++  L    TE  +  L   F    G  +     TG  +G  F  + +  +   A   
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 356 LNGLKMGDKTLTVRRATASGQSKTEQES 383
           +NG K+  K L +       Q  +   S
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQRSSGPSS 114

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 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

>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

>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 = 68.2 bits (167), Expect = 3e-14
 Identities = 22/104 (21%), Positives = 40/104 (38%), Gaps = 5/104 (4%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
             G   G E   ++ V  L +  ++  I+EL   FGTL    +  DR +G S G     +
Sbjct: 25  GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHF 83

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQ 387
           +  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

>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 = 67.3 bits (165), Expect = 4e-14
 Identities = 23/90 (25%), Positives = 45/90 (50%), Gaps = 2/90 (2%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG       P R+ V  +P+ F +  ++++   FG +   +++ +     SKG+GF  +
Sbjct: 5   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTF 62

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATA 373
           ++ A  D A   L+G  +  + + V  ATA
Sbjct: 63  ENSADADRAREKLHGTVVEGRKIEVNNATA 92

>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 = 46.5 bits (111), 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

>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 = 67.0 bits (164), Expect = 5e-14
 Identities = 26/98 (26%), Positives = 41/98 (41%), Gaps = 5/98 (5%)

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----RATASGQSK 378
           D A  +     +NG  +   T   R     AT SG S 
Sbjct: 61  DLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPSS 98

>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

>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

>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 = 66.9 bits (164), Expect = 5e-14
 Identities = 26/103 (25%), Positives = 45/103 (43%), Gaps = 9/103 (8%)

Query: 284 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G      +   + V GLP+  TE  +KE   +FG +    + KD  TG+SKG+GF
Sbjct: 2   SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQES 383
             + +        +  +   +  +    +       SK  Q+S
Sbjct: 62  VRFTEYETQVKVMSQRH--MIDGRWCDCKLP----NSKQSQDS 98

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 67.0 bits (164), Expect = 8e-14
 Identities = 28/89 (31%), Positives = 38/89 (42%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG          VFVG L    T   IK     FG +    +VKD  TG SKGYGF  +
Sbjct: 5   SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT 372
            +    + A   + G  +G + +    AT
Sbjct: 65  FNKWDAENAIQQMGGQWLGGRQIRTNWAT 93

>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

>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 = 66.1 bits (162), Expect = 1e-13
 Identities = 22/88 (25%), Positives = 45/88 (51%), Gaps = 5/88 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGG+P+   ET+++E  + FG +    ++ D +    +G+GF  ++D    D A   
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71

Query: 356 LNGLKMGDKTLTVRRATASGQSKTEQES 383
            +   +  K + V+RA    + +  + S
Sbjct: 72  -HFHDIMGKKVEVKRA----EPRDSKSS 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 = 7e-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

>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 = 46.7 bits (111), 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

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 67.6 bits (165), Expect = 2e-13
 Identities = 35/161 (21%), Positives = 57/161 (35%), Gaps = 17/161 (10%)

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 AVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQ 387
           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

>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

>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 = 65.9 bits (161), Expect = 2e-13
 Identities = 19/102 (18%), Positives = 44/102 (43%), Gaps = 8/102 (7%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
             +++  LPY  T  ++ ++   +G +    +     T  ++G  + VY+D      A  
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVD 65

Query: 355 ALNGLKMGDKTLTV-----RRATASGQSKTEQESILAQAQQH 391
            L+G  + ++ L V      RA     +K ++E +    +++
Sbjct: 66  HLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKY 107

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 46.6 bits (111), Expect = 1e-06
 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: 444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 503
           E+M +  GKYG +  + +        ET G    ++ Y D      A + LSG       
Sbjct: 23  EEMYDIFGKYGPIRQIRVGNT----PETRGTA--YVVYEDIFDAKNAVDHLSGFNVSNRY 76

Query: 504 VNAFYYPEDKYFNK 517
           +   YY  ++ F K
Sbjct: 77  LVVLYYNANRAFQK 90

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 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

>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

>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 = 3e-13
 Identities = 15/90 (16%), Positives = 32/90 (35%), Gaps = 4/90 (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--GLKMGDKTLTVRRATASGQSKTE 380
              L    +++    + V  A        +
Sbjct: 69  RRKLMPGRIQLWGHQIAVDWAEPEIDVDED 98

>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

>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 = 55.0 bits (132), Expect = 1e-08
 Identities = 25/239 (10%), Positives = 60/239 (25%), Gaps = 34/239 (14%)

Query: 272 PSPNLNLAAVGLASGAIGGAEGPDR-------VFVGGL-PYYFTETQIKELLESFGTLHG 323
              + + + +      +G    P         + V  L P   T   +  L   +G +  
Sbjct: 5   HHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQR 64

Query: 324 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQES 383
             ++ +      K        D     +A + LNG K+  K + +  +         +  
Sbjct: 65  VKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQ 119

Query: 384 ILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEIL 443
                 +      +       +     +     TL  +  +  +++ + L          
Sbjct: 120 EDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLH-LSNIPPSVSEEDL---------- 168

Query: 444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGN 502
              +      G +V        ++           ++         A   L     G N
Sbjct: 169 ---KVLFSSNGGVVKGFK-FFQKDR------KMALIQMGSVEEAVQALIDLHNHDLGEN 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

>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

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 64.0 bits (156), 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 = 2e-05
 Identities = 14/88 (15%), Positives = 30/88 (34%), Gaps = 7/88 (7%)

Query: 434 ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA 493
               +   + + +     K G +VN+  P  D+  G+T G    F+E            +
Sbjct: 17  IPSAKVPVLKKALTSLFSKAGKVVNMEFPI-DEATGKTKGFL--FVECGSMNDAKKIIKS 73

Query: 494 LSGRKFGGN---TVNAFYYPEDKYFNKD 518
             G++        +       ++Y + D
Sbjct: 74  FHGKRLDLKHRLFLYTM-KDVERYNSDD 100

>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 = 67.8 bits (165), Expect = 5e-13
 Identities = 21/157 (13%), Positives = 48/157 (30%), Gaps = 2/157 (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 GQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGM 411
             S+ E +S        ++ +  A    G +      
Sbjct: 151 FLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQ 187

>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

>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

>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 = 63.8 bits (156), Expect = 7e-13
 Identities = 22/101 (21%), Positives = 44/101 (43%), 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 GFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKT 379
           GF  ++DP       A+     +  + +  +  T  G   +
Sbjct: 61  GFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGMQPS 100

>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 = 66.8 bits (163), Expect = 7e-13
 Identities = 30/87 (34%), Positives = 49/87 (56%), Gaps = 2/87 (2%)

Query: 437 EEYEEILE-DMREECGKYGTLVNVVIPRPDQNGGE-TPGVGKVFLEYYDAVGCATAKNAL 494
           ++ ++ LE ++ EECGK+G +  V+I +  Q   E    + K+F+E+  A     A  AL
Sbjct: 136 KDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 195

Query: 495 SGRKFGGNTVNAFYYPEDKYFNKDYSA 521
           +GR F G  V A  Y ++++ N D SA
Sbjct: 196 NGRWFAGRKVVAEVYDQERFDNSDLSA 222

>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 = 63.5 bits (155), Expect = 1e-12
 Identities = 23/102 (22%), Positives = 44/102 (43%), Gaps = 2/102 (1%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCV 342
           +SG +   +   ++ V  +P+   + +I+EL  +FG L    L K    TG  +G+GF  
Sbjct: 5   SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64

Query: 343 YQDPAVTDIACAAL-NGLKMGDKTLTVRRATASGQSKTEQES 383
           +        A  AL +   +  + L +  A +    ++   S
Sbjct: 65  FITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 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

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 63.0 bits (154), Expect = 2e-12
 Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 1/82 (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 LNGLKMGDKTLTVRRATASGQS 377
            +  ++  KT+  + A      
Sbjct: 87  -SRHELDSKTIDPKVAFPRRAQ 107

>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 = 62.0 bits (151), Expect = 2e-12
 Identities = 14/87 (16%), Positives = 26/87 (29%), Gaps = 7/87 (8%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   + V  LP      ++ +LL+ +        +K      +K   F    +    
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQA 53

Query: 350 DIACAALNGLKMGDKTLTVRRATASGQ 376
             A    +      K L V+       
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQPTDAL 80

>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

>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 = 62.7 bits (153), Expect = 3e-12
 Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 1/84 (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 LNGLKMGDKTLTVRRATASGQSKT 379
                +  + +  +RA A  +S +
Sbjct: 89  -RPHSIDGRVVEPKRAVAREESGS 111

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 61.2 bits (149), Expect = 4e-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

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 15/88 (17%), Positives = 36/88 (40%), Gaps = 2/88 (2%)

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           +  P  +F+G L    +  ++K  +      +    V D  TG ++ +G+  ++     +
Sbjct: 14  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLE 72

Query: 351 IACAALNGLKMGDKTLTVRRATASGQSK 378
            A   L GLK+    + + +      ++
Sbjct: 73  KA-LELTGLKVFGNEIKLEKPKGRDGTR 99

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 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

>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 = 60.4 bits (147), Expect = 1e-11
 Identities = 24/97 (24%), Positives = 42/97 (43%), Gaps = 4/97 (4%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG+        ++FVG L    +E  +  L + FG +    +++  D G+SKG  F  +
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKF 63

Query: 344 QDPAVTDIACAALNG---LKMGDKTLTVRRATASGQS 377
                   A  AL+G   +     +L V+ A    +S
Sbjct: 64  SSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES 100

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 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

>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 = 58.0 bits (141), Expect = 6e-11
 Identities = 29/92 (31%), Positives = 46/92 (50%), Gaps = 9/92 (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 CVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
              +   + +IA   L+ + +  K L VR A 
Sbjct: 56  IRLETRTLAEIAKVELDNMPLRGKQLRVRFAC 87

>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 = 51.6 bits (124), Expect = 1e-08
 Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 6/88 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+ GG+    T+  +++    FG +    +  +      KGY F  +        A  +
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS 80

Query: 356 LNGLKMGDKTLTVRRATASGQSKTEQES 383
           +NG  +    +       S    +   S
Sbjct: 81  VNGTTIEGHVVKCYWGKESPDMTSGPSS 108

>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

>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: 434 ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA 493
              +  E++   + +   K+G + N   P  D   G+T G    FLEY        A   
Sbjct: 26  VGPDRLEKLKNVIHKIFSKFGKITNDFYPEED---GKTKGYI--FLEYASPAHAVDAVKN 80

Query: 494 LSGRKFGGN---TVNAF 507
             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

>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 = 23/91 (25%), Positives = 41/91 (45%), Gaps = 6/91 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++V  L     + ++++    FGT+    ++   + G SKG+GF  +  P     A   
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEEATKAVTE 74

Query: 356 LNGLKMGDKTLTVRRATASGQSKTEQESILA 386
           +NG  +  K L V  A    Q K E++S  +
Sbjct: 75  MNGRIVATKPLYVALA----QRKEERQSGPS 101

>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

>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 = 54.3 bits (131), Expect = 1e-09
 Identities = 20/86 (23%), Positives = 31/86 (36%), Gaps = 6/86 (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 AVTDIACAALNGLKMGDKTLTVRRAT 372
              +    + +   +G   L VR   
Sbjct: 56  GAREAVL-SQSQHSLGGHRLRVRPRE 80

>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 = 58.4 bits (142), Expect = 4e-11
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 8/83 (9%)

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 DIACAALNGLKMGDKTLTVRRAT 372
           + A   L+  K+    + V  + 
Sbjct: 56  EDAIRNLHHYKLHGVNINVEASK 78

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 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

>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

>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

>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

>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 = 56.3 bits (136), Expect = 4e-10
 Identities = 14/97 (14%), Positives = 30/97 (30%), Gaps = 1/97 (1%)

Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
           SG            +  +P+  T+  + + LE          V   + G   G     ++
Sbjct: 6   SGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFK 65

Query: 345 DPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQ 381
           +      +   L+  K+  +   V   T     + E+
Sbjct: 66  NEDDARKS-ERLHRKKLNGREAFVHVVTLEDMREIEK 101

>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

>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 = 55.3 bits (134), Expect = 4e-10
 Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 7/83 (8%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   VFVG      TE +++E    +G +    + K       + + F  + D  + 
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIA 55

Query: 350 DIACAALNGLKMGDKTLTVRRAT 372
              C     L +   ++ +  A 
Sbjct: 56  QSLCG--EDLIIKGISVHISNAE 76

>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

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 55.3 bits (134), Expect = 4e-10
 Identities = 15/98 (15%), Positives = 32/98 (32%), Gaps = 14/98 (14%)

Query: 289 GGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           G          VFVG      T  ++++    +G +    + K       + + F  + D
Sbjct: 3   GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFAD 57

Query: 346 PAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQES 383
             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

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 55.9 bits (135), Expect = 5e-10
 Identities = 19/85 (22%), Positives = 28/85 (32%), Gaps = 2/85 (2%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V++ G P   T   IKE LE  G +    + +       KG  F V+             
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAK-KFVET 71

Query: 357 NGLKMGDKTLTVRRATASGQSKTEQ 381
            G K  +  L +         K E+
Sbjct: 72  PGQKYKETDLLILFKDDYFAKKNEE 96

>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

>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 = 55.8 bits (135), Expect = 5e-10
 Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 13/99 (13%)

Query: 284 ASGAIGGAEGPD----------RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG 333
           +SG+ G + G            R++VG LP       I+++   +G +   DL   R   
Sbjct: 2   SSGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--- 58

Query: 334 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
               + F  ++DP   + A    +G       L V    
Sbjct: 59  GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 97

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 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

>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 = 55.3 bits (134), Expect = 5e-10
 Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 8/87 (9%)

Query: 286 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           G+ G +    ++FVG +    T  +++ L E  G +   D+V        K Y F   + 
Sbjct: 1   GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEK 52

Query: 346 PAVTDIACAALNGLKMGDKTLTVRRAT 372
            A    A A LNG ++  K + V  +T
Sbjct: 53  EADAKAAIAQLNGKEVKGKRINVELST 79

>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 = 8e-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

>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 = 60.2 bits (145), Expect = 6e-10
 Identities = 17/72 (23%), Positives = 34/72 (47%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  + Y  TE++++   E +G +    +V  + +G  +GY F  Y+       A    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 357 NGLKMGDKTLTV 368
           +G K+  + + V
Sbjct: 165 DGKKIDGRRVLV 176

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 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 = 8e-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 = 2e-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 = 51.0 bits (121), 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

>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 = 42.0 bits (99), Expect = 2e-05
 Identities = 18/75 (24%), Positives = 26/75 (34%), Gaps = 8/75 (10%)

Query: 434 ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA 493
              +  E++   + +   K+G + N   P  D   G+T G    FLEY        A   
Sbjct: 12  VGPDRLEKLKNVIHKIFSKFGKITNDFYPEED---GKTKGYI--FLEYASPAHAVDAVKN 66

Query: 494 LSGRKFGGN---TVN 505
             G K        VN
Sbjct: 67  ADGYKLDKQHTFRVN 81

>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 = 8e-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

>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 = 54.4 bits (131), Expect = 3e-09
 Identities = 16/92 (17%), Positives = 32/92 (34%), Gaps = 5/92 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDL-----VKDRDTGNSKGYGFCVYQDPAVTD 350
           R++V  L  +  E  +K +   +             ++    G  KG  F    +     
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 351 IACAALNGLKMGDKTLTVRRATASGQSKTEQE 382
            A    NG  +  K + V+ A ++   +  +E
Sbjct: 107 KALKEANGYVLFGKPMVVQFARSARPKQDPKE 138

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 53.1 bits (128), Expect = 5e-09
 Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 5/80 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +V+VG L     + +++     +G L    + ++       G+ F  ++DP   + A   
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 356 LNGLKMGDKTLTVRRATASG 375
           L+G  +    + V  +T   
Sbjct: 57  LDGKVICGSRVRVELSTGMP 76

>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

>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

>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

>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 = 51.5 bits (124), Expect = 2e-08
 Identities = 21/108 (19%), Positives = 37/108 (34%), Gaps = 8/108 (7%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
            S    G      +FV  L    TE  +++    FG L     +KD        Y F  +
Sbjct: 1   GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHF 52

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQH 391
            +      A   +NG  +  + + +  A    Q + E+++    A   
Sbjct: 53  DERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGP 100

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 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

>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: 440 EEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF 499
           +  +    E  GK+G +  VVI       G        ++ Y  +     A   ++    
Sbjct: 29  DPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV 88

Query: 500 GGNTVNAFY 508
            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 = 50.9 bits (122), Expect = 3e-08
 Identities = 14/92 (15%), Positives = 37/92 (40%), Gaps = 4/92 (4%)

Query: 284 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G +        V + GLP+  ++ +I +       +     +     G S G  F
Sbjct: 2   SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
             +    + + A    +  ++G + + + +++
Sbjct: 62  VQFASQEIAEKAL-KKHKERIGHRYIEIFKSS 92

>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

>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 = 50.6 bits (121), Expect = 4e-08
 Identities = 17/100 (17%), Positives = 28/100 (28%), Gaps = 11/100 (11%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +    LP      +I+E    FG+      +               + +P     A   L
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGS------LGRVLLPEGGITAIVEFLEPLEARKAFRHL 66

Query: 357 NGLKMGDKTLTVRRA-----TASGQSKTEQESILAQAQQH 391
              K     L +  A      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: 444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 503
            +++E   ++G+L  V++P          G     +E+ + +    A   L+  KF    
Sbjct: 25  AEIQETFSRFGSLGRVLLP---------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVP 75

Query: 504 VNAFYYPEDKY 514
           +   + P   +
Sbjct: 76  LYLEWAPIGVF 86

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 49.5 bits (118), Expect = 1e-07
 Identities = 16/92 (17%), Positives = 33/92 (35%), Gaps = 1/92 (1%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           E    V++ GLP+      + +  +    +     +     G + G GF  +++ A    
Sbjct: 23  EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKA 82

Query: 352 ACAALNGLKMGDKTLTVRRATASGQSKTEQES 383
           A    +   MG++ + V   T  G  +     
Sbjct: 83  AL-CRHKQYMGNRFIQVHPITKKGMLEKIDMI 113

>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

>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

>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 = 18/78 (23%), Positives = 31/78 (39%), Gaps = 9/78 (11%)

Query: 296 RVFVGGLPYYF-TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           RVF+G L      ++ ++ +   +G + G  +         KGY F  Y +      A  
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80

Query: 355 ALNGLKMGDKTLTVRRAT 372
             NG  +  +TL +  A 
Sbjct: 81  GENGRVLAGQTLDINMAG 98

>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 = 44.9 bits (106), Expect = 4e-06
 Identities = 23/118 (19%), Positives = 46/118 (38%), Gaps = 15/118 (12%)

Query: 284 ASGAIGGAEGPDR-----VFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNS 335
           +SG+ G   GP+      V + GLP+  +   ++  L        + G   +  R+ G  
Sbjct: 2   SSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQ 60

Query: 336 KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIA 393
            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 = 15/124 (12%), Positives = 43/124 (34%), Gaps = 9/124 (7%)

Query: 296 RVFVGGLPYYFTETQIKELL----ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
            +++  L     + ++K+ L      FG +     +    +   +G  F ++++ +    
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFKEVSSATN 67

Query: 352 ACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGM 411
           A  ++ G    DK + ++ A     S    +      ++    +K   ++         +
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKT--DSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAV 125

Query: 412 SLFG 415
              G
Sbjct: 126 QGGG 129

>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 = 5e-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 = 48.7 bits (116), 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 = 47.9 bits (114), Expect = 6e-07
 Identities = 19/118 (16%), Positives = 34/118 (28%), Gaps = 7/118 (5%)

Query: 268 GPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLV 327
                +    +      S     +     V + GLPY  TE  I         +    + 
Sbjct: 20  HMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIE 78

Query: 328 KDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLTVRRATASGQSKTEQES 383
              D G   G     +      + A AA+  +   M  + + +   + +G S     S
Sbjct: 79  IGPD-GRVTGEADVEFATH---EEAVAAMSKDRANMQHRYIELFLNSTTGASNGAYSS 132

>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 = 4e-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

>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

>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 = 46.5 bits (111), Expect = 7e-07
 Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 9/79 (11%)

Query: 296 RVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           R+F+G LP    ++  +  +   +G +   ++           +GF  + +P     A  
Sbjct: 24  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE 75

Query: 355 ALNGLKMGDKTLTVRRATA 373
             +      K L +  +++
Sbjct: 76  XESQEMNFGKKLILEVSSS 94

>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

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 46.5 bits (111), Expect = 7e-07
 Identities = 23/92 (25%), Positives = 36/92 (39%), Gaps = 9/92 (9%)

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--NGLKMGDKTLTVRRATASGQS 377
             +    AL  N   MG + + V R  +   S
Sbjct: 61  --EEVKQALKCNREYMGGRYIEVFREKSGPSS 90

>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

>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 = 46.6 bits (111), Expect = 8e-07
 Identities = 20/101 (19%), Positives = 34/101 (33%), Gaps = 7/101 (6%)

Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
           SG+   +     V + GLPY  TE  I              +    D G   G     + 
Sbjct: 6   SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFA 63

Query: 345 DPAVTDIACAAL--NGLKMGDKTLTVRRATASGQSKTEQES 383
                + A AA+  +   M  + + +   + +G S +   S
Sbjct: 64  TH---EDAVAAMAKDKANMQHRYVELFLNSTAGTSGSGPSS 101

>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

>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 = 8e-07
 Identities = 12/78 (15%), Positives = 29/78 (37%), Gaps = 9/78 (11%)

Query: 296 RVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           R+F+G LP    ++  +  +   +G +   ++           +GF  + +P     A  
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE 63

Query: 355 ALNGLKMGDKTLTVRRAT 372
             +      K L +  ++
Sbjct: 64  CESQEMNFGKKLILEVSS 81

>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 = 22/92 (23%), Positives = 34/92 (36%), Gaps = 11/92 (11%)

Query: 284 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G    P +   ++V G     T T ++     FG       + D      +   F
Sbjct: 2   SSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGN------IIDLSMDPPRNCAF 53

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
             Y+     D A A LNG ++    L V  A 
Sbjct: 54  VTYEKMESADQAVAELNGTQVESVQLKVNIAR 85

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 12/80 (15%), Positives = 33/80 (41%), Gaps = 7/80 (8%)

Query: 296 RVFVGGLPYYFTETQIKELL----ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
            +++  L     + ++K+ L      FG +     +    +   +G  F ++++ +    
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATN 66

Query: 352 ACAALNGLKMGDKTLTVRRA 371
           A  ++ G    DK + ++ A
Sbjct: 67  ALRSMQGFPFYDKPMRIQYA 86

>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

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 3/90 (3%)

Query: 296 RVFVGGLPYYFTETQIKEL-LESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
            +FVG L     +  + E  ++ + +  G  +V D+ TG SKGYGF  + D      A  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69

Query: 355 ALNG-LKMGDKTLTVRRATASGQSKTEQES 383
              G + +G K + +  A          ES
Sbjct: 70  ECQGAVGLGSKPVRLSVAIPKASRVKPVES 99

>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 = 46.0 bits (109), Expect = 2e-06
 Identities = 14/97 (14%), Positives = 31/97 (31%), Gaps = 10/97 (10%)

Query: 297 VFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           +   GLP+  T   +             +G   + +RD G  +G      +       A 
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKAL 72

Query: 354 AALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQ 390
              + + 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

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 41.7 bits (97), Expect = 2e-04
 Identities = 19/85 (22%), Positives = 27/85 (31%), Gaps = 2/85 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V++ G P   T   IKE LE  G +    + +       KG  F V+            
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVET 169

Query: 356 LNGLKMGDKTLTVRRATASGQSKTE 380
             G K  +  L +         K E
Sbjct: 170 P-GQKYKETDLLILFKDDYFAKKNE 193

>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

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

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 16/100 (16%), Positives = 32/100 (32%), Gaps = 7/100 (7%)

Query: 296 RVFVGGLPYYFTETQIKELL----ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
            V +  +     + +++ LL     S G +   D+V D  + ++ G  + V+        
Sbjct: 31  VVLITNINPEVPKEKLQALLYALASSQGDI--LDIVVDL-SDDNSGKAYIVFATQESAQA 87

Query: 352 ACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQH 391
              A  G       L +  +        E  S+      H
Sbjct: 88  FVEAFQGYPFQGNPLVITFSETPQSQVAEDGSLEHHHHHH 127

>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 = 45.6 bits (107), Expect = 4e-05
 Identities = 65/511 (12%), Positives = 129/511 (25%), Gaps = 163/511 (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 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL-TVRRATASGQSKTEQES 383
           DL ++  T N           P    I  A    ++ G  T    +       +   + S
Sbjct: 317 DLPREVLTTN-----------PRRLSI-IAES--IRDGLATWDNWKHVNCDKLTTIIESS 362

Query: 384 ILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETL---AKVLCLTEAITADALADDEEYE 440
           +     +    +KM  +          +S+F  +      +L L        +  D    
Sbjct: 363 L--NVLEPAEYRKMFDR----------LSVFPPSAHIPTILLSL--------IWFDVIKS 402

Query: 441 EILEDMREECGKYGTLVN-------VVIP----RPDQNGGETPGVGKVFLEYYDAVGCAT 489
           ++   +  +  KY  LV        + IP               + +  +++Y+      
Sbjct: 403 DV-MVVVNKLHKYS-LVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIP---- 456

Query: 490 AKNALSGRKFGGNTVNAFYYPEDKYFNKDYS 520
                  + 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 = 40.0 bits (93), Expect = 3e-04
 Identities = 17/95 (17%), Positives = 34/95 (35%), Gaps = 10/95 (10%)

Query: 297 VFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           V + GLP+  +   ++  L          G   +  R+ G   G  F          +A 
Sbjct: 47  VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMAL 105

Query: 354 AALNGLKMGDKTLTVRRATASGQSKTEQESILAQA 388
              +   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	521
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
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.97
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
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
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.97
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	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
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
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
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.95
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.95
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.95
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.95
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.95
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.95
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.95
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.95
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.94
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.94
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	99.87
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.84
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
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.8
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.79
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.79
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.79
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.78
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.78
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.77
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.77
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.77
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.77
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.76
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.76
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.76
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.76
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.76
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.76
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.76
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.76
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.76
2div_A	99	TRNA selenocysteine associated protein; structural	99.76
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.76
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.75
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.75
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.75
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.75
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.75
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.75
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.75
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.75
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.75
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.75
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.75
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.75
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.75
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.74
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.74
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.74
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.74
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.74
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.74
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.74
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.73
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.73
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.73
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.73
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.73
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.73
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.73
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.73
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.73
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.73
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.73
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.73
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.73
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.73
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.73
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.73
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.73
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.73
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.72
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	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
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.72
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.72
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.72
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.72
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.72
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.72
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.71
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.71
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.71
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.71
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.71
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.71
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.71
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.71
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.7
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.7
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.7
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.7
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.7
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.7
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.7
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.7
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.69
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.69
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.69
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.69
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.69
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.69
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.69
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.69
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.69
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.68
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.68
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.68
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.68
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.68
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.68
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.67
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.67
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.67
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.67
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.67
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.67
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.67
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.67
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.66
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.66
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.66
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.66
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.66
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.66
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.66
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.66
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.65
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.65
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.65
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.65
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.65
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.65
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.65
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.65
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.65
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.64
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.64
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.64
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.64
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.64
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.64
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.64
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.64
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.63
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.63
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.63
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.63
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.62
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.62
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.62
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.42
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.62
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.61
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.61
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.61
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.61
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.61
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.61
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.61
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.61
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.6
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.6
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.6
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.6
1x5p_A	97	Negative elongation factor E; structure genomics,	99.6
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.6
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.59
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.59
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.58
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.58
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.58
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.57
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.57
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.57
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.57
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.56
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.56
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.55
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.54
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.53
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.53
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.53
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.53
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.53
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.53
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.52
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.52
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.52
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.52
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.52
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.51
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.51
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.51
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.51
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.51
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.51
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.51
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.5
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.5
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.5
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.5
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.5
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.5
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.5
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.5
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.5
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.49
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.49
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.49
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.49
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.49
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.49
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.49
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.49
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.49
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.49
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.49
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.48
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.48
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.48
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.48
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.48
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.48
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.48
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.48
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.48
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.48
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.48
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.47
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.47
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.47
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.47
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.47
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.47
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.47
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.47
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.47
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.47
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.47
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.46
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.46
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.46
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.46
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.46
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.46
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.46
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.46
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.46
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.46
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.46
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.46
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.46
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.46
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.45
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.45
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.45
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.45
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.45
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.45
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.45
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.44
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.44
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.44
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.44
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.44
1x5p_A	97	Negative elongation factor E; structure genomics,	99.44
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.44
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.43
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.43
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.43
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.43
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.43
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.43
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.43
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.43
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.43
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.43
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.43
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.43
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.42
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.42
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.42
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.42
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.42
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.42
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.42
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.42
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.42
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.42
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.42
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.42
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.41
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.41
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.41
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.41
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.4
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.4
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.4
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.4
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.4
2div_A	99	TRNA selenocysteine associated protein; structural	99.39
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.39
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.39
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.39
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.39
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.39
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.38
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.38
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.38
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.38
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.38
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.37
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.37
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.37
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.36
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.36
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.35
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.35
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.35
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.35
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.34
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.33
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.33
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.32
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.32
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.31
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.31
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.31
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.3
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.28
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.27
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.26
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.26
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.26
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.23
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.21
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.18
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.11
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.09
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.02
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.02
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.01
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.92
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.86
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.84
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.55
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.54
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.53
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.0
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.89
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.63
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.55
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.53
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.34
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.32
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.08
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.92
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.63
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.22
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.84
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.07
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.06
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	93.18
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	92.72
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	92.18
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	92.1
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	86.73

>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=2.4e-41  Score=325.91  Aligned_cols=248  Identities=23%  Similarity=0.321  Sum_probs=210.7

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      .....++|||+|||.++|+++|+++|..||             |..+.++.++|||||+|.+.++|..|+ .|+|..+.|
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             455666899999999999999999999 699999999


Q ss_pred             ceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 009954          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (521)
Q Consensus       249 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~  328 (521)
                      +.|.|.++.                                   ..++|||+|||..+++++|.++|+.||.|..+.++.
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            999998632                                   125899999999999999999999999999999999


Q ss_pred             cCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCC
Q 009954          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG  408 (521)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  408 (521)
                      ++.+|.++|||||+|.+.++|.+|+..|+|..|.|+.|.|.|+.+......                             
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            988999999999999999999999999999999999999999975221100                             


Q ss_pred             CCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHH
Q 009954          409 GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCA  488 (521)
Q Consensus       409 ~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~  488 (521)
                             .....++.+.|+...  +       +++++|+++|+.||.|..|.|+.+. +|.   .+|+|||+|.+.++|.
T Consensus       181 -------~~~~~~l~v~nlp~~--~-------~~~~~l~~~f~~~G~i~~v~i~~~~-~g~---~~g~afV~f~~~~~A~  240 (284)
T 3smz_A          181 -------LLHSRCLCVDRLPPG--F-------NDVDALCRALSAVHSPTFCQLACGQ-DGQ---LKGFAVLEYETAEMAE  240 (284)
T ss_dssp             -------TTSCSEEEEECCCTT--C-------CCHHHHHHHTCSSSCCSEEEEEECS-SCC---EEEEEEEECSSHHHHH
T ss_pred             -------cCCccEEEEecCCcc--c-------CCHHHHHHHhhCCCCeEEEEEEECC-CCC---cccEEEEEeCCHHHHH
Confidence                   022233344443221  0       0115999999999999999999876 443   3689999999999999


Q ss_pred             HHHHHHhCCeeCCcEEEEEEcCCCCc
Q 009954          489 TAKNALSGRKFGGNTVNAFYYPEDKY  514 (521)
Q Consensus       489 ~Ai~~lng~~~~gr~l~v~~~~~~~~  514 (521)
                      +|+..|||..|+|+.|+|.|+.....
T Consensus       241 ~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          241 EAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             HHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             HHHHHhCCCccCCeEEEEEEecCCCc
Confidence            99999999999999999999987654

>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=9.1e-41  Score=323.16  Aligned_cols=248  Identities=16%  Similarity=0.240  Sum_probs=196.2

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC----CCCeEEEEecCHHHHHHHHHccCce
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH----EKKFAFVEMRTVEEASNAMALDGII  245 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~----~~g~afV~f~~~~~a~~A~~l~g~~  245 (521)
                      .....++|||+|||+.+|+++|+++|..||.            |..+.+..    ++|||||+|.+.++|.+|++++|..
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~  104 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGP------------IIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKV  104 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSC------------EEEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEECCCCCcEEEEEEECCHHHHHHHHHhCCcE
Confidence            4566889999999999999999999999997            44444433    5799999999999999999999999


Q ss_pred             ecCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcC-CeeEE
Q 009954          246 FEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-TLHGF  324 (521)
Q Consensus       246 ~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G-~i~~v  324 (521)
                      +.|+.|.|.++                                    ..++|||+|||..+++++|.++|+.|| .|..|
T Consensus       105 ~~g~~i~v~~~------------------------------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v  148 (292)
T 2ghp_A          105 VGQNEIIVSHL------------------------------------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSI  148 (292)
T ss_dssp             ETTEECEEEEC------------------------------------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEE
T ss_pred             eCCcEEEEEEC------------------------------------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEE
Confidence            99999999863                                    136899999999999999999999999 99999


Q ss_pred             EEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCC
Q 009954          325 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGM  404 (521)
Q Consensus       325 ~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  404 (521)
                      .|+.+. .|.++|||||+|.+.++|.+|+..|+|..|.|+.|.|.|+.+.......                  .     
T Consensus       149 ~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~------------------~-----  204 (292)
T 2ghp_A          149 RLPSLR-FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRT------------------D-----  204 (292)
T ss_dssp             ECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC------------------------------
T ss_pred             EEEeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccc------------------c-----
Confidence            999886 4889999999999999999999999999999999999999763221110                  0     


Q ss_pred             CCCCCCCCCCCCCcceEEEeeCc-CCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCC-CCCCCCCccEEEEEec
Q 009954          405 NTLGGGMSLFGETLAKVLCLTEA-ITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQ-NGGETPGVGKVFLEYY  482 (521)
Q Consensus       405 ~~~~~~~~~~~~~~~~v~~l~~~-~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~-~~~~~~g~g~afV~F~  482 (521)
                            ..........|.+|+.. ++.             ++|+++|+.||.|..|.|+.+.. ++..   +|+|||+|.
T Consensus       205 ------~~~~~~~~l~v~nlp~~~~t~-------------~~l~~~F~~~G~v~~v~i~~~~~~tg~~---~g~afV~F~  262 (292)
T 2ghp_A          205 ------SATLEGREIMIRNLSTELLDE-------------NLLRESFEGFGSIEKINIPAGQKEHSFN---NCCAFMVFE  262 (292)
T ss_dssp             --------CCTTTEEEEEEECTTTCCH-------------HHHHHHHGGGSCEEEEECCSCCC---CC---CEEEEEEES
T ss_pred             ------ccCCCCceEEEECCCcccCCH-------------HHHHHHHhccCCeeEEEEEecCCcCCCC---ceEEEEEeC
Confidence                  00001123333344433 333             59999999999999999999764 2443   588999999


Q ss_pred             CHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          483 DAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       483 ~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      +.++|.+|+ .|||..|+|+.|.|.|+...
T Consensus       263 ~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          263 NKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             SHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             CHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            999999999 99999999999999998764

>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=5.9e-32  Score=239.97  Aligned_cols=170  Identities=52%  Similarity=0.917  Sum_probs=152.7

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~  252 (521)
                      +.++|||+|||+.+|+++|+++|++||.+.+... .++..+.++.+..++|||||+|.+.++|.+|+.++|..+.|+.|.
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            4679999999999999999999999998876421 223358999999999999999999999999999999999999999


Q ss_pred             EeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 009954          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (521)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~  332 (521)
                      |.++..+...                             ...++|||+|||..+++++|+++|++||.|..|.++.++.+
T Consensus        82 v~~~~~~~~~-----------------------------~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~  132 (172)
T 2g4b_A           82 IRRPHDYQPL-----------------------------PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSAT  132 (172)
T ss_dssp             EECCSSCCCC-----------------------------TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTT
T ss_pred             ecCCcccCCC-----------------------------CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCC
Confidence            9986543321                             22468999999999999999999999999999999999889


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      |.++|||||+|.+.++|.+|++.|||..|+|+.|.|.||.
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            9999999999999999999999999999999999999983

>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=1.3e-31  Score=243.45  Aligned_cols=194  Identities=46%  Similarity=0.795  Sum_probs=161.0

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~  252 (521)
                      ..++|||+|||+.+|+++|+++|..||.+.+... .++..+.++.++.++|||||+|.+.++|.+|+.|||..|.|+.|.
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            4689999999999999999999999999877532 233458999999999999999999999999999999999999999


Q ss_pred             EeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 009954          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (521)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~  332 (521)
                      |.++..+.........+....+         ...........++|||+|||..+++++|+++|++||.|..|.+..++.+
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            9998776443221111100000         0011122345689999999999999999999999999999999999889


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCC
Q 009954          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQ  376 (521)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~  376 (521)
                      |.++|||||+|.+.++|.+|++.|||..|+|+.|.|.|+.+...
T Consensus       153 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          153 GLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             CSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            99999999999999999999999999999999999999987543

>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=7.6e-32  Score=247.47  Aligned_cols=167  Identities=20%  Similarity=0.359  Sum_probs=140.0

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      .+.++|||+|||+++|+++|+++|++||.|..+.      .+.+..++.++|||||+|.+.++|.+|+ .+++..+.|+.
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            3467899999999999999999999999843311      0111223556799999999999999999 79999999999


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~  330 (521)
                      |++.++........                           ....+|||+|||..+++++|+++|++||.|..|+|+.+ 
T Consensus        87 i~~~~~~~~~~~~~---------------------------~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d-  138 (213)
T 4f02_A           87 VRIMWSQRDPSLRK---------------------------SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-  138 (213)
T ss_dssp             CEEEECCCCTHHHH---------------------------HCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-
T ss_pred             cccccccccccccc---------------------------cccccceECCcccccHHHHHHHHHhhcCCeEEEEeecc-
Confidence            99987543322110                           12358999999999999999999999999999999998 


Q ss_pred             CCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                       .+.++|||||+|.+.++|.+||+.|||..|+|+.|.|.|+.+
T Consensus       139 -~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          139 -ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             -TTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             -CCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence             355899999999999999999999999999999999999965

>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=9.6e-31  Score=230.64  Aligned_cols=159  Identities=23%  Similarity=0.427  Sum_probs=141.8

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      ++|||+|||.++|+++|+++|++||.            |..+.+     +.++|||||+|.+.++|..|+ .|+|..+.|
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            444444     446799999999999999999 899999999


Q ss_pred             ceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 009954          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (521)
Q Consensus       249 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~  328 (521)
                      +.|.|.++......                           ......+|||+|||..+++++|.++|++||.|..+.++.
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                           123346899999999999999999999999999999999


Q ss_pred             cCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       329 ~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.|++
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=1.1e-30  Score=239.63  Aligned_cols=169  Identities=15%  Similarity=0.197  Sum_probs=140.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      .+.++|||+|||.++|+++|+++|++||.|.+|+|++++.+|.++|||||+|.+.++|.+||+.|+|..+.|+.|.|.++
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             cCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhc
Q 009954          372 TASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  451 (521)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~  451 (521)
                      ......    ..               ..               .....|-+|+..++.             ++|+++|+
T Consensus        93 ~~~~~~----~~---------------~~---------------~~~l~v~nl~~~~t~-------------~~l~~~F~  125 (213)
T 4f02_A           93 QRDPSL----RK---------------SG---------------VGNIFIKNLDKSIDN-------------KALYDTFS  125 (213)
T ss_dssp             CCCTHH----HH---------------HC---------------TTEEEEESCCTTCCH-------------HHHHHHHG
T ss_pred             cccccc----cc---------------cc---------------cccceECCcccccHH-------------HHHHHHHh
Confidence            642110    00               00               022222233333222             59999999


Q ss_pred             cccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          452 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       452 ~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      .||.|..|.|+.+..     ..+|+|||+|.+.++|.+||+.|||..|+|++|.|.|+...
T Consensus       126 ~~G~i~~~~i~~d~~-----~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          126 AFGNILSCKVVCDEN-----GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             GGSCEEEEEEEEETT-----EEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             hcCCeEEEEeeccCC-----CCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            999999999998752     23689999999999999999999999999999999998754

>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=2.9e-30  Score=229.74  Aligned_cols=165  Identities=18%  Similarity=0.360  Sum_probs=145.8

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      ....++|||+|||..+|+++|+++|..||.+.+.       .+.+..++.++|||||+|.+.++|.+|++|||..+.|+.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-------~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~   82 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-------AVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNE   82 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-------CCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-------EEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeE
Confidence            3457899999999999999999999999998762       377888999999999999999999999999999999999


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~  330 (521)
                      |.|.++......                           .....++|||+|||..+++++|+++|++||.|..+     .
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                           01233689999999999999999999999988766     3


Q ss_pred             CCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      .+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+.++
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            58999999999999999999999999999999999999999763

>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=1.1e-30  Score=230.91  Aligned_cols=164  Identities=20%  Similarity=0.323  Sum_probs=141.0

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+|||+.+|+++|+++|++||.|..+.+      +.+...+.++|||||+|.+.++|..|+ .|+|..+.|+.|
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 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRI------MRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL   75 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEEC------CEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE------EEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEE
Confidence            3578999999999999999999999997432111      111123446799999999999999999 699999999999


Q ss_pred             EEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC
Q 009954          252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD  331 (521)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~  331 (521)
                      .|.++.....                             ....++|||+|||..+++++|+++|++||.|..+.++.++.
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            9998653221                             12346899999999999999999999999999999999988


Q ss_pred             CCCcceEEEEEEcChHHHHHHHHHHcCCeeCC--eEEEEEEc
Q 009954          332 TGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  371 (521)
Q Consensus       332 ~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~  371 (521)
                      +|.++|||||+|.+.++|.+|++.|||..|.|  ++|.|.||
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            99999999999999999999999999999987  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=5.4e-31  Score=239.02  Aligned_cols=176  Identities=21%  Similarity=0.392  Sum_probs=141.6

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      ....++|||+|||+.+|+++|+++|+.||.|..+.      .+.+..++.++|||||+|.+.++|.+|+++++..+.|+.
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~   83 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV------VMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRV   83 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE------EEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEE
Confidence            34578999999999999999999999999843210      011111244578999999999999999988999999999


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~  330 (521)
                      |.|.++........                       .......++|||+|||..+++++|+++|++||.|..|.|+.+.
T Consensus        84 l~v~~~~~~~~~~~-----------------------~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~  140 (196)
T 1l3k_A           84 VEPKRAVSREDSQR-----------------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR  140 (196)
T ss_dssp             CEEEECCC----------------------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECT
T ss_pred             eeeecccCcccccc-----------------------cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecC
Confidence            99998654332110                       0112334789999999999999999999999999999999998


Q ss_pred             CCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCC
Q 009954          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQ  376 (521)
Q Consensus       331 ~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~  376 (521)
                      .+|.++|||||+|.+.++|.+||.. +|..|+|+.|.|.|+.++.+
T Consensus       141 ~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~  185 (196)
T 1l3k_A          141 GSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQE  185 (196)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC----
T ss_pred             CCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhH
Confidence            8999999999999999999999986 89999999999999987443

>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=3.6e-31  Score=244.09  Aligned_cols=184  Identities=26%  Similarity=0.395  Sum_probs=148.7

Q ss_pred             hhhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCcee
Q 009954          168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (521)
Q Consensus       168 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~  246 (521)
                      .......++|||+|||.++|+++|+++|..||.|..+.+      +.+...+.++|||||+|.+.++|.+|+ .|++..|
T Consensus        22 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i------~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~   95 (216)
T 2qfj_A           22 QGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM------SWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVML   95 (216)
T ss_dssp             HHHHHHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEE------CCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCC
T ss_pred             CcccCcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEE------eecCCCCccCceEEEEeCCHHHHHHHHHHccCCee
Confidence            345567889999999999999999999999998432110      111123557899999999999999999 5999999


Q ss_pred             cCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 009954          247 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (521)
Q Consensus       247 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i  326 (521)
                      .|+.|.|.++...........          .        ........++|||+|||..+++++|+++|++||.|..|.|
T Consensus        96 ~g~~l~v~~~~~~~~~~~~~~----------~--------~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i  157 (216)
T 2qfj_A           96 GGRNIKVGRPSNIGQAQPIID----------Q--------LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATL  157 (216)
T ss_dssp             C-CCCEEECCSCCGGGHHHHH----------H--------HHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEE
T ss_pred             CCeeEEEecCCCccccchhhh----------h--------hhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEE
Confidence            999999988665432211000          0        0000133468999999999999999999999999999999


Q ss_pred             eecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCC
Q 009954          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASG  375 (521)
Q Consensus       327 ~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (521)
                      +.++.+|.++|||||+|.+.++|.+|++.|||..|+|+.|.|.|+.+..
T Consensus       158 ~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          158 ARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             EecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            9998899999999999999999999999999999999999999998743

>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=9.7e-30  Score=224.41  Aligned_cols=157  Identities=22%  Similarity=0.387  Sum_probs=138.7

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCCeEEEEecCHHHHHHHH-HccCcee
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~A~-~l~g~~~  246 (521)
                      .++|||+|||+.+|+++|+++|+.||.|            ..+.+      +.++|||||+|.+.++|..|+ .|+|..+
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            5789999999999999999999999974            44443      334599999999999999999 5999999


Q ss_pred             cCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 009954          247 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (521)
Q Consensus       247 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i  326 (521)
                      .|+.|.|.++......                             ....+|||+|||..+++++|+++|++||.|..+.+
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            9999999986533211                             22368999999999999999999999999999999


Q ss_pred             eecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeE--EEEEEc
Q 009954          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT--LTVRRA  371 (521)
Q Consensus       327 ~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~--l~v~~~  371 (521)
                      +.+..+|.++|||||+|.+.++|.+|++.|||..|.|+.  |.|.||
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            999889999999999999999999999999999999965  888886

>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=7.7e-30  Score=225.35  Aligned_cols=164  Identities=24%  Similarity=0.349  Sum_probs=140.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.|+.+
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            46899999999999999999999999999999999988999999999999999999999999999999999999999975


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccc
Q 009954          374 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  453 (521)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~f  453 (521)
                      ....                                       .+...+.+.++....          ++++|+++|++|
T Consensus        83 ~~~~---------------------------------------~~~~~l~v~nl~~~~----------t~~~l~~~f~~~  113 (168)
T 1b7f_A           83 GGES---------------------------------------IKDTNLYVTNLPRTI----------TDDQLDTIFGKY  113 (168)
T ss_dssp             CSST---------------------------------------TTTCEEEEESCCTTC----------CHHHHHHHHTSS
T ss_pred             Cccc---------------------------------------CCCCCEEEeCCCCCC----------CHHHHHHhhhcC
Confidence            3211                                       222334444432211          125999999999


Q ss_pred             cceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCC--cEEEEEEc
Q 009954          454 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYY  509 (521)
Q Consensus       454 G~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~g--r~l~v~~~  509 (521)
                      |.|..|.|+++..++..   .|+|||+|.+.++|.+|++.|||..|+|  ++|+|.|+
T Consensus       114 G~i~~~~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          114 GSIVQKNILRDKLTGRP---RGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             SCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CcEEEEEEEEcCCCCCc---ceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            99999999998766553   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=1.5e-29  Score=223.22  Aligned_cols=164  Identities=27%  Similarity=0.423  Sum_probs=138.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||..+++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+
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            36899999999999999999999999999999999988999999999999999999999999999999999999999975


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccc
Q 009954          374 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  453 (521)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~f  453 (521)
                      ....                                       .....+.+.++....          ++++|+++|++|
T Consensus        82 ~~~~---------------------------------------~~~~~l~v~nl~~~~----------t~~~l~~~f~~~  112 (167)
T 1fxl_A           82 SSAS---------------------------------------IRDANLYVSGLPKTM----------TQKELEQLFSQY  112 (167)
T ss_dssp             CCGG---------------------------------------GTTCEEEEESCCTTC----------CHHHHHHHHGGG
T ss_pred             Cccc---------------------------------------CCCCcEEECCCCCcC----------CHHHHHHHHHhc
Confidence            3210                                       111223333332211          125999999999


Q ss_pred             cceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcE--EEEEEc
Q 009954          454 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT--VNAFYY  509 (521)
Q Consensus       454 G~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~--l~v~~~  509 (521)
                      |.|..|.|+.+..++..   .|+|||+|.+.++|.+|++.|||..|+|+.  |+|.|+
T Consensus       113 G~i~~~~i~~~~~~g~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          113 GRIITSRILVDQVTGVS---RGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             SCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEeEEEEEecCCCCCc---cceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            99999999988766543   689999999999999999999999999975  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=2.8e-29  Score=221.27  Aligned_cols=166  Identities=18%  Similarity=0.284  Sum_probs=140.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      ++|||+|||.++++++|.++|++||.|.+|.|+.++ ++.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++...
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            479999999999999999999999999999999986 5889999999999999999999999999999999999999653


Q ss_pred             CCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhcccc
Q 009954          375 GQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYG  454 (521)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG  454 (521)
                      ...                                     ...+...+.+.|+....          ++++|+++|+.||
T Consensus        80 ~~~-------------------------------------~~~~~~~l~v~nl~~~~----------t~~~l~~~f~~~G  112 (166)
T 3md3_A           80 QQS-------------------------------------SSDDTFNLFVGDLNVNV----------DDETLRNAFKDFP  112 (166)
T ss_dssp             CCC-------------------------------------CCTTCEEEEEESCCTTC----------CHHHHHHHHTTST
T ss_pred             CCC-------------------------------------CCCCCceEEECCCCCCC----------CHHHHHHHHhccC
Confidence            221                                     01233344444432221          1259999999999


Q ss_pred             ceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCC
Q 009954          455 TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       455 ~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~  511 (521)
                      .|..|.|+.+..++..   +|+|||+|.+.++|.+|+..|||..|+|+.|+|.|+.+
T Consensus       113 ~i~~~~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          113 SYLSGHVMWDMQTGSS---RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             TEEEEEEEECTTTCCE---EEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             CeeEEEEEecCCCCCc---ceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            9999999988766553   68999999999999999999999999999999999863

>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=3.5e-29  Score=230.76  Aligned_cols=179  Identities=20%  Similarity=0.353  Sum_probs=143.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||.++++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|+|..|.|+.|.|.++..
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            36899999999999999999999999999999999988999999999999999999999999999999999999999876


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccc
Q 009954          374 SGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKY  453 (521)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~f  453 (521)
                      .....+......          .  ..                .....+.+.++....          ++++|+++|+.|
T Consensus       108 ~~~~~~~~~~~~----------~--~~----------------~~~~~l~v~nlp~~~----------t~~~l~~~f~~~  149 (216)
T 2qfj_A          108 IGQAQPIIDQLA----------E--EA----------------RAFNRIYVASVHQDL----------SDDDIKSVFEAF  149 (216)
T ss_dssp             CGGGHHHHHHHH----------H--HH----------------TTSCEEEEECCCTTC----------CHHHHHHHHTTS
T ss_pred             ccccchhhhhhh----------c--cc----------------CCCcEEEEeCCCCcC----------CHHHHHHHHhcc
Confidence            433222111100          0  00                222333344332211          125999999999


Q ss_pred             cceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          454 GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       454 G~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      |.|..|.|+.+..++..   +|+|||+|.+.++|.+|+..|||..|+|+.|.|.|+....
T Consensus       150 G~v~~v~i~~~~~~g~~---~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          150 GKIKSATLARDPTTGKH---KGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             SCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             CCeeEEEEEecCCCCCc---CceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            99999999998766554   6899999999999999999999999999999999987654

>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=7.3e-31  Score=231.73  Aligned_cols=165  Identities=20%  Similarity=0.443  Sum_probs=139.0

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~  252 (521)
                      ++++|||+|||+++|+++|+++|++||.|..+.+      +.+..++.++|||||+|.+.++|..|+. ++..+.|+.|.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~   74 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKI------MKDPATGRSRGFGFLSFEKPSSVDEVVK-TQHILDGKVID   74 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEEC------CCCTTTSSCCSCEEEEESSTHHHHHHHH-SCCEETTEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEE------EECCCCCCccceEEEEEccHHHHHHHHh-cccccCCeEcc
Confidence            4679999999999999999999999997432111      1111234568999999999999999996 46789999999


Q ss_pred             EeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 009954          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (521)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~  332 (521)
                      |.++......                             ....+|||+|||..+++++|.++|++||.|..|.|+.++.+
T Consensus        75 v~~~~~~~~~-----------------------------~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~  125 (167)
T 2cjk_A           75 PKRAIPRDEQ-----------------------------DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDT  125 (167)
T ss_dssp             CEECCCHHHH-----------------------------HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSS
T ss_pred             cccccchhhc-----------------------------cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCC
Confidence            8875432110                             12358999999999999999999999999999999999889


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      |.++|||||+|.+.++|.+|++ |+|..|+|+.|.|.|+.++
T Consensus       126 g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          126 GQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             STTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             CccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            9999999999999999999998 8999999999999999763

>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=5.8e-29  Score=225.59  Aligned_cols=175  Identities=19%  Similarity=0.299  Sum_probs=138.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||+. ++..|.|+.|.|.++
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            3446899999999999999999999999999999999998999999999999999999999985 999999999999999


Q ss_pred             cCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhc
Q 009954          372 TASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  451 (521)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~  451 (521)
                      .........                                . ...+...+.+.|+....          ++++|+++|+
T Consensus        90 ~~~~~~~~~--------------------------------~-~~~~~~~l~V~nLp~~~----------t~~~l~~~F~  126 (196)
T 1l3k_A           90 VSREDSQRP--------------------------------G-AHLTVKKIFVGGIKEDT----------EEHHLRDYFE  126 (196)
T ss_dssp             CC--------------------------------------------CCSEEEEECCTTTC----------CHHHHHHHHT
T ss_pred             cCccccccc--------------------------------c-cCCCcceEEEeCCCCCC----------CHHHHHHHHh
Confidence            653211100                                0 00222333334332111          1259999999


Q ss_pred             cccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCc
Q 009954          452 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  514 (521)
Q Consensus       452 ~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~  514 (521)
                      .||.|..|.|+.+..++..   +|+|||+|.+.++|.+||.. +|..|+|+.|.|.|+....-
T Consensus       127 ~~G~i~~v~i~~~~~~g~~---~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~  185 (196)
T 1l3k_A          127 QYGKIEVIEIMTDRGSGKK---RGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQE  185 (196)
T ss_dssp             TTSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC----
T ss_pred             cCCCeEEEEEeecCCCCCc---cceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhH
Confidence            9999999999998766553   68999999999999999986 89999999999999876543

>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=6.5e-29  Score=220.94  Aligned_cols=165  Identities=21%  Similarity=0.325  Sum_probs=135.0

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec--CCCCeEEEEecCHHHHHHHH-HccCceec--
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--HEKKFAFVEMRTVEEASNAM-ALDGIIFE--  247 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~--~~~g~afV~f~~~~~a~~A~-~l~g~~~~--  247 (521)
                      +.++|||+|||+++|+++|+++|.+||.|..+.      .+.+...+  .++|||||+|.+.++|.+|+ .|++..+.  
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            357899999999999999999999999843211      01111111  56799999999999999999 69998876  


Q ss_pred             -CceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 009954          248 -GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (521)
Q Consensus       248 -g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i  326 (521)
                       ++.+.+.++......                            ....++|||+|||..+++++|+++|++||.|..|.+
T Consensus        76 ~~~~~~~~~~~~~~~~----------------------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~  127 (175)
T 3nmr_A           76 MHHPIQMKPADSEKNN----------------------------AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRI  127 (175)
T ss_dssp             CSSCCEEEECGGGCCS----------------------------CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEE
T ss_pred             CccceEEccccccccc----------------------------cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEE
Confidence             577777764322110                            122368999999999999999999999999999999


Q ss_pred             eecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC---CeEEEEEEcc
Q 009954          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG---DKTLTVRRAT  372 (521)
Q Consensus       327 ~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~---g~~l~v~~~~  372 (521)
                      +.++ +|.++|||||+|.+.++|.+|++.|||..+.   |++|.|.||.
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   4999999983

>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=1.7e-28  Score=222.50  Aligned_cols=184  Identities=15%  Similarity=0.126  Sum_probs=137.9

Q ss_pred             CCeEEEeCCC-ccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          174 ARRVYVGGLP-PLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       174 ~~~l~v~nlp-~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~-~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      .++|||+||| ..+|+++|+++|++||.            |.++.+.. .+|||||+|.+.++|..|+ .|||..+.|++
T Consensus         4 ~~~l~V~nL~~~~~~~~~L~~~F~~~G~------------v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~   71 (205)
T 3tyt_A            4 SPVLMVYGLDQSKMNCDRVFNVFCLYGN------------VEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQK   71 (205)
T ss_dssp             CSEEEEECCCTTTCCHHHHHHHHTTTSC------------EEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhcCC------------eEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCce
Confidence            5789999999 79999999999999998            66666654 5799999999999999999 69999999999


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCC-cccccc---cCC----CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCe-
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPN-LNLAAV---GLA----SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL-  321 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~-~~~~~~---~~~----~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i-  321 (521)
                      |.|.++................... ......   ...    ........+..+|||+|||..+++++|+++|++||.| 
T Consensus        72 l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~  151 (205)
T 3tyt_A           72 MNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKR  151 (205)
T ss_dssp             CEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCC
T ss_pred             EEEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcc
Confidence            9999876433211000000000000 000000   000    0001112345789999999999999999999999999 


Q ss_pred             -eEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCe----EEEEEEc
Q 009954          322 -HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK----TLTVRRA  371 (521)
Q Consensus       322 -~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~----~l~v~~~  371 (521)
                       ..|+++.+.  +.++|+|||+|.+.++|.+||..|||..|.|.    ++.|.++
T Consensus       152 ~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          152 PTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             eEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence             899998874  56679999999999999999999999999886    5666654

>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=7.3e-29  Score=218.82  Aligned_cols=163  Identities=21%  Similarity=0.347  Sum_probs=138.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      ++|||+|||.++++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.  +..+.|+.|.|.++.+.
T Consensus         4 ~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~~~   81 (167)
T 2cjk_A            4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAIPR   81 (167)
T ss_dssp             GEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECCCH
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccccch
Confidence            6899999999999999999999999999999999988999999999999999999999984  68999999999998641


Q ss_pred             CCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhcccc
Q 009954          375 GQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYG  454 (521)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG  454 (521)
                          ...                ..                .....|-+|+..++.             ++|+++|+.||
T Consensus        82 ----~~~----------------~~----------------~~~l~V~nlp~~~t~-------------~~l~~~F~~~G  112 (167)
T 2cjk_A           82 ----DEQ----------------DK----------------TGKIFVGGIGPDVRP-------------KEFEEFFSQWG  112 (167)
T ss_dssp             ----HHH----------------HH----------------CEEEEEEEECTTCCH-------------HHHHHHHHTTS
T ss_pred             ----hhc----------------cC----------------CCeEEECCCCCCCCH-------------HHHHHHHHhCc
Confidence                000                00                023334444444433             49999999999


Q ss_pred             ceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          455 TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       455 ~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      .|..|.|+.+..++..   +|+|||+|.+.++|.+|++ |+|..|+|+.|+|.|+.+.
T Consensus       113 ~i~~~~i~~~~~~g~~---~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          113 TIIDAQLMLDKDTGQS---RGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             CCSEEECCCSSSSSTT---SEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             cEEEEEEEEcCCCCcc---ceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            9999999998766654   6889999999999999998 8999999999999998764

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.95  E-value=2.1e-27  Score=220.39  Aligned_cols=185  Identities=19%  Similarity=0.205  Sum_probs=142.2

Q ss_pred             ccCCeEEEeCCCc-cCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC-CCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          172 RHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-KKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~-~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~-~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      ...++|||+|||+ .+|+++|+++|++||.            |..+.+... +|||||+|.+.++|.+|+ .|+|..|.|
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~------------i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g   99 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGD------------VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHG   99 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTC------------EEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSS
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCC------------eEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            4568999999999 9999999999999997            667766555 699999999999999999 599999999


Q ss_pred             ceEEEeCCCCCCccccccCCCCCCCC------CcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcC-Ce
Q 009954          249 VAVRVRRPTDYNPTLAAALGPGQPSP------NLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-TL  321 (521)
Q Consensus       249 ~~i~v~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G-~i  321 (521)
                      +.|.|.++..................      ..................+.++|||+|||..+++++|+++|++|| .|
T Consensus       100 ~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i  179 (229)
T 2adc_A          100 KPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVV  179 (229)
T ss_dssp             SBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCE
T ss_pred             eEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCe
Confidence            99999987654322111000000000      000000000000011233467899999999999999999999999 99


Q ss_pred             eEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC-CeEEEEEEccC
Q 009954          322 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRATA  373 (521)
Q Consensus       322 ~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~~~~  373 (521)
                      ..|.|+..     .+|||||+|.+.++|.+|++.|+|..|. |+.|.|.|+.+
T Consensus       180 ~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          180 KGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             EEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             eEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            99999653     2689999999999999999999999999 99999999975

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.95  E-value=6.5e-28  Score=228.40  Aligned_cols=155  Identities=23%  Similarity=0.366  Sum_probs=141.1

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....++|||+|||+++|+++|+++|..||.            |..+.+..++|||||+|.+.++|..|+ .|+|..|.|+
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            345678999999999999999999999987            667777889999999999999999999 5999999999


Q ss_pred             eEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec
Q 009954          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (521)
Q Consensus       250 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~  329 (521)
                      .|.|.++..                                   ..+|||+|||..+++++|.++|+.||.|..|.|+.+
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            999997531                                   258999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEEcChHHHHHHHHHHc-CCeeC---CeEEEEEEccC
Q 009954          330 RDTGNSKGYGFCVYQDPAVTDIACAALN-GLKMG---DKTLTVRRATA  373 (521)
Q Consensus       330 ~~~g~~~g~afV~f~~~~~A~~Al~~l~-g~~~~---g~~l~v~~~~~  373 (521)
                       .+|.++|||||+|.+.++|.+|+..|+ |..+.   +++|.|.++..
T Consensus       132 -~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~  178 (261)
T 3sde_A          132 -DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQ  178 (261)
T ss_dssp             -TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCC
T ss_pred             -CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccc
Confidence             599999999999999999999999995 55554   99999999976

>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=99.95  E-value=8.5e-28  Score=213.69  Aligned_cols=164  Identities=20%  Similarity=0.306  Sum_probs=134.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCC--CcceEEEEEEcChHHHHHHHHHHcCCeeC---CeEEEEE
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG--NSKGYGFCVYQDPAVTDIACAALNGLKMG---DKTLTVR  369 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g--~~~g~afV~f~~~~~A~~Al~~l~g~~~~---g~~l~v~  369 (521)
                      ++|||+|||..+++++|+++|++||.|..|.|+.++.+|  .++|||||+|.+.++|.+|++.|+|..+.   ++.+.+.
T Consensus         4 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~   83 (175)
T 3nmr_A            4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMK   83 (175)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEc
Confidence            689999999999999999999999999999999998776  89999999999999999999999998775   6888888


Q ss_pred             EccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHh
Q 009954          370 RATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREE  449 (521)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~  449 (521)
                      ++.......                                      .....+.+.++....          ++++|+++
T Consensus        84 ~~~~~~~~~--------------------------------------~~~~~l~v~nl~~~~----------t~~~l~~~  115 (175)
T 3nmr_A           84 PADSEKNNA--------------------------------------VEDRKLFIGMISKKC----------TENDIRVM  115 (175)
T ss_dssp             ECGGGCCSC--------------------------------------GGGSEEEEESCCTTC----------CHHHHHHH
T ss_pred             ccccccccc--------------------------------------CCCCeEEEcCCCCcC----------CHHHHHHH
Confidence            876422110                                      122233333332111          12599999


Q ss_pred             hccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeC---CcEEEEEEcC
Q 009954          450 CGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG---GNTVNAFYYP  510 (521)
Q Consensus       450 f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~---gr~l~v~~~~  510 (521)
                      |++||.|..|.|+++. ++.   .+|+|||+|.+.++|.+|++.|||..+.   |++|+|.|++
T Consensus       116 F~~~G~i~~v~~~~~~-~g~---~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          116 FSSFGQIEECRILRGP-DGL---SRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HGGGSCEEEEEEEECT-TSC---EEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             HHhCCCEEEEEEEECC-CCC---EEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            9999999999999885 443   3688999999999999999999998776   4999999975

>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=3.2e-27  Score=226.79  Aligned_cols=187  Identities=22%  Similarity=0.364  Sum_probs=140.9

Q ss_pred             hccCCeEEEeCCCccCcHHHHH----HHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII  245 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~----~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~  245 (521)
                      ....++|||+|||..+|+++|+    ++|..||.|..         |.....+.++|||||+|.+.++|.+|+ .|||..
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            3457899999999999999976    89999998432         222235668899999999999999999 799999


Q ss_pred             ecCceEEEeCCCCCCccccccCCCC-------------------------------------------------------
Q 009954          246 FEGVAVRVRRPTDYNPTLAAALGPG-------------------------------------------------------  270 (521)
Q Consensus       246 ~~g~~i~v~~~~~~~~~~~~~~~~~-------------------------------------------------------  270 (521)
                      |.|+.|+|.++...........+..                                                       
T Consensus        77 ~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (282)
T 3pgw_A           77 FYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHH  156 (282)
T ss_pred             eCCcEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCccccccccccc
Confidence            9999999998765442100000000                                                       


Q ss_pred             -------CCCCCcccccccCCCC---------------------CCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCee
Q 009954          271 -------QPSPNLNLAAVGLASG---------------------AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLH  322 (521)
Q Consensus       271 -------~~~~~~~~~~~~~~~~---------------------~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~  322 (521)
                             .+.+.. ....+..+.                     ........++|||+|||..+++++|+++|++||.|.
T Consensus       157 ~~g~~~~~~~p~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~  235 (282)
T 3pgw_A          157 MPGQPPYMPPPGM-IPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFK  235 (282)
T ss_pred             CCCCCCCCCCCCC-CCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeE
Confidence                   000000 000000000                     001223457899999999999999999999999999


Q ss_pred             EEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC-CeEEEEEEcc
Q 009954          323 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRAT  372 (521)
Q Consensus       323 ~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~~~  372 (521)
                      .|.|+.+.     +|||||+|.+.++|.+|++.|||..|. |+.|+|.|++
T Consensus       236 ~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          236 EVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            99998763     589999999999999999999999999 9999999985

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

Probab=99.95  E-value=2.1e-27  Score=229.36  Aligned_cols=172  Identities=15%  Similarity=0.320  Sum_probs=139.1

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHH-HhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVM-TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G-~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ..++|||+|||+.+|+++|+++|..|| .|..+.+      +.+ ..+.++|||||+|.+.++|.+|+ .|+|..+.|+.
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------PSL-RFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYT  188 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEEC------C--------CCEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEE------EeC-CCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            578999999999999999999999999 7543211      111 12557899999999999999999 59999999999


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeec
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKD  329 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~-~te~~l~~~F~~~G~i~~v~i~~~  329 (521)
                      |.|.++.........                      .......++|||+|||.. +++++|+++|++||.|..|.|+.+
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            999986543321110                      011234578999999999 999999999999999999999998


Q ss_pred             CC-CCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          330 RD-TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       330 ~~-~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      .. ||.++|||||+|.+.++|.+|+ .|||..|+|+.|.|.|+.++
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            75 5999999999999999999999 99999999999999999763

>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=1.4e-27  Score=229.64  Aligned_cols=172  Identities=18%  Similarity=0.179  Sum_probs=144.2

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||+.+|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|..|+ .|+|..+.|+.
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            3467899999999999999999999999843210      0111123446789999999999999999 79999999999


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCC-CHHHHHHHHHhcCCeeEEEEeec
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYF-TETQIKELLESFGTLHGFDLVKD  329 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~-te~~l~~~F~~~G~i~~v~i~~~  329 (521)
                      |.|.++......                          ......++|||+|||..+ ++++|+++|+.||.|..|.|+.+
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            999986532211                          011334689999999995 99999999999999999999998


Q ss_pred             CCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCC
Q 009954          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQ  376 (521)
Q Consensus       330 ~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~  376 (521)
                      . +|.++|+|||+|.+.++|.+|+..|||..|+|+.|.|.|+.++..
T Consensus       221 ~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          221 Q-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             S-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             C-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            6 899999999999999999999999999999999999999987544

>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=4.2e-27  Score=208.59  Aligned_cols=158  Identities=19%  Similarity=0.325  Sum_probs=130.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESF----G-------TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~----G-------~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  362 (521)
                      .++|||+|||..+++++|+++|++|    |       .|..+.+..      ++|||||+|.+.++|.+|+ .|+|..|.
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~~   76 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEec
Confidence            3689999999999999999999999    6       677776643      4799999999999999999 79999999


Q ss_pred             CeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHH
Q 009954          363 DKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEI  442 (521)
Q Consensus       363 g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~  442 (521)
                      |+.|.|.++........                                    .....|-+|+..++.            
T Consensus        77 g~~i~v~~~~~~~~~~~------------------------------------~~~l~v~nlp~~~t~------------  108 (172)
T 2g4b_A           77 GQSLKIRRPHDYQPLPG------------------------------------AHKLFIGGLPNYLND------------  108 (172)
T ss_dssp             TEECEEECCSSCCCCTT------------------------------------TTCEEEECCCTTCCH------------
T ss_pred             CceeeecCCcccCCCCC------------------------------------CCEEEEEcCCCcCCH------------
Confidence            99999999865321100                                    122333333333332            


Q ss_pred             HHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcC
Q 009954          443 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  510 (521)
Q Consensus       443 ~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~  510 (521)
                       ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|.+|++.|||..|+|++|.|.|++
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             599999999999999999998766553   6889999999999999999999999999999999974

>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=2.8e-27  Score=214.82  Aligned_cols=182  Identities=19%  Similarity=0.212  Sum_probs=139.8

Q ss_pred             CCeEEEeCCCc-cCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC-CCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          174 ARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-KKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       174 ~~~l~v~nlp~-~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~-~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      .++|||+|||+ .+|+++|+++|..||.            |..+.+... +|||||+|.+.++|.+|+ .|+|..+.|+.
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            57899999999 9999999999999987            555555444 699999999999999999 59999999999


Q ss_pred             EEEeCCCCCCccccccCCCCCCCCCccccc-------ccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcC-Cee
Q 009954          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAA-------VGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-TLH  322 (521)
Q Consensus       251 i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G-~i~  322 (521)
                      |.|.++................ .......       ............+.++|||+|||..+++++|+++|++|| .|.
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            9999876543221110000000 0000000       000000111223467899999999999999999999999 999


Q ss_pred             EEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC-CeEEEEEEccC
Q 009954          323 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRATA  373 (521)
Q Consensus       323 ~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~v~~~~~  373 (521)
                      .|.|+.+.     +|+|||+|.+.++|.+|+..|||..|+ |+.|.|.|+.+
T Consensus       150 ~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          150 GFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             EEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             EEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence            99997642     789999999999999999999999999 99999999975

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.95  E-value=2.4e-26  Score=220.74  Aligned_cols=198  Identities=15%  Similarity=0.235  Sum_probs=138.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~----~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      ...++|||+|||..+++++|+    ++|++||.|..|.|.+   +|.++|||||+|.+.++|.+||+.|||..|.|+.|.
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            445799999999999999966    9999999999999876   688999999999999999999999999999999999


Q ss_pred             EEEccCCCCCchHHHHH-----------HHHHHHHHHHHHHhhhccCC----CCCCC-----------------------
Q 009954          368 VRRATASGQSKTEQESI-----------LAQAQQHIAIQKMALQTSGM----NTLGG-----------------------  409 (521)
Q Consensus       368 v~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~----~~~~~-----------------------  409 (521)
                      |.|+.............           ....................    ..++.                       
T Consensus        84 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  163 (282)
T 3pgw_A           84 IQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPY  163 (282)
T ss_pred             EEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCC
Confidence            99997633211100000           00000000000000000000    00000                       


Q ss_pred             ------------CC----------------------CCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccc
Q 009954          410 ------------GM----------------------SLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGT  455 (521)
Q Consensus       410 ------------~~----------------------~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~  455 (521)
                                  ..                      ......+..++.+.|+..          ..++++|+++|+.||.
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                        00                      000111234444444422          2234699999999999


Q ss_pred             eeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeC-CcEEEEEEcC
Q 009954          456 LVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG-GNTVNAFYYP  510 (521)
Q Consensus       456 I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~-gr~l~v~~~~  510 (521)
                      |..|.|+.+.        .|+|||+|.+.++|.+||+.|||..|+ |+.|+|.|+.
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            9999998754        378899999999999999999999999 9999999974

>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=99.94  E-value=4.3e-27  Score=209.14  Aligned_cols=164  Identities=18%  Similarity=0.290  Sum_probs=130.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|+.||.|..+ ++.+..+|.++|||||+|.+.++|.+||+ |+|..|.|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecC
Confidence            445789999999999999999999999987663 33444588899999999999999999995 9999999999999999


Q ss_pred             cCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhc
Q 009954          372 TASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  451 (521)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~  451 (521)
                      .......                                     ..+...+.+.|+....          ++++|+++|+
T Consensus        89 ~~~~~~~-------------------------------------~~~~~~l~v~nlp~~~----------t~~~l~~~F~  121 (175)
T 1fje_B           89 KGRDSKK-------------------------------------VRAARTLLAKNLSFNI----------TEDELKEVFE  121 (175)
T ss_dssp             CCSSCST-------------------------------------TGGGGEEEEESCCSSC----------CHHHHHHHCT
T ss_pred             CCccccc-------------------------------------cccCCEEEEeCCCCCC----------CHHHHHHHHH
Confidence            7632210                                     0223334444432211          1259999999


Q ss_pred             cccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          452 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       452 ~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      .||.|..+     ..++.   .+|+|||+|.+.++|.+|+..|||..|+|+.|+|.|+.+.
T Consensus       122 ~~g~v~~~-----~~~~~---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          122 DALEIRLV-----SQDGK---SKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             TCSEEEEE-----CSSSS---CCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             hcCeEEEe-----cCCCC---CceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            99999877     22333   3588899999999999999999999999999999998764

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.94  E-value=3.8e-26  Score=207.35  Aligned_cols=181  Identities=18%  Similarity=0.265  Sum_probs=135.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESF----G-------TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~----G-------~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  362 (521)
                      .++|||+|||..+++++|+++|++|    |       .|..+.+      +.++|||||+|.+.++|.+|| .|||..|.
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            4799999999999999999999999    4       5555554      445899999999999999999 79999999


Q ss_pred             CeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHH
Q 009954          363 DKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEI  442 (521)
Q Consensus       363 g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~  442 (521)
                      |+.|.|.++.........                  ........++. .+.....+...+.+.++....          +
T Consensus        77 g~~i~v~~~~~~~~~~~~------------------~~~~~~~~~~~-~~~~~~~~~~~l~v~nl~~~~----------~  127 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGM------------------SENPSVYVPGV-VSTVVPDSAHKLFIGGLPNYL----------N  127 (198)
T ss_dssp             TEEEEEECCCCCCCCCCS------------------SSCSSCCCTTS-SCCCSSCCCCEEEEECCCTTC----------C
T ss_pred             CceEEEeCCCCCCCCCCC------------------cCCCcCCCCCC-ccCCCCCCCCEEEEeCCCCCC----------C
Confidence            999999998764322111                  00000011111 111112333344444443211          1


Q ss_pred             HHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          443 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       443 ~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      +++|+++|++||.|..|.|+.+..++..   .|+|||+|.+.++|.+|++.|||..|+|+.|+|.|+....
T Consensus       128 ~~~l~~~f~~~G~v~~~~~~~~~~~~~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          128 DDQVKELLTSFGPLKAFNLVKDSATGLS---KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             HHHHHHHHHTBSCEEEEEEEECTTTCSE---EEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             HHHHHHHHHHcCCccEEEEeecCCCCCc---ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            2599999999999999999998756543   6899999999999999999999999999999999987653

>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=4.6e-26  Score=206.50  Aligned_cols=181  Identities=13%  Similarity=0.118  Sum_probs=125.9

Q ss_pred             CCeEEEcCCC-CCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          294 PDRVFVGGLP-YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       294 ~~~l~v~nLp-~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      .++|||+||| ..+++++|+++|++||.|.+|+|+.+     .+|||||+|.+.++|++||+.|||..|.|+.|.|.|+.
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            3689999999 79999999999999999999999875     37999999999999999999999999999999999997


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCC------CCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHH
Q 009954          373 ASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG------GGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDM  446 (521)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl  446 (521)
                      .....+.........     .+..........+...      ......+.....|.+|+..++.             ++|
T Consensus        79 ~~~~~p~~~~~~~~~-----~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~-------------~~L  140 (205)
T 3tyt_A           79 QPAIMPGQSYGLEDG-----SCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTE-------------ENF  140 (205)
T ss_dssp             CSCCCCCSCCBCTTS-----CBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCH-------------HHH
T ss_pred             CCccCCCcccccccC-----CccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCH-------------HHH
Confidence            532110000000000     0000000000000000      0000001122333334433333             599


Q ss_pred             HHhhccccce--eEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCc
Q 009954          447 REECGKYGTL--VNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGN  502 (521)
Q Consensus       447 ~~~f~~fG~I--~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr  502 (521)
                      +++|++||.|  ..|.|+.+.  +.   ..|+|||+|.+.++|.+||..|||..|+|.
T Consensus       141 ~~~F~~~G~v~~~~v~~~~~~--~~---~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~  193 (205)
T 3tyt_A          141 FEICDELGVKRPTSVKVFSGK--SE---RSSSGLLEWDSKSDALETLGFLNHYQMKNP  193 (205)
T ss_dssp             HHHHHHHTCCCCSEEEECSCC--SS---SSEEEEEECSSHHHHHHHHHHHTTCEECCS
T ss_pred             HHHHHhcCCcceEEEEEEcCC--CC---CceEEEEEeCCHHHHHHHHHHhCCCCccCC
Confidence            9999999999  899998875  22   238889999999999999999999999998

>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=6e-26  Score=210.59  Aligned_cols=193  Identities=12%  Similarity=0.116  Sum_probs=137.2

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          292 EGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       292 ~~~~~l~v~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ...++|||+|||. .+++++|+++|++||.|..|.|+.++     +|||||+|.+.++|.+|++.|+|..|.|+.|.|.|
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            4457999999999 99999999999999999999999874     78999999999999999999999999999999999


Q ss_pred             ccCCCCCchHHHHHHHHHHHHHHHHHHhhh-ccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHh
Q 009954          371 ATASGQSKTEQESILAQAQQHIAIQKMALQ-TSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREE  449 (521)
Q Consensus       371 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~  449 (521)
                      +.......+........     ........ ......++.........+..++.+.|+....          ++++|+++
T Consensus       107 a~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~----------t~~~l~~~  171 (229)
T 2adc_A          107 SKHQNVQLPREGQEDQG-----LTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSV----------SEEDLKVL  171 (229)
T ss_dssp             CSCCCCCCCCSSSSTTT-----TEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTC----------CHHHHHHH
T ss_pred             ecCccccCccccccccc-----cccccccCcccccCCccccccccCCCCCCEEEEeCCCccC----------CHHHHHHH
Confidence            97632111100000000     00000000 0000000000000111233444455443221          12699999


Q ss_pred             hcccc-ceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeC-CcEEEEEEcCCC
Q 009954          450 CGKYG-TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG-GNTVNAFYYPED  512 (521)
Q Consensus       450 f~~fG-~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~-gr~l~v~~~~~~  512 (521)
                      |+.|| .|..|.|....        .|+|||+|.+.++|.+|+..|||..|+ |+.|+|.|+...
T Consensus       172 f~~~G~~i~~v~i~~~~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          172 FSSNGGVVKGFKFFQKD--------RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             HHTTSCCEEEEEECSSS--------TTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             HHHcCCCeeEEEEEECC--------CcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            99999 99999996632        378899999999999999999999999 999999998754

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

Probab=99.93  E-value=1.3e-25  Score=203.76  Aligned_cols=186  Identities=13%  Similarity=0.123  Sum_probs=136.4

Q ss_pred             CeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ++|||+|||. .+++++|+++|++||.|..|.|+.++     +|||||+|.+.++|.+|+..|+|..|.|+.|.|.|+..
T Consensus         4 ~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~   78 (198)
T 1qm9_A            4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   78 (198)
T ss_dssp             CEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCC
T ss_pred             cEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecC
Confidence            6899999999 99999999999999999999998874     78999999999999999999999999999999999976


Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHHhhhcc-----CCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHH
Q 009954          374 SGQSKTEQESILAQAQQHIAIQKMALQTS-----GMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMRE  448 (521)
Q Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~  448 (521)
                      .....+......         ........     ....++.........+..++.+.|+....          ++++|++
T Consensus        79 ~~~~~~~~~~~~---------~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~----------~~~~l~~  139 (198)
T 1qm9_A           79 QNVQLPREGQED---------QGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSV----------SEEDLKV  139 (198)
T ss_dssp             CSCCCSSSSSSS---------SSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTC----------CHHHHHH
T ss_pred             CCcCCCCcCCcc---------ccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCC----------CHHHHHH
Confidence            322111000000         00000000     00001110011111234455555543221          2269999


Q ss_pred             hhcccc-ceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeC-CcEEEEEEcCCC
Q 009954          449 ECGKYG-TLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFG-GNTVNAFYYPED  512 (521)
Q Consensus       449 ~f~~fG-~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~-gr~l~v~~~~~~  512 (521)
                      +|+.|| .|..|.|.++.        .|+|||+|.+.++|.+|+..|||..|+ |+.|+|.|+...
T Consensus       140 ~f~~~G~~v~~v~i~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          140 LFSSNGGVVKGFKFFQKD--------RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             HHHHTTSCCCEEEESSTT--------SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             HHHHcCCCceEEEEEeCC--------CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            999999 99999997643        378899999999999999999999999 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=4.4e-25  Score=208.93  Aligned_cols=157  Identities=25%  Similarity=0.359  Sum_probs=131.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||.++|+++|.++|++||.|..|.|.++      +|||||+|.+.++|.+|+..|+|..|.|+.|.|.|+
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            34468999999999999999999999999999998654      789999999999999999999999999999999999


Q ss_pred             cCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhc
Q 009954          372 TASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECG  451 (521)
Q Consensus       372 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~  451 (521)
                      .+                                          .....|-+|+..++.             ++|+++|+
T Consensus        94 ~~------------------------------------------~~~l~v~nl~~~~t~-------------~~l~~~F~  118 (261)
T 3sde_A           94 TH------------------------------------------GAALTVKNLSPVVSN-------------ELLEQAFS  118 (261)
T ss_dssp             CC------------------------------------------SSEEEEESCCTTCCH-------------HHHHHHHG
T ss_pred             cc------------------------------------------CCcccccCCCCCCCH-------------HHHHHHHH
Confidence            53                                          022222233333222             59999999


Q ss_pred             cccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHH-hCCeeC---CcEEEEEEcCCCC
Q 009954          452 KYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL-SGRKFG---GNTVNAFYYPEDK  513 (521)
Q Consensus       452 ~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~l-ng~~~~---gr~l~v~~~~~~~  513 (521)
                      .||.|..|.|+.+. +|..   .|+|||+|.+.++|.+||..| +|..+.   |++|.|.++...+
T Consensus       119 ~~G~i~~v~i~~~~-~g~~---~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          119 QFGPVEKAVVVVDD-RGRA---TGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             GGSCEEEEEEEEET-TSCE---EEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             hcCCeEEEEeeeCC-CCCc---CcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            99999999999984 5543   688999999999999999999 566665   9999999987653

>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=7e-22  Score=172.05  Aligned_cols=142  Identities=18%  Similarity=0.171  Sum_probs=107.1

Q ss_pred             ecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCe
Q 009954          218 INHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDR  296 (521)
Q Consensus       218 ~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  296 (521)
                      ....+|||||+|.+.++|++|+ .+++.......+.+..........   ..             .............++
T Consensus         9 ~~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~---~~-------------~~~~~~~~~~~~~~~   72 (158)
T 2kn4_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVT---EG-------------SHHHHHHMDVEGMTS   72 (158)
T ss_dssp             CSSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEE---CC-------------CCCSSCCCCCCBCCE
T ss_pred             CccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCcccccccc---cc-------------ccccccccCCCCCCE
Confidence            3457899999999999999999 566543322222222111000000   00             000001112234578


Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCC
Q 009954          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASG  375 (521)
Q Consensus       297 l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (521)
                      |||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.|+.+..
T Consensus        73 l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             EEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            9999999999999999999999999999999998899999999999999999999999999999999999999998743

>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=99.87  E-value=4.7e-22  Score=158.92  Aligned_cols=102  Identities=42%  Similarity=0.821  Sum_probs=95.0

Q ss_pred             CcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhC
Q 009954          417 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  496 (521)
Q Consensus       417 ~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng  496 (521)
                      .+++|++|.|+++++++.++.+|++|++||+++|++||+|.+|.|+++..++. ..++|+|||+|.+.++|.+|++.|||
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            78999999999999999999999999999999999999999999999874322 24578999999999999999999999


Q ss_pred             CeeCCcEEEEEEcCCCCcccccC
Q 009954          497 RKFGGNTVNAFYYPEDKYFNKDY  519 (521)
Q Consensus       497 ~~~~gr~l~v~~~~~~~~~~~~~  519 (521)
                      +.|+||+|+|.|+++++|..++|
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=99.84  E-value=1.8e-20  Score=148.55  Aligned_cols=80  Identities=31%  Similarity=0.542  Sum_probs=77.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||.++|+++|+++|++||.|..|+|++++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.||+|
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            36899999999999999999999999999999999999999999999999999999999999999999999999999965

>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=1.8e-20  Score=161.34  Aligned_cols=136  Identities=15%  Similarity=0.159  Sum_probs=109.8

Q ss_pred             CCCCeEEEEecCHHHHHHHH-Hc-cCceecCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeE
Q 009954          220 HEKKFAFVEMRTVEEASNAM-AL-DGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRV  297 (521)
Q Consensus       220 ~~~g~afV~f~~~~~a~~A~-~l-~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  297 (521)
                      .-+|+++|+|.+.++|++|+ ++ ||..+.| .+.+.++.............             ............++|
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 99998765422111000000             000111223455799


Q ss_pred             EEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       298 ~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      ||+|||..+++++|+++|++||.|..|.|+.+     ++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+.+.
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     5899999999999999999999999999999999999763

>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=3.8e-20  Score=150.51  Aligned_cols=100  Identities=30%  Similarity=0.499  Sum_probs=88.1

Q ss_pred             CcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCC-CCCCCccEEEEEecCHHHHHHHHHHHh
Q 009954          417 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNG-GETPGVGKVFLEYYDAVGCATAKNALS  495 (521)
Q Consensus       417 ~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~-~~~~g~g~afV~F~~~~~A~~Ai~~ln  495 (521)
                      .+++|++|.|+++++++.+     +|++||+++|++||+|.+|.|+++..+. ...+++|+|||+|.+.++|.+|++.||
T Consensus        18 ~ps~vl~L~Nm~~~~el~d-----dleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~Ln   92 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDD-----DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN   92 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCT-----THHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCHHHHHH-----HHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHC
Confidence            5789999999999988764     3678999999999999999999986421 112456899999999999999999999


Q ss_pred             CCeeCCcEEEEEEcCCCCcccccCCC
Q 009954          496 GRKFGGNTVNAFYYPEDKYFNKDYSA  521 (521)
Q Consensus       496 g~~~~gr~l~v~~~~~~~~~~~~~~~  521 (521)
                      |+.|+||+|.|.|+++++|.+++|+.
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            99999999999999999999999983

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

Probab=99.80  E-value=3.7e-19  Score=143.71  Aligned_cols=82  Identities=11%  Similarity=0.123  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      .+.++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++|++.|||..|.|+.|.|.++
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            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      ..
T Consensus        84 ~~   85 (110)
T 3s8s_A           84 IK   85 (110)
T ss_dssp             ST
T ss_pred             CC
Confidence            54

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.79  E-value=6e-20  Score=143.20  Aligned_cols=82  Identities=20%  Similarity=0.329  Sum_probs=76.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHc-CCeeCCeEEEEEEcc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN-GLKMGDKTLTVRRAT  372 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G-~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~-g~~~~g~~l~v~~~~  372 (521)
                      ++|||+|||+++|+++|+++|++|| .|.+|+|++++.+|.++|||||+|.+.++|++||+.|+ +..|+|+.|.|.|+.
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 79999999999999999999999999999999999874 578999999999998


Q ss_pred             CCCC
Q 009954          373 ASGQ  376 (521)
Q Consensus       373 ~~~~  376 (521)
                      ++..
T Consensus        82 ~~~~   85 (91)
T 2lxi_A           82 PKPK   85 (91)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7543

>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=99.79  E-value=1.8e-19  Score=145.34  Aligned_cols=94  Identities=26%  Similarity=0.430  Sum_probs=87.5

Q ss_pred             CCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHh
Q 009954          416 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  495 (521)
Q Consensus       416 ~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~ln  495 (521)
                      +.+++|++|.|+++.+++.++.+|++|++||+++|++||.|.+|.|+++.       ++|+|||+|.+.++|.+|++.||
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            47899999999999999999999999999999999999999999998864       24788999999999999999999


Q ss_pred             CCeeCCcEEEEEEcCCCCccc
Q 009954          496 GRKFGGNTVNAFYYPEDKYFN  516 (521)
Q Consensus       496 g~~~~gr~l~v~~~~~~~~~~  516 (521)
                      |+.|+||.|.|.|+++.+|..
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            999999999999999988864

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.79  E-value=2.7e-19  Score=139.86  Aligned_cols=81  Identities=20%  Similarity=0.322  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCC--eeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCC----eeCCeEE
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGT--LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL----KMGDKTL  366 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~--i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~----~~~g~~l  366 (521)
                      .-.+|||+|||+.+|+++|+++|++||.  |.+|+|++|+.+|.++|||||+|.+.++|.+||+.|||.    .|+|+.|
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            3468999999999999999999999995  679999999999999999999999999999999999996    5899999


Q ss_pred             EEEEccC
Q 009954          367 TVRRATA  373 (521)
Q Consensus       367 ~v~~~~~  373 (521)
                      .|.||+.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999964

>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=99.78  E-value=9.6e-19  Score=142.98  Aligned_cols=80  Identities=23%  Similarity=0.468  Sum_probs=74.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||+.+++++|+++|++||.|.+|+|+.+.  +.++|||||+|.+.++|++||+.|+|..|.|+.|.|.++..
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999984  55899999999999999999999999999999999999976


Q ss_pred             CC
Q 009954          374 SG  375 (521)
Q Consensus       374 ~~  375 (521)
                      ..
T Consensus        83 ~~   84 (115)
T 4f25_A           83 RK   84 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.78  E-value=1.4e-18  Score=134.68  Aligned_cols=81  Identities=31%  Similarity=0.460  Sum_probs=76.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+.
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            34689999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      +
T Consensus        85 ~   85 (87)
T 3bs9_A           85 R   85 (87)
T ss_dssp             -
T ss_pred             C
Confidence            5

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.78  E-value=1.8e-18  Score=132.71  Aligned_cols=80  Identities=21%  Similarity=0.408  Sum_probs=77.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      .+|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+.++
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            48999999999999999999999999999999999889999999999999999999999999999999999999999764

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=2.8e-18  Score=135.38  Aligned_cols=84  Identities=33%  Similarity=0.642  Sum_probs=79.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+
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 009954          372 TASG  375 (521)
Q Consensus       372 ~~~~  375 (521)
                      .++.
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            8743

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=3.3e-18  Score=134.95  Aligned_cols=83  Identities=20%  Similarity=0.418  Sum_probs=78.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|
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            34457899999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ccC
Q 009954          371 ATA  373 (521)
Q Consensus       371 ~~~  373 (521)
                      ++.
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            863

>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=99.77  E-value=2.3e-18  Score=132.79  Aligned_cols=81  Identities=19%  Similarity=0.336  Sum_probs=77.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+
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            34578999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             c
Q 009954          372 T  372 (521)
Q Consensus       372 ~  372 (521)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.77  E-value=3.8e-18  Score=134.74  Aligned_cols=84  Identities=32%  Similarity=0.538  Sum_probs=79.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|+|..|+|+.|.|.|+.+
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            36899999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CCCC
Q 009954          374 SGQS  377 (521)
Q Consensus       374 ~~~~  377 (521)
                      ....
T Consensus        82 ~~~~   85 (96)
T 2x1f_A           82 SDIS   85 (96)
T ss_dssp             SSGG
T ss_pred             CCCC
Confidence            5443

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.7e-18  Score=137.63  Aligned_cols=86  Identities=29%  Similarity=0.427  Sum_probs=80.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.|
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            34457899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009954          371 ATASGQ  376 (521)
Q Consensus       371 ~~~~~~  376 (521)
                      +.+...
T Consensus        92 a~~~~~   97 (103)
T 2cq0_A           92 AKPSTN   97 (103)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=2.5e-18  Score=135.35  Aligned_cols=82  Identities=23%  Similarity=0.448  Sum_probs=77.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|
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            34557899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cc
Q 009954          371 AT  372 (521)
Q Consensus       371 ~~  372 (521)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            84

>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=2.6e-18  Score=137.46  Aligned_cols=86  Identities=28%  Similarity=0.539  Sum_probs=80.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEE
Q 009954          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       290 ~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      .....++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34556799999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EccCCC
Q 009954          370 RATASG  375 (521)
Q Consensus       370 ~~~~~~  375 (521)
                      |+.+..
T Consensus        88 ~a~~~~   93 (102)
T 1x5s_A           88 QAGKSS   93 (102)
T ss_dssp             EEECCC
T ss_pred             ECCCCC
Confidence            997743

>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=2e-18  Score=138.09  Aligned_cols=86  Identities=19%  Similarity=0.310  Sum_probs=80.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|
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            34567899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009954          371 ATASGQ  376 (521)
Q Consensus       371 ~~~~~~  376 (521)
                      +.+...
T Consensus        89 a~~~~~   94 (102)
T 2cqb_A           89 AKPMRI   94 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987443

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.76  E-value=7.2e-18  Score=138.07  Aligned_cols=85  Identities=31%  Similarity=0.448  Sum_probs=80.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++||+.|+|..|.|+.|.|.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   92 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            44578999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009954          372 TASGQ  376 (521)
Q Consensus       372 ~~~~~  376 (521)
                      .++..
T Consensus        93 ~~~~~   97 (115)
T 2dgo_A           93 TRKPP   97 (115)
T ss_dssp             SCCCC
T ss_pred             cCCCC
Confidence            87443

>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=5.2e-19  Score=137.84  Aligned_cols=81  Identities=17%  Similarity=0.335  Sum_probs=73.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFG--TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G--~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      .+|||+|||..+++++|+++|++||  .|.+|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.++.
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 009954          373 ASG  375 (521)
Q Consensus       373 ~~~  375 (521)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            643

>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=99.76  E-value=3.8e-18  Score=135.66  Aligned_cols=84  Identities=26%  Similarity=0.435  Sum_probs=79.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.++
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            34578999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009954          372 TASG  375 (521)
Q Consensus       372 ~~~~  375 (521)
                      .+..
T Consensus        86 ~~~~   89 (99)
T 1whw_A           86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCc
Confidence            8743

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.76  E-value=6e-18  Score=138.49  Aligned_cols=85  Identities=25%  Similarity=0.481  Sum_probs=80.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.|||..|.|+.|.|.|+
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            34578999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009954          372 TASGQ  376 (521)
Q Consensus       372 ~~~~~  376 (521)
                      .++..
T Consensus       103 ~~~~~  107 (115)
T 2cpz_A          103 RSKND  107 (115)
T ss_dssp             CCSCC
T ss_pred             CCCCc
Confidence            87443

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=3e-18  Score=137.37  Aligned_cols=83  Identities=20%  Similarity=0.392  Sum_probs=79.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.|||..|.|+.|.|.|+
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA   90 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEC
Confidence            45579999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      ...
T Consensus        91 ~~~   93 (103)
T 2dnm_A           91 RYG   93 (103)
T ss_dssp             SSC
T ss_pred             CcC
Confidence            863

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=3e-18  Score=136.25  Aligned_cols=84  Identities=24%  Similarity=0.396  Sum_probs=79.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCee-EEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeE----
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLH-GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT----  365 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~-~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~----  365 (521)
                      ....++|||+|||..+++++|+++|++||.|. .|.|+.++.+|.++|||||+|.+.++|++|++.|||..|.|+.    
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 009954          366 LTVRRATAS  374 (521)
Q Consensus       366 l~v~~~~~~  374 (521)
                      |+|.|+.+.
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999999763

>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=99.76  E-value=4.6e-18  Score=147.80  Aligned_cols=150  Identities=17%  Similarity=0.136  Sum_probs=101.1

Q ss_pred             EEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhcc
Q 009954          323 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTS  402 (521)
Q Consensus       323 ~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  402 (521)
                      .++|+.+.  ..++|||||+|.+.++|++|++.+++....+..+.+.........                         
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~-------------------------   54 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTV-------------------------   54 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEE-------------------------
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccc-------------------------
Confidence            46677763  468999999999999999999998864333333333222110000                         


Q ss_pred             CCCCCCCCCCCCCCCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEec
Q 009954          403 GMNTLGGGMSLFGETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYY  482 (521)
Q Consensus       403 ~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~  482 (521)
                       ..................+.+.|+....          ++++|+++|+.||.|..|.|+.+..++..   +|+|||+|.
T Consensus        55 -~~~~~~~~~~~~~~~~~~l~v~nl~~~~----------~~~~l~~~F~~~G~v~~~~i~~~~~~g~~---~g~afV~f~  120 (158)
T 2kn4_A           55 -TEGSHHHHHHMDVEGMTSLKVDNLTYRT----------SPDTLRRVFEKYGRVGDVYIPRDRYTKES---RGFAFVRFH  120 (158)
T ss_dssp             -ECCCCCSSCCCCCCBCCEEEEESCCTTC----------CHHHHHHHHHHHSCEEEEECCCCSSCTTS---CCEEEEEES
T ss_pred             -cccccccccccCCCCCCEEEEeCCCCCC----------CHHHHHHHHHhcCCeEEEEEeecCCCCcc---ceEEEEEEC
Confidence             0000000001111223333333332211          12599999999999999999998766654   688899999


Q ss_pred             CHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          483 DAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       483 ~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      +.++|+.||+.|||..|+|+.|+|.|+....
T Consensus       121 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A          121 DKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             BHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             CHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            9999999999999999999999999988754

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.75  E-value=5.8e-19  Score=148.43  Aligned_cols=122  Identities=20%  Similarity=0.308  Sum_probs=80.1

Q ss_pred             eEEEEecCHHHHHHHH-HccCceecCceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCC
Q 009954          224 FAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGL  302 (521)
Q Consensus       224 ~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL  302 (521)
                      ++|++|.+...+..|| .++|....|+.- +.+.              .+               .......++|||+||
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~--------------~~---------------~~~~~~~~~l~V~nL   55 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYG--------------RP---------------PPDVEGMTSLKVDNL   55 (135)
T ss_dssp             ------------------------------CCSC--------------CS---------------CSSGGGCCCEEEECC
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCC-CCcC--------------CC---------------CCCCCCCCEEEEeCC
Confidence            6788888888899999 677766554321 1110              00               011233468999999


Q ss_pred             CCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCC
Q 009954          303 PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASG  375 (521)
Q Consensus       303 p~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (521)
                      |..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++||+.|+|..|.|+.|.|.|+.+..
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            9999999999999999999999999998899999999999999999999999999999999999999998743

>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=5.5e-18  Score=134.69  Aligned_cols=84  Identities=25%  Similarity=0.535  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+ |+|..|.|+.|.|.|+
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            445789999999999999999999999999999999998899999999999999999999999 9999999999999999


Q ss_pred             cCCCC
Q 009954          372 TASGQ  376 (521)
Q Consensus       372 ~~~~~  376 (521)
                      .++..
T Consensus        87 ~~~~~   91 (99)
T 2dgs_A           87 EPRDS   91 (99)
T ss_dssp             CCCCC
T ss_pred             CCCcc
Confidence            87443

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=3.4e-18  Score=135.15  Aligned_cols=83  Identities=30%  Similarity=0.521  Sum_probs=78.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGF-DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ..++|||+|||..+++++|.++|++||.|..| .|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+
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             cCCC
Q 009954          372 TASG  375 (521)
Q Consensus       372 ~~~~  375 (521)
                      .+..
T Consensus        84 ~~~~   87 (96)
T 1x5t_A           84 FKKD   87 (96)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            8744

>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=5.3e-18  Score=136.42  Aligned_cols=85  Identities=29%  Similarity=0.444  Sum_probs=80.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|
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             ccCCC
Q 009954          371 ATASG  375 (521)
Q Consensus       371 ~~~~~  375 (521)
                      +.+..
T Consensus        92 a~~~~   96 (105)
T 1x5u_A           92 ASAHN   96 (105)
T ss_dssp             TTTTS
T ss_pred             CCCCC
Confidence            97743

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=1.4e-17  Score=132.68  Aligned_cols=83  Identities=22%  Similarity=0.534  Sum_probs=78.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+
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            345789999999999999999999999999999999997 9999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009954          372 TASG  375 (521)
Q Consensus       372 ~~~~  375 (521)
                      .+..
T Consensus        94 ~~~~   97 (100)
T 2do4_A           94 NSGP   97 (100)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7643

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=6e-18  Score=136.37  Aligned_cols=83  Identities=27%  Similarity=0.381  Sum_probs=78.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+.
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             CCC
Q 009954          373 ASG  375 (521)
Q Consensus       373 ~~~  375 (521)
                      ++.
T Consensus       102 ~~~  104 (106)
T 1p27_B          102 VRG  104 (106)
T ss_dssp             ESS
T ss_pred             CCC
Confidence            643

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=5.4e-18  Score=134.53  Aligned_cols=84  Identities=24%  Similarity=0.447  Sum_probs=77.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC---CCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~---~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++.   ++.++|||||+|.+.++|.+|++.|||..|.|+.|.|
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            3457899999999999999999999999999999999876   6689999999999999999999999999999999999


Q ss_pred             EEccCCC
Q 009954          369 RRATASG  375 (521)
Q Consensus       369 ~~~~~~~  375 (521)
                      .|+....
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9998743

>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=99.75  E-value=5.4e-18  Score=136.66  Aligned_cols=85  Identities=28%  Similarity=0.465  Sum_probs=79.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee---CCeEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM---GDKTLT  367 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~---~g~~l~  367 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..+   .|+.|.
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            34457899999999999999999999999999999999988999999999999999999999999999887   899999


Q ss_pred             EEEccCCC
Q 009954          368 VRRATASG  375 (521)
Q Consensus       368 v~~~~~~~  375 (521)
                      |.|+....
T Consensus        90 v~~a~~~~   97 (106)
T 2dgp_A           90 VKPADSES   97 (106)
T ss_dssp             EEECCCCS
T ss_pred             EEECCccc
Confidence            99997643

>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=99.75  E-value=7e-18  Score=133.03  Aligned_cols=80  Identities=31%  Similarity=0.553  Sum_probs=75.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++. |.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+
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            4457899999999999999999999999999999999974 999999999999999999999999999999999999998


Q ss_pred             c
Q 009954          372 T  372 (521)
Q Consensus       372 ~  372 (521)
                      .
T Consensus        93 ~   93 (95)
T 2ywk_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.75  E-value=8.4e-18  Score=133.61  Aligned_cols=81  Identities=25%  Similarity=0.427  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHG--------FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~--------v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  363 (521)
                      ...++|||+|||..+++++|+++|++||.|..        |.|+.++.+|.++|||||+|.+.++|++|++.|||..|.|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            44578999999999999999999999999999        9999998899999999999999999999999999999999


Q ss_pred             eEEEEEEcc
Q 009954          364 KTLTVRRAT  372 (521)
Q Consensus       364 ~~l~v~~~~  372 (521)
                      +.|.|.+|+
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999984

>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=99.75  E-value=7.5e-18  Score=147.27  Aligned_cols=141  Identities=21%  Similarity=0.203  Sum_probs=79.7

Q ss_pred             EEecCHHHHHHHH-HccCceec--CceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCC
Q 009954          227 VEMRTVEEASNAM-ALDGIIFE--GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLP  303 (521)
Q Consensus       227 V~f~~~~~a~~A~-~l~g~~~~--g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp  303 (521)
                      .+|.+.++|..|+ .+++....  |+...+.+.......   ..   .+..+.   ...............++|||+|||
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~---~~---~~~~~s---~~~~~~~~~~~~~~~~~l~V~nLp   81 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIH---SY---ERVRNE---DDDELEPGPQRSVEGWILFVTSIH   81 (165)
T ss_dssp             ----------------------------------------------------------------CCCCC-CEEEEEESCC
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCcccccccc---Cc---cccccC---CCCCCCCCCCCCCCCCEEEEeCCC
Confidence            7899999999999 67776554  555544432110000   00   000000   000000011112344689999999


Q ss_pred             CCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCCC
Q 009954          304 YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQ  376 (521)
Q Consensus       304 ~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~~  376 (521)
                      ..+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.|+.....
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            9999999999999999999999999988999999999999999999999999999999999999999987443

>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=99.75  E-value=6.8e-18  Score=136.07  Aligned_cols=84  Identities=33%  Similarity=0.693  Sum_probs=79.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|+|..|.|+.|.|.+
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            34557899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 009954          371 ATAS  374 (521)
Q Consensus       371 ~~~~  374 (521)
                      +.++
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            9763

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=8.7e-18  Score=132.57  Aligned_cols=82  Identities=18%  Similarity=0.241  Sum_probs=75.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~----~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      ...++|||+|||..+++++|+    ++|++||.|..|.|+.++.+   +|||||+|.+.++|++|++.|||..|.|+.|.
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            345689999999999999999    99999999999999998655   88999999999999999999999999999999


Q ss_pred             EEEccCCCC
Q 009954          368 VRRATASGQ  376 (521)
Q Consensus       368 v~~~~~~~~  376 (521)
                      |.++.+...
T Consensus        84 V~~a~~~~~   92 (96)
T 2dgx_A           84 VSLATGASG   92 (96)
T ss_dssp             EEECCCSSC
T ss_pred             EEEcCCCCC
Confidence            999977443

>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=1.2e-17  Score=135.81  Aligned_cols=86  Identities=28%  Similarity=0.424  Sum_probs=80.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHc------CCeeCCe
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN------GLKMGDK  364 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~------g~~~~g~  364 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.||      |..|.|+
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            3455789999999999999999999999999999999999899999999999999999999999999      9999999


Q ss_pred             EEEEEEccCCCC
Q 009954          365 TLTVRRATASGQ  376 (521)
Q Consensus       365 ~l~v~~~~~~~~  376 (521)
                      .|.|.|+.++..
T Consensus        92 ~l~v~~a~~~~~  103 (111)
T 1x4h_A           92 QLKVDLAVTRDE  103 (111)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEECCCCcc
Confidence            999999987443

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.74  E-value=1.3e-18  Score=138.36  Aligned_cols=80  Identities=16%  Similarity=0.268  Sum_probs=76.8

Q ss_pred             CCeEEEcCCCC------CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC-eEE
Q 009954          294 PDRVFVGGLPY------YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD-KTL  366 (521)
Q Consensus       294 ~~~l~v~nLp~------~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g-~~l  366 (521)
                      .++|||+|||.      .+++++|+++|++||.|..|.|+.++.||.++|||||+|.+.++|.+||+.|||..|.| +.|
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 009954          367 TVRRATA  373 (521)
Q Consensus       367 ~v~~~~~  373 (521)
                      .|.++.+
T Consensus        86 ~V~~a~~   92 (100)
T 3ns6_A           86 FLYTMKD   92 (100)
T ss_dssp             EEEESHH
T ss_pred             EEEECch
Confidence            9999964

>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=99.74  E-value=1.7e-17  Score=134.01  Aligned_cols=81  Identities=25%  Similarity=0.393  Sum_probs=77.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|.++|++||.|..|.|+.++ +|.++|||||+|.+.++|++|++.|||..|.|+.|.|.+
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 009954          371 AT  372 (521)
Q Consensus       371 ~~  372 (521)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.74  E-value=1.5e-17  Score=133.18  Aligned_cols=83  Identities=25%  Similarity=0.510  Sum_probs=77.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++|| |..|.|+.++.+|.++|||||+|.+.++|.+|| .|||..|.|+.|.|.|
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            34457899999999999999999999997 999999999989999999999999999999999 8999999999999999


Q ss_pred             ccCCC
Q 009954          371 ATASG  375 (521)
Q Consensus       371 ~~~~~  375 (521)
                      +.+..
T Consensus        90 a~~~~   94 (103)
T 2dng_A           90 AEGRK   94 (103)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            98743

>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=99.74  E-value=1.2e-17  Score=135.59  Aligned_cols=83  Identities=29%  Similarity=0.365  Sum_probs=78.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+.
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            34689999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             CCC
Q 009954          373 ASG  375 (521)
Q Consensus       373 ~~~  375 (521)
                      ++.
T Consensus       105 ~~~  107 (110)
T 1oo0_B          105 VKG  107 (110)
T ss_dssp             ESS
T ss_pred             cCC
Confidence            643

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.74  E-value=2.1e-17  Score=132.86  Aligned_cols=84  Identities=24%  Similarity=0.393  Sum_probs=78.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC---eEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD---KTLTV  368 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g---~~l~v  368 (521)
                      ...++|||+|||..+++++|.++|++||.|..|.|+.++ +|.++|||||+|.+.++|.+||+.|||..|.|   +.|.|
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            345789999999999999999999999999999999997 89999999999999999999999999999988   99999


Q ss_pred             EEccCCCC
Q 009954          369 RRATASGQ  376 (521)
Q Consensus       369 ~~~~~~~~  376 (521)
                      .|+.....
T Consensus        92 ~~a~~~~~   99 (105)
T 2dnh_A           92 KFADTDKE   99 (105)
T ss_dssp             EESCSSCC
T ss_pred             EECccCcc
Confidence            99987543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=1.5e-17  Score=134.26  Aligned_cols=84  Identities=24%  Similarity=0.457  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec-CCCCCcceEEEEEEcChHHHHHHHHHH-cCCeeCCeEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVR  369 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-~~~g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v~  369 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.+ +.+|.++|||||+|.+.++|.+||+.| ||..|.|+.|.|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~   92 (107)
T 2cph_A           13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   92 (107)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEE
Confidence            44578999999999999999999999999999999998 789999999999999999999999999 9999999999999


Q ss_pred             EccCCC
Q 009954          370 RATASG  375 (521)
Q Consensus       370 ~~~~~~  375 (521)
                      |+.+..
T Consensus        93 ~a~~~~   98 (107)
T 2cph_A           93 WADSEV   98 (107)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            998743

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.2e-17  Score=134.35  Aligned_cols=85  Identities=24%  Similarity=0.531  Sum_probs=79.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||.. +|..|.|+.|.|.+
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            34567999999999999999999999999999999999988999999999999999999999998 99999999999999


Q ss_pred             ccCCCC
Q 009954          371 ATASGQ  376 (521)
Q Consensus       371 ~~~~~~  376 (521)
                      +.++..
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            987543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.6e-17  Score=133.13  Aligned_cols=83  Identities=23%  Similarity=0.412  Sum_probs=78.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.+  +|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             SSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            45678999999999999999999999999999999998  8999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009954          372 TASGQ  376 (521)
Q Consensus       372 ~~~~~  376 (521)
                      .++..
T Consensus        91 ~~~~~   95 (103)
T 2d9p_A           91 QRKEE   95 (103)
T ss_dssp             SSCCC
T ss_pred             ccccc
Confidence            87443

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

Probab=99.73  E-value=1.9e-17  Score=129.64  Aligned_cols=82  Identities=29%  Similarity=0.581  Sum_probs=76.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.+  +|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+
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            44579999999999999999999999999999999985  8999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009954          372 TASG  375 (521)
Q Consensus       372 ~~~~  375 (521)
                      .+..
T Consensus        84 ~~~~   87 (92)
T 2dgv_A           84 RNAS   87 (92)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            7743

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.73  E-value=2.5e-17  Score=127.52  Aligned_cols=79  Identities=24%  Similarity=0.566  Sum_probs=74.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++ +++..|.|+.|.|.+|
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            455799999999999999999999999999999999998899999999999999999999996 5888999999999986

>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=99.73  E-value=4.5e-17  Score=130.43  Aligned_cols=83  Identities=25%  Similarity=0.386  Sum_probs=76.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++  +.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|
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            3456799999999999999999999999999999999984  34689999999999999999999999999999999999


Q ss_pred             ccCCC
Q 009954          371 ATASG  375 (521)
Q Consensus       371 ~~~~~  375 (521)
                      +.+..
T Consensus        90 a~~~~   94 (103)
T 2cqi_A           90 ATTPS   94 (103)
T ss_dssp             CCCTT
T ss_pred             CCCCc
Confidence            98743

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.73  E-value=5.7e-18  Score=135.03  Aligned_cols=98  Identities=29%  Similarity=0.451  Sum_probs=84.7

Q ss_pred             CCcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHh
Q 009954          416 ETLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  495 (521)
Q Consensus       416 ~~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~ln  495 (521)
                      +.+++|++|.|+++++++.+     +++++|+++|++||.|.+|.|+.+..++.  .++|+|||+|.+.++|.+|++.||
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            36888999999998876643     46789999999999999999998753321  236888999999999999999999


Q ss_pred             CCeeCCcEEEEEEcCCCCcccccCC
Q 009954          496 GRKFGGNTVNAFYYPEDKYFNKDYS  520 (521)
Q Consensus       496 g~~~~gr~l~v~~~~~~~~~~~~~~  520 (521)
                      |+.|+|+.|.|.|+++++|..++|+
T Consensus        78 G~~~~Gr~i~v~~a~~~~f~~~~~~  102 (105)
T 2pe8_A           78 GRYFGGRVVKACFYNLDKFRVLDLA  102 (105)
T ss_dssp             TCEETTEECEEEECCHHHHHTTCCC
T ss_pred             CCEECCcEEEEEEcCHHHhhhhhcc
Confidence            9999999999999999999999986

>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=99.73  E-value=1.8e-17  Score=128.93  Aligned_cols=78  Identities=17%  Similarity=0.378  Sum_probs=75.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.++.+
T Consensus         7 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            68999999999999999999999999999999999889999999999999999999999 8999999999999999975

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.73  E-value=1.4e-17  Score=143.21  Aligned_cols=81  Identities=25%  Similarity=0.430  Sum_probs=77.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFG--TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G--~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ..++|||+|||..+++++|+++|+.||  .|..|+|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.+
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  999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 009954          371 ATA  373 (521)
Q Consensus       371 ~~~  373 (521)
                      +.+
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            964

>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=99.73  E-value=8.4e-18  Score=139.99  Aligned_cols=84  Identities=20%  Similarity=0.397  Sum_probs=79.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++||+.|+|..|.|+.|.|.|
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 009954          371 ATAS  374 (521)
Q Consensus       371 ~~~~  374 (521)
                      +.++
T Consensus       123 a~~~  126 (129)
T 2kxn_B          123 SITK  126 (129)
T ss_dssp             CSSS
T ss_pred             ecCC
Confidence            9763

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.73  E-value=1.8e-17  Score=136.38  Aligned_cols=82  Identities=28%  Similarity=0.501  Sum_probs=77.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++|++.|||..|.|+.|+|.|
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            34557899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cc
Q 009954          371 AT  372 (521)
Q Consensus       371 ~~  372 (521)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            73

>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=1.4e-17  Score=136.13  Aligned_cols=82  Identities=29%  Similarity=0.571  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|.++|++||.|..|.|+.+. +|.++|||||+|.+.++|++|++.|+|..|.|+.|.|.|+
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            345799999999999999999999999999999999997 9999999999999999999999999999999999999999


Q ss_pred             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      ...
T Consensus        84 ~~~   86 (116)
T 2fy1_A           84 KKP   86 (116)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            763

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.73  E-value=1.4e-17  Score=129.22  Aligned_cols=80  Identities=24%  Similarity=0.495  Sum_probs=75.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCC-cceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN-SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~-~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      .++|||+|||..+++++|.++|++||.|..|.|+.+..++. ++|||||+|.+.++|.+|++.|||..|.|+.|.|.++.
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 89999999999999999999999999999999999996


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      +
T Consensus        84 ~   84 (88)
T 4a8x_A           84 A   84 (88)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.9e-17  Score=135.06  Aligned_cols=84  Identities=21%  Similarity=0.371  Sum_probs=79.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~--------~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  363 (521)
                      ...++|||+|||..+++++|+++|++||.|.        .|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   92 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCC
Confidence            4557999999999999999999999999999        69999998899999999999999999999999999999999


Q ss_pred             eEEEEEEccCCC
Q 009954          364 KTLTVRRATASG  375 (521)
Q Consensus       364 ~~l~v~~~~~~~  375 (521)
                      +.|.|.|+..+.
T Consensus        93 ~~l~V~~a~~~~  104 (113)
T 2cpe_A           93 SKLKVSLARKKP  104 (113)
T ss_dssp             EECEEECSSCCC
T ss_pred             CEEEEEECCCCC
Confidence            999999998743

>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=99.73  E-value=5.2e-18  Score=133.81  Aligned_cols=81  Identities=16%  Similarity=0.345  Sum_probs=75.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++||+.|||..|.|+.|.|.++
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            34578999999999999999999999999999999988889999999999999999999999999999999999999988


Q ss_pred             c
Q 009954          372 T  372 (521)
Q Consensus       372 ~  372 (521)
                      .
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.73  E-value=5.2e-17  Score=130.05  Aligned_cols=84  Identities=25%  Similarity=0.557  Sum_probs=77.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.  .++|||||+|.+.++|.+|+..|||..|.|+.|.|.|
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            44567999999999999999999999999999999999853  4899999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009954          371 ATASGQ  376 (521)
Q Consensus       371 ~~~~~~  376 (521)
                      +.+...
T Consensus        90 a~~~~~   95 (103)
T 2cq3_A           90 ATARVM   95 (103)
T ss_dssp             CCSSCC
T ss_pred             cccCCC
Confidence            987443

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.4e-17  Score=131.28  Aligned_cols=78  Identities=13%  Similarity=0.180  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcC--CeeCCeEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVR  369 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v~  369 (521)
                      ...++|||+|||..+++++|+++|++||.|.+|.|+++      +|||||+|.+.++|.+|++.|++  ..|.|++|.|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            44579999999999999999999999999999999875      78999999999999999998864  78999999999


Q ss_pred             EccCCC
Q 009954          370 RATASG  375 (521)
Q Consensus       370 ~~~~~~  375 (521)
                      |+..+.
T Consensus        88 ~A~~~~   93 (105)
T 1sjq_A           88 FSNHKE   93 (105)
T ss_dssp             CCSSSS
T ss_pred             EcCCCC
Confidence            998743

>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=2.1e-17  Score=123.73  Aligned_cols=72  Identities=18%  Similarity=0.303  Sum_probs=68.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      .-|||+||++.+|+++|+++|.+||+|.++.+..      ++|||||+|.+.++|.+|++.|||..+.|++|.|.+|.
T Consensus         8 ~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            8 SWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            5699999999999999999999999999999865      58999999999999999999999999999999999994

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=2.3e-17  Score=135.18  Aligned_cols=82  Identities=33%  Similarity=0.613  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.|++ .|.|+.|.|.|+
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a   93 (116)
T 2cqd_A           15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   93 (116)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEc
Confidence            4557899999999999999999999999999999999988999999999999999999999999998 899999999999


Q ss_pred             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      ...
T Consensus        94 ~~~   96 (116)
T 2cqd_A           94 YLG   96 (116)
T ss_dssp             TTT
T ss_pred             ccC
Confidence            764

>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=9.7e-18  Score=133.04  Aligned_cols=82  Identities=16%  Similarity=0.329  Sum_probs=77.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++||+.|||..|.|+.|.|.++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            44578999999999999999999999999998888888889999999999999999999999999999999999999998


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      ..
T Consensus        93 ~~   94 (98)
T 2cqp_A           93 SG   94 (98)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=6.2e-17  Score=132.25  Aligned_cols=82  Identities=23%  Similarity=0.372  Sum_probs=77.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.+
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            3455789999999999999999999999999999999997 699999999999999999999999999999999999999


Q ss_pred             ccC
Q 009954          371 ATA  373 (521)
Q Consensus       371 ~~~  373 (521)
                      +..
T Consensus        91 a~~   93 (114)
T 2do0_A           91 DER   93 (114)
T ss_dssp             CSC
T ss_pred             ccc
Confidence            975

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=1.6e-17  Score=133.27  Aligned_cols=83  Identities=27%  Similarity=0.395  Sum_probs=78.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHh-cCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCe-eCCeEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLES-FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK-MGDKTLTVR  369 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~-~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~-~~g~~l~v~  369 (521)
                      ...++|||+|||..+++++|+++|++ ||.|..|.|+.++ +|.++|||||+|.+.++|.+||+.|+|.. |.|+.|.|.
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             EccCCC
Q 009954          370 RATASG  375 (521)
Q Consensus       370 ~~~~~~  375 (521)
                      |+.+..
T Consensus        86 ~a~~~~   91 (104)
T 2dhg_A           86 VAIPKA   91 (104)
T ss_dssp             BCCCCC
T ss_pred             EccCCC
Confidence            997643

>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=1.9e-17  Score=132.80  Aligned_cols=82  Identities=28%  Similarity=0.492  Sum_probs=76.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC-CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT-GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ...++|||+|||..+++++|+++|++|| |..|.|+.++.+ |.++|||||+|.+.++|++|| .|||..|.|+.|.|.+
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            3457899999999999999999999999 999999999887 999999999999999999999 8999999999999999


Q ss_pred             ccCCC
Q 009954          371 ATASG  375 (521)
Q Consensus       371 ~~~~~  375 (521)
                      +.++.
T Consensus        91 a~~~~   95 (104)
T 1wi8_A           91 ADQAQ   95 (104)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            98743

>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=99.72  E-value=3.2e-18  Score=139.90  Aligned_cols=104  Identities=19%  Similarity=0.254  Sum_probs=64.6

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~----~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      ..+|||+|||+.+|+++|+++|.+||.|.            ++.+    +.++|||||+|.+.++|.+|+ .|+|..|.|
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 SGNIFIKNLDKSIDNKALYDTFSAFGNIL------------SCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLND   72 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEE------------EEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEE------------EEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECC
Confidence            45799999999999999999999999843            3332    335799999999999999999 799999999


Q ss_pred             ceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHH
Q 009954          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQ  310 (521)
Q Consensus       249 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~  310 (521)
                      +.|.|.++.........                     ........++|||+|||+.+|++.
T Consensus        73 ~~i~V~~a~~~~~~~~~---------------------~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           73 RKVFVGRFKSRKEREAE---------------------LGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             EECEEEESSCCCC-------------------------------------------------
T ss_pred             EEEEEEECCCccccccc---------------------cccccCCCCceEeCCCCCCccccc
Confidence            99999986643321110                     000112335799999999999863

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.72  E-value=1.7e-17  Score=138.30  Aligned_cols=86  Identities=27%  Similarity=0.381  Sum_probs=80.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|++||+.|||..|.|+.|.|.|+.
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            34689999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCCCCc
Q 009954          373 ASGQSK  378 (521)
Q Consensus       373 ~~~~~~  378 (521)
                      +.....
T Consensus       101 ~~~~~~  106 (126)
T 3ex7_B          101 VRGPPK  106 (126)
T ss_dssp             ESSSCC
T ss_pred             CCCCCC
Confidence            755443

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=5.3e-17  Score=126.77  Aligned_cols=81  Identities=23%  Similarity=0.356  Sum_probs=76.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|+.| .|..|.|+.+ .+|.++|||||+|.+.++|.+||+ |||..|+|+.|.|.++
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            345789999999999999999999999 9999999999 799999999999999999999999 9999999999999999


Q ss_pred             cCCC
Q 009954          372 TASG  375 (521)
Q Consensus       372 ~~~~  375 (521)
                      .+..
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7643

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.72  E-value=6.3e-17  Score=134.26  Aligned_cols=85  Identities=21%  Similarity=0.338  Sum_probs=79.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.+. +|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|
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            3455789999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 009954          371 ATASGQ  376 (521)
Q Consensus       371 ~~~~~~  376 (521)
                      +.....
T Consensus       111 a~~~~~  116 (124)
T 2kt5_A          111 VASQID  116 (124)
T ss_dssp             ECCTTC
T ss_pred             eCCCCC
Confidence            987443

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.72  E-value=6.9e-18  Score=126.64  Aligned_cols=75  Identities=25%  Similarity=0.585  Sum_probs=72.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      +|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|++|++ |+|..|+|+.|.|.+|
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 9999999999999985

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.72  E-value=5.1e-17  Score=137.81  Aligned_cols=85  Identities=31%  Similarity=0.526  Sum_probs=80.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.|
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            34567999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 009954          371 ATASG  375 (521)
Q Consensus       371 ~~~~~  375 (521)
                      +....
T Consensus       119 a~~~~  123 (139)
T 1u6f_A          119 AASGH  123 (139)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            98743

>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=128.31  Aligned_cols=83  Identities=23%  Similarity=0.385  Sum_probs=77.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||.  ++..|.|+.|.|.|
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            3456789999999999999999999999999999999998899999999999999999999998  47899999999999


Q ss_pred             ccCCC
Q 009954          371 ATASG  375 (521)
Q Consensus       371 ~~~~~  375 (521)
                      +.++.
T Consensus        90 a~~~~   94 (103)
T 2cqg_A           90 PNSKQ   94 (103)
T ss_dssp             CCTTC
T ss_pred             cCCCC
Confidence            98744

>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=99.71  E-value=1.4e-17  Score=133.69  Aligned_cols=80  Identities=43%  Similarity=0.735  Sum_probs=77.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+..
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

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

Probab=99.71  E-value=4.8e-17  Score=126.85  Aligned_cols=77  Identities=17%  Similarity=0.161  Sum_probs=70.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCe--eCCeEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK--MGDKTLTVR  369 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~--~~g~~l~v~  369 (521)
                      .+.++|||+|||..+++++|.++|++||.|.+|.+++.      +|||||+|.+.++|.+|++.|+|..  |.|++|.|.
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 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            34468999999999999999999999999999998853      7899999999999999999999875  889999999


Q ss_pred             EccCC
Q 009954          370 RATAS  374 (521)
Q Consensus       370 ~~~~~  374 (521)
                      |++.+
T Consensus        93 ~S~~k   97 (100)
T 3r27_A           93 YSTSQ   97 (100)
T ss_dssp             ECSCS
T ss_pred             ecccc
Confidence            99763

>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=1.3e-17  Score=132.70  Aligned_cols=78  Identities=22%  Similarity=0.261  Sum_probs=74.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||.++|+++|.++|++||.|.+|.|+.++. |.++|||||+|.+.++|.+||. ++|..|.|+.|.|.++..
T Consensus        11 ~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             GGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEchH
Confidence            36899999999999999999999999999999999986 9999999999999999999999 899999999999999853

>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=99.71  E-value=8.1e-17  Score=139.42  Aligned_cols=84  Identities=24%  Similarity=0.374  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.|||..|.|+.|.|.|+
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            45579999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009954          372 TASG  375 (521)
Q Consensus       372 ~~~~  375 (521)
                      .+..
T Consensus       117 ~~~~  120 (156)
T 1h2v_Z          117 AGFK  120 (156)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8743

>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=99.71  E-value=7.2e-17  Score=138.77  Aligned_cols=138  Identities=20%  Similarity=0.147  Sum_probs=100.1

Q ss_pred             CCCcceEEEEEEcChHHHHHHHHHH-cCCeeCCeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCC
Q 009954          332 TGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGG  410 (521)
Q Consensus       332 ~g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (521)
                      ...-+|+++|+|.+.++|++|++.| ||..+.| .|.+.++.......                      ..........
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~----------------------~~~~~~~~~~   65 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVT----------------------EGSHHHHHHM   65 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEE----------------------CSSSSCCCCS
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccc----------------------cccccccccc
Confidence            3456899999999999999999999 9999999 99999885411000                      0000000001


Q ss_pred             CCCCCCCcceEEEeeCcC-CcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHH
Q 009954          411 MSLFGETLAKVLCLTEAI-TADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCAT  489 (521)
Q Consensus       411 ~~~~~~~~~~v~~l~~~~-~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~  489 (521)
                      .+.......+|++ .|+. +.++           ++|+++|+.||.|..|.|+.+.        +|+|||+|.+.++|..
T Consensus        66 ~~~~~~~~~~l~V-~nl~~~~t~-----------~~l~~~F~~~G~i~~v~i~~~~--------~g~afV~f~~~~~a~~  125 (150)
T 2i2y_A           66 HRDSCPLDCKVYV-GNLGNNGNK-----------TELERAFGYYGPLRSVWVARNP--------PGFAFVEFEDPRDAAD  125 (150)
T ss_dssp             CSSSSTTSCEEEE-ESCCSCCSC-----------HHHHHHHHHHSCEEEEEECSSS--------CSEEEEEESSHHHHHH
T ss_pred             cccCCCCCCEEEE-eCCCCCCCH-----------HHHHHHHHhhCCEEEEEEeeCC--------CcEEEEEECCHHHHHH
Confidence            1111122333333 3332 2221           5999999999999999999862        4788999999999999


Q ss_pred             HHHHHhCCeeCCcEEEEEEcCCC
Q 009954          490 AKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       490 Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      ||..|||..|+|++|+|.|+...
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            99999999999999999998765

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=5e-18  Score=130.82  Aligned_cols=81  Identities=21%  Similarity=0.420  Sum_probs=76.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|+|.++
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            34579999999999999999999999999999999999889999999999999999999999999999999999988876


Q ss_pred             c
Q 009954          372 T  372 (521)
Q Consensus       372 ~  372 (521)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.71  E-value=5e-17  Score=138.16  Aligned_cols=82  Identities=20%  Similarity=0.343  Sum_probs=77.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEE
Q 009954          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       290 ~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      .....++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.
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            34566899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             Ec
Q 009954          370 RA  371 (521)
Q Consensus       370 ~~  371 (521)
                      ||
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            85

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=2.9e-17  Score=134.21  Aligned_cols=79  Identities=18%  Similarity=0.365  Sum_probs=75.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|| .|||..|.|+.|.|.|+.+
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            368999999999999999999999999999999999989999999999999999999999 8999999999999999954

>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=5.8e-18  Score=170.31  Aligned_cols=83  Identities=20%  Similarity=0.425  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.|+
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 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      ...
T Consensus       180 ~~~  182 (437)
T 3pgw_S          180 RGR  182 (437)
T ss_pred             CCC
Confidence            763

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=5.1e-17  Score=131.31  Aligned_cols=82  Identities=26%  Similarity=0.585  Sum_probs=75.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++  +.++|||||+|.+.++|++|++.|+|..|.|+.|.|.+
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            3456789999999999999999999999999999999884  45899999999999999999999999999999999999


Q ss_pred             ccCC
Q 009954          371 ATAS  374 (521)
Q Consensus       371 ~~~~  374 (521)
                      +.++
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9763

>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=99.70  E-value=4.5e-17  Score=132.12  Aligned_cols=84  Identities=18%  Similarity=0.262  Sum_probs=76.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH---HHHHhcCCeeEEEEeecCCCC---CcceEEEEEEcChHHHHHHHHHHcCCeeCCeE
Q 009954          292 EGPDRVFVGGLPYYFTETQIK---ELLESFGTLHGFDLVKDRDTG---NSKGYGFCVYQDPAVTDIACAALNGLKMGDKT  365 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~---~~F~~~G~i~~v~i~~~~~~g---~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~  365 (521)
                      ...++|||+|||+.+++++|.   ++|++||.|..|.|+.+..++   .++|||||+|.+.++|++||+.|||..|.|+.
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 009954          366 LTVRRATASG  375 (521)
Q Consensus       366 l~v~~~~~~~  375 (521)
                      |.|.|+.++.
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            9999998744

>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=5.3e-17  Score=131.14  Aligned_cols=83  Identities=25%  Similarity=0.431  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.+ |..|+|+.|.|.++
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVA  101 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEc
Confidence            44578999999999999999999999999999999999889999999999999999999999975 69999999999999


Q ss_pred             cCCC
Q 009954          372 TASG  375 (521)
Q Consensus       372 ~~~~  375 (521)
                      .+..
T Consensus       102 ~~~~  105 (109)
T 2rs2_A          102 FPRR  105 (109)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8743

>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=99.70  E-value=1.3e-16  Score=126.13  Aligned_cols=78  Identities=14%  Similarity=0.169  Sum_probs=70.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHc--CCeeCCeEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTVR  369 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~v~  369 (521)
                      .+.++|||+|||..+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|++.|+  +..|.|+.|.|.
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            44578999999999999999999999999999988865      7899999999999999999874  678999999999


Q ss_pred             EccCCC
Q 009954          370 RATASG  375 (521)
Q Consensus       370 ~~~~~~  375 (521)
                      |+....
T Consensus        87 ~a~~~~   92 (101)
T 2cq1_A           87 YSNHKE   92 (101)
T ss_dssp             ECSCSS
T ss_pred             EcCccc
Confidence            998643

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=1.5e-17  Score=125.47  Aligned_cols=76  Identities=28%  Similarity=0.494  Sum_probs=73.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ++|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|++.++ ..|.|+.|.|.++
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            479999999999999999999999999999999998899999999999999999999999998 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=99.70  E-value=1.9e-16  Score=128.15  Aligned_cols=81  Identities=20%  Similarity=0.394  Sum_probs=74.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|..   ++.++|||||+|.+.++|++||+.|||..|.|+.|.|.|+
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            4457899999999999999999999999999999965   4568999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009954          372 TASG  375 (521)
Q Consensus       372 ~~~~  375 (521)
                      .+..
T Consensus        97 ~~~~  100 (109)
T 1x4a_A           97 RSGR  100 (109)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8743

>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=7.9e-18  Score=131.25  Aligned_cols=79  Identities=33%  Similarity=0.567  Sum_probs=74.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      ++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.+ |.+|+..|||..|.|+.|.|.++.+.
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            47999999999999999999999999999999999889999999999999999 99999999999999999999999763

>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=99.69  E-value=6.5e-17  Score=132.33  Aligned_cols=79  Identities=20%  Similarity=0.408  Sum_probs=73.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|.++|++||.|..|.|+.+   +.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+
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            34579999999999999999999999999999999875   456999999999999999999999999999999999999


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      .+
T Consensus        83 ~~   84 (115)
T 3lqv_A           83 NA   84 (115)
T ss_dssp             CH
T ss_pred             cC
Confidence            64

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.69  E-value=1.7e-17  Score=138.98  Aligned_cols=83  Identities=22%  Similarity=0.291  Sum_probs=78.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE--EEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCC----eeCCe
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHG--FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL----KMGDK  364 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~--v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~----~~~g~  364 (521)
                      ....++|||+|||..+++++|+++|++||.|..  |+|+.++.+|.++|||||+|.+. +|.+|+..|||.    .|.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            345678999999999999999999999999976  99999999999999999999999 999999999999    99999


Q ss_pred             EEEEEEccCC
Q 009954          365 TLTVRRATAS  374 (521)
Q Consensus       365 ~l~v~~~~~~  374 (521)
                      .|.|.|+.+.
T Consensus        99 ~l~V~~a~~~  108 (131)
T 2m2b_A           99 TINVEFAKGS  108 (131)
T ss_dssp             CCCCEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999999763

>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=99.69  E-value=4.5e-17  Score=129.63  Aligned_cols=80  Identities=16%  Similarity=0.205  Sum_probs=73.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||+.+++++|+++|++||.| .|.|+.++ +|.++|||||+|.+.++|++||+ +|+..|+|+.|.|.+
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 99999999999999999999995 799999999999999


Q ss_pred             ccC
Q 009954          371 ATA  373 (521)
Q Consensus       371 ~~~  373 (521)
                      +..
T Consensus        89 ~~~   91 (102)
T 1wez_A           89 NST   91 (102)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            865

>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=99.69  E-value=5.6e-17  Score=127.94  Aligned_cols=76  Identities=14%  Similarity=0.112  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCC--eeCCeEEEE
Q 009954          292 EGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL--KMGDKTLTV  368 (521)
Q Consensus       292 ~~~~~l~v~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~--~~~g~~l~v  368 (521)
                      .+.++|||+|||. .+++++|+++|++||.|.+|.|+++      +|||||+|.+.++|..|++.|++.  .|.|+.|.|
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            3557899999999 9999999999999999999999875      579999999999999999999864  599999999


Q ss_pred             EEccC
Q 009954          369 RRATA  373 (521)
Q Consensus       369 ~~~~~  373 (521)
                      .|+..
T Consensus        87 ~~a~~   91 (102)
T 1x4d_A           87 HLSQK   91 (102)
T ss_dssp             EEECC
T ss_pred             EECCC
Confidence            99985

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.69  E-value=6.8e-17  Score=132.46  Aligned_cols=80  Identities=18%  Similarity=0.308  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGT---LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~---i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (521)
                      ...++|||+|||..+++++|+++|+.||.   |..|.|+.++. |.++|||||+|.+.++|++||+ |||..|+|+.|.|
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            44578999999999999999999999999   89999999975 9999999999999999999999 9999999999999


Q ss_pred             EEccC
Q 009954          369 RRATA  373 (521)
Q Consensus       369 ~~~~~  373 (521)
                      .++..
T Consensus        93 ~~a~~   97 (118)
T 2db1_A           93 FKSHR   97 (118)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            99853

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=6.4e-17  Score=131.01  Aligned_cols=83  Identities=19%  Similarity=0.327  Sum_probs=76.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEe-ecCCCCCcceEEEEEEcChHHHHHHHHHHc--CCeeCCeEEEE
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLV-KDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTV  368 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~-i~~v~i~-~~~~~g~~~g~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~v  368 (521)
                      ..++|||+|||..+++++|+++|++||. |..|.|+ .+..+|.++|||||+|.+.++|.+|++.|+  +..|.|+.|.|
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 009954          369 RRATASG  375 (521)
Q Consensus       369 ~~~~~~~  375 (521)
                      .|+.+..
T Consensus        87 ~~a~~~~   93 (109)
T 2dis_A           87 DWAEPEI   93 (109)
T ss_dssp             EESCSSC
T ss_pred             EEcCCCC
Confidence            9998744

>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=6.9e-17  Score=129.60  Aligned_cols=78  Identities=24%  Similarity=0.362  Sum_probs=73.4

Q ss_pred             CCeEEEcCCCCCC------CHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCe-EE
Q 009954          294 PDRVFVGGLPYYF------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK-TL  366 (521)
Q Consensus       294 ~~~l~v~nLp~~~------te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~-~l  366 (521)
                      .++|||+|||..+      ++++|+++|++||.|..|.|+.  .+|.++|||||+|.+.++|.+|+..|||..|.|+ .|
T Consensus        15 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l   92 (105)
T 2nlw_A           15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   92 (105)
T ss_dssp             CSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEE
T ss_pred             CCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceE
Confidence            4789999999999      7899999999999999999883  5899999999999999999999999999999998 99


Q ss_pred             EEEEccC
Q 009954          367 TVRRATA  373 (521)
Q Consensus       367 ~v~~~~~  373 (521)
                      .|.++..
T Consensus        93 ~V~~a~~   99 (105)
T 2nlw_A           93 RVNLFTD   99 (105)
T ss_dssp             EEECSCC
T ss_pred             EEEEcch
Confidence            9999975

>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=99.69  E-value=1.8e-17  Score=131.75  Aligned_cols=81  Identities=27%  Similarity=0.506  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC-CCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ...++|||+|||..+++++|+++|++|| |..|.|+.++ .+|.++|||||+|.+.++|.+|| .|+|..|+|+.|.|.+
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 9999999997 58999999999999999999999 8999999999999999


Q ss_pred             ccCC
Q 009954          371 ATAS  374 (521)
Q Consensus       371 ~~~~  374 (521)
                      +.+.
T Consensus        95 a~~~   98 (100)
T 2j76_E           95 ADQA   98 (100)
T ss_dssp             CCCS
T ss_pred             ccCC
Confidence            9763

>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=99.68  E-value=1.2e-16  Score=127.01  Aligned_cols=78  Identities=17%  Similarity=0.151  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCC--eeCCeEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL--KMGDKTLTVR  369 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~--~~~g~~l~v~  369 (521)
                      .+.++|||+|||..+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|++.|++.  .|.|+.|.|.
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            34578999999999999999999999999999998764      789999999999999999998764  5999999999


Q ss_pred             EccCCC
Q 009954          370 RATASG  375 (521)
Q Consensus       370 ~~~~~~  375 (521)
                      |+..+.
T Consensus        87 ~a~~~~   92 (104)
T 1wex_A           87 YSTSKR   92 (104)
T ss_dssp             ECSSSS
T ss_pred             EccCcc
Confidence            997643

>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=3.9e-17  Score=133.23  Aligned_cols=81  Identities=12%  Similarity=0.215  Sum_probs=75.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCe-eEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTL-HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i-~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      ....++|||+|||..+++++|+++|+.||.| ..|.|+.++ +|.++|||||+|.+.++|.+||+. ||..|.|+.|.|.
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            3455789999999999999999999999999 899999997 999999999999999999999996 9999999999999


Q ss_pred             EccC
Q 009954          370 RATA  373 (521)
Q Consensus       370 ~~~~  373 (521)
                      ++..
T Consensus        90 ~a~~   93 (114)
T 2cpy_A           90 VVTL   93 (114)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            9964

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.68  E-value=1e-16  Score=133.03  Aligned_cols=79  Identities=22%  Similarity=0.423  Sum_probs=76.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|| .|||..|.|+.|.|.|+..
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            368999999999999999999999999999999999889999999999999999999999 7999999999999999975

>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=1.1e-16  Score=129.55  Aligned_cols=79  Identities=13%  Similarity=0.165  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHc--CCeeCCeEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTVR  369 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~v~  369 (521)
                      .+.++|||+|||+.+++++|+++|++||.|.+|.|+.+      +|||||+|.+.++|.+|++.|+  +..|.|++|.|.
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      7899999999999999999987  478999999999


Q ss_pred             EccCCCC
Q 009954          370 RATASGQ  376 (521)
Q Consensus       370 ~~~~~~~  376 (521)
                      |+..+..
T Consensus       103 ~a~~k~~  109 (119)
T 2ad9_A          103 FSNHKEL  109 (119)
T ss_dssp             ECSSSSC
T ss_pred             EccCCCC
Confidence            9987443

>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=99.68  E-value=1.9e-16  Score=129.34  Aligned_cols=81  Identities=20%  Similarity=0.481  Sum_probs=76.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee--------CC
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--------GD  363 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--------~g  363 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++|.+||+.|||..|        .+
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            445799999999999999999999999999999999997 999999999999999999999999999999        68


Q ss_pred             eEEEEEEccC
Q 009954          364 KTLTVRRATA  373 (521)
Q Consensus       364 ~~l~v~~~~~  373 (521)
                      ++|.|.|+.+
T Consensus       102 ~~l~v~~a~p  111 (114)
T 1x5o_A          102 EPLLCKFSGP  111 (114)
T ss_dssp             SCBEEEECCC
T ss_pred             CceeEEccCC
Confidence            8899999975

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1e-16  Score=131.27  Aligned_cols=81  Identities=27%  Similarity=0.507  Sum_probs=77.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+. +|..|.|+.|.|.++.+
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            47899999999999999999999999999999999988999999999999999999999997 99999999999999987


Q ss_pred             CC
Q 009954          374 SG  375 (521)
Q Consensus       374 ~~  375 (521)
                      +.
T Consensus       106 ~~  107 (116)
T 1x4b_A          106 RE  107 (116)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>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=99.68  E-value=3.2e-16  Score=126.42  Aligned_cols=76  Identities=21%  Similarity=0.283  Sum_probs=71.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC-----eEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD-----KTL  366 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g-----~~l  366 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.+       |||||+|.+.++|++||+.|||..|.|     +.|
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            44578999999999999999999999999999999876       799999999999999999999999999     999


Q ss_pred             EEEEccCC
Q 009954          367 TVRRATAS  374 (521)
Q Consensus       367 ~v~~~~~~  374 (521)
                      .|.++.+.
T Consensus        86 ~V~~a~~~   93 (108)
T 1x4c_A           86 RVKVDGPR   93 (108)
T ss_dssp             EEEESSCC
T ss_pred             EEEeCCCC
Confidence            99999873

>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=1.1e-16  Score=128.07  Aligned_cols=80  Identities=16%  Similarity=0.332  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~-v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ...++|||+|||..+++++|+++|++||.|.. |.|+.+ .+|.++|||||+|.+.++|++||+. +|..|+|+.|.|.+
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            44578999999999999999999999999987 888888 6999999999999999999999997 99999999999999


Q ss_pred             ccC
Q 009954          371 ATA  373 (521)
Q Consensus       371 ~~~  373 (521)
                      +..
T Consensus        91 ~~~   93 (104)
T 1wg5_A           91 SSR   93 (104)
T ss_dssp             ECT
T ss_pred             CCH
Confidence            865

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1.9e-16  Score=126.29  Aligned_cols=81  Identities=19%  Similarity=0.333  Sum_probs=73.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|   .++.+ .++.++|||||+|.+.++|++||+.|||..|.|+.|.|.|
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            3456799999999999999999999999987   56666 5899999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 009954          371 ATASG  375 (521)
Q Consensus       371 ~~~~~  375 (521)
                      +.+..
T Consensus        88 a~~~~   92 (101)
T 2fc9_A           88 QGPRG   92 (101)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            98743

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.6e-16  Score=122.52  Aligned_cols=77  Identities=27%  Similarity=0.514  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+        +|||||+|.+.++|++|++.|||..|.|+.|.|.|+
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            445789999999999999999999999999999987        569999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009954          372 TASGQ  376 (521)
Q Consensus       372 ~~~~~  376 (521)
                      .+...
T Consensus        78 ~~~~~   82 (90)
T 2dnq_A           78 KNKSK   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87443

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

Probab=99.67  E-value=2.1e-16  Score=130.42  Aligned_cols=79  Identities=13%  Similarity=0.233  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~----~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      .+.++|||+|||..+++++|+    ++|++||.|..|.+..   ++.++|||||+|.+.++|..|+..|||..|.|+.|.
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    7999999999988753   688999999999999999999999999999999999


Q ss_pred             EEEccC
Q 009954          368 VRRATA  373 (521)
Q Consensus       368 v~~~~~  373 (521)
                      |.|+..
T Consensus       104 V~~a~~  109 (127)
T 2a3j_A          104 ITFSET  109 (127)
T ss_dssp             EEECCC
T ss_pred             EEEccC
Confidence            999976

>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=9.4e-17  Score=134.10  Aligned_cols=80  Identities=18%  Similarity=0.279  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGT---LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~---i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (521)
                      ...++|||+|||+++|+++|+++|++||.   |..|.|+.++. |.++|||||+|.+.++|++||+ |||..|+|+.|.|
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            34578999999999999999999999999   89999999976 9999999999999999999999 9999999999999


Q ss_pred             EEccC
Q 009954          369 RRATA  373 (521)
Q Consensus       369 ~~~~~  373 (521)
                      .++..
T Consensus       120 ~~a~~  124 (136)
T 2hgl_A          120 FKSHR  124 (136)
T ss_dssp             EECCH
T ss_pred             EECCh
Confidence            99853

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.67  E-value=4.1e-17  Score=122.39  Aligned_cols=75  Identities=23%  Similarity=0.432  Sum_probs=71.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      +|||+|||..+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|.+|++ +++..|.|+.|.|.+|
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

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3.3e-16  Score=125.10  Aligned_cols=82  Identities=28%  Similarity=0.426  Sum_probs=74.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|+.|+   .|.++.++.++.++|||||+|.+.++|++||+.|||..|.|+.|.|.|
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            34557899999999999999999999874   677888888999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 009954          371 ATASG  375 (521)
Q Consensus       371 ~~~~~  375 (521)
                      +.++.
T Consensus        89 a~~~~   93 (102)
T 2fc8_A           89 AKPKG   93 (102)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            98743

>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=99.67  E-value=3.2e-16  Score=120.66  Aligned_cols=75  Identities=21%  Similarity=0.403  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHH-cCCeeCCeEEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVRR  370 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v~~  370 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|++.| +|..|.|+.|.|.|
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            34578999999999999999999999999999999874      789999999999999999999 99999999999999


Q ss_pred             cc
Q 009954          371 AT  372 (521)
Q Consensus       371 ~~  372 (521)
                      ++
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            84

>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=1.3e-16  Score=128.01  Aligned_cols=75  Identities=25%  Similarity=0.394  Sum_probs=71.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      .+|||+|||+.+++++|+++|+.| .|..|.|+.++ +|.++|||||+|.+.++|.+|| .|||..|+|+.|.|..+.
T Consensus        17 ~~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           17 LYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            589999999999999999999999 89999999997 4999999999999999999999 599999999999999885

>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=4.7e-17  Score=134.92  Aligned_cols=81  Identities=19%  Similarity=0.316  Sum_probs=74.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||+.+++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+||+ |||..|+|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            455799999999999999999999999999986666666799999999999999999999999 9999999999999999


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      ..
T Consensus       102 ~~  103 (124)
T 1wel_A          102 TK  103 (124)
T ss_dssp             CH
T ss_pred             CH
Confidence            64

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.66  E-value=1.9e-16  Score=127.20  Aligned_cols=77  Identities=17%  Similarity=0.160  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G-~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ..++|||+|||+.+++++|+++|++|| .|..+.|...    .++|||||+|.+.++|++||+.|||..|.|+.|.|.++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            346899999999999999999999999 8999988543    47899999999999999999999999999999999999


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      ..
T Consensus       103 ~~  104 (111)
T 2jvr_A          103 DN  104 (111)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.66  E-value=4e-16  Score=123.32  Aligned_cols=77  Identities=26%  Similarity=0.528  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC--CeEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG--DKTLTVR  369 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~--g~~l~v~  369 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.+..+      +|||||+|.+.++|++|++.|||..|.  |+.|.|.
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            34578999999999999999999999999999998764      689999999999999999999999999  9999999


Q ss_pred             EccCC
Q 009954          370 RATAS  374 (521)
Q Consensus       370 ~~~~~  374 (521)
                      |+.++
T Consensus        89 ~a~~~   93 (97)
T 1why_A           89 FAKSG   93 (97)
T ss_dssp             ECCCC
T ss_pred             ECCCC
Confidence            99764

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.66  E-value=6.3e-17  Score=123.25  Aligned_cols=72  Identities=25%  Similarity=0.405  Sum_probs=67.5

Q ss_pred             CeEEEcCCCCCC------CHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCe-EEE
Q 009954          295 DRVFVGGLPYYF------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK-TLT  367 (521)
Q Consensus       295 ~~l~v~nLp~~~------te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~-~l~  367 (521)
                      ++|||+|||..+      ++++|+++|++||.|..|.|+.  .+|.++|||||+|.+.++|.+|++.|||..|.|+ .|+
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 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            589999999999      7799999999999999999883  5899999999999999999999999999999999 887


Q ss_pred             E
Q 009954          368 V  368 (521)
Q Consensus       368 v  368 (521)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=6.6e-16  Score=120.22  Aligned_cols=75  Identities=29%  Similarity=0.432  Sum_probs=70.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+++        ||||+|.+.++|.+|++.|||..|.|+.|.|.|+
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 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            44578999999999999999999999999999999744        8999999999999999999999999999999999


Q ss_pred             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      .+.
T Consensus        79 ~~~   81 (90)
T 2dnp_A           79 TKG   81 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            874

>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=99.66  E-value=3.7e-16  Score=124.04  Aligned_cols=77  Identities=34%  Similarity=0.551  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|.++      +|||||+|.+.++|.+|++.|||..|.|+.|.|.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            45579999999999999999999999999999999864      789999999999999999999999999999999999


Q ss_pred             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      .+.
T Consensus        87 ~~~   89 (99)
T 2cpj_A           87 CHS   89 (99)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            763

>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=99.66  E-value=1.8e-16  Score=145.64  Aligned_cols=81  Identities=17%  Similarity=0.334  Sum_probs=76.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFG--TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G--~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ..++|||+|||..+|+++|+++|++||  .|..|+|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.+
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 009954          371 ATA  373 (521)
Q Consensus       371 ~~~  373 (521)
                      +..
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            964

>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=3.8e-17  Score=130.36  Aligned_cols=81  Identities=19%  Similarity=0.310  Sum_probs=74.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|+++|++||.|.. .++.+..+|.++|||||+|.+.++|.+||+ |||..|.|+.|.|.++.
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~   93 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcC
Confidence            4568999999999999999999999999888 666666789999999999999999999999 99999999999999997


Q ss_pred             CCC
Q 009954          373 ASG  375 (521)
Q Consensus       373 ~~~  375 (521)
                      +..
T Consensus        94 ~~~   96 (101)
T 1fj7_A           94 GRD   96 (101)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=9e-16  Score=119.97  Aligned_cols=76  Identities=21%  Similarity=0.356  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+++        ||||+|.+.++|.+|++.|||..|.|+.|.|.|+
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 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            34578999999999999999999999999999998743        9999999999999999999999999999999999


Q ss_pred             cCCC
Q 009954          372 TASG  375 (521)
Q Consensus       372 ~~~~  375 (521)
                      .+..
T Consensus        80 ~~~~   83 (92)
T 2dgt_A           80 TSRL   83 (92)
T ss_dssp             SCCC
T ss_pred             cCCC
Confidence            8743

>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=99.65  E-value=6.6e-16  Score=124.90  Aligned_cols=78  Identities=18%  Similarity=0.368  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|+..|+|..|.|+.|.|.|+
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            34579999999999999999999999999999999876      789999999999999999999999999999999999


Q ss_pred             cCCC
Q 009954          372 TASG  375 (521)
Q Consensus       372 ~~~~  375 (521)
                      .+..
T Consensus        97 ~~~~  100 (109)
T 1x4g_A           97 KESP  100 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8743

>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=99.65  E-value=3.8e-17  Score=136.87  Aligned_cols=80  Identities=16%  Similarity=0.198  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||+++|+++|+++|++|| |..|.|+.++. |.++|||||+|.+.++|++|| .||+..|+|+.|.|.++
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            4457899999999999999999999999 67999999975 999999999999999999999 68999999999999998


Q ss_pred             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      ...
T Consensus       121 ~~~  123 (139)
T 2hgn_A          121 STT  123 (139)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            763

>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=99.65  E-value=2.2e-16  Score=124.92  Aligned_cols=80  Identities=14%  Similarity=0.360  Sum_probs=73.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~----~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      ...++|||+|||..+++++|.    ++|++||.|..|.+..   +|.++|||||+|.+.++|.+|++.|||..|.|+.|.
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            345789999999999999999    9999999999998873   577889999999999999999999999999999999


Q ss_pred             EEEccCC
Q 009954          368 VRRATAS  374 (521)
Q Consensus       368 v~~~~~~  374 (521)
                      |.|+.+.
T Consensus        83 v~~a~~~   89 (97)
T 1nu4_A           83 IQYAKTD   89 (97)
T ss_dssp             EEECSSC
T ss_pred             EEEccCC
Confidence            9999764

>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=99.65  E-value=6.7e-17  Score=130.16  Aligned_cols=80  Identities=16%  Similarity=0.268  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGT---LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~---i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (521)
                      ...++|||+|||+.+++++|+++|+.||.   |..|.|+.++. |.++|||||+|.+.++|.+||+ |||..|+|+.|.|
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            45578999999999999999999999998   89999999976 9999999999999999999999 9999999999999


Q ss_pred             EEccC
Q 009954          369 RRATA  373 (521)
Q Consensus       369 ~~~~~  373 (521)
                      .++.+
T Consensus        87 ~~a~~   91 (107)
T 2lmi_A           87 YEINN   91 (107)
T ss_dssp             EECCH
T ss_pred             EECCH
Confidence            99853

>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=1.1e-15  Score=122.31  Aligned_cols=77  Identities=21%  Similarity=0.326  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|..|.|++        |||||+|.+.++|.+||+.|||..|.|+.|.|.|+
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            4557899999999999999999999999999999874        48999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009954          372 TASGQ  376 (521)
Q Consensus       372 ~~~~~  376 (521)
                      .+...
T Consensus        81 ~~~~~   85 (103)
T 2dgu_A           81 KPPDQ   85 (103)
T ss_dssp             CCCCC
T ss_pred             CCCcc
Confidence            87443

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.65  E-value=3.5e-16  Score=125.11  Aligned_cols=79  Identities=13%  Similarity=0.092  Sum_probs=72.4

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcC----hHH----HHHHHH--HHcCCe
Q 009954          295 DRVFVGGL----PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD----PAV----TDIACA--ALNGLK  360 (521)
Q Consensus       295 ~~l~v~nL----p~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~----~~~----A~~Al~--~l~g~~  360 (521)
                      +.|||+||    |+.+++++|+++|+.||.|.++.++.|+.||.++|||||+|.+    +++    |.+|+.  .|+|..
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    433    788988  789999


Q ss_pred             eCCeEEEEEEccC
Q 009954          361 MGDKTLTVRRATA  373 (521)
Q Consensus       361 ~~g~~l~v~~~~~  373 (521)
                      |+|+.|+|.+-..
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            9999999998865

>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=99.65  E-value=1.3e-15  Score=120.15  Aligned_cols=75  Identities=16%  Similarity=0.363  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          292 EGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       292 ~~~~~l~v~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ...++|||+|||. .+++++|+++|++||.|..|.|.        +|||||+|.+.++|.+|++.|||..|.|+.|.|.|
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            3457899999998 99999999999999999999883        68999999999999999999999999999999999


Q ss_pred             ccCC
Q 009954          371 ATAS  374 (521)
Q Consensus       371 ~~~~  374 (521)
                      +...
T Consensus        92 a~~~   95 (97)
T 2xnq_A           92 SSSN   95 (97)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9753

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.64  E-value=6.4e-16  Score=135.94  Aligned_cols=82  Identities=22%  Similarity=0.364  Sum_probs=77.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.+. +|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3455789999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             ccC
Q 009954          371 ATA  373 (521)
Q Consensus       371 ~~~  373 (521)
                      +..
T Consensus       164 a~~  166 (177)
T 2f3j_A          164 VAS  166 (177)
T ss_dssp             ESS
T ss_pred             ecC
Confidence            976

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.64  E-value=3.2e-16  Score=124.95  Aligned_cols=75  Identities=20%  Similarity=0.379  Sum_probs=71.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      ++|||+|||..+++++|+++|++||.|..|.|+.+     ++|||||+|.+.++|.+|++.|+|..|.|+.|.|.|+...
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            47999999999999999999999999999999886     6899999999999999999999999999999999999763

>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=99.64  E-value=9.1e-17  Score=131.47  Aligned_cols=85  Identities=21%  Similarity=0.268  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|.++|++||.|..+.+..+..+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.|+
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            34579999999999999999999999999944322222227889999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009954          372 TASGQ  376 (521)
Q Consensus       372 ~~~~~  376 (521)
                      .+...
T Consensus       103 ~~~~~  107 (115)
T 2cpx_A          103 KNKKQ  107 (115)
T ss_dssp             CCCSC
T ss_pred             cCCCC
Confidence            87443

>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=3e-16  Score=125.11  Aligned_cols=75  Identities=20%  Similarity=0.403  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|+++|++||.|..|.+..      ++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+.
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            357899999999999999999999999999999873      47899999999999999999999999999999999986


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (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=8e-16  Score=123.82  Aligned_cols=76  Identities=18%  Similarity=0.447  Sum_probs=70.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||..+++++|+++|++||.|..|.|.        +|||||+|.+.++|.+|++.|||..|.|+.|.|.|
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            3455799999999999999999999999999999987        67999999999999999999999999999999999


Q ss_pred             ccCC
Q 009954          371 ATAS  374 (521)
Q Consensus       371 ~~~~  374 (521)
                      +.+.
T Consensus       100 a~~~  103 (108)
T 2jvo_A          100 SKLP  103 (108)
T ss_dssp             CSCC
T ss_pred             ecCC
Confidence            9763

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=8.4e-16  Score=121.40  Aligned_cols=78  Identities=28%  Similarity=0.441  Sum_probs=70.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||..+++++|+++|++||.|. +.++.+    .++|||||+|.+.++|++|++.|||..|.|+.|.|.++
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-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            3457999999999999999999999999997 666643    57899999999999999999999999999999999999


Q ss_pred             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      .+.
T Consensus        92 ~~~   94 (97)
T 2e5j_A           92 RQQ   94 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            763

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.64  E-value=4e-16  Score=123.13  Aligned_cols=78  Identities=17%  Similarity=0.333  Sum_probs=71.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|+++|++||.|..+     ..++.++|||||+|.+.++|.+|++.|+|..|.|+.|.|.|+.
T Consensus        15 ~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   89 (96)
T 1fjc_A           15 AARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcC
Confidence            44789999999999999999999999988766     2478899999999999999999999999999999999999997


Q ss_pred             CCC
Q 009954          373 ASG  375 (521)
Q Consensus       373 ~~~  375 (521)
                      +..
T Consensus        90 ~~~   92 (96)
T 1fjc_A           90 EKG   92 (96)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            643

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.64  E-value=9.3e-16  Score=114.83  Aligned_cols=71  Identities=18%  Similarity=0.229  Sum_probs=67.3

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      +..|||+||++.+|+++|+++|.+||+            |.++.+..++|||||+|.+.++|.+|+ .||+..+.|++|+
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            457999999999999999999999998            788888889999999999999999999 7999999999999


Q ss_pred             EeCC
Q 009954          253 VRRP  256 (521)
Q Consensus       253 v~~~  256 (521)
                      |+.+
T Consensus        75 V~~A   78 (89)
T 2wbr_A           75 AESP   78 (89)
T ss_dssp             EECC
T ss_pred             EEEC
Confidence            9986

>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=99.63  E-value=2.3e-16  Score=126.18  Aligned_cols=77  Identities=14%  Similarity=0.212  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcC--CeeCCeEEEE
Q 009954          292 EGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTV  368 (521)
Q Consensus       292 ~~~~~l~v~nLp~~-~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v  368 (521)
                      .+.++|||+|||.+ +++++|+++|++||.|.+|.|++.      +|||||+|.+.++|.+|++.|++  ..|.|+.|.|
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   96 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   96 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            44578999999998 999999999999999999999753      78999999999999999998864  5699999999


Q ss_pred             EEccCC
Q 009954          369 RRATAS  374 (521)
Q Consensus       369 ~~~~~~  374 (521)
                      .|+..+
T Consensus        97 ~~a~~~  102 (112)
T 1x4f_A           97 DLSEKY  102 (112)
T ss_dssp             EEECSC
T ss_pred             EECccc
Confidence            999763

>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=99.63  E-value=7.6e-16  Score=120.70  Aligned_cols=77  Identities=23%  Similarity=0.412  Sum_probs=69.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcC-CeeCCeEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG-LKMGDKTLTVR  369 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~-i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g-~~~~g~~l~v~  369 (521)
                      ...++|||+|||..+++++|+++|++||. |..+.+.       ++|||||+|.+.++|.+|++.||| ..|.|+.|.|.
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       378999999999999999999999 99999999999


Q ss_pred             EccCCC
Q 009954          370 RATASG  375 (521)
Q Consensus       370 ~~~~~~  375 (521)
                      |+.++.
T Consensus        79 ~a~~~~   84 (93)
T 2cqh_A           79 YSVSKK   84 (93)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            998743

>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=128.30  Aligned_cols=79  Identities=19%  Similarity=0.287  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCe----eEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTL----HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i----~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      ....+|||+|||+++|+++|+++|++||.|    ..|.|+.+ .+|.++|||||+|.+.++|++||+. |+..|+|+.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            345789999999999999999999999975    68999998 4899999999999999999999995 99999999999


Q ss_pred             EEEcc
Q 009954          368 VRRAT  372 (521)
Q Consensus       368 v~~~~  372 (521)
                      |..+.
T Consensus        99 V~~a~  103 (123)
T 2dha_A           99 LFRST  103 (123)
T ss_dssp             CEEEC
T ss_pred             EEECC
Confidence            99885

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.63  E-value=4.4e-16  Score=124.38  Aligned_cols=79  Identities=29%  Similarity=0.581  Sum_probs=74.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||..+++++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++|++|+.  +|..|+|+.|.|.++..
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            3689999999999999999999999999999999998 99999999999999999999999  99999999999999976


Q ss_pred             CC
Q 009954          374 SG  375 (521)
Q Consensus       374 ~~  375 (521)
                      +.
T Consensus        86 ~~   87 (102)
T 2xs2_A           86 KQ   87 (102)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>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=99.62  E-value=6.1e-16  Score=125.23  Aligned_cols=75  Identities=19%  Similarity=0.172  Sum_probs=69.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||..+++++|+++|++||.|..|.|+.      ++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+..
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            35899999999999999999999999999998874      478999999999999999999999999999999999976


Q ss_pred             C
Q 009954          374 S  374 (521)
Q Consensus       374 ~  374 (521)
                      .
T Consensus        84 ~   84 (111)
T 1whx_A           84 G   84 (111)
T ss_dssp             T
T ss_pred             C
Confidence            3

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=4.4e-15  Score=117.77  Aligned_cols=76  Identities=18%  Similarity=0.283  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhc--CCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESF--GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~--G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      ...++|||+|||..+++++|+++|++|  |.|..|.+.        +|||||+|.+.++|.+|+..|||..|.|+.|.|.
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            445789999999999999999999999  899998865        5699999999999999999999999999999999


Q ss_pred             EccCCC
Q 009954          370 RATASG  375 (521)
Q Consensus       370 ~~~~~~  375 (521)
                      |+.+..
T Consensus        85 ~a~~~~   90 (99)
T 2cpd_A           85 LAKPVD   90 (99)
T ss_dssp             CCCCCC
T ss_pred             ECCCCC
Confidence            998743

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.62  E-value=3.1e-15  Score=119.12  Aligned_cols=81  Identities=15%  Similarity=0.093  Sum_probs=72.1

Q ss_pred             CCCeEEEcCCCC-----CCCHHHHHHHHHhcCCeeEEEEeecCCC-CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEE
Q 009954          293 GPDRVFVGGLPY-----YFTETQIKELLESFGTLHGFDLVKDRDT-GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (521)
Q Consensus       293 ~~~~l~v~nLp~-----~~te~~l~~~F~~~G~i~~v~i~~~~~~-g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (521)
                      +.++|+|.||..     +.++++|+++|++||.|.+|.|+.++.+ +.++|||||+|.+.++|.+|++.|||.+|.|+.|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            446899999963     2378999999999999999999998654 6899999999999999999999999999999999


Q ss_pred             EEEEccC
Q 009954          367 TVRRATA  373 (521)
Q Consensus       367 ~v~~~~~  373 (521)
                      .|.|+..
T Consensus        87 ~v~~a~~   93 (105)
T 2pe8_A           87 KACFYNL   93 (105)
T ss_dssp             EEEECCH
T ss_pred             EEEEcCH
Confidence            9999953

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.42  E-value=3.3e-17  Score=134.27  Aligned_cols=81  Identities=25%  Similarity=0.423  Sum_probs=77.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCe
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHG--------FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK  364 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~--------v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~  364 (521)
                      ..++|||+|||..+++++|+++|++||.|..        |.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+
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            3468999999999999999999999999998        99999988999999999999999999999999999999999


Q ss_pred             EEEEEEccC
Q 009954          365 TLTVRRATA  373 (521)
Q Consensus       365 ~l~v~~~~~  373 (521)
                      .|.|.|+.+
T Consensus        86 ~l~V~~a~~   94 (116)
T 2lcw_A           86 PIKVSFATR   94 (116)
Confidence            999999975

>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=99.62  E-value=1.2e-15  Score=121.95  Aligned_cols=77  Identities=23%  Similarity=0.332  Sum_probs=69.3

Q ss_pred             CCCCeEEE--cCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee-----CCe
Q 009954          292 EGPDRVFV--GGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-----GDK  364 (521)
Q Consensus       292 ~~~~~l~v--~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~-----~g~  364 (521)
                      .+.++|||  +||+..+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|++|++.|||..|     .|+
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 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            34568999  779999999999999999999999987642      78999999999999999999999988     789


Q ss_pred             EEEEEEccCC
Q 009954          365 TLTVRRATAS  374 (521)
Q Consensus       365 ~l~v~~~~~~  374 (521)
                      +|.|.|+...
T Consensus        97 ~l~v~~a~~~  106 (114)
T 2cq2_A           97 TLYLNFVEKV  106 (114)
T ss_dssp             ECEEEEESCC
T ss_pred             EEEEEecccC
Confidence            9999999763

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=2e-15  Score=119.03  Aligned_cols=78  Identities=18%  Similarity=0.252  Sum_probs=71.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGF-DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ..++|||+|||..+++++|+++|++||.|..| .|+.++.+|    .|||+|.+.++|.+|++.|||..|.|+.|.|.|+
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 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45789999999999999999999999999999 588776543    4999999999999999999999999999999999


Q ss_pred             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      .++
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=99.61  E-value=2.6e-15  Score=121.63  Aligned_cols=73  Identities=25%  Similarity=0.470  Sum_probs=68.9

Q ss_pred             CCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          293 GPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       293 ~~~~l~v~nLp~~-~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ..++|||+|||.. +++++|+++|++||.|..|.|        ++|||||+|.+.++|++|++.|+|..|.|+.|.|.|+
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 999999999999999999998        4789999999999999999999999999999999999


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      ..
T Consensus        98 ~~   99 (110)
T 1wf1_A           98 GE   99 (110)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.61  E-value=2.6e-15  Score=122.92  Aligned_cols=75  Identities=21%  Similarity=0.324  Sum_probs=69.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceE-EEEEEcChHHHHHHHHHHcCCeeCC--eEEEEEEc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY-GFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  371 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~-afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~  371 (521)
                      ..|||+||++.+|+++|+++|++||.|..|.|+...     +|| |||+|.+.++|.+|++.|||..|.|  +.|+|.|+
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~a  103 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  103 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEEC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEec
Confidence            468899999999999999999999999999887652     677 9999999999999999999999988  99999999


Q ss_pred             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      ++.
T Consensus       104 k~~  106 (130)
T 3zzy_A          104 KLT  106 (130)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            863

>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=99.61  E-value=6.2e-16  Score=126.93  Aligned_cols=79  Identities=19%  Similarity=0.376  Sum_probs=72.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCee--EEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLH--GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~--~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      ...++|||+|||+.+|+++|+++|++| .|.  .|.|+.++. |.++|||||+|.+.++|++||+ +++..|+|+.|.|.
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 666  899999976 9999999999999999999998 57899999999999


Q ss_pred             EccC
Q 009954          370 RATA  373 (521)
Q Consensus       370 ~~~~  373 (521)
                      ++..
T Consensus       117 ~a~~  120 (126)
T 2hgm_A          117 KSSQ  120 (126)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8853

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

Probab=99.61  E-value=1e-15  Score=120.65  Aligned_cols=76  Identities=16%  Similarity=0.378  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          293 GPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       293 ~~~~l~v~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ..++|||+|||. .+++++|+++|++||.|..|.|.        +|||||+|.+.++|.+|++.|||..|.|+.|.|.|+
T Consensus         9 ~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   80 (96)
T 2kvi_A            9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVS   80 (96)
T ss_dssp             CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEc
Confidence            446899999998 99999999999999999999984        679999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009954          372 TASGQ  376 (521)
Q Consensus       372 ~~~~~  376 (521)
                      .....
T Consensus        81 ~~~~~   85 (96)
T 2kvi_A           81 SSNAR   85 (96)
T ss_dssp             ECCCC
T ss_pred             CcCCC
Confidence            77443

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.61  E-value=8.8e-16  Score=119.45  Aligned_cols=80  Identities=21%  Similarity=0.199  Sum_probs=66.9

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHH-HhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHH-c-cCceecCce
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVM-TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-L-DGIIFEGVA  250 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G-~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~-l-~g~~~~g~~  250 (521)
                      +++|||+|||+++|+++|+++|++|| .|..+.      .+.+..++.++|||||+|.+.++|.+|++ + ++..+.|++
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 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVR------LMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQK   74 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCC------SSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEE------EEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEE
Confidence            46899999999999999999999999 554432      24455667889999999999999999994 5 567799999


Q ss_pred             EEEeCCCCC
Q 009954          251 VRVRRPTDY  259 (521)
Q Consensus       251 i~v~~~~~~  259 (521)
                      |.|.++.+.
T Consensus        75 i~V~~a~~~   83 (91)
T 2lxi_A           75 VSMHYSDPK   83 (91)
T ss_dssp             EEEECCCSC
T ss_pred             EEEEEcCCC
Confidence            999987643

>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=99.61  E-value=2.1e-16  Score=124.92  Aligned_cols=79  Identities=18%  Similarity=0.348  Sum_probs=65.1

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+|||+++|+++|+++|++||.|..+.      .+.+..++.++|||||+|.+.++|.+|+ .|||..|.|++|
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~------i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l   91 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAK------LIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI   91 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEE------EEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeE------eeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            356899999999999999999999999853311      0122223566799999999999999999 699999999999


Q ss_pred             EEeCCC
Q 009954          252 RVRRPT  257 (521)
Q Consensus       252 ~v~~~~  257 (521)
                      +|.+++
T Consensus        92 ~V~~Ak   97 (99)
T 4fxv_A           92 KVSYAR   97 (99)
T ss_dssp             EEEECC
T ss_pred             EEEEee
Confidence            999864

>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=1.7e-15  Score=114.46  Aligned_cols=71  Identities=13%  Similarity=0.170  Sum_probs=64.1

Q ss_pred             CCe-EEEcCCCCCCCHHH----HHHHHHhcC-CeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          294 PDR-VFVGGLPYYFTETQ----IKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       294 ~~~-l~v~nLp~~~te~~----l~~~F~~~G-~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      ..+ |||+|||..+++++    |+++|++|| .|.+|       +|   |+|||+|.+.++|++|++.|+|..|.|++|+
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            345 99999999999987    558999995 99888       34   8999999999999999999999999999999


Q ss_pred             EEEccCC
Q 009954          368 VRRATAS  374 (521)
Q Consensus       368 v~~~~~~  374 (521)
                      |.||+..
T Consensus        78 v~~A~~~   84 (96)
T 2diu_A           78 VSFTPKN   84 (96)
T ss_dssp             EESSCCS
T ss_pred             EEecCCC
Confidence            9999763

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.60  E-value=1.3e-15  Score=121.31  Aligned_cols=74  Identities=34%  Similarity=0.468  Sum_probs=65.1

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCCeEEEEecCHHHHHHHH-HccCceecCceEE
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~-~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      ++|||+|||..+|+++|+++|++||.            |..+.+.. ++|||||+|.+.++|.+|+ .|++..+.|+.|.
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            44455444 5999999999999999999 5999999999999


Q ss_pred             EeCCCCCC
Q 009954          253 VRRPTDYN  260 (521)
Q Consensus       253 v~~~~~~~  260 (521)
                      |.++....
T Consensus        69 V~~a~~~~   76 (101)
T 2hvz_A           69 VELSTGMP   76 (101)
T ss_dssp             EEESSSCC
T ss_pred             EEEccCCC
Confidence            99876544

>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=99.60  E-value=3.3e-15  Score=127.05  Aligned_cols=76  Identities=21%  Similarity=0.278  Sum_probs=69.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC--eEEEEEEcc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRAT  372 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~~  372 (521)
                      .+|||+||++.+++++|+++|++||.|..|.|....    ++|||||+|.+.++|++|++.|||..|.|  +.|+|.|++
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            468999999999999999999999999999987542    57899999999999999999999999965  999999998


Q ss_pred             CC
Q 009954          373 AS  374 (521)
Q Consensus       373 ~~  374 (521)
                      +.
T Consensus       123 ~~  124 (164)
T 1sjr_A          123 LT  124 (164)
T ss_dssp             SS
T ss_pred             CC
Confidence            74

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.60  E-value=1.9e-15  Score=116.98  Aligned_cols=74  Identities=18%  Similarity=0.242  Sum_probs=69.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|+++|++| .|..+.|.      .++|||||+|.+.++|.+|++.|||..+.|+.|.|.|+.
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      468999999999999999999999999999999999996


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      .
T Consensus        77 ~   77 (88)
T 1wg1_A           77 T   77 (88)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=7.6e-16  Score=131.17  Aligned_cols=81  Identities=21%  Similarity=0.265  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEE--------EEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGF--------DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v--------~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g  363 (521)
                      ...++|||+|||..+++++|.++|++||.|..+        .+.   .+|.++|||||+|.+.++|.+||..|||..|.|
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            445789999999999999999999999998764        332   378899999999999999999999999999999


Q ss_pred             eEEEEEEccCCC
Q 009954          364 KTLTVRRATASG  375 (521)
Q Consensus       364 ~~l~v~~~~~~~  375 (521)
                      +.|.|.|+....
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

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

Probab=99.60  E-value=6.8e-15  Score=116.16  Aligned_cols=77  Identities=22%  Similarity=0.340  Sum_probs=69.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+||  .+++++|+++|++||.|..|.|.      .++|||||+|.+.++|.+||+.|+|..|.|+.|.|.|+
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            34578999996  89999999999999999999984      45789999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009954          372 TASGQ  376 (521)
Q Consensus       372 ~~~~~  376 (521)
                      .+...
T Consensus        85 ~~~~~   89 (97)
T 1x5p_A           85 RKQPM   89 (97)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            87443

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=3.5e-15  Score=117.10  Aligned_cols=76  Identities=25%  Similarity=0.429  Sum_probs=68.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|+++|++||.|..|  +.++.+|.   ||||+|.+.++|.+||+ |+|..|.|+.|.|.++.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECC
Confidence            44689999999999999999999999999987  55555665   99999999999999999 99999999999999987


Q ss_pred             CC
Q 009954          373 AS  374 (521)
Q Consensus       373 ~~  374 (521)
                      ..
T Consensus        81 ~~   82 (94)
T 2e5g_A           81 QK   82 (94)
T ss_dssp             CS
T ss_pred             cC
Confidence            63

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=2.9e-15  Score=118.00  Aligned_cols=77  Identities=19%  Similarity=0.231  Sum_probs=68.3

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-Hcc--CceecC
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD--GIIFEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~--g~~~~g  248 (521)
                      ...++|||+|||+.+|+++|+++|++||.            |.++.+..++|||||+|.+.++|..|+ .|+  +..|.|
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            34679999999999999999999999998            778888888999999999999999999 465  478999


Q ss_pred             ceEEEeCCCCCC
Q 009954          249 VAVRVRRPTDYN  260 (521)
Q Consensus       249 ~~i~v~~~~~~~  260 (521)
                      ++|.|.++....
T Consensus        82 r~l~V~~A~~~~   93 (105)
T 1sjq_A           82 QPIYIQFSNHKE   93 (105)
T ss_dssp             EECCBCCCSSSS
T ss_pred             EEEEEEEcCCCC
Confidence            999999876543

>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=99.59  E-value=8.2e-15  Score=118.88  Aligned_cols=96  Identities=22%  Similarity=0.362  Sum_probs=80.9

Q ss_pred             CCCcceEEEeeCcCCcccC-CChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHH
Q 009954          415 GETLAKVLCLTEAITADAL-ADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNA  493 (521)
Q Consensus       415 ~~~~~~v~~l~~~~~~~~~-~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~  493 (521)
                      .+.++++++|.|+++..++ .+..+|++++++|+++|++||.|..|.|+ +..      .+|+|||+|.+.++|.+|+..
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~-~~~------~~G~afV~f~~~~~A~~Ai~~   83 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLF-DRH------PDGVASVSFRDPEEADYCIQT   83 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEE-TTC------TTCEEEEECSCHHHHHHHHHH
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEe-cCC------CCEEEEEEECCHHHHHHHHHH
Confidence            4578899999999888765 34567899999999999999999999774 321      258889999999999999999


Q ss_pred             HhCCeeCCcEEEEEEcCC-CCcccc
Q 009954          494 LSGRKFGGNTVNAFYYPE-DKYFNK  517 (521)
Q Consensus       494 lng~~~~gr~l~v~~~~~-~~~~~~  517 (521)
                      |||..|+|++|+|.|+.. .+|..+
T Consensus        84 lng~~~~gr~l~v~~a~~~~~~~~~  108 (112)
T 2dit_A           84 LDGRWFGGRQITAQAWDGTTDYQSG  108 (112)
T ss_dssp             STTCEETTEECEEEECCSCCCSSCC
T ss_pred             cCCCEECCcEEEEEEeCCCCCcccC
Confidence            999999999999999876 455443

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.58  E-value=8.8e-15  Score=119.42  Aligned_cols=73  Identities=19%  Similarity=0.234  Sum_probs=66.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceE-EEEEEcChHHHHHHHHHHcCCeeCC--eEEEEEEcc
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY-GFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRAT  372 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~-afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~~  372 (521)
                      .|||+||++.+++++|+++|++||.|..|.|+..      .|| |||+|.+.++|..|++.|||..|.|  +.|+|.|+.
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            4789999999999999999999999999998753      276 9999999999999999999999977  699999998


Q ss_pred             CC
Q 009954          373 AS  374 (521)
Q Consensus       373 ~~  374 (521)
                      +.
T Consensus       101 ~~  102 (124)
T 2e5i_A          101 PT  102 (124)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>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=5e-15  Score=117.88  Aligned_cols=70  Identities=26%  Similarity=0.407  Sum_probs=62.0

Q ss_pred             HHHHHHHHHHHHhh-ccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcC
Q 009954          437 EEYEEILEDMREEC-GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  510 (521)
Q Consensus       437 ~~~~~~~~dl~~~f-~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~  510 (521)
                      ..|.+++++|+++| ++||+|.+|.|+++.. +   ..+|+|||+|.+.++|.+|+..|||+.|+|++|+|.|++
T Consensus        34 ~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~---~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~sp  104 (104)
T 1jmt_A           34 EHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-D---HLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP  104 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-S---SSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEECC
T ss_pred             HHHHHHHHHHHHHhhccCCceEEEEEEeCCC-C---CccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            34677888899999 9999999999998753 3   346889999999999999999999999999999999975

>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=99.58  E-value=2.4e-15  Score=122.58  Aligned_cols=74  Identities=22%  Similarity=0.302  Sum_probs=66.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeE-----EE
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT-----LT  367 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~-----l~  367 (521)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.+       |||||+|.+.++|++||+.|||..|.|+.     |+
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            3478999999999999999999999999999999765       89999999999999999999999999988     66


Q ss_pred             EEEccC
Q 009954          368 VRRATA  373 (521)
Q Consensus       368 v~~~~~  373 (521)
                      |..+.+
T Consensus        88 v~~~~~   93 (115)
T 3beg_B           88 VKVDGP   93 (115)
T ss_dssp             EEECC-
T ss_pred             eccCCC
Confidence            666644

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.57  E-value=1.3e-14  Score=115.44  Aligned_cols=81  Identities=21%  Similarity=0.431  Sum_probs=73.1

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ...++|||+|||..+|+++|+++|.+||.|.. .      .+.+..++.++|||||+|.+.++|.+|++||+..|.|+.|
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      2677788999999999999999999999999999999999


Q ss_pred             EEeCCCCC
Q 009954          252 RVRRPTDY  259 (521)
Q Consensus       252 ~v~~~~~~  259 (521)
                      .|.++...
T Consensus        88 ~V~~a~~~   95 (101)
T 1fj7_A           88 KLEKPKGR   95 (101)
T ss_dssp             EEECCSCC
T ss_pred             EEEEcCCC
Confidence            99987654

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

Probab=99.57  E-value=3.9e-15  Score=116.02  Aligned_cols=75  Identities=21%  Similarity=0.159  Sum_probs=67.5

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCce--ecC
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII--FEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~--~~g  248 (521)
                      .++++|||+|||..+|+++|+++|++||.            |.++.+.+.+|||||+|.+.++|..|+ .|++..  +.|
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            34679999999999999999999999998            777888889999999999999999999 688764  789


Q ss_pred             ceEEEeCCCC
Q 009954          249 VAVRVRRPTD  258 (521)
Q Consensus       249 ~~i~v~~~~~  258 (521)
                      ++|.|++++.
T Consensus        87 r~i~V~~S~~   96 (100)
T 3r27_A           87 HPAFVNYSTS   96 (100)
T ss_dssp             EEEEEEECSC
T ss_pred             cEEEEEeccc
Confidence            9999998764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.57  E-value=7.8e-16  Score=120.18  Aligned_cols=82  Identities=17%  Similarity=0.279  Sum_probs=67.2

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHh--hcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCc---
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTA--IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI---  244 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~--~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~---  244 (521)
                      .....+|||+|||+.+|+++|+++|++||.+  ...      ..+.+..++.++|||||+|.+.++|.+|+ .|||.   
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v------~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~   79 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNI------RLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPP   79 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGE------ECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSC
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEE------EEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCC
Confidence            4557799999999999999999999999953  221      11334445778999999999999999999 68886   


Q ss_pred             -eecCceEEEeCCCC
Q 009954          245 -IFEGVAVRVRRPTD  258 (521)
Q Consensus       245 -~~~g~~i~v~~~~~  258 (521)
                       .+.|++|.|.++++
T Consensus        80 ~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           80 LKIDGKTIGVDFAKS   94 (95)
T ss_dssp             EEETTEEEEEEECCC
T ss_pred             ceECCEEEEEEEccC
Confidence             58999999998753

>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=99.57  E-value=9.8e-15  Score=112.91  Aligned_cols=74  Identities=18%  Similarity=0.344  Sum_probs=63.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCe--eCCeEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK--MGDKTLTVR  369 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~--~~g~~l~v~  369 (521)
                      ...++|||+|||.++++++|+++|++||.|.+|.|+.+     ++|||||+|.+.++|.+    |+|..  +.|+.|.|.
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            44579999999999999999999999999999999875     68999999999999983    56654  569999999


Q ss_pred             EccCC
Q 009954          370 RATAS  374 (521)
Q Consensus       370 ~~~~~  374 (521)
                      ++.++
T Consensus        80 ~a~~k   84 (89)
T 3d2w_A           80 NAEPK   84 (89)
T ss_dssp             ECC--
T ss_pred             EcCCC
Confidence            99764

>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=99.56  E-value=1.9e-15  Score=123.52  Aligned_cols=99  Identities=19%  Similarity=0.242  Sum_probs=83.4

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe---cCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~---~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      ..++|||+|||..+|+++|+++|..||.            |..+.+   +.++|||||+|.+.++|..|+ .|||..+.|
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            3579999999999999999999999998            444444   556899999999999999999 599999999


Q ss_pred             ceEEEeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCC
Q 009954          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT  320 (521)
Q Consensus       249 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~  320 (521)
                      +.|.|.++.....                                     ..+++...++++|.++|++||.
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            9999998542211                                     0367777889999999999985

>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=7.7e-15  Score=113.36  Aligned_cols=71  Identities=24%  Similarity=0.541  Sum_probs=65.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESF----G-------TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM  361 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~----G-------~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~  361 (521)
                      ..++|||+|||..+++++|+++|++|    |       .|..+.+..+      +|||||+|.+.++|.+|+ .|||..|
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            34689999999999999999999999    8       8999988765      789999999999999999 8999999


Q ss_pred             CCeEEEEEE
Q 009954          362 GDKTLTVRR  370 (521)
Q Consensus       362 ~g~~l~v~~  370 (521)
                      .|+.|.|..
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            999999975

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=6.9e-15  Score=119.79  Aligned_cols=77  Identities=27%  Similarity=0.432  Sum_probs=65.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC---CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT---GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~---g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (521)
                      ...++|||+|||..+++++|+++|++||.|. +.++.+..+   |.++|||||+|.+.++|++||+.|+  .++|+.|.+
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  255555555


Q ss_pred             EEc
Q 009954          369 RRA  371 (521)
Q Consensus       369 ~~~  371 (521)
                      ..+
T Consensus        83 ~~~   85 (114)
T 2dnl_A           83 VSS   85 (114)
T ss_dssp             ECC
T ss_pred             ccC
Confidence            443

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.54  E-value=2.6e-14  Score=110.37  Aligned_cols=84  Identities=46%  Similarity=0.825  Sum_probs=71.6

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ...++|||+|||+.+|+++|+++|.+||.+.+... .++..+..+.+..++|||||+|.+.++|.+|+.|||..+.|+.|
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            34679999999999999999999999975544211 12234888999999999999999999999999999999999999


Q ss_pred             EEeCC
Q 009954          252 RVRRP  256 (521)
Q Consensus       252 ~v~~~  256 (521)
                      +|++|
T Consensus        83 ~V~rp   87 (87)
T 2hzc_A           83 KIRRP   87 (87)
T ss_dssp             EEECC
T ss_pred             EEeCC
Confidence            99863

>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=99.53  E-value=1.5e-14  Score=114.85  Aligned_cols=77  Identities=18%  Similarity=0.172  Sum_probs=67.3

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccC--ceecC
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG--IIFEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g--~~~~g  248 (521)
                      .+.++|||+|||+.+|+++|+++|.+||.            |..+.+...+|||||+|.+.++|.+|+ .|++  ..|.|
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 5765  45999


Q ss_pred             ceEEEeCCCCCC
Q 009954          249 VAVRVRRPTDYN  260 (521)
Q Consensus       249 ~~i~v~~~~~~~  260 (521)
                      ++|.|.++....
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=99.53  E-value=5.6e-15  Score=116.43  Aligned_cols=77  Identities=22%  Similarity=0.235  Sum_probs=68.5

Q ss_pred             ccCCeEEEeCCCc-cCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccC--ceec
Q 009954          172 RHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG--IIFE  247 (521)
Q Consensus       172 ~~~~~l~v~nlp~-~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g--~~~~  247 (521)
                      .+.++|||+|||+ .+|+++|+++|.+||.            |.++.+..++|||||+|.+.++|..|+ .|++  ..|.
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 9999999999999998            788888888999999999999999999 5775  5699


Q ss_pred             CceEEEeCCCCCC
Q 009954          248 GVAVRVRRPTDYN  260 (521)
Q Consensus       248 g~~i~v~~~~~~~  260 (521)
                      |++|.|.++..+.
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

>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=99.53  E-value=1.6e-14  Score=114.08  Aligned_cols=77  Identities=17%  Similarity=0.163  Sum_probs=68.0

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-Hc--cCceecC
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-AL--DGIIFEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l--~g~~~~g  248 (521)
                      .+.++|||+|||+.+|+++|+++|.+||.            |.++.+...+|||||+|.+.++|..|+ .|  ++..+.|
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            34679999999999999999999999997            677777788999999999999999999 45  5788999


Q ss_pred             ceEEEeCCCCCC
Q 009954          249 VAVRVRRPTDYN  260 (521)
Q Consensus       249 ~~i~v~~~~~~~  260 (521)
                      ++|.|.++....
T Consensus        81 r~l~V~~a~~~~   92 (101)
T 2cq1_A           81 QPIYIQYSNHKE   92 (101)
T ss_dssp             EECEEEECSCSS
T ss_pred             cEEEEEEcCccc
Confidence            999999976543

>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=99.53  E-value=2.3e-14  Score=144.15  Aligned_cols=67  Identities=21%  Similarity=0.313  Sum_probs=61.0

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      ++|.++|+.||.|+.|.|+.+..++..   +|||||+|.+.++|.+||..|||..|+|+.|.|.|+....
T Consensus       117 ~~L~~~F~~~G~I~~v~i~~d~~tg~~---kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          117 SKLRREFEVYGPIKRIHMVYSKRSGKP---RGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRT  183 (437)
T ss_pred             HHHHHHHHHcCCeeEEEeeccCCCCCc---cceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            599999999999999999998766654   6889999999999999999999999999999999987543

>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=99.53  E-value=5.5e-14  Score=113.51  Aligned_cols=79  Identities=24%  Similarity=0.409  Sum_probs=71.6

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      .....++|||+|||..+|+++|+++|.+||.            |..+.+...+|||||+|.+.++|.+|+ .|+|..|.|
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~------------i~~v~i~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   88 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQ------------IMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEG   88 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEeCCCCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3456789999999999999999999999997            778888888999999999999999999 799999999


Q ss_pred             ceEEEeCCCCCC
Q 009954          249 VAVRVRRPTDYN  260 (521)
Q Consensus       249 ~~i~v~~~~~~~  260 (521)
                      +.|.|.++....
T Consensus        89 ~~l~v~~a~~~~  100 (109)
T 1x4g_A           89 HVVKCYWGKESP  100 (109)
T ss_dssp             EECEEECCCCCC
T ss_pred             cEEEEEecCCCC
Confidence            999999976543

>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=99.53  E-value=6.6e-15  Score=120.27  Aligned_cols=84  Identities=17%  Similarity=0.264  Sum_probs=68.0

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....++|||+|||..+|+++|+++|.+||.|..+.      .+.+...+.++|||||+|.+.++|.+|+ .||+..|.|+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   95 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAK------VFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMK   95 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEE------EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            34568999999999999999999999999854311      0111123456799999999999999999 7999999999


Q ss_pred             eEEEeCCCCCC
Q 009954          250 AVRVRRPTDYN  260 (521)
Q Consensus       250 ~i~v~~~~~~~  260 (521)
                      .|+|.++....
T Consensus        96 ~l~V~~a~~~~  106 (115)
T 2cpz_A           96 RLKVQLKRSKN  106 (115)
T ss_dssp             ECEEECCCCSC
T ss_pred             EEEEEEcCCCC
Confidence            99999876543

>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=99.52  E-value=3e-14  Score=113.51  Aligned_cols=81  Identities=11%  Similarity=0.205  Sum_probs=70.3

Q ss_pred             CCCeEEEcCC--CCCCC--------HHHHHHHHHhcCCeeEEEEeecCCC--CCcceEEEEEEcChHHHHHHHHHHcCCe
Q 009954          293 GPDRVFVGGL--PYYFT--------ETQIKELLESFGTLHGFDLVKDRDT--GNSKGYGFCVYQDPAVTDIACAALNGLK  360 (521)
Q Consensus       293 ~~~~l~v~nL--p~~~t--------e~~l~~~F~~~G~i~~v~i~~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~g~~  360 (521)
                      ++++|.|.||  |..+.        +++|+++|++||.|.+|.|+++..+  +.++|+|||+|.+.++|.+|++.|||..
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            4568999999  33332        3789999999999999999988654  4689999999999999999999999999


Q ss_pred             eCCeEEEEEEccC
Q 009954          361 MGDKTLTVRRATA  373 (521)
Q Consensus       361 ~~g~~l~v~~~~~  373 (521)
                      |+|+.|.|.|+..
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

>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=99.52  E-value=5.9e-14  Score=112.11  Aligned_cols=77  Identities=27%  Similarity=0.387  Sum_probs=66.8

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec----CCCCeEEEEecCHHHHHHHH-HccCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAM-ALDGII  245 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~----~~~g~afV~f~~~~~a~~A~-~l~g~~  245 (521)
                      ....++|||+|||..+|+++|+++|.+||.            |..+.+.    .++|||||+|.+.++|.+|+ .||+..
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   79 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGP------------CKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRK   79 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSC------------EEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCC------------EeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCC
Confidence            345789999999999999999999999998            4444443    35799999999999999999 599999


Q ss_pred             ecCceEEEeCCCCC
Q 009954          246 FEGVAVRVRRPTDY  259 (521)
Q Consensus       246 ~~g~~i~v~~~~~~  259 (521)
                      |.|+.|.|.++...
T Consensus        80 ~~g~~l~V~~a~~~   93 (103)
T 2cqi_A           80 ILGKEVKVNWATTP   93 (103)
T ss_dssp             ETTEEEEEEECCCT
T ss_pred             cCCCeEEEEECCCC
Confidence            99999999987654

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

Probab=99.52  E-value=1.7e-14  Score=114.86  Aligned_cols=75  Identities=23%  Similarity=0.405  Sum_probs=68.0

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||.++|+++|+++|.+||.            |..+.+..++|||||+|.+.++|..|+ .|||..|.|+.
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            34679999999999999999999999997            566677789999999999999999999 79999999999


Q ss_pred             EEEeCCCC
Q 009954          251 VRVRRPTD  258 (521)
Q Consensus       251 i~v~~~~~  258 (521)
                      |+|.++..
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

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=3.1e-14  Score=112.32  Aligned_cols=77  Identities=21%  Similarity=0.274  Sum_probs=67.4

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||..+|+++|+++|.+||.|.           ..+.++.++|||||+|.+.++|.+|+ .|||..|.|+.
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-----------~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   85 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-----------LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDT   85 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-----------SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-----------EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            4467999999999999999999999999751           23445688999999999999999999 79999999999


Q ss_pred             EEEeCCCCC
Q 009954          251 VRVRRPTDY  259 (521)
Q Consensus       251 i~v~~~~~~  259 (521)
                      |.|.++...
T Consensus        86 l~V~~a~~~   94 (97)
T 2e5j_A           86 LRVALARQQ   94 (97)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEEcCCC
Confidence            999986543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.51  E-value=3.4e-14  Score=114.06  Aligned_cols=74  Identities=18%  Similarity=0.191  Sum_probs=64.6

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHH-HhhcCCCCCCCCceEEEEe--cCCCCeEEEEecCHHHHHHHH-HccCceec
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVM-TAIGGNSAGPGDAVVNVYI--NHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G-~~~~~~~~~~~~~v~~~~~--~~~~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      ....+|||+|||+.+|+++|+++|.+|| .|            ..+.+  ..++|||||+|.+.++|++|+ .|||..|.
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            3457899999999999999999999999 63            33333  357899999999999999999 69999999


Q ss_pred             CceEEEeCCC
Q 009954          248 GVAVRVRRPT  257 (521)
Q Consensus       248 g~~i~v~~~~  257 (521)
                      |+.|.|.++.
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            9999999764

>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=6.3e-14  Score=114.45  Aligned_cols=83  Identities=16%  Similarity=0.268  Sum_probs=71.4

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||..+|+++|+++|.+||.|..+.      ..++...+.++|||||+|.+.++|.+|+ .|||..|.|+.
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            3467999999999999999999999999975432      1455557888999999999999999999 69999999999


Q ss_pred             EEEeCCCCCC
Q 009954          251 VRVRRPTDYN  260 (521)
Q Consensus       251 i~v~~~~~~~  260 (521)
                      |.|.++....
T Consensus        97 l~v~~a~~~~  106 (115)
T 2cpx_A           97 LVIEFGKNKK  106 (115)
T ss_dssp             CEEEECCCCS
T ss_pred             EEEEEccCCC
Confidence            9999876543

>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=99.51  E-value=1.9e-14  Score=110.58  Aligned_cols=73  Identities=22%  Similarity=0.367  Sum_probs=67.0

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-Hc-cCceecCc
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-AL-DGIIFEGV  249 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l-~g~~~~g~  249 (521)
                      ...++|||+|||..+|+++|+++|.+||.            |..+.+..++|||||+|.+.++|.+|+ .| ++..+.|+
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~------------i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~   77 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGE------------IRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGR   77 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSC------------EEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETTE
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCC------------EeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECCC
Confidence            44679999999999999999999999987            777777788999999999999999999 48 99999999


Q ss_pred             eEEEeCC
Q 009954          250 AVRVRRP  256 (521)
Q Consensus       250 ~i~v~~~  256 (521)
                      .|.|.++
T Consensus        78 ~l~v~~a   84 (85)
T 2ytc_A           78 RLNVKWG   84 (85)
T ss_dssp             ECCEEEC
T ss_pred             EEEEEec
Confidence            9999875

>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=99.51  E-value=4.8e-14  Score=111.25  Aligned_cols=75  Identities=21%  Similarity=0.352  Sum_probs=68.3

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceec--Cc
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE--GV  249 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~--g~  249 (521)
                      ..++|||+|||..+|+++|+++|.+||.            |..+.+...+|||||+|.+.++|.+|+ .||+..|.  |+
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~   83 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGS------------IRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDR   83 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSC------------EEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCCCc
Confidence            4578999999999999999999999997            777777778999999999999999999 59999999  99


Q ss_pred             eEEEeCCCCC
Q 009954          250 AVRVRRPTDY  259 (521)
Q Consensus       250 ~i~v~~~~~~  259 (521)
                      .|.|.++...
T Consensus        84 ~l~V~~a~~~   93 (97)
T 1why_A           84 RLRVDFAKSG   93 (97)
T ss_dssp             BCEEEECCCC
T ss_pred             EEEEEECCCC
Confidence            9999987643

>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=99.51  E-value=3.7e-14  Score=114.55  Aligned_cols=77  Identities=29%  Similarity=0.500  Sum_probs=66.7

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe---cCCCCeEEEEecCHHHHHHHH-HccCceec
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~---~~~~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      ...++|||+|||..+|+++|+++|.+||.            |..+.+   ..++|||||+|.+.++|.+|+ .||+..|.
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~   87 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGA------------IRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYD   87 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            45689999999999999999999999998            444443   335789999999999999999 79999999


Q ss_pred             CceEEEeCCCCCC
Q 009954          248 GVAVRVRRPTDYN  260 (521)
Q Consensus       248 g~~i~v~~~~~~~  260 (521)
                      |+.|.|.++....
T Consensus        88 g~~l~V~~a~~~~  100 (109)
T 1x4a_A           88 GYRLRVEFPRSGR  100 (109)
T ss_dssp             TEECEEECCCCCC
T ss_pred             CeEEEEEEcccCC
Confidence            9999999876543

>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=7.4e-15  Score=109.92  Aligned_cols=75  Identities=15%  Similarity=0.280  Sum_probs=63.6

Q ss_pred             eEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEEEeC
Q 009954          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (521)
Q Consensus       176 ~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v~~  255 (521)
                      +|||+|||+.+|+++|+++|++||.|..+.+      +.+...+.++|||||+|.+.++|++|+++++..+.|+.|.|++
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            5899999999999999999999998644321      2222346678999999999999999999999999999999987


Q ss_pred             C
Q 009954          256 P  256 (521)
Q Consensus       256 ~  256 (521)
                      +
T Consensus        75 A   75 (75)
T 2mss_A           75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.51  E-value=4.1e-14  Score=111.40  Aligned_cols=74  Identities=15%  Similarity=0.332  Sum_probs=66.0

Q ss_pred             hccCCeEEEeCCCc-cCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          171 TRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       171 ~~~~~~l~v~nlp~-~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      ....++|||+|||. .+++++|+++|.+||.            |..+.+  .+|||||+|.+.++|.+|+ .|||..+.|
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~------------v~~v~i--~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGH------------IMQINI--KNAFGFIQFDNPQSVRDAIEXESQEMNFG   84 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSC------------EEEEEE--CSSEEEEEESSHHHHHHHHHHHTTSEETT
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCC------------EEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            34578999999998 9999999999999997            566666  4899999999999999999 699999999


Q ss_pred             ceEEEeCCCC
Q 009954          249 VAVRVRRPTD  258 (521)
Q Consensus       249 ~~i~v~~~~~  258 (521)
                      +.|.|.++..
T Consensus        85 ~~l~V~~a~~   94 (97)
T 2xnq_A           85 KKLILEVSSS   94 (97)
T ss_dssp             EECEEEECCC
T ss_pred             EEEEEEecCC
Confidence            9999998653

>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=99.50  E-value=1.1e-14  Score=116.82  Aligned_cols=83  Identities=25%  Similarity=0.384  Sum_probs=66.8

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||..+|+++|+++|.+||.|..+.+      +.+...+.++|||||+|.+.++|.+|+ .||+..|.|+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   86 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHM------PKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKP   86 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEEC------CBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE------EecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            45679999999999999999999999998432111      111123456799999999999999999 59999999999


Q ss_pred             EEEeCCCCCC
Q 009954          251 VRVRRPTDYN  260 (521)
Q Consensus       251 i~v~~~~~~~  260 (521)
                      |.|.++....
T Consensus        87 l~v~~a~~~~   96 (105)
T 1x5u_A           87 IRVNKASAHN   96 (105)
T ss_dssp             CEEEETTTTS
T ss_pred             EEEEECCCCC
Confidence            9999876543

>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=99.50  E-value=7e-14  Score=109.96  Aligned_cols=75  Identities=17%  Similarity=0.174  Sum_probs=65.9

Q ss_pred             cCCeEEEeCCCccCcHHHHH----HHHHHHHHhhcCCCCCCCCceEEEEecCC---CCeEEEEecCHHHHHHHH-HccCc
Q 009954          173 HARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVYINHE---KKFAFVEMRTVEEASNAM-ALDGI  244 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~----~~f~~~G~~~~~~~~~~~~~v~~~~~~~~---~g~afV~f~~~~~a~~A~-~l~g~  244 (521)
                      ..++|||+|||..+++++|+    ++|.+||.            |..+.+...   +|||||+|.+.++|.+|+ .|||.
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            35689999999999999999    99999997            566665433   899999999999999999 69999


Q ss_pred             eecCceEEEeCCCCC
Q 009954          245 IFEGVAVRVRRPTDY  259 (521)
Q Consensus       245 ~~~g~~i~v~~~~~~  259 (521)
                      .|.|+.|+|.++...
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

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

Probab=99.50  E-value=2.8e-14  Score=117.67  Aligned_cols=80  Identities=15%  Similarity=0.213  Sum_probs=66.0

Q ss_pred             cCCeEEEeCCCccCcHHHHH----HHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceec
Q 009954          173 HARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~----~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      ..++|||+|||+.+++++|+    ++|++||.|..         |.....+.++|||||+|.+.++|..|+ .|||..|.
T Consensus        28 p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~---------v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~   98 (127)
T 2a3j_A           28 PSQVVLITNINPEVPKEKLQALLYALASSQGDILD---------IVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQ   98 (127)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEE---------EEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEE---------EEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeC
Confidence            35789999999999999876    69999998432         111223567899999999999999999 79999999


Q ss_pred             CceEEEeCCCCCCc
Q 009954          248 GVAVRVRRPTDYNP  261 (521)
Q Consensus       248 g~~i~v~~~~~~~~  261 (521)
                      |++|.|.++.....
T Consensus        99 gr~l~V~~a~~~~~  112 (127)
T 2a3j_A           99 GNPLVITFSETPQS  112 (127)
T ss_dssp             TSCCEEEECCCCCH
T ss_pred             CCEEEEEEccCcch
Confidence            99999999775543

>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=99.50  E-value=1.6e-14  Score=116.78  Aligned_cols=77  Identities=19%  Similarity=0.231  Sum_probs=66.9

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-Hcc--CceecC
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD--GIIFEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~--g~~~~g  248 (521)
                      .+.++|||+|||+.+|+++|+++|++||.            |.++.+...+|||||+|.+.++|.+|+ .|+  +..|.|
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            34678999999999999999999999998            566666667999999999999999999 576  468999


Q ss_pred             ceEEEeCCCCCC
Q 009954          249 VAVRVRRPTDYN  260 (521)
Q Consensus       249 ~~i~v~~~~~~~  260 (521)
                      ++|.|.++....
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

>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=1.3e-14  Score=112.18  Aligned_cols=76  Identities=20%  Similarity=0.423  Sum_probs=65.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.+     ++|||||+|.+.++|++|+..  +..+.|+.|.|.++.
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            3579999999999999999999999999999998865     689999999999999864321  345699999999997


Q ss_pred             CCC
Q 009954          373 ASG  375 (521)
Q Consensus       373 ~~~  375 (521)
                      ++.
T Consensus        77 ~~~   79 (88)
T 1wf0_A           77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            743

>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=99.50  E-value=1.7e-14  Score=114.37  Aligned_cols=76  Identities=29%  Similarity=0.496  Sum_probs=69.1

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||..+|+++|+++|.+||.            |..+.+..++|||||+|.+.++|.+|+ .|++..|.|+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~   80 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGK------------AGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQ   80 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCC------------CSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCC------------eEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeCCce
Confidence            45679999999999999999999999987            667777788999999999999999999 79999999999


Q ss_pred             EEEeCCCCC
Q 009954          251 VRVRRPTDY  259 (521)
Q Consensus       251 i~v~~~~~~  259 (521)
                      |.|.++...
T Consensus        81 l~v~~a~~~   89 (99)
T 2cpj_A           81 LRVRFACHS   89 (99)
T ss_dssp             CEEEESSCC
T ss_pred             EEEEEcCCC
Confidence            999987653

>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=99.50  E-value=7.1e-14  Score=113.41  Aligned_cols=79  Identities=14%  Similarity=0.145  Sum_probs=69.9

Q ss_pred             CCeEEEcCCCCC--C---CHHHHHHHHHhcCCeeEEEEeecCC----CCCcceEEEEEEcChHHHHHHHHHHcCCeeCCe
Q 009954          294 PDRVFVGGLPYY--F---TETQIKELLESFGTLHGFDLVKDRD----TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK  364 (521)
Q Consensus       294 ~~~l~v~nLp~~--~---te~~l~~~F~~~G~i~~v~i~~~~~----~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~  364 (521)
                      .++|+|.||-..  +   .++||+++|++||.|.+|.|+.+..    ++.++|+|||+|.+.++|.+|++.|||.+|+|+
T Consensus        20 s~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR   99 (118)
T 3ue2_A           20 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR   99 (118)
T ss_dssp             CCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            468999999422  2   3689999999999999999998864    457789999999999999999999999999999


Q ss_pred             EEEEEEcc
Q 009954          365 TLTVRRAT  372 (521)
Q Consensus       365 ~l~v~~~~  372 (521)
                      .|.|.|+.
T Consensus       100 ~i~v~~~~  107 (118)
T 3ue2_A          100 KVVAEVYD  107 (118)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEcC
Confidence            99999985

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.50  E-value=9e-15  Score=122.70  Aligned_cols=68  Identities=22%  Similarity=0.353  Sum_probs=61.2

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  514 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~  514 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|++||+.|||..|+|++|+|.|+....-
T Consensus        62 ~~L~~~F~~~G~i~~v~i~~~~~~g~~---~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~  129 (135)
T 2lea_A           62 DTLRRVFEKYGRVGDVYIPRDRYTKES---RGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  129 (135)
T ss_dssp             HHHHHHHGGGSCCSEEECCCCSSSSSC---CSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCC
T ss_pred             HHHHHHHHhcCCEEEEEEEecCCCCcc---ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            699999999999999999998766553   57789999999999999999999999999999999876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=1.3e-14  Score=114.29  Aligned_cols=83  Identities=16%  Similarity=0.305  Sum_probs=67.6

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+|||..+|+++|+++|.+||.|..+.     ..+.+...+.++|||||+|.+.++|.+|+ .||+..|.|+.|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~-----~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   78 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTP-----KIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPI   78 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCC-----EECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE-----EEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            467999999999999999999999999864320     11122234567899999999999999999 599999999999


Q ss_pred             EEeCCCCCC
Q 009954          252 RVRRPTDYN  260 (521)
Q Consensus       252 ~v~~~~~~~  260 (521)
                      .|.++....
T Consensus        79 ~v~~a~~~~   87 (96)
T 1x5t_A           79 TVSYAFKKD   87 (96)
T ss_dssp             EEEESCCCC
T ss_pred             EEEEecccC
Confidence            999876543

>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=99.49  E-value=8.6e-14  Score=124.24  Aligned_cols=77  Identities=22%  Similarity=0.267  Sum_probs=72.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ++|||+|||..+++++|.++|++||.|..|.|+.+. +|.++|||||+|.+.++|.+|++.+ +..|+|+.|.|.+...
T Consensus       110 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             CEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            689999999999999999999999999999999986 6999999999999999999999865 5699999999999875

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=4.5e-14  Score=110.98  Aligned_cols=74  Identities=27%  Similarity=0.407  Sum_probs=64.6

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCCeEEEEecCHHHHHHHH-HccCc
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGI  244 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~A~-~l~g~  244 (521)
                      ...++|||+|||..+|+++|+++|.+||.|            ..+.+      +.++|||||+|.+.++|.+|+ .|||.
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v------------~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   80 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPI------------ADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM   80 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCE------------EEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCe------------eEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCC
Confidence            346789999999999999999999999974            44433      455789999999999999999 59999


Q ss_pred             eecCceEEEeCCC
Q 009954          245 IFEGVAVRVRRPT  257 (521)
Q Consensus       245 ~~~g~~i~v~~~~  257 (521)
                      .|.|+.|.|.+++
T Consensus        81 ~~~g~~l~v~~a~   93 (95)
T 2cqc_A           81 ELDGRRIRVSGPS   93 (95)
T ss_dssp             EETTEEEEEECCS
T ss_pred             EECCEEEEEEecC
Confidence            9999999999864

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

Probab=99.49  E-value=4.8e-14  Score=113.55  Aligned_cols=67  Identities=18%  Similarity=0.239  Sum_probs=61.4

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|++||+.|||..|+|+.|+|.++....
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            599999999999999999999877654   6889999999999999999999999999999999987543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=1.2e-13  Score=107.36  Aligned_cols=74  Identities=23%  Similarity=0.417  Sum_probs=65.9

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||..+|+++|+++|.+||.            |..+.+.  ++||||+|.+.++|.+|+ .|||..|.|+.
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~~~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~   72 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGR------------VIECDVV--KDYAFVHMEKEADAKAAIAQLNGKEVKGKR   72 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSC------------EEEEEEC--SSCEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCC------------EEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            45678999999999999999999999997            6666665  569999999999999999 69999999999


Q ss_pred             EEEeCCCCC
Q 009954          251 VRVRRPTDY  259 (521)
Q Consensus       251 i~v~~~~~~  259 (521)
                      |.|.++...
T Consensus        73 l~v~~a~~~   81 (90)
T 2dnp_A           73 INVELSTKG   81 (90)
T ss_dssp             CEEEESCCC
T ss_pred             EEEEECCCC
Confidence            999987654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=1.7e-14  Score=117.39  Aligned_cols=91  Identities=21%  Similarity=0.208  Sum_probs=69.4

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCC--CCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCcee
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAG--PGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~--~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~  246 (521)
                      .....++|||+|||..+|+++|+++|.+||.|.......  .+..+.+..++.++|||||+|.+.++|.+|+ .||+..|
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            345678999999999999999999999999864110000  0001122233556899999999999999999 5999999


Q ss_pred             cCceEEEeCCCCCC
Q 009954          247 EGVAVRVRRPTDYN  260 (521)
Q Consensus       247 ~g~~i~v~~~~~~~  260 (521)
                      .|+.|.|.++....
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            99999999876544

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=1.3e-13  Score=109.28  Aligned_cols=76  Identities=26%  Similarity=0.401  Sum_probs=66.2

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHH--HHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceec
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQV--MTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~--G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      ....++|||+|||..+|+++|+++|.+|  |.            |..+.+  .+|||||+|.+.++|.+|+ .|||..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~------------v~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~   77 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGA------------VERVKK--IRDYAFVHFSNREDAVEAMKALNGKVLD   77 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTC------------EEEEEE--CSSEEEEEESSHHHHHHHHHHHSSEEET
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcc------------eEEEEE--eCCeEEEEeCCHHHHHHHHHHhCCCEeC
Confidence            3457899999999999999999999999  65            555554  4789999999999999999 59999999


Q ss_pred             CceEEEeCCCCCC
Q 009954          248 GVAVRVRRPTDYN  260 (521)
Q Consensus       248 g~~i~v~~~~~~~  260 (521)
                      |+.|.|.++....
T Consensus        78 g~~l~v~~a~~~~   90 (99)
T 2cpd_A           78 GSPIEVTLAKPVD   90 (99)
T ss_dssp             TEEEEEECCCCCC
T ss_pred             CcEEEEEECCCCC
Confidence            9999999876543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.49  E-value=4.1e-14  Score=113.73  Aligned_cols=76  Identities=24%  Similarity=0.310  Sum_probs=66.0

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      .....++|||+|||..+|+++|+++|.+||.|            ..+.+.  +|||||+|.+.++|.+|+ .|||..|.|
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 009954          249 VAVRVRRPTDY  259 (521)
Q Consensus       249 ~~i~v~~~~~~  259 (521)
                      +.|.|.++...
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

>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=99.49  E-value=9.1e-14  Score=111.01  Aligned_cols=78  Identities=24%  Similarity=0.388  Sum_probs=67.5

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC----CCCeEEEEecCHHHHHHHH-HccCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH----EKKFAFVEMRTVEEASNAM-ALDGII  245 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~----~~g~afV~f~~~~~a~~A~-~l~g~~  245 (521)
                      ....++|||+|||..+|+++|+++|.+||.            |..+.+..    ++|||||+|.+.++|.+|+ .||+..
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~------------v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   79 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGK------------ILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTV   79 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSC------------EEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            445689999999999999999999999997            45555433    4899999999999999999 699999


Q ss_pred             ecCceEEEeCCCCCC
Q 009954          246 FEGVAVRVRRPTDYN  260 (521)
Q Consensus       246 ~~g~~i~v~~~~~~~  260 (521)
                      |.|+.|.|.++....
T Consensus        80 ~~g~~l~v~~a~~~~   94 (103)
T 2cq3_A           80 VEGRKIEVNNATARV   94 (103)
T ss_dssp             ETTEECEEEECCSSC
T ss_pred             ECCEEEEEEEcccCC
Confidence            999999999876543

>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=99.49  E-value=6.8e-15  Score=113.65  Aligned_cols=80  Identities=11%  Similarity=0.319  Sum_probs=64.4

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      ....++|||+|||+.+|+++|+++|++||.|..+.      .+.+..++.++|||||+|.+.++|.+|+++++..+.|+.
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~   81 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCT------IKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRV   81 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEE------EEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE------EeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEE
Confidence            45578999999999999999999999999843210      011111244579999999999999999988999999999


Q ss_pred             EEEeCC
Q 009954          251 VRVRRP  256 (521)
Q Consensus       251 i~v~~~  256 (521)
                      |.|+++
T Consensus        82 i~v~~A   87 (87)
T 3s7r_A           82 IDPKKA   87 (87)
T ss_dssp             EEEEEC
T ss_pred             EEEEeC
Confidence            999863

>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=99.49  E-value=3.9e-15  Score=115.73  Aligned_cols=79  Identities=15%  Similarity=0.154  Sum_probs=61.2

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHH--HhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVM--TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G--~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      .+|||+|||.++|+++|+++|++||  .|..+      ..+.+..++.++|||||+|.+.++|.+|+ .|||..|.|+.|
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v------~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i   75 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEI------KFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNP   75 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCE------EEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEE------EEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEE
Confidence            3799999999999999999999999  64321      11222225567899999999999999999 799999999999


Q ss_pred             EEeCCCCC
Q 009954          252 RVRRPTDY  259 (521)
Q Consensus       252 ~v~~~~~~  259 (521)
                      .|.++...
T Consensus        76 ~V~~~~~~   83 (90)
T 3p5t_L           76 VVTPSNKL   83 (90)
T ss_dssp             EECCC---
T ss_pred             EEEECCCC
Confidence            99986543

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=8e-14  Score=108.30  Aligned_cols=74  Identities=27%  Similarity=0.455  Sum_probs=66.2

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+|||.++|+++|+++|.+||.            |..+.+.  +|||||+|.+.++|.+|+ .||+..|.|+.|
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   72 (90)
T 2dnq_A            7 GMVKLFIGNLPREATEQEIRSLFEQYGK------------VLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNI   72 (90)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHHHTSSC------------EEEEEEE--TTEEEEEESSHHHHHHHHHHHTTCBCSSCBC
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEE--CCEEEEEECCHHHHHHHHHHhcCCccCCcEE
Confidence            4679999999999999999999999997            5555555  899999999999999999 799999999999


Q ss_pred             EEeCCCCCC
Q 009954          252 RVRRPTDYN  260 (521)
Q Consensus       252 ~v~~~~~~~  260 (521)
                      .|.++....
T Consensus        73 ~v~~a~~~~   81 (90)
T 2dnq_A           73 NVEASKNKS   81 (90)
T ss_dssp             EEECSSCCC
T ss_pred             EEEECCCCC
Confidence            999876544

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.48  E-value=8.9e-14  Score=111.94  Aligned_cols=78  Identities=22%  Similarity=0.337  Sum_probs=67.3

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-------cCCCCeEEEEecCHHHHHHHH-Hc-
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVEMRTVEEASNAM-AL-  241 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~-------~~~~g~afV~f~~~~~a~~A~-~l-  241 (521)
                      ....++|||+|||..+|+++|+++|.+||.            |..+.+       +.++|||||+|.+.++|.+|+ .| 
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~   79 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGE------------LKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALC   79 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCC------------eEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhc
Confidence            345789999999999999999999999998            444444       345899999999999999999 68 


Q ss_pred             cCceecCceEEEeCCCCCC
Q 009954          242 DGIIFEGVAVRVRRPTDYN  260 (521)
Q Consensus       242 ~g~~~~g~~i~v~~~~~~~  260 (521)
                      |+..|.|+.|.|.++....
T Consensus        80 ~~~~~~g~~l~v~~a~~~~   98 (107)
T 2cph_A           80 HSTHLYGRRLVLEWADSEV   98 (107)
T ss_dssp             TCCBSSSCBCEEEECCCCC
T ss_pred             cCCeECCCEEEEEeCCCCC
Confidence            9999999999999876543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.48  E-value=7.1e-14  Score=118.30  Aligned_cols=85  Identities=15%  Similarity=0.239  Sum_probs=67.6

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      .....++|||+|||..+|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|.+|+ .|||..|.|
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g  111 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVK------IVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN  111 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEE------EEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            345678999999999999999999999999843210      0111112345799999999999999999 599999999


Q ss_pred             ceEEEeCCCCCC
Q 009954          249 VAVRVRRPTDYN  260 (521)
Q Consensus       249 ~~i~v~~~~~~~  260 (521)
                      +.|+|.++....
T Consensus       112 ~~l~v~~a~~~~  123 (139)
T 1u6f_A          112 KRLKVALAASGH  123 (139)
T ss_dssp             CEEEEEESSCCC
T ss_pred             eEEEEEECCCCC
Confidence            999999876543

>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=99.48  E-value=1.7e-14  Score=115.32  Aligned_cols=78  Identities=23%  Similarity=0.312  Sum_probs=67.8

Q ss_pred             hccCCeEEEeCCCcc-CcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-Hcc--Ccee
Q 009954          171 TRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD--GIIF  246 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~-~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~--g~~~  246 (521)
                      ....++|||+|||++ +|+++|+++|.+||.            |.++.+..++|||||+|.+.++|..|+ .|+  +..|
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            345789999999998 999999999999998            667777788999999999999999999 565  5669


Q ss_pred             cCceEEEeCCCCCC
Q 009954          247 EGVAVRVRRPTDYN  260 (521)
Q Consensus       247 ~g~~i~v~~~~~~~  260 (521)
                      .|++|.|.++....
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            99999999876544

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.48  E-value=8.9e-14  Score=114.09  Aligned_cols=74  Identities=18%  Similarity=0.289  Sum_probs=65.0

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCCeEEEEecCHHHHHHHH-HccC
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG  243 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~A~-~l~g  243 (521)
                      ....++|||+|||.++|+++|+++|.+||.|            ..+.+      +.++|||||+|.+.++|.+|+ .|||
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i------------~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g  104 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNV------------ISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNG  104 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEE------------EEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCE------------EEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCC
Confidence            4457899999999999999999999999984            44443      456899999999999999999 6999


Q ss_pred             ceecCceEEEeCC
Q 009954          244 IIFEGVAVRVRRP  256 (521)
Q Consensus       244 ~~~~g~~i~v~~~  256 (521)
                      ..|.|+.|+|.++
T Consensus       105 ~~~~g~~l~V~~a  117 (118)
T 2khc_A          105 FQVGTKRLKVQLK  117 (118)
T ss_dssp             CEETTEECCEEEC
T ss_pred             CEECCEEEEEEec
Confidence            9999999999875

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.48  E-value=2.4e-14  Score=118.64  Aligned_cols=85  Identities=21%  Similarity=0.350  Sum_probs=68.8

Q ss_pred             hhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecC
Q 009954          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (521)
Q Consensus       169 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g  248 (521)
                      ......++|||+|||..+|+++|+++|.+||.|..+.      .+.+...+.++|||||+|.+.++|.+|++|||..|.|
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      0111123556899999999999999999999999999


Q ss_pred             ceEEEeCCCCC
Q 009954          249 VAVRVRRPTDY  259 (521)
Q Consensus       249 ~~i~v~~~~~~  259 (521)
                      +.|.|.++...
T Consensus       105 ~~l~V~~a~~~  115 (124)
T 2jwn_A          105 RTIKVLPKRTN  115 (124)
T ss_dssp             EECEEEESSCC
T ss_pred             eEEEEEECCCC
Confidence            99999986643

>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=99.48  E-value=1.3e-14  Score=112.69  Aligned_cols=81  Identities=23%  Similarity=0.400  Sum_probs=66.2

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ...++|||+|||..+|+++|+++|++||.|..+.      .+.+...+.++|||||+|.+.++|.+|+.|||..+.|+.|
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            3467999999999999999999999999843210      0111123456899999999999999999999999999999


Q ss_pred             EEeCCCC
Q 009954          252 RVRRPTD  258 (521)
Q Consensus       252 ~v~~~~~  258 (521)
                      .|.++..
T Consensus        78 ~V~~a~~   84 (89)
T 3ucg_A           78 KVIPKRT   84 (89)
T ss_dssp             EEEETTT
T ss_pred             EEEEccC
Confidence            9998654

>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=99.48  E-value=3.7e-14  Score=114.67  Aligned_cols=75  Identities=21%  Similarity=0.160  Sum_probs=69.0

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||+.+|+++|+++|.+||.            |..+.+..++|||||+|.+.++|..|+ .|||..|.|+.
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~------------i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   75 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGS------------LGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHVP   75 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCeE
Confidence            34679999999999999999999999997            777888889999999999999999999 69999999999


Q ss_pred             EEEeCCCC
Q 009954          251 VRVRRPTD  258 (521)
Q Consensus       251 i~v~~~~~  258 (521)
                      |.|.|+..
T Consensus        76 l~V~~a~~   83 (111)
T 1whx_A           76 LYLEWAPI   83 (111)
T ss_dssp             CEEEEEET
T ss_pred             EEEEECCC
Confidence            99998654

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.48  E-value=1e-13  Score=111.68  Aligned_cols=75  Identities=24%  Similarity=0.323  Sum_probs=67.1

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC---
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG---  248 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g---  248 (521)
                      ..++|||+|||+++|+++|+++|.+||.            |..+.+... |||||+|.+.++|++|| .||+..|.|   
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~   80 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGD------------VCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEG   80 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSC------------EEEEEEETT-TEEEEEESSHHHHHHHHHHSSSEEEECTTS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EeEEEEecC-CEEEEEECCHHHHHHHHHHHCcCCccCCcC
Confidence            3679999999999999999999999997            666666665 99999999999999999 599999999   


Q ss_pred             --ceEEEeCCCCCC
Q 009954          249 --VAVRVRRPTDYN  260 (521)
Q Consensus       249 --~~i~v~~~~~~~  260 (521)
                        +.|+|.++....
T Consensus        81 ~~~~i~V~~a~~~~   94 (108)
T 1x4c_A           81 ETAYIRVKVDGPRS   94 (108)
T ss_dssp             CEEEEEEEESSCCS
T ss_pred             cceEEEEEeCCCCC
Confidence              999999876644

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=4.4e-14  Score=112.26  Aligned_cols=75  Identities=20%  Similarity=0.296  Sum_probs=65.6

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCCeEEEEecCHHHHHHHHHccCcee
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDGIIF  246 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~A~~l~g~~~  246 (521)
                      ...++|||+|||+++|+++|+++|++||.|            ..+.+     +.++|||||+|.+.++|..|+.+++..|
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            345789999999999999999999999984            44433     5578999999999999999999999999


Q ss_pred             cCceEEEeCCCC
Q 009954          247 EGVAVRVRRPTD  258 (521)
Q Consensus       247 ~g~~i~v~~~~~  258 (521)
                      .|+.|.|.++..
T Consensus        77 ~gr~l~V~~~~~   88 (103)
T 1s79_A           77 KETDLLILFKDD   88 (103)
T ss_dssp             TTTTCEEEEHHH
T ss_pred             CCEEEEEEEchH
Confidence            999999987554

>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=99.48  E-value=2.5e-13  Score=110.03  Aligned_cols=80  Identities=18%  Similarity=0.297  Sum_probs=68.8

Q ss_pred             CCCCCeEEEcCCCCCCC-----------HHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCC
Q 009954          291 AEGPDRVFVGGLPYYFT-----------ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL  359 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~t-----------e~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~  359 (521)
                      ....++|+|.||....+           +++|+++|++||.|..|.| .++   .++|||||+|.+.++|.+|++.|||.
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            34557899999954432           5899999999999999966 443   37999999999999999999999999


Q ss_pred             eeCCeEEEEEEccCC
Q 009954          360 KMGDKTLTVRRATAS  374 (521)
Q Consensus       360 ~~~g~~l~v~~~~~~  374 (521)
                      .|.|+.|.|.|+.+.
T Consensus        88 ~~~gr~l~v~~a~~~  102 (112)
T 2dit_A           88 WFGGRQITAQAWDGT  102 (112)
T ss_dssp             EETTEECEEEECCSC
T ss_pred             EECCcEEEEEEeCCC
Confidence            999999999999763

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=2.9e-14  Score=114.97  Aligned_cols=82  Identities=21%  Similarity=0.340  Sum_probs=66.9

Q ss_pred             hhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceec
Q 009954          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       169 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      ......++|||+|||..+|+++|+++|++||.|..+.        +....+.++|||||+|.+.++|.+|+ .|||..|.
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            3445678999999999999999999999999854311        11111336899999999999999999 59999999


Q ss_pred             CceEEEeCCCC
Q 009954          248 GVAVRVRRPTD  258 (521)
Q Consensus       248 g~~i~v~~~~~  258 (521)
                      |+.|.|.++..
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

>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=99.47  E-value=2.4e-14  Score=113.32  Aligned_cols=79  Identities=16%  Similarity=0.123  Sum_probs=67.9

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+|||+.+|+++|+++|.+||.|..+      ..+.+...+.++|||||+|.+.++|.+|+ .||+..|.|+.|
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~------~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   87 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGS------VCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKV   87 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTT------CEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccce------EEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEE
Confidence            45789999999999999999999999986532      22444455667899999999999999999 799999999999


Q ss_pred             EEeCCC
Q 009954          252 RVRRPT  257 (521)
Q Consensus       252 ~v~~~~  257 (521)
                      +|.++.
T Consensus        88 ~V~~a~   93 (98)
T 2cqp_A           88 KLVLGS   93 (98)
T ss_dssp             EEEESS
T ss_pred             EEEEcC
Confidence            999864

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.47  E-value=1.2e-13  Score=112.75  Aligned_cols=79  Identities=24%  Similarity=0.373  Sum_probs=67.6

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCCeEEEEecCHHHHHHHH-HccC
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG  243 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~A~-~l~g  243 (521)
                      ....++|||+|||..+|+++|+++|..||.|            ..+.+      +.++|||||+|.+.++|.+|+ .||+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i------------~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   79 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRI------------SDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG   79 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCE------------EEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCC
Confidence            3457899999999999999999999999984            44433      344789999999999999999 6999


Q ss_pred             ceecCceEEEeCCCCCCc
Q 009954          244 IIFEGVAVRVRRPTDYNP  261 (521)
Q Consensus       244 ~~~~g~~i~v~~~~~~~~  261 (521)
                      ..|.|+.|.|.++.....
T Consensus        80 ~~~~g~~l~V~~a~~~~~   97 (115)
T 2dgo_A           80 QWLGGRQIRTNWATRKPP   97 (115)
T ss_dssp             CEETTEECEEEESSCCCC
T ss_pred             CEECCEEEEEEEccCCCC
Confidence            999999999999776543

>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=99.47  E-value=3.9e-14  Score=113.83  Aligned_cols=84  Identities=17%  Similarity=0.233  Sum_probs=67.5

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCcee---
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF---  246 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~---  246 (521)
                      ....++|||+|||..+|+++|+++|.+||.|..+.+      +.+..++.++|||||+|.+.++|.+|+ .||+..+   
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~   83 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTV------LKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPG   83 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEEC------CCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE------EecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCC
Confidence            345678999999999999999999999998533211      112223557899999999999999999 6999987   


Q ss_pred             cCceEEEeCCCCCC
Q 009954          247 EGVAVRVRRPTDYN  260 (521)
Q Consensus       247 ~g~~i~v~~~~~~~  260 (521)
                      .|+.|.|.++....
T Consensus        84 ~g~~l~v~~a~~~~   97 (106)
T 2dgp_A           84 MNRPIQVKPADSES   97 (106)
T ss_dssp             CSSCCEEEECCCCS
T ss_pred             CCceEEEEECCccc
Confidence            88999999876543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.47  E-value=7.3e-14  Score=110.47  Aligned_cols=82  Identities=21%  Similarity=0.280  Sum_probs=66.1

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE---ecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~---~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      +.++|||+|||..+|+++|+++|.+||.|..+.      .+.+..   ++.++|||||+|.+.++|.+|+ .||+..|.|
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            467899999999999999999999999853211      011111   2256789999999999999999 599999999


Q ss_pred             ceEEEeCCCCCC
Q 009954          249 VAVRVRRPTDYN  260 (521)
Q Consensus       249 ~~i~v~~~~~~~  260 (521)
                      +.|.|.++....
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

>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=99.47  E-value=1.1e-13  Score=112.75  Aligned_cols=82  Identities=21%  Similarity=0.392  Sum_probs=66.9

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||..+|+++|+++|++||.|..+.+      +.+ ..+.++|||||+|.+.++|++|+ .|||..|.|+.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i------~~~-~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~   77 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLL------IKD-RTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKA   77 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEE------ECS-TTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE------EEC-CCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            44679999999999999999999999998532110      111 13456799999999999999999 69999999999


Q ss_pred             EEEeCCCCCC
Q 009954          251 VRVRRPTDYN  260 (521)
Q Consensus       251 i~v~~~~~~~  260 (521)
                      |.|.++....
T Consensus        78 l~V~~a~~~~   87 (116)
T 2fy1_A           78 IKVEQAKKPS   87 (116)
T ss_dssp             CEEEECCCSS
T ss_pred             EEEEECCCCC
Confidence            9999876544

>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=99.47  E-value=6.3e-14  Score=107.09  Aligned_cols=72  Identities=18%  Similarity=0.403  Sum_probs=63.2

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCCeEEEEecCHHHHHHHH-HccCceec
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      .+|||+|||..+|+++|+++|.+||.|            ..+.+      +.++|||||+|.+.++|..|+ .|||..+.
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i------------~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~   69 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSY------------LSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN   69 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTE------------EEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEET
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCe------------eEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeC
Confidence            579999999999999999999999984            34333      345799999999999999999 59999999


Q ss_pred             CceEEEeCCCC
Q 009954          248 GVAVRVRRPTD  258 (521)
Q Consensus       248 g~~i~v~~~~~  258 (521)
                      |+.|.|.++..
T Consensus        70 g~~l~v~~a~~   80 (83)
T 3md1_A           70 GRPLRINWAAK   80 (83)
T ss_dssp             TEECEEEECCC
T ss_pred             CcEEEEEecCc
Confidence            99999998754

>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=99.47  E-value=3.4e-13  Score=107.61  Aligned_cols=75  Identities=21%  Similarity=0.318  Sum_probs=66.4

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+|||+.+|+++|+++|.+||.            |..+.+.  ++||||+|.+.++|.+|+ .||+..|.|+.|
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~------------i~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l   75 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGK------------LERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEGENI   75 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSC------------EEEEEEC--SSCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEE--CCEEEEEeCCHHHHHHHHHHHCCCccCCCEE
Confidence            4678999999999999999999999997            5566554  679999999999999999 599999999999


Q ss_pred             EEeCCCCCCc
Q 009954          252 RVRRPTDYNP  261 (521)
Q Consensus       252 ~v~~~~~~~~  261 (521)
                      .|.++.....
T Consensus        76 ~v~~a~~~~~   85 (103)
T 2dgu_A           76 EIVFAKPPDQ   85 (103)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEcCCCcc
Confidence            9998765443

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.47  E-value=1.1e-13  Score=111.45  Aligned_cols=79  Identities=11%  Similarity=0.262  Sum_probs=63.8

Q ss_pred             hhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCCeEEEEecCHHHHHHHHHcc
Q 009954          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALD  242 (521)
Q Consensus       169 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~A~~l~  242 (521)
                      ......++|||+|||..+|+++|+++|..||.|            ..+.+      +.++|||||+|.+.++|.+|+..+
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i------------~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~   87 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEV------------KECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS   87 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCE------------EEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCe------------EEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC
Confidence            344567899999999999999999999999984            44443      456899999999999999999766


Q ss_pred             CceecCceEEEeCCCCC
Q 009954          243 GIIFEGVAVRVRRPTDY  259 (521)
Q Consensus       243 g~~~~g~~i~v~~~~~~  259 (521)
                      +..|.|+.|.|.++...
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            79999999999986543

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

Probab=99.47  E-value=7e-14  Score=127.34  Aligned_cols=77  Identities=21%  Similarity=0.389  Sum_probs=70.0

Q ss_pred             CCCCeEEEcCCCCCC---------CHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee-
Q 009954          292 EGPDRVFVGGLPYYF---------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-  361 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~---------te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~-  361 (521)
                      ...++|||+||+..+         ++++|+++|++||.|.+|.|+..      +|||||+|.+.++|+.|+++|+|..| 
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 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            345799999999998         79999999999999999999864      79999999999999999999999999 


Q ss_pred             -----------CCeEEEEEEccCC
Q 009954          362 -----------GDKTLTVRRATAS  374 (521)
Q Consensus       362 -----------~g~~l~v~~~~~~  374 (521)
                                 .|+.|.|.||...
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                       8999999999763

>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=99.47  E-value=2.1e-14  Score=107.39  Aligned_cols=74  Identities=18%  Similarity=0.279  Sum_probs=62.7

Q ss_pred             eEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEEEeC
Q 009954          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (521)
Q Consensus       176 ~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v~~  255 (521)
                      +|||+|||+.+|+++|+++|++||.|..+.+      +.+..++.++|||||+|.+.++|.+|+++++..+.|+.|.|++
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            5999999999999999999999998543321      2223346678999999999999999998899999999999975

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.47  E-value=3.1e-14  Score=116.42  Aligned_cols=85  Identities=19%  Similarity=0.329  Sum_probs=68.1

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCc
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~  249 (521)
                      .....++|||+|||..+|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|.+|+..++..|.|+
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            345568999999999999999999999999853211      01111234568999999999999999996699999999


Q ss_pred             eEEEeCCCCCC
Q 009954          250 AVRVRRPTDYN  260 (521)
Q Consensus       250 ~i~v~~~~~~~  260 (521)
                      .|.|.++....
T Consensus        97 ~l~V~~a~~~~  107 (116)
T 1x4b_A           97 VVEPKRAVARE  107 (116)
T ss_dssp             EEEEECCSSCC
T ss_pred             EEEEEECCCCc
Confidence            99999876543

>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=99.46  E-value=1.2e-13  Score=110.30  Aligned_cols=75  Identities=19%  Similarity=0.291  Sum_probs=66.5

Q ss_pred             cCCeEEE--eCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCcee---
Q 009954          173 HARRVYV--GGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF---  246 (521)
Q Consensus       173 ~~~~l~v--~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~---  246 (521)
                      +.++|||  +||+..+|+++|+++|++||.            |..+.+..++|||||+|.+.++|.+|+ .|||..+   
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~------------v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~   91 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGL------------VDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDD   91 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSC------------EEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEECT
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCC------------eEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEccc
Confidence            4678999  779999999999999999997            677777778999999999999999999 7999988   


Q ss_pred             --cCceEEEeCCCCC
Q 009954          247 --EGVAVRVRRPTDY  259 (521)
Q Consensus       247 --~g~~i~v~~~~~~  259 (521)
                        .|++|.|.++...
T Consensus        92 lg~g~~l~v~~a~~~  106 (114)
T 2cq2_A           92 LGQKITLYLNFVEKV  106 (114)
T ss_dssp             TSCEEECEEEEESCC
T ss_pred             cCCCcEEEEEecccC
Confidence              6789999886543

>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=99.46  E-value=2.3e-14  Score=112.70  Aligned_cols=78  Identities=18%  Similarity=0.184  Sum_probs=66.5

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      .++|||+|||+.+|+++|+++|.+||.|..+      ..+.+...+.++|||||+|.+.++|.+|+ .||+..|.|+.|+
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~------~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~   88 (95)
T 2ek1_A           15 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGS------VCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   88 (95)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHTTTSCBCTTC------CEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCccce------EEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEE
Confidence            5789999999999999999999999986532      22344445567899999999999999999 6999999999999


Q ss_pred             EeCCC
Q 009954          253 VRRPT  257 (521)
Q Consensus       253 v~~~~  257 (521)
                      |.++.
T Consensus        89 v~~a~   93 (95)
T 2ek1_A           89 LSGPS   93 (95)
T ss_dssp             EECCC
T ss_pred             EEecc
Confidence            98754

>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=99.46  E-value=1.6e-14  Score=119.66  Aligned_cols=81  Identities=19%  Similarity=0.190  Sum_probs=69.0

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ...++|||+|||+.+|+++|+++|..||.|..+.      .+.+...+.++|||||+|.+.++|.+||.||+..|.|+.|
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~------~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i   96 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSI------YIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFI   96 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTC------EEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCB
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceE------EEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEE
Confidence            4467999999999999999999999999865421      2444456677899999999999999999999999999999


Q ss_pred             EEeCCCC
Q 009954          252 RVRRPTD  258 (521)
Q Consensus       252 ~v~~~~~  258 (521)
                      .|.++..
T Consensus        97 ~V~~a~~  103 (124)
T 1wel_A           97 QVHPITK  103 (124)
T ss_dssp             EEEEECH
T ss_pred             EEEECCH
Confidence            9987643

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=5e-13  Score=104.73  Aligned_cols=63  Identities=21%  Similarity=0.364  Sum_probs=58.3

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  509 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~  509 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|++|++.|||..|+|++|+|.|+
T Consensus        31 ~~l~~~f~~~G~v~~v~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           31 NDLYRIFSKYGKVVKVTIMKDKDTRKS---KGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             HHHHHHTTTTSCEEEEEECCCSSSCCC---TTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             HHHHHHHHhcCCeEEEEEEeCCCCCCc---ccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            599999999999999999998766554   578899999999999999999999999999999986

>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=99.46  E-value=4.6e-13  Score=108.33  Aligned_cols=70  Identities=19%  Similarity=0.274  Sum_probs=62.4

Q ss_pred             HHHH---HhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          444 EDMR---EECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       444 ~dl~---~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      ++|+   ++|++||+|..|.|+++..++.....+|+|||+|.+.++|++||+.|||..|+|++|+|.|+....
T Consensus        30 ~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           30 PEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             HHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCS
T ss_pred             HHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEeccccc
Confidence            4888   999999999999999987655444456899999999999999999999999999999999987764

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.46  E-value=1.4e-13  Score=109.32  Aligned_cols=77  Identities=18%  Similarity=0.344  Sum_probs=66.1

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCCeEEEEecCHHHHHHHH-HccCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDGI  244 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~A~-~l~g~  244 (521)
                      ....++|||+|||..+|+++|+++|.+||.|            ..+.+     +.++|||||+|.+.++|.+|+ .||+.
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            3456789999999999999999999999974            44433     345699999999999999999 79999


Q ss_pred             eecCceEEEeCCCCC
Q 009954          245 IFEGVAVRVRRPTDY  259 (521)
Q Consensus       245 ~~~g~~i~v~~~~~~  259 (521)
                      .|.|+.|.|.++...
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            999999999986543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.46  E-value=1.9e-13  Score=108.34  Aligned_cols=86  Identities=13%  Similarity=0.208  Sum_probs=70.9

Q ss_pred             eEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCee
Q 009954          420 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKF  499 (521)
Q Consensus       420 ~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~  499 (521)
                      +++.+.|++..    .+..+.+++++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|++||+.|||..|
T Consensus         7 ~~vfV~nLp~v----~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~---kG~afV~f~~~~~A~~Ai~~lng~~~   79 (100)
T 3ns6_A            7 QYIVVNGAPVI----PSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKT---KGFLFVECGSMNDAKKIIKSFHGKRL   79 (100)
T ss_dssp             GEEEEESCCCC----BGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEE---CSEEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             cEEEEeCCCcC----ChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCcc---ceEEEEEECCHHHHHHHHHHhCCccc
Confidence            34555555332    223457788999999999999999999998876654   68889999999999999999999999


Q ss_pred             CC-cEEEEEEcCCC
Q 009954          500 GG-NTVNAFYYPED  512 (521)
Q Consensus       500 ~g-r~l~v~~~~~~  512 (521)
                      +| +.|+|.++.+.
T Consensus        80 ~g~r~l~V~~a~~~   93 (100)
T 3ns6_A           80 DLKHRLFLYTMKDV   93 (100)
T ss_dssp             SSSCBCEEEESHHH
T ss_pred             CCCeEEEEEECchh
Confidence            99 99999998653

>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=99.46  E-value=1.1e-13  Score=107.00  Aligned_cols=72  Identities=24%  Similarity=0.368  Sum_probs=63.4

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cC-CCCeEEEEecCHHHHHHHH-HccCce
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NH-EKKFAFVEMRTVEEASNAM-ALDGII  245 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~------~~-~~g~afV~f~~~~~a~~A~-~l~g~~  245 (521)
                      .++|||+|||.++|+++|+++|.+||.|            ..+.+      +. ++|||||+|.+.++|.+|+ .|||..
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i------------~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~   71 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKI------------KMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQ   71 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCE------------EEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCE------------EEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCe
Confidence            5789999999999999999999999974            44443      22 7899999999999999999 599999


Q ss_pred             ecCceEEEeCCC
Q 009954          246 FEGVAVRVRRPT  257 (521)
Q Consensus       246 ~~g~~i~v~~~~  257 (521)
                      +.|+.|.|.++.
T Consensus        72 ~~g~~l~v~~a~   83 (88)
T 4a8x_A           72 IDGQEITATAVL   83 (88)
T ss_dssp             ETTEECEEEEEC
T ss_pred             ECCeEEEEEECC
Confidence            999999999754

>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=99.46  E-value=2.2e-13  Score=110.38  Aligned_cols=77  Identities=22%  Similarity=0.364  Sum_probs=67.1

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCCeEEEEecCHHHHHHHH-Hcc--
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALD--  242 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~A~-~l~--  242 (521)
                      ...++|||+|||+.+|+++|+++|.+||.            |..+.+      +.++|||||+|.+.++|.+|+ .||  
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~   80 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGD------------LKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLE   80 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTT
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccc
Confidence            45679999999999999999999999997            444444      456899999999999999999 699  


Q ss_pred             ----CceecCceEEEeCCCCCC
Q 009954          243 ----GIIFEGVAVRVRRPTDYN  260 (521)
Q Consensus       243 ----g~~~~g~~i~v~~~~~~~  260 (521)
                          +..|.|+.|.|.++....
T Consensus        81 ~~~~~~~~~g~~l~v~~a~~~~  102 (111)
T 1x4h_A           81 AEGGGLKLDGRQLKVDLAVTRD  102 (111)
T ss_dssp             TTTCCEESSSCEEEEECCCCCC
T ss_pred             cccCCcEEcCEEEEEEECCCCc
Confidence                999999999999876543

>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=99.46  E-value=8.7e-14  Score=111.56  Aligned_cols=77  Identities=22%  Similarity=0.282  Sum_probs=66.0

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCCeEEEEecCHHHHHHHH-HccCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDGII  245 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~A~-~l~g~~  245 (521)
                      ...++|||+|||..+|+++|+++|.+||.|            ..+.+     +.++|||||+|.+.++|.+|+ .||+..
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i------------~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   80 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVI------------DECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQ   80 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCE------------EEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCc
Confidence            457899999999999999999999999984            33333     344799999999999999999 699999


Q ss_pred             ecC---ceEEEeCCCCCC
Q 009954          246 FEG---VAVRVRRPTDYN  260 (521)
Q Consensus       246 ~~g---~~i~v~~~~~~~  260 (521)
                      +.|   +.|.|.++....
T Consensus        81 ~~gg~~~~l~V~~a~~~~   98 (105)
T 2dnh_A           81 TMPGASSSLVVKFADTDK   98 (105)
T ss_dssp             CCTTCSSCCEEEESCSSC
T ss_pred             cCCCCCccEEEEECccCc
Confidence            998   999999876543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=6.8e-14  Score=111.74  Aligned_cols=78  Identities=22%  Similarity=0.260  Sum_probs=67.3

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE----ecCCCCeEEEEecCHHHHHHHH-HccCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY----INHEKKFAFVEMRTVEEASNAM-ALDGII  245 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~----~~~~~g~afV~f~~~~~a~~A~-~l~g~~  245 (521)
                      ....++|||+|||+.+|+++|+++|.+||.|            ..+.    .+.++|||||+|.+.++|.+|+ .||+..
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i------------~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~   79 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTI------------TSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRI   79 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCE------------EEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCE------------EEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCE
Confidence            3457899999999999999999999999984            3333    3456899999999999999999 699999


Q ss_pred             ecCceEEEeCCCCCC
Q 009954          246 FEGVAVRVRRPTDYN  260 (521)
Q Consensus       246 ~~g~~i~v~~~~~~~  260 (521)
                      |.|+.|.|.++....
T Consensus        80 ~~g~~l~V~~a~~~~   94 (103)
T 2d9p_A           80 VATKPLYVALAQRKE   94 (103)
T ss_dssp             SSSSBCEEEECSSCC
T ss_pred             eCCcEEEEEEecccc
Confidence            999999999876544

>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=99.46  E-value=7.8e-14  Score=109.62  Aligned_cols=75  Identities=31%  Similarity=0.461  Sum_probs=64.9

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCCeEEEEecCHHHHHHHH-HccCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDGI  244 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~A~-~l~g~  244 (521)
                      ....++|||+|||+.+++++|+++|.+||.|            ..+.+     +.++|||||+|.+.++|.+|+ .||+.
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i------------~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~   80 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPL------------TKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGI   80 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCE------------EEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCE------------EEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCC
Confidence            3456799999999999999999999999974            44443     344789999999999999999 59999


Q ss_pred             eecCceEEEeCCC
Q 009954          245 IFEGVAVRVRRPT  257 (521)
Q Consensus       245 ~~~g~~i~v~~~~  257 (521)
                      .|.|+.|.|.++.
T Consensus        81 ~~~g~~l~V~~a~   93 (95)
T 2ywk_A           81 RLYGRPINVSGPS   93 (95)
T ss_dssp             EETTEECEEECCC
T ss_pred             EECCCEEEEEEcC
Confidence            9999999999864

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.46  E-value=4.4e-14  Score=112.38  Aligned_cols=79  Identities=20%  Similarity=0.298  Sum_probs=67.5

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....++|||+|||..+|+++|+++|.+||.|.          +.....+.++|||||+|.+.++|.+|+ .||+..|.|+
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            34578999999999999999999999998752          222245677999999999999999999 5999999999


Q ss_pred             eEEEeCCCCC
Q 009954          250 AVRVRRPTDY  259 (521)
Q Consensus       250 ~i~v~~~~~~  259 (521)
                      .|.|.++...
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

>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=99.46  E-value=5.8e-15  Score=117.20  Aligned_cols=81  Identities=17%  Similarity=0.250  Sum_probs=64.6

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEE-EecCCCCeEEEEecCHHHHHHHHHccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV-YINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~-~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~  249 (521)
                      ....++|||+|||.++|+++|+++|..|| |..+.+      +.+. ..+.++|||||+|.+.++|.+|+.|+|..|.|+
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i------~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~   88 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRL------PREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNR   88 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEEC------SCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTB
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEE------EecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCe
Confidence            44568999999999999999999999998 643211      1111 245578999999999999999999999999999


Q ss_pred             eEEEeCCCC
Q 009954          250 AVRVRRPTD  258 (521)
Q Consensus       250 ~i~v~~~~~  258 (521)
                      .|.|.++..
T Consensus        89 ~l~V~~a~~   97 (100)
T 2j76_E           89 RIRVDVADQ   97 (100)
T ss_dssp             CCCCEECCC
T ss_pred             EEEEEeccC
Confidence            999998654

>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=99.45  E-value=8e-14  Score=113.57  Aligned_cols=76  Identities=29%  Similarity=0.412  Sum_probs=66.8

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCCeEEEEecCHHHHHHHHHccC
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDG  243 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~A~~l~g  243 (521)
                      .....++|||+|||..+|+++|+++|..||.            |..+.+      +.++|||||+|.+.++|.+|+.||+
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            444444      5678999999999999999999999


Q ss_pred             ceecCceEEEeCCC
Q 009954          244 IIFEGVAVRVRRPT  257 (521)
Q Consensus       244 ~~~~g~~i~v~~~~  257 (521)
                      ..|.|+.|.|.++.
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

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=2.2e-13  Score=107.04  Aligned_cols=67  Identities=19%  Similarity=0.312  Sum_probs=61.5

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|++||+.|||..|+|+.|+|.|+.+..
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            599999999999999999998766654   6899999999999999999999999999999999987754

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.45  E-value=4.1e-13  Score=117.99  Aligned_cols=79  Identities=15%  Similarity=0.163  Sum_probs=64.9

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+|||+.+|+++|+++|.+||.|..+.+      +.+. .+.++|||||+|.+.++|.+|+ .||+..|.|+.|
T Consensus        87 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i------~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l  159 (177)
T 2f3j_A           87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAV------DYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM  159 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEE------CCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE------EECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEE
Confidence            3578999999999999999999999998532110      1111 3557899999999999999999 599999999999


Q ss_pred             EEeCCCC
Q 009954          252 RVRRPTD  258 (521)
Q Consensus       252 ~v~~~~~  258 (521)
                      +|.++..
T Consensus       160 ~V~~a~~  166 (177)
T 2f3j_A          160 DIQLVAS  166 (177)
T ss_dssp             EEEEESS
T ss_pred             EEEEecC
Confidence            9998654

>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=99.45  E-value=1.3e-13  Score=106.29  Aligned_cols=65  Identities=12%  Similarity=0.345  Sum_probs=59.2

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~  511 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|+.|++.|||..|+|+.|+|.|+..
T Consensus        21 ~~l~~~F~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   85 (87)
T 3bs9_A           21 AAIAAAFAPFGRISDARVVKDMATGKS---KGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR   85 (87)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC-
T ss_pred             HHHHHHHHhcCCEeEEEEEecCCCCcc---ceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCC
Confidence            599999999999999999998766553   68999999999999999999999999999999999865

>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=99.45  E-value=2.5e-14  Score=116.40  Aligned_cols=81  Identities=12%  Similarity=0.090  Sum_probs=66.6

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHh-hcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTA-IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~-~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      ...++|||+|||+.+|+++|+++|..||.| ..+.      ++.+. .+.++|||||+|.+.++|.+||++|+..|.|+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~------i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~   85 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVH------VLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGRE   85 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEE------ECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEE------EEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeE
Confidence            456899999999999999999999999875 2211      11222 466899999999999999999977999999999


Q ss_pred             EEEeCCCCC
Q 009954          251 VRVRRPTDY  259 (521)
Q Consensus       251 i~v~~~~~~  259 (521)
                      |.|.++...
T Consensus        86 i~v~~a~~~   94 (114)
T 2cpy_A           86 AFVHVVTLE   94 (114)
T ss_dssp             EEEEEECHH
T ss_pred             EEEEECCHH
Confidence            999986543

>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=99.45  E-value=5.3e-14  Score=110.07  Aligned_cols=75  Identities=21%  Similarity=0.396  Sum_probs=64.0

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccC-ceecCce
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG-IIFEGVA  250 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g-~~~~g~~  250 (521)
                      ..++|||+|||.++|+++|+++|.+||.++..        +..    .++|||||+|.+.++|.+|+ .||| ..|.|+.
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--------QVL----LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKI   74 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSS--------CEE----EETTEEEECCSCHHHHHHHHHHHTTTCEETTEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEE--------EEE----cCCCEEEEEECCHHHHHHHHHHccCCeeECCEE
Confidence            45789999999999999999999999973211        111    35899999999999999999 6999 9999999


Q ss_pred             EEEeCCCCC
Q 009954          251 VRVRRPTDY  259 (521)
Q Consensus       251 i~v~~~~~~  259 (521)
                      |.|.++...
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

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.45  E-value=5.1e-14  Score=112.02  Aligned_cols=72  Identities=13%  Similarity=0.259  Sum_probs=62.9

Q ss_pred             EcCCCCCCCHHHHHHHH------------HhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEE
Q 009954          299 VGGLPYYFTETQIKELL------------ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (521)
Q Consensus       299 v~nLp~~~te~~l~~~F------------~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (521)
                      +.||+..+++++|+++|            ++||.|.+|.|+.+. ++.++|||||+|.+.++|.+|++.|||..|+|+.|
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            45666667776666555            999999999999885 58899999999999999999999999999999999


Q ss_pred             EEEEc
Q 009954          367 TVRRA  371 (521)
Q Consensus       367 ~v~~~  371 (521)
                      .|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99987

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.44  E-value=3.3e-14  Score=122.14  Aligned_cols=81  Identities=20%  Similarity=0.251  Sum_probs=63.9

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHH--HhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVM--TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G--~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      ...++|||+|||+.+|+++|+++|..||  .|..+.      .+.+..++.++|||||+|.+.++|.+|| .|||..|.|
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~------i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~G  126 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELK------FAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNG  126 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEE------EEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEE------EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            4568999999999999999999999999  632210      0111123556899999999999999999 689999999


Q ss_pred             ceEEEeCCCC
Q 009954          249 VAVRVRRPTD  258 (521)
Q Consensus       249 ~~i~v~~~~~  258 (521)
                      +.|.|.++..
T Consensus       127 r~l~V~~a~~  136 (156)
T 3n9u_C          127 EKVDVRPATR  136 (156)
T ss_dssp             EECEEEECCH
T ss_pred             eEeEEEEcCC
Confidence            9999998653

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=2.8e-13  Score=107.96  Aligned_cols=69  Identities=16%  Similarity=0.205  Sum_probs=62.4

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCcc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYF  515 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~  515 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|++||+.|||..|+|+.|+|.|+....-.
T Consensus        27 ~~l~~~f~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   95 (102)
T 2cqb_A           27 KVLHAAFIPFGDITDIQIPLDYETEKH---RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK   95 (102)
T ss_dssp             HHHHHHHTTTSCCCCEECCCCSSSCCC---SSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             HHHHHHhhccCCEEEEEEEecCCCCCc---ceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCCC
Confidence            599999999999999999998766654   688999999999999999999999999999999998876543

>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=99.44  E-value=1.7e-13  Score=125.83  Aligned_cols=100  Identities=32%  Similarity=0.506  Sum_probs=86.6

Q ss_pred             CcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCC-CCCccEEEEEecCHHHHHHHHHHHh
Q 009954          417 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGE-TPGVGKVFLEYYDAVGCATAKNALS  495 (521)
Q Consensus       417 ~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~-~~g~g~afV~F~~~~~A~~Ai~~ln  495 (521)
                      ..+.++.|.+.++.+++.++     +.++|.++|++||.|..|.|+++..++.. ..++|++||+|.+.++|.+|++.||
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            56678899999998877543     55799999999999999999876544322 2457889999999999999999999


Q ss_pred             CCeeCCcEEEEEEcCCCCcccccCCC
Q 009954          496 GRKFGGNTVNAFYYPEDKYFNKDYSA  521 (521)
Q Consensus       496 g~~~~gr~l~v~~~~~~~~~~~~~~~  521 (521)
                      |+.|+||+|.|.|+++++|.+++|++
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

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=2.7e-13  Score=102.38  Aligned_cols=69  Identities=14%  Similarity=0.158  Sum_probs=60.4

Q ss_pred             EEEeCCCccCcHHH----HHHHHHHHH-HhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          177 VYVGGLPPLANEQA----IATFFSQVM-TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       177 l~v~nlp~~~t~~~----l~~~f~~~G-~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      |||+|||..+++++    |+++|.+|| .            |+++ +   .|+|||+|.+.++|+.|+ .|+|..+.|++
T Consensus        12 lYV~NL~~~~~~~~lk~~L~~lF~~yGG~------------Vl~V-t---gG~AfV~F~~~esA~~A~~~l~G~~l~gr~   75 (96)
T 2diu_A           12 LYVYNLPANKDGKSVSNRLRRLSDNCGGK------------VLSI-T---GCSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             EEEESCCTTSCHHHHHHHHHHHHHTTTCC------------EEEC-C---TTCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             EEEeCCCCcCCHHHHHHHHHHHHHHcCCe------------eEEE-e---cCEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            99999999999988    558999995 7            5555 2   299999999999999999 79999999999


Q ss_pred             EEEeCCCCCCc
Q 009954          251 VRVRRPTDYNP  261 (521)
Q Consensus       251 i~v~~~~~~~~  261 (521)
                      |+|.+++....
T Consensus        76 i~v~~A~~~sd   86 (96)
T 2diu_A           76 IIVSFTPKNRE   86 (96)
T ss_dssp             CEEESSCCSCC
T ss_pred             EEEEecCCCcc
Confidence            99999876554

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.44  E-value=3.5e-14  Score=116.20  Aligned_cols=79  Identities=18%  Similarity=0.198  Sum_probs=65.6

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHH---hhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecC
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMT---AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~---~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g  248 (521)
                      ...++|||+|||+.+|+++|+++|..||.   |..+.      .+.+ ..+.++|||||+|.+.++|.+||++|+..|.|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~------i~~~-~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~g   87 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVH------FIYT-REGRQSGEAFVELESEDDVKLALKKDRESMGH   87 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEE------EEEC-SSSCEEEEEEEEBSSHHHHHHHGGGTTEEETT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEE------EEEC-CCCCCCeEEEEEECCHHHHHHHHhcCCCeECC
Confidence            45678999999999999999999999987   43311      1122 22567899999999999999999999999999


Q ss_pred             ceEEEeCCC
Q 009954          249 VAVRVRRPT  257 (521)
Q Consensus       249 ~~i~v~~~~  257 (521)
                      +.|+|.++.
T Consensus        88 r~i~V~~a~   96 (118)
T 2db1_A           88 RYIEVFKSH   96 (118)
T ss_dssp             EEEEEEEEC
T ss_pred             eEEEEEECC
Confidence            999998764

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

Probab=99.44  E-value=3.9e-13  Score=105.97  Aligned_cols=74  Identities=23%  Similarity=0.362  Sum_probs=67.4

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+||  .+|+++|+++|.+||.            |..+.+..++|||||+|.+.++|.+|+ .||+..|.|+.
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            35679999996  8999999999999997            777888899999999999999999999 79999999999


Q ss_pred             EEEeCCCCC
Q 009954          251 VRVRRPTDY  259 (521)
Q Consensus       251 i~v~~~~~~  259 (521)
                      |.|.++...
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

>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=99.44  E-value=3.6e-13  Score=106.66  Aligned_cols=68  Identities=19%  Similarity=0.275  Sum_probs=62.0

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  514 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~  514 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|++||..|||..|+|+.|+|.|+....-
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            599999999999999999998766654   68999999999999999999999999999999999887653

>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=99.43  E-value=2e-13  Score=104.76  Aligned_cols=63  Identities=17%  Similarity=0.253  Sum_probs=57.9

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  509 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~  509 (521)
                      ++|+++|++||.|..|.|+.+..++..   +|+|||+|.+.++|++|++.|||..|+|++|+|.|+
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            599999999999999999988666543   688999999999999999999999999999999986

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.43  E-value=1.8e-13  Score=109.57  Aligned_cols=80  Identities=20%  Similarity=0.241  Sum_probs=66.0

Q ss_pred             ccCCeEEEeCCCccC------cHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCc
Q 009954          172 RHARRVYVGGLPPLA------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI  244 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~------t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~  244 (521)
                      ...++|||+|||..+      |+++|+++|++||.|..+.+       . ..++.++|||||+|.+.++|.+|+ .|||.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i-------~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~   84 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY-------P-EEDGKTKGYIFLEYASPAHAVDAVKNADGY   84 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEEC-------C-CBTTBSCCEEEEEECSSSHHHHHHHHCSSE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEe-------e-CCCCCeeeEEEEEECCHHHHHHHHHHhCCc
Confidence            346799999999999      88999999999998533211       0 123467899999999999999999 69999


Q ss_pred             eecCc-eEEEeCCCCC
Q 009954          245 IFEGV-AVRVRRPTDY  259 (521)
Q Consensus       245 ~~~g~-~i~v~~~~~~  259 (521)
                      .|.|+ .|.|.++...
T Consensus        85 ~~~g~~~l~V~~a~~~  100 (105)
T 2nlw_A           85 KLDKQHTFRVNLFTDF  100 (105)
T ss_dssp             ECSTTCEEEEECSCCC
T ss_pred             ccCCCceEEEEEcchH
Confidence            99998 9999987654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=6.9e-13  Score=108.32  Aligned_cols=77  Identities=18%  Similarity=0.334  Sum_probs=65.8

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCCeEEEEecCHHHHHHHH-Hcc
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALD  242 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~A~-~l~  242 (521)
                      .....++|||+|||..+|+++|+++|.+||.            |..+.+      +.++|||||+|.+.++|++|+ .++
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~   80 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGD------------IEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN   80 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSC------------EEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCC------------eeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCC
Confidence            3455789999999999999999999999998            444444      446799999999999999999 588


Q ss_pred             CceecCceEEEeCCCCC
Q 009954          243 GIIFEGVAVRVRRPTDY  259 (521)
Q Consensus       243 g~~~~g~~i~v~~~~~~  259 (521)
                      + .|.|+.|.|.++...
T Consensus        81 ~-~~~g~~l~V~~a~~~   96 (116)
T 2cqd_A           81 P-IIDGRKANVNLAYLG   96 (116)
T ss_dssp             C-EETTEECEEEESTTT
T ss_pred             C-cCCCEEEEEEEcccC
Confidence            7 899999999987643

>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=99.43  E-value=3.1e-13  Score=117.85  Aligned_cols=141  Identities=14%  Similarity=0.108  Sum_probs=66.8

Q ss_pred             EEEcChHHHHHHHHHHcCCeeC--CeEEEEEEccCCCCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCc
Q 009954          341 CVYQDPAVTDIACAALNGLKMG--DKTLTVRRATASGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETL  418 (521)
Q Consensus       341 V~f~~~~~A~~Al~~l~g~~~~--g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  418 (521)
                      .+|.+.++|..|+..|++....  |+.+.+.+.....      .....         ....  .... .....|... .+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~------~~~~~---------~~~~--s~~~-~~~~~~~~~-~~   71 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREA------IHSYE---------RVRN--EDDD-ELEPGPQRS-VE   71 (165)
T ss_dssp             -------------------------------------------------------------------------CCCC-C-
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCcccccc------ccCcc---------cccc--CCCC-CCCCCCCCC-CC
Confidence            7899999999999999886554  6666555532100      00000         0000  0000 000011111 22


Q ss_pred             ceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCe
Q 009954          419 AKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRK  498 (521)
Q Consensus       419 ~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~  498 (521)
                      ...|.+.|+....          ++++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|+.||..|||..
T Consensus        72 ~~~l~V~nLp~~~----------t~~~L~~~F~~~G~i~~v~i~~~~~~g~~---~g~afV~f~~~~~A~~Ai~~l~g~~  138 (165)
T 1rk8_A           72 GWILFVTSIHEEA----------QEDEIQEKFCDYGEIKNIHLNLDRRTGFS---KGYALVEYETHKQALAAKEALNGAE  138 (165)
T ss_dssp             CEEEEEESCCTTC----------CHHHHHHHHGGGSCEEEEEEEECTTTSSE---EEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCEEEEeCCCCCC----------CHHHHHHHhhcCCCEEEEEEEecCCCCcE---eeEEEEEECCHHHHHHHHHHhCCCE
Confidence            3344444442221          22699999999999999999998766654   6899999999999999999999999


Q ss_pred             eCCcEEEEEEcCCCC
Q 009954          499 FGGNTVNAFYYPEDK  513 (521)
Q Consensus       499 ~~gr~l~v~~~~~~~  513 (521)
                      |+|+.|.|.|+....
T Consensus       139 ~~g~~l~V~~a~~~~  153 (165)
T 1rk8_A          139 IMGQTIQVDWCFVKG  153 (165)
T ss_dssp             ETTEECEEEESEECC
T ss_pred             ECCEEEEEEEecCCC
Confidence            999999999986543

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

Probab=99.43  E-value=8.9e-14  Score=108.56  Aligned_cols=80  Identities=18%  Similarity=0.219  Sum_probs=65.8

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||..+|+++|+++|.+||.|..+        .+....+.++|||||+|.+.++|.+|+ .||+..|.|+.
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        111123446799999999999999999 69999999999


Q ss_pred             EEEeCCCCC
Q 009954          251 VRVRRPTDY  259 (521)
Q Consensus       251 i~v~~~~~~  259 (521)
                      |.|.++...
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

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.43  E-value=4.9e-14  Score=117.83  Aligned_cols=85  Identities=15%  Similarity=0.277  Sum_probs=69.8

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCc----e
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI----I  245 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~----~  245 (521)
                      ....++|||+|||+.+|+++|+++|.+||.|...+    +.++.+..++.++|||||+|.+. +|.+|+ .|||.    .
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            35567999999999999999999999999863210    11234444677899999999999 999999 79999    9


Q ss_pred             ecCceEEEeCCCCCC
Q 009954          246 FEGVAVRVRRPTDYN  260 (521)
Q Consensus       246 ~~g~~i~v~~~~~~~  260 (521)
                      |.|+.|.|.++....
T Consensus        95 ~~gr~l~V~~a~~~~  109 (131)
T 2m2b_A           95 IDGKTINVEFAKGSK  109 (131)
T ss_dssp             GGGCCCCCEECCCSC
T ss_pred             CCCEEEEEEECCCCC
Confidence            999999999876644

>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=99.43  E-value=2e-13  Score=110.38  Aligned_cols=72  Identities=22%  Similarity=0.414  Sum_probs=64.7

Q ss_pred             cCCeEEEeCCCcc-CcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          173 HARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       173 ~~~~l~v~nlp~~-~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ..++|||+|||+. +|+++|+++|.+||.            |..+.+  .+|||||+|.+.++|.+|+ .|++..|.|+.
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~------------v~~v~i--~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   91 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGR------------VAGCSV--HKGYAFVQYSNERHARAAVLGENGRVLAGQT   91 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSC------------CSEEEE--ETTEEEEECSSSHHHHHHHHHHTTCEETTEE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCC------------eEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCEECCeE
Confidence            4579999999999 999999999999997            444444  7899999999999999999 79999999999


Q ss_pred             EEEeCCCC
Q 009954          251 VRVRRPTD  258 (521)
Q Consensus       251 i~v~~~~~  258 (521)
                      |.|.++..
T Consensus        92 l~V~~a~~   99 (110)
T 1wf1_A           92 LDINMAGE   99 (110)
T ss_dssp             CCEEESCC
T ss_pred             EEEEECCC
Confidence            99998754

>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=99.43  E-value=2.3e-14  Score=114.72  Aligned_cols=85  Identities=31%  Similarity=0.434  Sum_probs=67.8

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....++|||+|||..+|+++|+++|.+||.|..+.      .+.+...+.++|||||+|.+.++|.+|+ .|||..|.|+
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            34568999999999999999999999999853210      0111113445799999999999999999 6999999999


Q ss_pred             eEEEeCCCCCCc
Q 009954          250 AVRVRRPTDYNP  261 (521)
Q Consensus       250 ~i~v~~~~~~~~  261 (521)
                      .|.|.++.....
T Consensus        79 ~l~v~~a~~~~~   90 (104)
T 1p1t_A           79 ALRVDNAASEKN   90 (104)
T ss_dssp             CBEEEETTCTTH
T ss_pred             EEEEEeCCCccc
Confidence            999998765443

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=2.9e-13  Score=105.60  Aligned_cols=75  Identities=28%  Similarity=0.458  Sum_probs=65.6

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||..+|+++|+++|++||.            |..+.+.  ++||||+|.+.++|.+|+ .||+..|.|+.
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~   73 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGP------------VIECDIV--KDYAFVHMERAEDAVEAIRGLDNTEFQGKR   73 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSC------------CCEEEEC--SSEEEEEESCHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCeeCCcE
Confidence            44679999999999999999999999997            4455554  569999999999999999 79999999999


Q ss_pred             EEEeCCCCCC
Q 009954          251 VRVRRPTDYN  260 (521)
Q Consensus       251 i~v~~~~~~~  260 (521)
                      |.|.++....
T Consensus        74 l~V~~a~~~~   83 (92)
T 2dgt_A           74 MHVQLSTSRL   83 (92)
T ss_dssp             EEEEESSCCC
T ss_pred             EEEEEccCCC
Confidence            9999876543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=6.4e-13  Score=106.01  Aligned_cols=67  Identities=16%  Similarity=0.306  Sum_probs=61.3

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|++||..|||..|+|+.|+|.|+....
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            599999999999999999998766554   6899999999999999999999999999999999987754

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.43  E-value=8.8e-14  Score=109.54  Aligned_cols=78  Identities=18%  Similarity=0.283  Sum_probs=67.5

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....++|||+|||..+|+++|+++|..||.|.          ++ ...+.++|||||+|.+.++|.+|+ .|+|..|.|+
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~----------~~-~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   81 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIR----------LV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGR   81 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEEC----------CE-EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEE----------Ee-CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            34568999999999999999999999998752          22 455677899999999999999999 5999999999


Q ss_pred             eEEEeCCCCC
Q 009954          250 AVRVRRPTDY  259 (521)
Q Consensus       250 ~i~v~~~~~~  259 (521)
                      .|.|.++...
T Consensus        82 ~l~v~~a~~~   91 (96)
T 1fjc_A           82 SVSLYYTGEK   91 (96)
T ss_dssp             EEEEEECSSS
T ss_pred             EEEEEEcCCC
Confidence            9999986543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.43  E-value=2.8e-13  Score=106.06  Aligned_cols=76  Identities=25%  Similarity=0.406  Sum_probs=64.3

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCC-eEEEEecCHHHHHHHHHccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g-~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ..++|||+|||..+|+++|+++|.+||.            |..+......+ ||||+|.+.++|.+|++||+..|.|+.|
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~------------v~~v~~~~~~g~~afV~f~~~~~a~~ai~l~g~~~~g~~l   74 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGP------------VASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHSLGGHRL   74 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSC------------EEEEEECSSSCCEEEEEESSHHHHHHHHTCSCCEETTEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCC------------eEEEEEcCCCCcEEEEEECCHHHHHHHHhcCCeEECCEEE
Confidence            4579999999999999999999999998            44443333222 9999999999999999999999999999


Q ss_pred             EEeCCCCCC
Q 009954          252 RVRRPTDYN  260 (521)
Q Consensus       252 ~v~~~~~~~  260 (521)
                      .|.++....
T Consensus        75 ~V~~a~~~~   83 (94)
T 2e5g_A           75 RVRPREQKE   83 (94)
T ss_dssp             CCBCSCCSC
T ss_pred             EEEECCcCC
Confidence            999765443

>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=99.42  E-value=4.2e-13  Score=105.53  Aligned_cols=68  Identities=24%  Similarity=0.424  Sum_probs=61.7

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  514 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~  514 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|++|++.|||..|+|+.|+|.|+.....
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            599999999999999999998766543   68899999999999999999999999999999999887653

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.42  E-value=6.2e-13  Score=105.25  Aligned_cols=67  Identities=19%  Similarity=0.233  Sum_probs=60.7

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  514 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~  514 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|++||+ |||..|+|+.|+|.|+....-
T Consensus        25 ~~l~~~F~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~~   91 (99)
T 2dgs_A           25 TELREYFKKFGVVTEVVMIYDAEKQRP---RGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPRDS   91 (99)
T ss_dssp             HHHHHHHSSSSCEEEEEECCCTTTCSC---CSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECCCCCC
T ss_pred             HHHHHHHHhcCCeEEEEEEeCCCCCCC---CceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECCCCcc
Confidence            599999999999999999998766554   6899999999999999999 999999999999999876653

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=2.7e-13  Score=108.01  Aligned_cols=68  Identities=16%  Similarity=0.281  Sum_probs=61.5

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  514 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~  514 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|.+||+.|||..|+|++|+|.|+....-
T Consensus        27 ~~l~~~f~~~G~i~~v~i~~~~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   94 (102)
T 1x5s_A           27 QSLEQVFSKYGQISEVVVVKDRETQRS---RGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   94 (102)
T ss_dssp             HHHHHHHHHHSCCCEEEECCCSSSCSC---CSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             HHHHHHHHhcCCeEEEEEEeCCCCCCc---ccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            599999999999999999998766553   68999999999999999999999999999999999876543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.42  E-value=2.7e-14  Score=114.56  Aligned_cols=84  Identities=17%  Similarity=0.293  Sum_probs=66.5

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      ....++|||+|||+.+|+++|+++|.+||.|..+.      .+.+..++.++|||||+|.+.++|.+|+..++..|.|+.
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~   86 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCV------IMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRN   86 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEE------EEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEE
Confidence            34568999999999999999999999999843210      011112234578999999999999999955999999999


Q ss_pred             EEEeCCCCCC
Q 009954          251 VRVRRPTDYN  260 (521)
Q Consensus       251 i~v~~~~~~~  260 (521)
                      |.|.++....
T Consensus        87 l~V~~a~~~~   96 (105)
T 2dh8_A           87 IDPKPCTPRG   96 (105)
T ss_dssp             EBCCCSCCSS
T ss_pred             EEEEEccCCC
Confidence            9999876543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.42  E-value=1.4e-13  Score=104.56  Aligned_cols=71  Identities=20%  Similarity=0.261  Sum_probs=59.1

Q ss_pred             CeEEEeCCCccC------cHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceec
Q 009954          175 RRVYVGGLPPLA------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       175 ~~l~v~nlp~~~------t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      ++|||+|||..+      |+++|+++|++||.|..+.+        ...++.++|||||+|.+.++|.+|+ .|||..+.
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i--------~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~   73 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--------PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD   73 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEEC--------CCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCS
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEe--------cCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccC
Confidence            689999999999      78999999999998433210        0123456899999999999999999 69999999


Q ss_pred             Cc-eEEE
Q 009954          248 GV-AVRV  253 (521)
Q Consensus       248 g~-~i~v  253 (521)
                      |+ +|+|
T Consensus        74 g~~~l~V   80 (81)
T 2krb_A           74 KQHTFRV   80 (81)
T ss_dssp             SSSCCCC
T ss_pred             CceeEEe
Confidence            99 8876

>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=99.42  E-value=2.3e-13  Score=107.38  Aligned_cols=77  Identities=19%  Similarity=0.398  Sum_probs=66.8

Q ss_pred             ccCCeEEEeCCCccCcHHHHH----HHHHHHHHhhcCCCCCCCCceEEEEe---cCCCCeEEEEecCHHHHHHHH-HccC
Q 009954          172 RHARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDG  243 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~----~~f~~~G~~~~~~~~~~~~~v~~~~~---~~~~g~afV~f~~~~~a~~A~-~l~g  243 (521)
                      ...++|||+|||..+|+++|+    ++|.+||.            |..+.+   +.++|||||+|.+.++|..|+ .|||
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            346799999999999999999    99999997            445544   367899999999999999999 6999


Q ss_pred             ceecCceEEEeCCCCCC
Q 009954          244 IIFEGVAVRVRRPTDYN  260 (521)
Q Consensus       244 ~~~~g~~i~v~~~~~~~  260 (521)
                      ..+.|+.|.|.++....
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

>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=99.42  E-value=8.8e-13  Score=106.41  Aligned_cols=77  Identities=25%  Similarity=0.374  Sum_probs=65.2

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-------cCCCCeEEEEecCHHHHHHHH-Hcc--
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVEMRTVEEASNAM-ALD--  242 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~-------~~~~g~afV~f~~~~~a~~A~-~l~--  242 (521)
                      ..++|||+|||..+|+++|+++|.+||..           |..+.+       +.++|||||+|.+.++|..|+ .|+  
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            45789999999999999999999999861           333333       367899999999999999999 585  


Q ss_pred             CceecCceEEEeCCCCCC
Q 009954          243 GIIFEGVAVRVRRPTDYN  260 (521)
Q Consensus       243 g~~~~g~~i~v~~~~~~~  260 (521)
                      +..+.|+.|.|.++....
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            589999999999976544

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.42  E-value=3e-13  Score=108.22  Aligned_cols=82  Identities=21%  Similarity=0.370  Sum_probs=66.3

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHH-HHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCce-ecC
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQ-VMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII-FEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~-~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~-~~g  248 (521)
                      ...++|||+|||..+|+++|+++|.+ ||.|..+.      .+.+. .+.++|||||+|.+.++|.+|+ .|++.. |.|
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~------i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g   79 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGK------VVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGS   79 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEE------EEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEE------EEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCC
Confidence            34678999999999999999999999 99843211      01111 3456899999999999999999 599999 999


Q ss_pred             ceEEEeCCCCCC
Q 009954          249 VAVRVRRPTDYN  260 (521)
Q Consensus       249 ~~i~v~~~~~~~  260 (521)
                      +.|.|.++....
T Consensus        80 ~~l~v~~a~~~~   91 (104)
T 2dhg_A           80 KPVRLSVAIPKA   91 (104)
T ss_dssp             SCCCCCBCCCCC
T ss_pred             EeEEEEEccCCC
Confidence            999999876543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.42  E-value=3.8e-13  Score=109.56  Aligned_cols=76  Identities=18%  Similarity=0.215  Sum_probs=65.3

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCCeEEEEecCHHHHHHHH-HccCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-ALDGII  245 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~A~-~l~g~~  245 (521)
                      ...++|||+|||..+|+++|+++|.+||.|            ..+.+     +.++|||||+|.+.++|.+|+ .||+..
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i------------~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~   80 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVV------------VRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQL   80 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCE------------EEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            446799999999999999999999999974            33333     334789999999999999999 599999


Q ss_pred             ecCceEEEeCCCCC
Q 009954          246 FEGVAVRVRRPTDY  259 (521)
Q Consensus       246 ~~g~~i~v~~~~~~  259 (521)
                      |.|+.|.|.++...
T Consensus        81 ~~g~~l~v~~a~~~   94 (114)
T 2do0_A           81 LFDRPMHVKMDERA   94 (114)
T ss_dssp             ETTEECEEEECSCC
T ss_pred             eCCCEEEEEEcccC
Confidence            99999999987543

>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=99.42  E-value=1.1e-13  Score=110.51  Aligned_cols=83  Identities=20%  Similarity=0.309  Sum_probs=65.5

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      ....++|||+|||..+|+++|+++|.+||.|..+.      .+.+..++.++|||||+|.+.++|.+|+. ++..|.|+.
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~   84 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQ------VKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRW   84 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEE------EEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEE
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEE------EEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCeE
Confidence            44567899999999999999999999999843210      01111224557899999999999999996 578999999


Q ss_pred             EEEeCCCCCC
Q 009954          251 VRVRRPTDYN  260 (521)
Q Consensus       251 i~v~~~~~~~  260 (521)
                      |.|.++....
T Consensus        85 l~v~~a~~~~   94 (103)
T 2cqg_A           85 CDCKLPNSKQ   94 (103)
T ss_dssp             EEEECCCTTC
T ss_pred             EEEEecCCCC
Confidence            9999876543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.42  E-value=7e-13  Score=105.78  Aligned_cols=67  Identities=22%  Similarity=0.401  Sum_probs=61.1

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|++||+.|||..|+|+.|+|.|+....
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            599999999999999999998766553   5888999999999999999999999999999999988654

>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=99.42  E-value=9.9e-14  Score=107.19  Aligned_cols=73  Identities=23%  Similarity=0.361  Sum_probs=64.2

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+|||+.+|+++|+++|.+| .            |..+.+..++|||||+|.+.++|.+|+ .|||..+.|+.|
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            45789999999999999999999998 6            344444578999999999999999999 699999999999


Q ss_pred             EEeCCCC
Q 009954          252 RVRRPTD  258 (521)
Q Consensus       252 ~v~~~~~  258 (521)
                      +|.++..
T Consensus        71 ~V~~a~~   77 (88)
T 1wg1_A           71 IVQLQPT   77 (88)
T ss_dssp             EEEECCC
T ss_pred             EEEEcCC
Confidence            9998643

>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=99.41  E-value=4.4e-13  Score=111.30  Aligned_cols=67  Identities=22%  Similarity=0.370  Sum_probs=61.3

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|++||+.|||..|+|++|+|.|+..++
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            599999999999999999998766554   6889999999999999999999999999999999987764

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=7.9e-14  Score=108.60  Aligned_cols=80  Identities=19%  Similarity=0.268  Sum_probs=64.8

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ...++|||+|||..+|+++|+++|..| .|..+.      .+.+ ..+.++|||||+|.+.++|.+|+.||+..|.|+.|
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~------i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i   79 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIR------IVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYI   79 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEE------EEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEE------EEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEE
Confidence            346799999999999999999999998 643210      1111 23456899999999999999999999999999999


Q ss_pred             EEeCCCCC
Q 009954          252 RVRRPTDY  259 (521)
Q Consensus       252 ~v~~~~~~  259 (521)
                      .|.++...
T Consensus        80 ~v~~a~~~   87 (91)
T 2dgw_A           80 EVFREKSG   87 (91)
T ss_dssp             EEEEESSC
T ss_pred             EEEECCcC
Confidence            99986543

>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=99.41  E-value=2.3e-13  Score=113.00  Aligned_cols=76  Identities=25%  Similarity=0.286  Sum_probs=66.1

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCCeEEEEecCHHHHHHHH-HccCc
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDGI  244 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~A~-~l~g~  244 (521)
                      ...++|||+|||..+|+++|+++|.+||.            |..+.+      +.++|||||+|.+.++|.+|+ .|||.
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   87 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGE------------IKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQ   87 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            34679999999999999999999999997            444444      345899999999999999999 69999


Q ss_pred             eecCceEEEeCCCCC
Q 009954          245 IFEGVAVRVRRPTDY  259 (521)
Q Consensus       245 ~~~g~~i~v~~~~~~  259 (521)
                      .|.|+.|.|.++...
T Consensus        88 ~~~g~~l~v~~a~~~  102 (126)
T 3ex7_B           88 DLMGQPISVDWCFVR  102 (126)
T ss_dssp             BSSSSBCEEEESEES
T ss_pred             eeCCeEEEEEEecCC
Confidence            999999999987543

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

Probab=99.41  E-value=1.4e-13  Score=108.31  Aligned_cols=75  Identities=15%  Similarity=0.312  Sum_probs=64.4

Q ss_pred             hccCCeEEEeCCCc-cCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          171 TRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       171 ~~~~~~l~v~nlp~-~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      ....++|||+|||. .+|+++|+++|.+||.            |..+.+  .+|||||+|.+.++|..|+ .|||..+.|
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            34577999999998 9999999999999997            444444  3899999999999999999 699999999


Q ss_pred             ceEEEeCCCCC
Q 009954          249 VAVRVRRPTDY  259 (521)
Q Consensus       249 ~~i~v~~~~~~  259 (521)
                      +.|.|.++...
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

>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=99.40  E-value=4.7e-14  Score=117.68  Aligned_cols=79  Identities=19%  Similarity=0.198  Sum_probs=65.9

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHH---hhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecC
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMT---AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~---~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g  248 (521)
                      ...++|||+|||+++|+++|+++|.+||.   |..+      ..+.+.. ++++|||||+|.+.++|.+|+++|+..|.|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v------~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~g  114 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGV------HFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGH  114 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTE------EEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEE------EEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECC
Confidence            45679999999999999999999999987   3321      1122222 667899999999999999999999999999


Q ss_pred             ceEEEeCCC
Q 009954          249 VAVRVRRPT  257 (521)
Q Consensus       249 ~~i~v~~~~  257 (521)
                      +.|.|.++.
T Consensus       115 r~i~V~~a~  123 (136)
T 2hgl_A          115 RYIEVFKSH  123 (136)
T ss_dssp             SEEEEEECC
T ss_pred             EEEEEEECC
Confidence            999998754

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=8.5e-14  Score=110.96  Aligned_cols=81  Identities=21%  Similarity=0.330  Sum_probs=65.5

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....++|||+|||..+|+++|+++|..|+.+         ..+.+...+.++|||||+|.+.++|.+|+ .||+..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~---------~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   82 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSVRA---------RIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGN   82 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCSEE---------EEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCeEE---------EEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            3456899999999999999999999976431         11222234556799999999999999999 5999999999


Q ss_pred             eEEEeCCCCCC
Q 009954          250 AVRVRRPTDYN  260 (521)
Q Consensus       250 ~i~v~~~~~~~  260 (521)
                      .|.|.++....
T Consensus        83 ~l~V~~a~~~~   93 (102)
T 2fc8_A           83 KVTLDWAKPKG   93 (102)
T ss_dssp             ECEEEECCCCC
T ss_pred             EEEEEEecCCC
Confidence            99999976543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.40  E-value=6.8e-14  Score=107.43  Aligned_cols=79  Identities=18%  Similarity=0.328  Sum_probs=63.6

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+|||+.+|+++|+++|.+||.|..+.+      +.+...+.++|||||+|.+.++|.+|+ .|||..+.|+.|
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i------~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~   77 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKA------ILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   77 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEE------ECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE------EecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEE
Confidence            4679999999999999999999999998432100      111123456899999999999999999 699999999999


Q ss_pred             EEeCCC
Q 009954          252 RVRRPT  257 (521)
Q Consensus       252 ~v~~~~  257 (521)
                      ++.++.
T Consensus        78 ~~~~~~   83 (85)
T 1x4e_A           78 KQSGPS   83 (85)
T ss_dssp             CSSCCC
T ss_pred             eecCCC
Confidence            998753

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.40  E-value=1.1e-12  Score=103.73  Aligned_cols=64  Identities=16%  Similarity=0.327  Sum_probs=58.6

Q ss_pred             HHHHHhhccccceeE--------EEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcC
Q 009954          444 EDMREECGKYGTLVN--------VVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  510 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~--------v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~  510 (521)
                      ++|+++|+.||.|..        |.|+.+..++..   +|+|||+|.+.++|++||+.|||..|+|+.|+|.|+.
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            599999999999999        999998766553   6899999999999999999999999999999999874

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=2.9e-13  Score=108.36  Aligned_cols=76  Identities=17%  Similarity=0.211  Sum_probs=62.0

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  253 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v  253 (521)
                      ..+|||+|||+.+|+++|+++|..| .|....      ++.+ ..++++|||||+|.+.++|.+||++|+..|.|+.|.|
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~------i~~d-~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V   87 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVH------LLKD-HVGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEV   87 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEE------ECCC-TTCCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEE------EEEC-CCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEE
Confidence            4689999999999999999999998 432110      0111 1256789999999999999999999999999999999


Q ss_pred             eCCC
Q 009954          254 RRPT  257 (521)
Q Consensus       254 ~~~~  257 (521)
                      ..+.
T Consensus        88 ~~a~   91 (109)
T 2dnn_A           88 SPAT   91 (109)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            8754

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.39  E-value=2.7e-13  Score=107.35  Aligned_cols=68  Identities=21%  Similarity=0.271  Sum_probs=61.7

Q ss_pred             HHHHHhhcccccee-EEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcE----EEEEEcCCCCc
Q 009954          444 EDMREECGKYGTLV-NVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT----VNAFYYPEDKY  514 (521)
Q Consensus       444 ~dl~~~f~~fG~I~-~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~----l~v~~~~~~~~  514 (521)
                      ++|+++|++||.|. .|.|+++..++..   +|+|||+|.+.++|++||+.|||..|+|+.    |+|.|+....-
T Consensus        24 ~~l~~~F~~~G~i~~~v~i~~~~~~g~~---~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~~~   96 (99)
T 2div_A           24 NFISRAFATMGETVMSVKIIRNRLTGIP---AGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGP   96 (99)
T ss_dssp             HHHHHHHHHTTCCCCEEEEEECSSSCCE---EEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTCCSS
T ss_pred             HHHHHHHHHhCCcceEEEEeecCCCCCc---CCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCCCCC
Confidence            59999999999999 9999998766554   689999999999999999999999999999    99999887654

>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=99.39  E-value=5.6e-13  Score=107.17  Aligned_cols=63  Identities=17%  Similarity=0.308  Sum_probs=58.2

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  510 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~  510 (521)
                      ++|+++|+.||.|..|.|+.+. ++..   +|+|||+|.+.++|++||+.|||..|+|+.|+|.|++
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            5999999999999999999887 5543   6899999999999999999999999999999999975

>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=99.39  E-value=4.1e-13  Score=115.99  Aligned_cols=78  Identities=23%  Similarity=0.395  Sum_probs=67.5

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCCeEEEEecCHHHHHHHH-HccC
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG  243 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~a~~A~-~l~g  243 (521)
                      ....++|||+|||..+|+++|+++|.+||.|            ..+.+      +.++|||||+|.+.++|.+|+ .||+
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i------------~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g  103 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDI------------KKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYING  103 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCE------------EEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence            3467899999999999999999999999984            44443      445789999999999999999 5999


Q ss_pred             ceecCceEEEeCCCCCC
Q 009954          244 IIFEGVAVRVRRPTDYN  260 (521)
Q Consensus       244 ~~~~g~~i~v~~~~~~~  260 (521)
                      ..|.|+.|+|.++....
T Consensus       104 ~~~~g~~l~V~~a~~~~  120 (156)
T 1h2v_Z          104 TRLDDRIIRTDWDAGFK  120 (156)
T ss_dssp             SEETTEECEEEEESCCC
T ss_pred             CEECCeEEEEEECCCCC
Confidence            99999999999976544

>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=99.39  E-value=2.9e-14  Score=110.82  Aligned_cols=78  Identities=29%  Similarity=0.417  Sum_probs=62.2

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEE
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v  253 (521)
                      ++|||+|||..+++++|+++|++||.|..+.+      +.+..++.++|||||+|.+.+ |.+|+ .|||..+.|+.|.|
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V   74 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKL------IYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRV   74 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEE------CCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSE
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEE------EEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEE
Confidence            58999999999999999999999998532110      111123566899999999999 99999 69999999999999


Q ss_pred             eCCCCC
Q 009954          254 RRPTDY  259 (521)
Q Consensus       254 ~~~~~~  259 (521)
                      .++...
T Consensus        75 ~~a~~~   80 (90)
T 2ki2_A           75 TEANPK   80 (90)
T ss_dssp             EEC---
T ss_pred             EEcCCC
Confidence            987654

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.39  E-value=5.7e-13  Score=107.06  Aligned_cols=66  Identities=17%  Similarity=0.278  Sum_probs=60.1

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|++||+.|||..|+|+.|+|.|+.+.
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            599999999999999999988766543   689999999999999999999999999999999998764

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.39  E-value=4.6e-14  Score=106.14  Aligned_cols=75  Identities=11%  Similarity=0.238  Sum_probs=61.3

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEE
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v  253 (521)
                      ++|||+|||..+|+++|+++|++||.|..+.      .+.+...+.++|||||+|.+.++|.+|+ .++ ..+.|+.|.|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~------i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v   73 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECL------VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDP   73 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEE------EECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE------EecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEE
Confidence            4799999999999999999999999854311      1122234567899999999999999999 467 9999999999


Q ss_pred             eCC
Q 009954          254 RRP  256 (521)
Q Consensus       254 ~~~  256 (521)
                      +++
T Consensus        74 ~~a   76 (77)
T 1uaw_A           74 KVA   76 (77)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            874

>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=99.38  E-value=5.5e-14  Score=112.99  Aligned_cols=80  Identities=18%  Similarity=0.210  Sum_probs=66.3

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHH---hhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecC
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMT---AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~---~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g  248 (521)
                      ...++|||+|||+.+|+++|+++|..||.   |..+.      .+.+.. +.++|||||+|.+.++|.+||.+++..|.|
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~------i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~g   81 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIH------FLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQ   81 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEE------CCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSS
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEE------EEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCC
Confidence            45678999999999999999999999887   43221      122222 678899999999999999999999999999


Q ss_pred             ceEEEeCCCC
Q 009954          249 VAVRVRRPTD  258 (521)
Q Consensus       249 ~~i~v~~~~~  258 (521)
                      +.|.|.++..
T Consensus        82 r~i~V~~a~~   91 (107)
T 2lmi_A           82 RYVEVYEINN   91 (107)
T ss_dssp             SCCCCEECCH
T ss_pred             eEEEEEECCH
Confidence            9999987653

>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=99.38  E-value=4.5e-13  Score=113.91  Aligned_cols=88  Identities=16%  Similarity=0.181  Sum_probs=70.1

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||+.+|+++|+++|..||.|..+.+ .....+....++.++|||||+|.+.++|..|+ .|||..|.|+.
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            34678999999999999999999999997643100 00000333467889999999999999999999 59999999999


Q ss_pred             EEEeCCCCCC
Q 009954          251 VRVRRPTDYN  260 (521)
Q Consensus       251 i~v~~~~~~~  260 (521)
                      |.|.++....
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

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.38  E-value=1.4e-12  Score=104.70  Aligned_cols=66  Identities=20%  Similarity=0.342  Sum_probs=60.3

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|++||..|||..|+|+.|+|.|+...
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            599999999999999999998766553   689999999999999999999999999999999998654

>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=99.38  E-value=2.2e-12  Score=104.19  Aligned_cols=66  Identities=23%  Similarity=0.367  Sum_probs=60.2

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|..||..|||..|+|+.|+|.|+...
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            599999999999999999988766553   688999999999999999999999999999999998654

>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=1e-13  Score=113.41  Aligned_cols=84  Identities=24%  Similarity=0.188  Sum_probs=65.4

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      .....+|||+|||+++|+++|+++|++||.|.+..  ..+..+.+ ..++++|||||+|.+.++|.+||+.|+..|.|+.
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v--~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~   96 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGK--EGILFVTY-PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRY   96 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGG--GGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCc--ceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeE
Confidence            35578999999999999999999999998642100  00011122 3566789999999999999999977999999999


Q ss_pred             EEEeCCC
Q 009954          251 VRVRRPT  257 (521)
Q Consensus       251 i~v~~~~  257 (521)
                      |.|..+.
T Consensus        97 i~V~~a~  103 (123)
T 2dha_A           97 IELFRST  103 (123)
T ss_dssp             ECCEEEC
T ss_pred             EEEEECC
Confidence            9997653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.08  E-value=4e-14  Score=115.75  Aligned_cols=89  Identities=20%  Similarity=0.230  Sum_probs=70.3

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCC--CCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceec
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAG--PGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~--~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      ....++|||+|||..+|+++|+++|.+||.|..+....  .+..+.+..++.++|||||+|.+.++|.+|+ .||+..|.
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            34567999999999999999999999999875410000  0112334455678999999999999999999 59999999


Q ss_pred             CceEEEeCCCCC
Q 009954          248 GVAVRVRRPTDY  259 (521)
Q Consensus       248 g~~i~v~~~~~~  259 (521)
                      |+.|.|.++...
T Consensus        84 g~~l~V~~a~~~   95 (116)
T 2lcw_A           84 GNPIKVSFATRR   95 (116)
Confidence            999999987654

>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=99.37  E-value=1.5e-12  Score=103.97  Aligned_cols=67  Identities=18%  Similarity=0.191  Sum_probs=59.5

Q ss_pred             HHHHHhhccccceeEEEecCCCCC-CCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCcc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQN-GGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYF  515 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~-~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~  515 (521)
                      ++|+++|+.|| |..|.|+.+..+ +..   +|+|||+|.+.++|++|| .|||..|+|+.|+|.|+....-.
T Consensus        30 ~~l~~~F~~~G-i~~v~i~~~~~~~g~~---~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~   97 (104)
T 1wi8_A           30 ESIKEFFRGLN-ISAVRLPREPSNPERL---KGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDK   97 (104)
T ss_dssp             HHHHHHTTTSC-EEEEECCBCSSCTTSB---CSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCCC
T ss_pred             HHHHHHHHHCC-ceEEEEecCCCCCCCc---CeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccCCCCC
Confidence            59999999999 999999998765 443   578899999999999999 99999999999999998876543

>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=99.37  E-value=2.1e-12  Score=103.88  Aligned_cols=76  Identities=16%  Similarity=0.113  Sum_probs=65.8

Q ss_pred             CCCeEEEcCCCCCCC----------HHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeC
Q 009954          293 GPDRVFVGGLPYYFT----------ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (521)
Q Consensus       293 ~~~~l~v~nLp~~~t----------e~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~  362 (521)
                      +.++|.|.||-..-.          ++||+++|++||.|.+|.|.++.    ++|+|||+|.+.++|.+|++.|||.+|+
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            346899999954322          26899999999999999987652    4899999999999999999999999999


Q ss_pred             CeEEEEEEcc
Q 009954          363 DKTLTVRRAT  372 (521)
Q Consensus       363 g~~l~v~~~~  372 (521)
                      |+.|.|.|+.
T Consensus        82 GR~i~v~~~~   91 (114)
T 3s6e_A           82 GKMITAAYVP   91 (114)
T ss_dssp             TEECEEEEEC
T ss_pred             CEEEEEEEEc
Confidence            9999999985

>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=99.37  E-value=4.7e-13  Score=108.96  Aligned_cols=72  Identities=25%  Similarity=0.344  Sum_probs=62.3

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce-
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA-  250 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~-  250 (521)
                      ..++|||+|||+++|+++|+++|.+||.            |..+.+... |||||+|.+.++|++|| .||+..|.|+. 
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~   81 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGD------------VCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHEG   81 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSC------------EEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTTS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEecC-CEEEEEECCHHHHHHHHHHhCCCEECCcEe
Confidence            4578999999999999999999999997            667776655 99999999999999999 59999999988 


Q ss_pred             ----EEEeCCC
Q 009954          251 ----VRVRRPT  257 (521)
Q Consensus       251 ----i~v~~~~  257 (521)
                          |+|....
T Consensus        82 ~~~~i~v~~~~   92 (115)
T 3beg_B           82 ETAYIRVKVDG   92 (115)
T ss_dssp             CCCBCEEEECC
T ss_pred             eeEEEEeccCC
Confidence                6666543

>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=99.36  E-value=9.7e-14  Score=113.81  Aligned_cols=74  Identities=20%  Similarity=0.220  Sum_probs=61.9

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCCeEEEEecCHHHHHHHHHccCcee
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDGIIF  246 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~A~~l~g~~~  246 (521)
                      ...++|||+|||+.+|+++|+++|++| .|+          ..++.+     ++++|||||+|.+.++|.+|+++++..|
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~----------~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~~~~~l  108 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIV----------PNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERI  108 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEE----------EEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTTTTCCB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-Cce----------eeEEEEEECCCCCCceEEEEEECCHHHHHHHHHHCCCEE
Confidence            446789999999999999999999999 321          003333     5678999999999999999998888999


Q ss_pred             cCceEEEeCC
Q 009954          247 EGVAVRVRRP  256 (521)
Q Consensus       247 ~g~~i~v~~~  256 (521)
                      .|+.|.|.++
T Consensus       109 ~gR~I~V~~a  118 (126)
T 2hgm_A          109 GHRYIEVFKS  118 (126)
T ss_dssp             TTBCCCCEEE
T ss_pred             CCEEEEEEEC
Confidence            9999999764

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.36  E-value=1.6e-12  Score=103.62  Aligned_cols=67  Identities=13%  Similarity=0.132  Sum_probs=60.0

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCcc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYF  515 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~  515 (521)
                      ++|+++|+.|| |..|.|+.+..++..   +|+|||+|.+.++|++|| .|||..|+|+.|+|.|+....-.
T Consensus        30 ~~l~~~F~~~g-i~~v~i~~~~~~g~~---~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2dng_A           30 GDIDAIFKDLS-IRSVRLVRDKDTDKF---KGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQD   96 (103)
T ss_dssp             HHHHHHTTTSC-EEEEEEEECSSSCSE---EEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECCCCCCC
T ss_pred             HHHHHHHHhCC-ceEEEEeecCCCCcc---ceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEecCCCCC
Confidence            59999999997 999999998766554   689999999999999999 89999999999999998876543

>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=99.35  E-value=1.9e-12  Score=110.09  Aligned_cols=74  Identities=19%  Similarity=0.186  Sum_probs=63.8

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe--cCCCCeEEEEecCHHHHHHHH-HccCceecC--
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--  248 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~--~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g--  248 (521)
                      ..+|||+||++.+|+++|+++|++||.            |.++.+  ...+|||||+|.+.++|..|+ .|||..|.|  
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~------------V~~V~i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g  113 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGT------------VLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNAC  113 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSC------------EEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCC------------EEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCC
Confidence            457999999999999999999999998            444444  345789999999999999999 699999966  


Q ss_pred             ceEEEeCCCCC
Q 009954          249 VAVRVRRPTDY  259 (521)
Q Consensus       249 ~~i~v~~~~~~  259 (521)
                      +.|+|.+++..
T Consensus       114 ~~L~V~~Ak~~  124 (164)
T 1sjr_A          114 CTLRIDFSKLT  124 (164)
T ss_dssp             SCEEEEECSSS
T ss_pred             cEEEEEEecCC
Confidence            99999997754

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.35  E-value=1.5e-12  Score=106.14  Aligned_cols=73  Identities=18%  Similarity=0.125  Sum_probs=61.8

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCe-EEEEecCHHHHHHHH-HccCceecC--ce
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKF-AFVEMRTVEEASNAM-ALDGIIFEG--VA  250 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~-afV~f~~~~~a~~A~-~l~g~~~~g--~~  250 (521)
                      ..|||+||++.+|+++|+++|++||.            |.++.+....|| |||+|.+.++|..|+ .|||..|.|  +.
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            35789999999999999999999998            444443333596 999999999999999 799999988  68


Q ss_pred             EEEeCCCCC
Q 009954          251 VRVRRPTDY  259 (521)
Q Consensus       251 i~v~~~~~~  259 (521)
                      |+|.+++..
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

>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=99.35  E-value=7e-14  Score=117.00  Aligned_cols=81  Identities=25%  Similarity=0.194  Sum_probs=65.0

Q ss_pred             hhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCc
Q 009954          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (521)
Q Consensus       170 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~  249 (521)
                      .....++|||+|||+++|+++|+++|++|| ++.+.+      +.+. .++++|||||+|.+.++|++||++|+..|.|+
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i------~~d~-~g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR  113 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHI------EIGP-DGRVTGEADVEFATHEEAVAAMSKDRANMQHR  113 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEEC------CCSS-SSCSSCCCEEECSHHHHHHHHTTCCSCSSSSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEE------EECC-CCCCceEEEEEeCCHHHHHHHHhhCCCEECCE
Confidence            345568999999999999999999999998 432211      2222 26678999999999999999999999999999


Q ss_pred             eEEEeCCCC
Q 009954          250 AVRVRRPTD  258 (521)
Q Consensus       250 ~i~v~~~~~  258 (521)
                      .|.|.++..
T Consensus       114 ~i~V~~a~~  122 (139)
T 2hgn_A          114 YIELFLNST  122 (139)
T ss_dssp             CCCCEECCC
T ss_pred             EEEEEECCC
Confidence            999987543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.35  E-value=2.7e-12  Score=108.69  Aligned_cols=63  Identities=17%  Similarity=0.253  Sum_probs=57.6

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  509 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~  509 (521)
                      ++|+++|+.||.|..|.|+.+..++..   +|+|||+|.+.++|++||+.|||..|+|+.|+|.|+
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            599999999999999999998766654   688999999999999999999999999999999885

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.34  E-value=5.6e-12  Score=98.82  Aligned_cols=74  Identities=12%  Similarity=0.182  Sum_probs=62.7

Q ss_pred             CeEEEcCCC-------CCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          295 DRVFVGGLP-------YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       295 ~~l~v~nLp-------~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      .+|.|.-..       ..+++++|+++|++||.|..|.|+     +.++|||||+|.+.++|.+|++.+++  +.|+.|.
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            466665554       458999999999999999999987     35799999999999999999997554  6799999


Q ss_pred             EEEccCCC
Q 009954          368 VRRATASG  375 (521)
Q Consensus       368 v~~~~~~~  375 (521)
                      |.|+....
T Consensus        84 V~~a~~~~   91 (100)
T 2d9o_A           84 ISWLEGQP   91 (100)
T ss_dssp             EECSSCCC
T ss_pred             EEEccCCC
Confidence            99997643

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.33  E-value=3.2e-12  Score=105.69  Aligned_cols=67  Identities=15%  Similarity=0.261  Sum_probs=60.9

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  514 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~  514 (521)
                      ++|+++|+.||.|..|.|+.+. ++..   +|+|||+|.+.++|++|+..|||..|+|+.|+|.|+.....
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            5999999999999999999987 6543   68899999999999999999999999999999999877554

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.33  E-value=2.1e-13  Score=125.17  Aligned_cols=80  Identities=15%  Similarity=0.144  Sum_probs=64.2

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHH--HhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVM--TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G--~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ..++|||+|||+.+|+++|+++|.+||  .|..+.      ++.+..++.++|||||+|.+.++|.+|| .||+..|.|+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~------i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr  140 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIK------FFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQ  140 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEE------EEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTB
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEE------EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCE
Confidence            567899999999999999999999999  643211      1111124556899999999999999999 5999999999


Q ss_pred             eEEEeCCCC
Q 009954          250 AVRVRRPTD  258 (521)
Q Consensus       250 ~i~v~~~~~  258 (521)
                      .|+|.++..
T Consensus       141 ~l~V~~a~~  149 (229)
T 3q2s_C          141 NPVVTPVNK  149 (229)
T ss_dssp             CCEEEECCH
T ss_pred             EeEEEECCC
Confidence            999998653

>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=99.32  E-value=2.3e-12  Score=104.80  Aligned_cols=80  Identities=13%  Similarity=0.266  Sum_probs=63.7

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCcee---
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF---  246 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~---  246 (521)
                      ....++|||+|||..+|+++|+++|..||.|..+.+      +.+ ..+.++|||||+|.+.++|.+|+ .|||..|   
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i------~~~-~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~   94 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRI------LRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTP   94 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEE------EEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE------EEC-CCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCC
Confidence            445689999999999999999999999998432110      111 13455799999999999999999 6999999   


Q ss_pred             -----cCceEEEeCCC
Q 009954          247 -----EGVAVRVRRPT  257 (521)
Q Consensus       247 -----~g~~i~v~~~~  257 (521)
                           .+++|.|.++.
T Consensus        95 ~~~~~~~~~l~v~~a~  110 (114)
T 1x5o_A           95 PGVSAPTEPLLCKFSG  110 (114)
T ss_dssp             TTSCCCSSCBEEEECC
T ss_pred             ccccCCCCceeEEccC
Confidence                 57778888764

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.31  E-value=1.1e-11  Score=97.46  Aligned_cols=64  Identities=17%  Similarity=0.250  Sum_probs=57.1

Q ss_pred             HHHHHhhccccceeEE-EecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCc
Q 009954          444 EDMREECGKYGTLVNV-VIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  514 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v-~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~  514 (521)
                      ++|+++|+.||.|..| .|+.+..+       |.|||+|.+.++|..||..|||..|+|++|+|.|+.+.+.
T Consensus        30 ~~l~~~F~~~G~v~~~~~i~~~~~~-------~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~~   94 (96)
T 2e44_A           30 EVLDSLLVQYGVVESCEQVNTDSET-------AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMA   94 (96)
T ss_dssp             HHHHHHHHHHSCEEEEEEECCSSSS-------EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCCS
T ss_pred             HHHHHHHHhcCCeEEEEEeecCCCC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCcccc
Confidence            4999999999999999 58876532       4589999999999999999999999999999999988754

>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=99.31  E-value=3.1e-12  Score=98.70  Aligned_cols=74  Identities=27%  Similarity=0.425  Sum_probs=57.8

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCCeEEEEecCHHHHHHHHHccCce--ec
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAMALDGII--FE  247 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~-~~~g~afV~f~~~~~a~~A~~l~g~~--~~  247 (521)
                      .....+|||+|||+++|+++|+++|++||.            |.++.+. .++|||||+|.+.++|.+   +++..  +.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~------------i~~v~i~~~srGfaFV~F~~~~~A~~---~~~~~~~~~   72 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGE------------VVDVFIPKPFRAFAFVTFADDKVAQS---LCGEDLIIK   72 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSC------------EEEEECCSSCCSEEEEEESCHHHHHH---HTTCEEEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCC------------EEEEEEeeCCCCEEEEEECCHHHHHH---HcCCCcccC
Confidence            344678999999999999999999999998            5566554 369999999999999984   34444  56


Q ss_pred             CceEEEeCCCCC
Q 009954          248 GVAVRVRRPTDY  259 (521)
Q Consensus       248 g~~i~v~~~~~~  259 (521)
                      |+.|.|.++...
T Consensus        73 g~~v~v~~a~~k   84 (89)
T 3d2w_A           73 GISVHISNAEPK   84 (89)
T ss_dssp             TEEEEEEECC--
T ss_pred             CEEEEEEEcCCC
Confidence            899999886543

>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=99.31  E-value=5e-12  Score=100.87  Aligned_cols=68  Identities=13%  Similarity=0.226  Sum_probs=60.4

Q ss_pred             HHHHHhhccccceeE-EEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCccc
Q 009954          444 EDMREECGKYGTLVN-VVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFN  516 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~-v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~~  516 (521)
                      ++|+++|+.||.|.. |.|+.+ .++..   +|+|||+|.+.++|++||+. ||..|+|+.|.|.+++..++..
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            699999999999998 888887 46554   68899999999999999997 9999999999999998877653

>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=99.30  E-value=3.4e-12  Score=101.25  Aligned_cols=70  Identities=13%  Similarity=0.073  Sum_probs=61.0

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCcccccC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY  519 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~~~~~  519 (521)
                      ++|+++|++|| |+.|.|+.+. ++..   +|+|||+|.+.++|++||+ +|+..|+|+.|+|.++....-..+.|
T Consensus        30 ~~l~~~F~~~G-~~~v~i~~d~-~g~~---~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~~~~~~~~~~   99 (102)
T 1wez_A           30 NDIYNFFSPLN-PMRVHIEIGP-DGRV---TGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTSGSGP   99 (102)
T ss_dssp             HHHHHSSCSCC-CSEEEEEESS-SSCE---EEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCCCCCCS
T ss_pred             HHHHHHHHHcC-ceEEEEEECC-CCCE---eeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCCCCCCCCCC
Confidence            69999999999 5599999987 6543   6899999999999999995 79999999999999988877665554

>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=99.28  E-value=2.8e-12  Score=98.99  Aligned_cols=75  Identities=25%  Similarity=0.390  Sum_probs=61.2

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~-~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ..++|||+|||..+|+++|+++|.+||.            |..+.+. .++|||||+|.+.++|++|+.. ...+.|+.|
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 3689999999999999876532 455689999


Q ss_pred             EEeCCCCCC
Q 009954          252 RVRRPTDYN  260 (521)
Q Consensus       252 ~v~~~~~~~  260 (521)
                      .|.++....
T Consensus        71 ~v~~a~~~~   79 (88)
T 1wf0_A           71 HISNAEPKH   79 (88)
T ss_dssp             EEECCCCCC
T ss_pred             EEEecCCCC
Confidence            999876543

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

Probab=99.27  E-value=3.6e-12  Score=116.06  Aligned_cols=77  Identities=22%  Similarity=0.341  Sum_probs=68.9

Q ss_pred             hccCCeEEEeCCCccC---------cHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-H
Q 009954          171 TRHARRVYVGGLPPLA---------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-A  240 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~---------t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~  240 (521)
                      ....++|||+||+..+         ++++|+++|++||.            |.++.+..++|||||+|.+.++|+.|+ .
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         89999999999998            777787789999999999999999999 7


Q ss_pred             ccCcee------------cCceEEEeCCCCC
Q 009954          241 LDGIIF------------EGVAVRVRRPTDY  259 (521)
Q Consensus       241 l~g~~~------------~g~~i~v~~~~~~  259 (521)
                      |+|..|            .|+.|.|.|+...
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

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.26  E-value=2e-11  Score=99.80  Aligned_cols=63  Identities=19%  Similarity=0.289  Sum_probs=56.1

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccE-EEEEecCHHHHHHHHHHHhCCeeCC--cEEEEEEcCCCCc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGK-VFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYYPEDKY  514 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~-afV~F~~~~~A~~Ai~~lng~~~~g--r~l~v~~~~~~~~  514 (521)
                      ++|.++|++||.|.+|.|....        .|+ |||+|.+.++|+.|++.|||..|.|  ++|+|.|+.....
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            5999999999999999997642        356 9999999999999999999999988  9999999877643

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.26  E-value=1.1e-11  Score=119.29  Aligned_cols=77  Identities=21%  Similarity=0.282  Sum_probs=65.7

Q ss_pred             CCCCCeEEEcC--CCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee---CCe-
Q 009954          291 AEGPDRVFVGG--LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM---GDK-  364 (521)
Q Consensus       291 ~~~~~~l~v~n--Lp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~---~g~-  364 (521)
                      ..+..+|||+|  |+..+|+++|+++|++||.|.+|.+..      ++|||||+|.+.++|++|++.|||..+   .|+ 
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            34557899999  578999999999999999999987753      479999999999999999999999877   244 


Q ss_pred             -EEEEEEccC
Q 009954          365 -TLTVRRATA  373 (521)
Q Consensus       365 -~l~v~~~~~  373 (521)
                       .|.|.|+..
T Consensus        89 ~~ly~~~~~~   98 (345)
T 3tht_A           89 ITLYLNFVEK   98 (345)
T ss_dssp             EECEEEECSS
T ss_pred             eEEEEEEeec
Confidence             678888753

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.26  E-value=1.1e-12  Score=104.50  Aligned_cols=78  Identities=18%  Similarity=0.313  Sum_probs=63.5

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ...++|||+|||..+|+++|+++|..||.|..+.+      +.+ ..+.++|||||+|.+.++|.+|+. ++..+.|+.|
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i------~~~-~~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l   78 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKI------ITD-RTGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKL   78 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEE------EEC-TTSCEEEEEEEEESSCCCHHHHTT-CCCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEE------EEC-CCCCccceEEEEECCHHHHHHHHh-CCCeECCEEE
Confidence            44679999999999999999999999998432110      111 134467999999999999999999 9999999999


Q ss_pred             EEeCCC
Q 009954          252 RVRRPT  257 (521)
Q Consensus       252 ~v~~~~  257 (521)
                      .|.++.
T Consensus        79 ~v~~a~   84 (102)
T 2xs2_A           79 KLGPAI   84 (102)
T ss_dssp             EEEEEE
T ss_pred             EEEECC
Confidence            998754

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.23  E-value=4.2e-12  Score=103.20  Aligned_cols=75  Identities=21%  Similarity=0.248  Sum_probs=55.8

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe---cCCCCeEEEEecCHHHHHHHH-HccCceec
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~---~~~~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      ...++|||+|||+.+|+++|+++|.+||.|. ..+      +.+..+   +.++|||||+|.+.++|.+|+ .|+  .+.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~------~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~   76 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDW------PHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EED   76 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EEC------TTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EET
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEE------eecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcC
Confidence            3468999999999999999999999999853 110      111112   467899999999999999999 562  255


Q ss_pred             CceEEEeC
Q 009954          248 GVAVRVRR  255 (521)
Q Consensus       248 g~~i~v~~  255 (521)
                      |+.+.+..
T Consensus        77 G~~~~~~~   84 (114)
T 2dnl_A           77 GKLYLCVS   84 (114)
T ss_dssp             TEEEEEEC
T ss_pred             CcEEEecc
Confidence            55555543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.21  E-value=1.6e-11  Score=98.25  Aligned_cols=65  Identities=12%  Similarity=0.104  Sum_probs=57.0

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecC----HHH----HHHHHH--HHhCCeeCCcEEEEEEcCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYD----AVG----CATAKN--ALSGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~----~~~----A~~Ai~--~lng~~~~gr~l~v~~~~~  511 (521)
                      .+|+++|+.||+|..|.++.|+.+|.+   +|++||+|.+    +++    |.+|+.  .|||..|+|++|+|.+-..
T Consensus        21 ~~Lk~~Fs~fGeV~~~~li~Dp~Tg~s---lGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           21 ISIKNYFKKYGEISHFEAFNDPNSALP---LHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILNKH   95 (136)
T ss_dssp             HHHHHHHHTTSCCSEEEEEECTTTCCE---EEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEECCT
T ss_pred             HHHHHHHHhcCCeEEEEEEecCCCCce---eeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEECcc
Confidence            599999999999999999999999886   6888999996    544    899999  7999999999999997544

>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=99.18  E-value=1.8e-11  Score=109.17  Aligned_cols=78  Identities=21%  Similarity=0.304  Sum_probs=66.1

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCCeEEEEecCHHHHHHHHHccCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDGII  245 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~-----~~~~g~afV~f~~~~~a~~A~~l~g~~  245 (521)
                      ....++|||+|||+.+|+++|+++|++||.|            ..+.+     +.++|||||+|.+.++|.+|+.+.+..
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            3457899999999999999999999999984            33333     346799999999999999999766779


Q ss_pred             ecCceEEEeCCCCCC
Q 009954          246 FEGVAVRVRRPTDYN  260 (521)
Q Consensus       246 ~~g~~i~v~~~~~~~  260 (521)
                      +.|+.|.|.+...|.
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            999999999877664

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.11  E-value=6.4e-11  Score=92.76  Aligned_cols=61  Identities=16%  Similarity=0.248  Sum_probs=52.5

Q ss_pred             HHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          443 LEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       443 ~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      +++|+++|++||.|..|.|+..        .+|+|||+|.+.++|+.||+.+++  +.|+.|+|.|+....
T Consensus        31 e~~L~~~F~~~G~V~~v~i~~~--------~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           31 KDVLLRLLQKYGEVLNLVLSSK--------KPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQP   91 (100)
T ss_dssp             HHHHHHHHHTTSCEEEEEEESS--------SSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCC
T ss_pred             HHHHHHHHHhcCCEEEEEEccC--------CCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCC
Confidence            3699999999999999999842        258889999999999999998555  689999999987653

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.09  E-value=9e-10  Score=82.44  Aligned_cols=62  Identities=6%  Similarity=0.286  Sum_probs=55.5

Q ss_pred             HHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCc
Q 009954          441 EILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKY  514 (521)
Q Consensus       441 ~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~  514 (521)
                      .+..+|.+.|.+||+|..|+|..+.           +||+|.+.++|.+||+ |||..++|+.|+|.+.+++=-
T Consensus        27 ~l~~~L~~~F~~~G~Vi~vr~~~d~-----------~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt~dW~   88 (91)
T 2dnr_A           27 ALIDELLQQFASFGEVILIRFVEDK-----------MWVTFLEGSSALNVLS-LNGKELLNRTITIALKSPSGP   88 (91)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEECSSS-----------EEEEESSHHHHHHGGG-GTTCEETTEEEEEEECCCSSC
T ss_pred             HHHHHHHHHHHhCCCeEEEEEecCC-----------EEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCCCCcc
Confidence            3456899999999999999998853           4999999999999999 999999999999999987643

>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=99.02  E-value=4e-10  Score=108.36  Aligned_cols=74  Identities=18%  Similarity=0.239  Sum_probs=63.1

Q ss_pred             hccCCeEEEeC--CCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceec
Q 009954          171 TRHARRVYVGG--LPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       171 ~~~~~~l~v~n--lp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      ..++++|||+|  |+..+|+++|+++|++||.            |..+.+..++|||||+|.+.++|++|+ .|||..+.
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  5788999999999999998            677777778999999999999999999 79999884


Q ss_pred             ---Cc--eEEEeCC
Q 009954          248 ---GV--AVRVRRP  256 (521)
Q Consensus       248 ---g~--~i~v~~~  256 (521)
                         |+  .+.|.+.
T Consensus        83 ~~~g~~~~ly~~~~   96 (345)
T 3tht_A           83 DDLGQKITLYLNFV   96 (345)
T ss_dssp             CTTSCEEECEEEEC
T ss_pred             cccCCceEEEEEEe
Confidence               44  5667664

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.02  E-value=7.7e-10  Score=82.80  Aligned_cols=70  Identities=19%  Similarity=0.296  Sum_probs=60.0

Q ss_pred             CeEEEcCCCC----CCCH----HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEE
Q 009954          295 DRVFVGGLPY----YFTE----TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (521)
Q Consensus       295 ~~l~v~nLp~----~~te----~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (521)
                      -||+|.-.+.    ..-.    .+|.+.|++||.|..++++.+.        +||+|.+.++|.+||+ |||..++|+.|
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            3777766652    2222    6799999999999999999873        8999999999999999 99999999999


Q ss_pred             EEEEccC
Q 009954          367 TVRRATA  373 (521)
Q Consensus       367 ~v~~~~~  373 (521)
                      +|.++++
T Consensus        79 kV~lkt~   85 (91)
T 2dnr_A           79 TIALKSP   85 (91)
T ss_dssp             EEEECCC
T ss_pred             EEEeCCC
Confidence            9999876

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.01  E-value=9.2e-10  Score=88.35  Aligned_cols=75  Identities=13%  Similarity=0.127  Sum_probs=66.9

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcC-hHHHHHHHHHHc--CCeeCCeEEE
Q 009954          292 EGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD-PAVTDIACAALN--GLKMGDKTLT  367 (521)
Q Consensus       292 ~~~~~l~v~nLp~~-~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~-~~~A~~Al~~l~--g~~~~g~~l~  367 (521)
                      .....|+|+||+.. +++++|+++|++||.|..|.+..+..      .|||+|.+ .++|..|+..|+  |..|.|..++
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            34468999999999 99999999999999999999998854      59999999 899999999995  7889999988


Q ss_pred             EEEcc
Q 009954          368 VRRAT  372 (521)
Q Consensus       368 v~~~~  372 (521)
                      +....
T Consensus        90 ~evL~   94 (121)
T 1owx_A           90 WEVLE   94 (121)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            88763

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.92  E-value=3.7e-09  Score=96.76  Aligned_cols=67  Identities=16%  Similarity=0.170  Sum_probs=60.8

Q ss_pred             CCHHHHHHHHHhcCCeeEEEEeecC----CCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          306 FTETQIKELLESFGTLHGFDLVKDR----DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       306 ~te~~l~~~F~~~G~i~~v~i~~~~----~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      -.+++|.+.|++||.|.+|.|+.+.    .++.++|++||+|.+.++|.+|+..|||.+|+|+.|.|.|..
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            3568999999999999999998554    355899999999999999999999999999999999999985

>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=2.4e-09  Score=80.42  Aligned_cols=58  Identities=21%  Similarity=0.366  Sum_probs=52.1

Q ss_pred             HHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcC
Q 009954          441 EILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  510 (521)
Q Consensus       441 ~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~  510 (521)
                      .+..+|.+.|..||+|..|+|..+.           +||+|.+.++|.+||+ |||..++|+.|+|.+-.
T Consensus        36 ~l~~~L~~~F~~~G~Vilvr~v~d~-----------~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           36 DLRTELMQTLGSYGTIVLVRINQGQ-----------MLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHHHHSCCSEEEEETTE-----------EEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHHHHHHHCCCEEEEEEecCc-----------EEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccC
Confidence            3456899999999999999999863           5999999999999999 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=98.84  E-value=6.9e-09  Score=77.97  Aligned_cols=69  Identities=17%  Similarity=0.283  Sum_probs=59.6

Q ss_pred             CeEEEcCCCCC------CCH---HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeE
Q 009954          295 DRVFVGGLPYY------FTE---TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT  365 (521)
Q Consensus       295 ~~l~v~nLp~~------~te---~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~  365 (521)
                      -||+|.-++..      ..+   .+|.+.|++||.|..++++.+.        +||+|.+.++|.+||+ |||..++|+.
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      221   5699999999999999999883        9999999999999998 9999999999


Q ss_pred             EEEEEcc
Q 009954          366 LTVRRAT  372 (521)
Q Consensus       366 l~v~~~~  372 (521)
                      |+|.+-.
T Consensus        87 L~V~~k~   93 (95)
T 1ufw_A           87 VKISGPS   93 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEeccC
Confidence            9999754

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.55  E-value=8.5e-08  Score=76.90  Aligned_cols=71  Identities=10%  Similarity=0.022  Sum_probs=62.4

Q ss_pred             cCCeEEEeCCCcc-CcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecC-HHHHHHHH-Hc--cCceec
Q 009954          173 HARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT-VEEASNAM-AL--DGIIFE  247 (521)
Q Consensus       173 ~~~~l~v~nlp~~-~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~-~~~a~~A~-~l--~g~~~~  247 (521)
                      ..+.|+|+||+.. ++.++|+++|++||.            |..+.+......|||.|.+ ..+|..|+ .+  ++..|.
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~------------V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i~   84 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGE------------IKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLR   84 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCC------------EEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTT
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCC------------EEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEEe
Confidence            3568999999999 999999999999987            8888888888899999999 89999999 67  478888


Q ss_pred             CceEEEeC
Q 009954          248 GVAVRVRR  255 (521)
Q Consensus       248 g~~i~v~~  255 (521)
                      |..+++..
T Consensus        85 g~~~~~ev   92 (121)
T 1owx_A           85 NKEVTWEV   92 (121)
T ss_dssp             SSSEEEEE
T ss_pred             CcEEEEEE
Confidence            98888763

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.54  E-value=1.3e-07  Score=72.24  Aligned_cols=59  Identities=10%  Similarity=0.092  Sum_probs=54.6

Q ss_pred             HHHHHhhccc-----cceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCC
Q 009954          444 EDMREECGKY-----GTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       444 ~dl~~~f~~f-----G~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~  511 (521)
                      ..|+.++++|     |.|++|.+..+.         |-|+|+|.+...|.+|...|+|..|.|++|+|.-+.+
T Consensus        36 arIr~lve~~~~i~~g~i~KI~L~pDH---------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gTv~e   99 (117)
T 2l9w_A           36 SLICQFLQEEIHINEKDIRKILLVSDF---------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTIND   99 (117)
T ss_dssp             HHHHHHHHHHTCCCTTTCSEEEEETTT---------TEEEEECSCHHHHHHHHHHHSSEEETTEEEEEECHHH
T ss_pred             HHHHHHHhhhhccCccceeEEEEecCC---------CceEEEEccchhhHHHHhhcCCeeecCeEEEecCHHH
Confidence            3899999999     999999999986         6799999999999999999999999999999987654

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.53  E-value=5e-07  Score=69.07  Aligned_cols=73  Identities=15%  Similarity=0.129  Sum_probs=67.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhc-----CCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESF-----GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~-----G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      ..++|-|-|||..++...|+.+.+++     |.|..|.+..|.      +-|+|+|.+...|-+|.-+|+|..|.|+.|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            35789999999999999999999999     999999999884      3599999999999999999999999999999


Q ss_pred             EEEc
Q 009954          368 VRRA  371 (521)
Q Consensus       368 v~~~  371 (521)
                      |.-.
T Consensus        94 ~gTv   97 (117)
T 2l9w_A           94 SGTI   97 (117)
T ss_dssp             EECH
T ss_pred             ecCH
Confidence            9854

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.00  E-value=3.2e-05  Score=58.81  Aligned_cols=73  Identities=19%  Similarity=0.271  Sum_probs=59.4

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  253 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v  253 (521)
                      .++|.|.|||+.+.++.|.-+|+.--.       .-+..|..+....  +-|+|+|.+.+.|++.|+.....|.+..|.|
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rr-------sGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k~~H~L~~~~LsV   78 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRR-------SGGGPVLSWQRLG--CGGVLTFREPADAERVLAQADHELHGAQLSL   78 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTT-------TCCCCEEEEEEET--TEEEEEESSHHHHHHHHTCSCCBSSSSBCEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCc-------CCCceeeEEEEcC--CcEEEEEcChHHHHHHhcCCcceecCeEEEE
Confidence            468999999999999999999996200       1234577777665  8899999999999999977788888999999


Q ss_pred             eC
Q 009954          254 RR  255 (521)
Q Consensus       254 ~~  255 (521)
                      ..
T Consensus        79 ~P   80 (104)
T 2dhx_A           79 RP   80 (104)
T ss_dssp             EE
T ss_pred             Ec
Confidence            74

>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=97.89  E-value=3.5e-05  Score=58.95  Aligned_cols=76  Identities=12%  Similarity=0.097  Sum_probs=64.2

Q ss_pred             CCCCeEEEcCCCCCC-C----HHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEE
Q 009954          292 EGPDRVFVGGLPYYF-T----ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~-t----e~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (521)
                      ..+++|+|.||+..+ .    .+.+.++|..|+++......+.-      .-..|.|.++++|.+|...||+..|.|..|
T Consensus         3 ~~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~   76 (104)
T 1wey_A            3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCcee
Confidence            456799999998865 2    25789999999998887776642      137999999999999999999999999999


Q ss_pred             EEEEccC
Q 009954          367 TVRRATA  373 (521)
Q Consensus       367 ~v~~~~~  373 (521)
                      +|-|+++
T Consensus        77 r~YFgq~   83 (104)
T 1wey_A           77 KLYFAQT   83 (104)
T ss_dssp             EEECCCC
T ss_pred             EEEecCC
Confidence            9999964

>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=97.63  E-value=0.0003  Score=52.77  Aligned_cols=54  Identities=19%  Similarity=0.407  Sum_probs=45.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  357 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  357 (521)
                      ..++| ++|+.+...||.++|+.||.| .|..+.|.       .|||.|.+++.|..|++.+.
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            44556 999999999999999999965 56677763       59999999999999999763

>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=97.55  E-value=0.0003  Score=53.78  Aligned_cols=63  Identities=11%  Similarity=0.182  Sum_probs=55.5

Q ss_pred             HHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          442 ILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       442 ~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      +++.++++|..|+++......+.         +.-+.|.|.++++|.+|-..|++..|+|+.|+|.|.....
T Consensus        23 lk~~~e~Lf~~~~~~~tF~~lkS---------FRRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~~   85 (104)
T 1wey_A           23 TRAKFESLFRTYDKDTTFQYFKS---------FKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLH   85 (104)
T ss_dssp             HHHHHHHHHHTTCSSCEEEEETT---------TTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSS
T ss_pred             HHHHHHHHHHhhCcCcceeecCc---------ceEEEEEeCChHHHHHHHHHhccceecCceeEEEecCCCC
Confidence            44688999999999999888775         3678999999999999999999999999999999976443

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.53  E-value=0.00079  Score=51.20  Aligned_cols=72  Identities=21%  Similarity=0.281  Sum_probs=60.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHh-----cCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLES-----FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~-----~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      ...+|.|.|||+.+.++.|.-+|+.     -|.|..|....        +-|+|+|.+.+.|++.|+. ..+.|.|..|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEE
Confidence            3468999999999999999999996     25688888754        2599999999999999873 46889999999


Q ss_pred             EEEccC
Q 009954          368 VRRATA  373 (521)
Q Consensus       368 v~~~~~  373 (521)
                      |....+
T Consensus        78 V~P~~~   83 (104)
T 2dhx_A           78 LRPAPP   83 (104)
T ss_dssp             EEECCC
T ss_pred             EEcCCC
Confidence            987654

>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=97.34  E-value=0.0013  Score=49.52  Aligned_cols=67  Identities=13%  Similarity=0.229  Sum_probs=56.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCC--cceEEEEEEcChHHHHHHHHHHcCCee
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTDIACAALNGLKM  361 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~--~~g~afV~f~~~~~A~~Al~~l~g~~~  361 (521)
                      ++|.|++||+.+||+++.+.++.+..+........+.+..  .-.-|||.|.+.+++..-.+.++|..|
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            4799999999999999999999988887777666543322  235699999999999999999999877

>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=97.32  E-value=0.00094  Score=52.64  Aligned_cols=72  Identities=17%  Similarity=0.179  Sum_probs=59.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC-eEEEEEEcc
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD-KTLTVRRAT  372 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g-~~l~v~~~~  372 (521)
                      .+-|.|-+.|+.. ...|..+|++||.|.......    +  ..+-.|.|.+..+|++||. .||..|+| ..|-|.++.
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-ASYILLQFAQYGNILKHVMSN----T--GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS----S--SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC----C--CCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECC
Confidence            4579999999985 667899999999999887621    1  3489999999999999999 59999984 778888875


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      .
T Consensus        96 d   96 (119)
T 1wwh_A           96 D   96 (119)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=0.0021  Score=50.61  Aligned_cols=74  Identities=19%  Similarity=0.270  Sum_probs=60.3

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecC-c
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG-V  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g-~  249 (521)
                      ....+.|.|-|.|+.. ...|..+|++||.            |++........+-.|.|.+..+|++||..||..+.| -
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            3446789999999986 5678889999998            555555556789999999999999999999999985 6


Q ss_pred             eEEEeCCC
Q 009954          250 AVRVRRPT  257 (521)
Q Consensus       250 ~i~v~~~~  257 (521)
                      .|-|.+..
T Consensus        88 mIGV~p~~   95 (119)
T 1wwh_A           88 MIGVKPCI   95 (119)
T ss_dssp             ECEEEECC
T ss_pred             EEEEEECC
Confidence            77777643

>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=96.92  E-value=0.0018  Score=48.77  Aligned_cols=53  Identities=19%  Similarity=0.410  Sum_probs=45.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHc
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  357 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  357 (521)
                      .++| ++|+.+...||.++|+.||.| .|..+.|.       .|||.|.+++.|..|++.+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            3555 999999999999999999944 57777763       59999999999999999874

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.63  E-value=0.0018  Score=51.70  Aligned_cols=68  Identities=18%  Similarity=0.254  Sum_probs=50.1

Q ss_pred             HHHHHhhccccceeE-EEecCCCC--------CCCCC--CCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          444 EDMREECGKYGTLVN-VVIPRPDQ--------NGGET--PGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~-v~i~~~~~--------~~~~~--~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      ..|-++|++||.|.. +.+.+...        .....  .|.+...|+|++..+|.+||.. ||..|+|.-|=|..++..
T Consensus        21 ~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG~ii~G~mIGV~Py~~~   99 (132)
T 3p3d_A           21 NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NGAVFNGVLLGVIPYTKD   99 (132)
T ss_dssp             HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TTCEETTEECEEEECCHH
T ss_pred             HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CCeEeCcEEEEEEECCHH
Confidence            489999999999887 32322110        00000  1457899999999999999995 999999999989888654

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.22  E-value=0.0035  Score=50.08  Aligned_cols=82  Identities=15%  Similarity=0.237  Sum_probs=55.4

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceE------EEEec--CCCCeEEEEecCHHHHHHHHHccCce
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV------NVYIN--HEKKFAFVEMRTVEEASNAMALDGII  245 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~------~~~~~--~~~g~afV~f~~~~~a~~A~~l~g~~  245 (521)
                      ...|.|-|.|+..+ ..+.+.|++||.|+............      .....  ....+..|+|.+..+|.+||..||..
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            45688999977765 56778999999976432110000000      00000  13467899999999999999999999


Q ss_pred             ecCceEEEeCC
Q 009954          246 FEGVAVRVRRP  256 (521)
Q Consensus       246 ~~g~~i~v~~~  256 (521)
                      |.|..|-|.+.
T Consensus        86 i~G~mIGV~Py   96 (132)
T 3p3d_A           86 FNGVLLGVIPY   96 (132)
T ss_dssp             ETTEECEEEEC
T ss_pred             eCcEEEEEEEC
Confidence            99998888754

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.84  E-value=0.0058  Score=46.19  Aligned_cols=67  Identities=15%  Similarity=0.190  Sum_probs=49.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCC--cceEEEEEEcChHHHHHHHHHHcCCee
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTDIACAALNGLKM  361 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~--~~g~afV~f~~~~~A~~Al~~l~g~~~  361 (521)
                      -+|.|+.||+.+||+++.+.++.+-.+........+.+..  .-.-|||.|.+.++...-.+.++|..|
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F   78 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIF   78 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            4799999999999999888887655544333322222111  113489999999999999999999776

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.07  E-value=0.013  Score=58.31  Aligned_cols=55  Identities=15%  Similarity=0.240  Sum_probs=42.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHH
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA  355 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~  355 (521)
                      +.|+|. .|..+++.+|.++|++||+|.++.+..+  .|   -||.|||.+.+++..++..
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~--~g---~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES--FG---LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS--SS---EEEEEECC---CCHHHHSS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc--CC---eEEEEEeCCHHHHHHHHhc
Confidence            679997 6999999999999999999999988875  33   5999999999999977653

>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=95.06  E-value=0.017  Score=43.29  Aligned_cols=62  Identities=16%  Similarity=0.264  Sum_probs=46.2

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe--cC------CCCeEEEEecCHHHHHHHH-HccCce
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NH------EKKFAFVEMRTVEEASNAM-ALDGII  245 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~--~~------~~g~afV~f~~~~~a~~A~-~l~g~~  245 (521)
                      .+|.|++||+.+||+++.+.+..+..            +.....  ++      .-.-|||.|.+.+++.... .++|..
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            47999999999999999988876532            211111  11      1257999999999999888 699988


Q ss_pred             ecC
Q 009954          246 FEG  248 (521)
Q Consensus       246 ~~g  248 (521)
                      +.+
T Consensus        70 F~D   72 (91)
T 1uw4_A           70 FLD   72 (91)
T ss_dssp             EEC
T ss_pred             EEc
Confidence            754

>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=93.18  E-value=0.37  Score=36.15  Aligned_cols=41  Identities=12%  Similarity=0.173  Sum_probs=32.1

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHh
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  495 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~ln  495 (521)
                      .||.++|++||.|. |.-+-|          --|||.|.+++.|..|+..++
T Consensus        30 ~DI~~lFs~fggv~-I~WidD----------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           30 SDLYQLFSAFGNIQ-ISWIDD----------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             HHHHHHHTTTCSCC-CEEEET----------TEEEEECSCHHHHHHHHHHHH
T ss_pred             HHHHHHhhccCCEE-EEEEcC----------CeEEEEecCHHHHHHHHHhcc
Confidence            49999999999544 222233          268999999999999999774

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=92.72  E-value=0.031  Score=55.51  Aligned_cols=62  Identities=18%  Similarity=0.211  Sum_probs=44.1

Q ss_pred             hhhccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCC-eEEEEecCHHHHHHHHHccC
Q 009954          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEEASNAMALDG  243 (521)
Q Consensus       169 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g-~afV~f~~~~~a~~A~~l~g  243 (521)
                      ......++|+|. .|..+++.+|.++|++||.            |.++...+++| ||.|+|.+.+++..++...+
T Consensus        48 r~~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~------------i~~~~~~~~~g~~~~vef~~~~~~~~~~~~~~  110 (464)
T 3pq1_A           48 RREQAQRTVLIH-CPEKISENKFLKYLSQFGP------------INNHFFYESFGLYAVVEFCQKESIGSLQNGTH  110 (464)
T ss_dssp             HHHHHHTEEEEE-ECCC---CHHHHHHGGGSC------------CCCEEEECSSSEEEEEECC---CCHHHHSSCC
T ss_pred             HHHHhcceEEEE-cCCCCCHHHHHHHHHhcCC------------cceEEEEccCCeEEEEEeCCHHHHHHHHhccC
Confidence            345667899998 6999999999999999998            55555556665 99999999999998874433

>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=92.18  E-value=0.29  Score=36.84  Aligned_cols=41  Identities=12%  Similarity=0.171  Sum_probs=32.2

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHh
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  495 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~ln  495 (521)
                      .||.++|++||.|. |.-+-|          --|||.|.+++.|..|+..++
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            49999999999443 333333          268999999999999999875

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=92.10  E-value=0.099  Score=39.43  Aligned_cols=71  Identities=17%  Similarity=0.165  Sum_probs=44.6

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      +-+|.|+.||+.+||+++.+.+..+=.+--+.- -+++.-.   -...-.-|||.|.+.++..... .++|..+.+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~f-v~G~~s~---~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEF-FAADLSL---YPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCC-CCCCSSS---CCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEE-eCCccCC---CCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            457999999999999998766654311000000 0000000   0011257999999999999988 699988754

>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=86.73  E-value=1.5  Score=44.47  Aligned_cols=54  Identities=19%  Similarity=0.407  Sum_probs=44.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  357 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  357 (521)
                      ..++|+ +|..+...+|.++|+.||.| .|.++.+.       .|||.|.+.+.|..+++.+.
T Consensus       441 ~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt-------~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          441 HVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS-------EEEEECSCHHHHHHHHHHHT
T ss_pred             cEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC-------eEEEEECCHHHHHHHHHHHH
Confidence            445555 99999999999999999954 56665552       59999999999999999885

---

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	521
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	2e-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	6e-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
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-14
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	9e-07
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
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
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
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
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	4e-13
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	0.002
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
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	9e-13
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-04
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
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
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
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-05
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
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
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-12
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	7e-06
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
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	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
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
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	6e-12
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-05
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
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	9e-06
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	8e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-06
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	8e-12
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-06
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	8e-12
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
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-11
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-04
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-11
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-06
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
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
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-10
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
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	3e-10
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-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
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-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
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
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-09
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	0.001
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
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	9e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-04
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
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	7e-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
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	9e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	0.002
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:) 8e-07
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	2e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-07
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	7e-07
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-07
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-05
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
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-05
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	6e-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	2e-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	0.002
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: 420 KVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFL 479
           +VLCL   +  + L DDEEYEEI+ED+R+EC KYG + ++ IPR   +G E PG GK+F+
Sbjct: 5   EVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPR-PVDGVEVPGCGKIFV 63

Query: 480 EYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDY 519
           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 = 78.1 bits (191), Expect = 2e-17
 Identities = 41/211 (19%), Positives = 73/211 (34%), Gaps = 34/211 (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 CAALNGLKMGDKTLTVRRATASGQSKTEQES 383
                   +      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 = 70.8 bits (173), Expect = 6e-16
 Identities = 45/82 (54%), Positives = 58/82 (70%)

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 LNGLKMGDKTLTVRRATASGQS 377
           LNG+++GDK L V+RA+   ++
Sbjct: 63  LNGMQLGDKKLLVQRASVGAKN 84

>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 = 20/87 (22%), Positives = 38/87 (43%), Gaps = 4/87 (4%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCVYQDPAVTDIACA 354
           ++ V  +P+   + +I+EL  +FG L    L K    TG  +G+GF  +        A  
Sbjct: 10  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 355 AL-NGLKMGDKTLTVRRATASGQSKTE 380
           AL +   +  + L +  A +  +   +
Sbjct: 70  ALCHSTHLYGRRLVLEWADS--EVTVQ 94

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 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

>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 = 67.0 bits (163), Expect = 2e-14
 Identities = 25/82 (30%), Positives = 41/82 (50%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+VGGL    +E  + EL    G +    + KDR TG  +GYGF  +      D A   
Sbjct: 11  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 70

Query: 356 LNGLKMGDKTLTVRRATASGQS 377
           ++ +K+  K + V +A+A  ++
Sbjct: 71  MDMIKLYGKPIRVNKASAHNKN 92

>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

>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

>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 = 55.8 bits (134), 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

>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 = 57.4 bits (138), 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

>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

>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 = 62.8 bits (152), Expect = 4e-13
 Identities = 14/82 (17%), Positives = 28/82 (34%), Gaps = 7/82 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++++G L    T   +++L                      GY F  Y D      A   
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKL------PLAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 356 LNG-LKMGDKTLTVRRATASGQ 376
           L+G +++  K + V  + +   
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKL 78

>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

>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

>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 = 62.4 bits (151), Expect = 9e-13
 Identities = 29/97 (29%), Positives = 47/97 (48%), Gaps = 3/97 (3%)

Query: 285 SGAIGG-AEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
            GA G   EGP+   +F+  LP  F +  + ++   FG +    +  D+ T  SK +GF 
Sbjct: 6   IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFV 65

Query: 342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASGQSK 378
            Y +P     A  ++NG ++G K L V+   +   SK
Sbjct: 66  SYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 102

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 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

>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

>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

>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 = 23/89 (25%), Positives = 39/89 (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 DIACAALNGLKMGDKTLTVRRATASGQSK 378
             A A ++G     + L V  +T   ++ 
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 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

>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 = 3e-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

>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 = 22/87 (25%), Positives = 38/87 (43%), Gaps = 6/87 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            + V GLP+  TE  +KE   +FG +    + KD  TG+SKG+GF  + +        + 
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 356 LNGLKMGDKTLTVRRATASGQSKTEQE 382
            + +    +    +       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

>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

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (146), Expect = 3e-12
 Identities = 23/84 (27%), Positives = 47/84 (55%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +++      A  A
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 356 LNGLKMGDKTLTVRRATASGQSKT 379
           +NG  +  + + V +A  S  +++
Sbjct: 67  MNGKSVDGRQIRVDQAGKSSDNRS 90

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 7e-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

>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

>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 = 60.0 bits (145), Expect = 4e-12
 Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 3/77 (3%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACA 354
           F+  L +  TE  +K +    G +    + K ++      S G+GF  Y+ P     A  
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 355 ALNGLKMGDKTLTVRRA 371
            L G  +    L VR +
Sbjct: 62  QLQGHTVDGHKLEVRIS 78

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 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

>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 = 52.4 bits (125), 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

>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

>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 = 59.8 bits (144), Expect = 6e-12
 Identities = 28/86 (32%), Positives = 45/86 (52%), Gaps = 1/86 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGLPY+ T+  +++  E FG +    ++ DR TG S+GYGF    D A  + AC  
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 356 LNGLKMGDKTLTVRRATASGQSKTEQ 381
            N   +  +   V  A    + ++ Q
Sbjct: 72  PNP-IIDGRKANVNLAYLGAKPRSLQ 96

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 3e-05
 Identities = 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

>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

>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 = 59.3 bits (143), Expect = 7e-12
 Identities = 23/76 (30%), Positives = 33/76 (43%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            + V  L     ET ++EL   FG++    L KD+ TG SKG+ F  +        A A 
Sbjct: 10  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 69

Query: 356 LNGLKMGDKTLTVRRA 371
           ++G       L V  A
Sbjct: 70  VSGFGYDHLILNVEWA 85

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 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

>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 = 8e-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 = 42.4 bits (99), 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

>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 = 59.3 bits (143), Expect = 8e-12
 Identities = 22/85 (25%), Positives = 33/85 (38%), Gaps = 2/85 (2%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           P  ++VG L    TE  I +L    G           +  ++  Y F  + +      A 
Sbjct: 8   PRTLYVGNLSRDVTEVLILQLFSQIG--PCKSCKMITEHTSNDPYCFVEFYEHRDAAAAL 65

Query: 354 AALNGLKMGDKTLTVRRATASGQSK 378
           AA+NG K+  K + V  AT     K
Sbjct: 66  AAMNGRKILGKEVKVNWATTPSSQK 90

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 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

>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 = 60.0 bits (145), Expect = 8e-12
 Identities = 19/101 (18%), Positives = 45/101 (44%), Gaps = 6/101 (5%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +++  LPY  T  ++ ++   +G +         +T  ++G  + VY+D      AC  L
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKNACDHL 66

Query: 357 NGLKMGDKTLTVRRATASGQSKTEQESILAQAQQHIAIQKM 397
           +G  + ++ L V    A   ++  Q+    + ++ + + K 
Sbjct: 67  SGFNVCNRYLVVLYYNA---NRAFQKMDTKKKEEQLKLLKE 104

>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: 444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNT 503
           E+M +  GKYG +  + +    +        G  ++ Y D      A + LSG       
Sbjct: 22  EEMYDIFGKYGPIRQIRVGNTPET------RGTAYVVYEDIFDAKNACDHLSGFNVCNRY 75

Query: 504 VNAFYYPEDKYFNK 517
           +   YY  ++ F K
Sbjct: 76  LVVLYYNANRAFQK 89

>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 = 58.6 bits (141), Expect = 1e-11
 Identities = 24/80 (30%), Positives = 35/80 (43%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FV  +     E +I+E    +G +    L  DR TG SKGY    Y+       A  A
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 356 LNGLKMGDKTLTVRRATASG 375
           LNG ++  +T+ V      G
Sbjct: 69  LNGAEIMGQTIQVDWCFVKG 88

>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

>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 = 58.5 bits (141), Expect = 1e-11
 Identities = 11/78 (14%), Positives = 32/78 (41%), Gaps = 1/78 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLES-FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
            +++  L     + ++K+ L + F        +    +   +G  F ++++ +    A  
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 355 ALNGLKMGDKTLTVRRAT 372
           ++ G    DK + ++ A 
Sbjct: 65  SMQGFPFYDKPMRIQYAK 82

>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 = 3e-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

>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 = 57.0 bits (137), 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

>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

>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 = 56.3 bits (135), Expect = 1e-10
 Identities = 16/77 (20%), Positives = 28/77 (36%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +++  L    TE  +  L   F    G  +     TG  +G  F  + +  +   A   
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 356 LNGLKMGDKTLTVRRAT 372
           +NG K+  K L +    
Sbjct: 80  VNGYKLYGKILVIEFGK 96

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.1 bits (135), Expect = 1e-10
 Identities = 22/97 (22%), Positives = 36/97 (37%), Gaps = 9/97 (9%)

Query: 420 KVLCLTEAIT-ADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVF 478
           +V+ +       D   D     EI ED+R EC K+G +  +++     +       G   
Sbjct: 9   RVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPD-------GVAS 61

Query: 479 LEYYDAVGCATAKNALSGRKFGGNTVNA-FYYPEDKY 514
           + + 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

>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 = 56.3 bits (135), Expect = 1e-10
 Identities = 23/89 (25%), Positives = 37/89 (41%), Gaps = 1/89 (1%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG+      P   F+G LPY  TE  IKE              +  +    KG+G+  +
Sbjct: 5   SSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           +D      +  +LN   +G+K + V  A 
Sbjct: 65  EDLDSLL-SALSLNEESLGNKRIRVDVAD 92

>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

>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 = 55.0 bits (132), Expect = 2e-10
 Identities = 13/83 (15%), Positives = 32/83 (38%), Gaps = 5/83 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +    L +  TE ++KE+ E    +           G SKG  +  ++  A  +     
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 356 LNGLKMGDKTLTVRRATASGQSK 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

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.6 bits (131), Expect = 3e-10
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 6/77 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE ++++L E +G      + KD+       +GF   +   + +IA   
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVE 63

Query: 356 LNGLKMGDKTLTVRRAT 372
           L+ + +  K L VR A 
Sbjct: 64  LDNMPLRGKQLRVRFAC 80

>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 = 1e-07
 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

>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

>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 = 18/93 (19%), Positives = 35/93 (37%), Gaps = 12/93 (12%)

Query: 284 ASGAIGGAEGPD---RVFVGGLPYYFT-ETQIKELLESFGTLHGFDLVKDRDTGNSKGYG 339
           +SG+ G  +      RVF+G L      ++ ++ +   +G +              KG+ 
Sbjct: 2   SSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKI--------VGCSVHKGFA 53

Query: 340 FCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           F  Y +      A A  +G  +  + L +  A 
Sbjct: 54  FVQYVNERNARAAVAGEDGRMIAGQVLDINLAA 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 = 1e-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 = 52.7 bits (126), 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

>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 = 52.3 bits (125), Expect = 2e-09
 Identities = 16/90 (17%), Positives = 32/90 (35%), Gaps = 7/90 (7%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   VFVG      TE +++E    +G      ++        + + F  + D  + 
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGD-----VMDVFIPKPFRAFAFVTFADDQIA 55

Query: 350 DIACAALNGLKMGDKTLTVRRATASGQSKT 379
              C     L +   ++ +  A     S +
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

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 2e-09
 Identities = 14/83 (16%), Positives = 25/83 (30%), Gaps = 7/83 (8%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   + V  LP      ++ +LL+ +         K      +K   F    +    
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQA 53

Query: 350 DIACAALNGLKMGDKTLTVRRAT 372
             A    +      K L V+   
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQP 76

>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 = 52.5 bits (125), Expect = 3e-09
 Identities = 38/89 (42%), Positives = 50/89 (56%), Gaps = 1/89 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC YQD      A   
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 356 LNGLKMGDKTLTVRRATASGQSKTEQESI 384
           LNG +   + L V  A  S ++K E +S+
Sbjct: 70  LNGREFSGRALRVDNAA-SEKNKEELKSL 97

>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

>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 = 51.8 bits (123), Expect = 4e-09
 Identities = 12/85 (14%), Positives = 28/85 (32%), Gaps = 1/85 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
             +  +P+  T+  + + LE          V   + G   G     +++      +   L
Sbjct: 11  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-RL 69

Query: 357 NGLKMGDKTLTVRRATASGQSKTEQ 381
           +  K+  +   V   T     + E+
Sbjct: 70  HRKKLNGREAFVHVVTLEDMREIEK 94

>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

>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 = 50.9 bits (121), 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 = 47.0 bits (111), 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

>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 = 51.8 bits (123), Expect = 9e-09
 Identities = 27/85 (31%), Positives = 43/85 (50%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           +    + V  +P    E Q+++L E +G +    +V DR+T  S+GYGF  +Q  +    
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 352 ACAALNGLKMGDKTLTVRRATASGQ 376
           A A LNG  + +K L V  A +  Q
Sbjct: 100 AIAGLNGFNILNKRLKVALAASGHQ 124

>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

>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

>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 = 7e-08
 Identities = 24/88 (27%), Positives = 37/88 (42%), Gaps = 6/88 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VF+  L +   E  + E+L+ FG L    +V   DT +SKG  F  +          AA
Sbjct: 10  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 69

Query: 356 LN------GLKMGDKTLTVRRATASGQS 377
            +      GLK+  + L V  A    ++
Sbjct: 70  ASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 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

>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 = 48.1 bits (114), Expect = 9e-08
 Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 4/82 (4%)

Query: 288 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 347
           + G     R+ V  L Y  T   + ++   FGT+             ++      Y DP 
Sbjct: 1   MAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPV 56

Query: 348 VTDIACAALNGLKMGDKTLTVR 369
               A  +L+G  + +   T+R
Sbjct: 57  SAQHAKLSLDGQNIYNACCTLR 78

>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

>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 = 8e-07
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 5/76 (6%)

Query: 436 DEEYEEILEDMREEC-GKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNAL 494
            E Y+E  E++  E   KYG +  + +     +          ++++        A   L
Sbjct: 33  QEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNV----YVKFRREEDAEKAVIDL 88

Query: 495 SGRKFGGNTVNAFYYP 510
           + R F G  ++A   P
Sbjct: 89  NNRWFNGQPIHAELSP 104

>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 = 46.1 bits (108), Expect = 2e-07
 Identities = 12/77 (15%), Positives = 28/77 (36%), Gaps = 7/77 (9%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + + GLP   T  ++ +LL  +   +             KG  F    +    + A    
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKY-------CFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 357 NGLKMGDKTLTVRRATA 373
           +  ++ ++ L+V+    
Sbjct: 54  HQSRLRERELSVQLQPT 70

>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 = 12/89 (13%), Positives = 33/89 (37%), Gaps = 1/89 (1%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG          V + GLP+  ++ +I +       +     +     G S G  F  +
Sbjct: 5   SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT 372
               + +      +  ++G + + + +++
Sbjct: 65  ASQEIAE-KALKKHKERIGHRYIEIFKSS 92

>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 = 46.0 bits (108), Expect = 7e-07
 Identities = 16/106 (15%), Positives = 29/106 (27%), 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 PAVTDIACAALNGLKMGDKTLTVRRATASGQSKTEQESILAQAQQH 391
                      N   +  +   V      G+ + E    + + QQ 
Sbjct: 58  AKEALGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQE 103

>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 = 45.5 bits (107), Expect = 7e-07
 Identities = 15/82 (18%), Positives = 25/82 (30%), Gaps = 3/82 (3%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V + GLPY  TE  I               ++    G   G     +        A  A 
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLN--PMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AK 74

Query: 357 NGLKMGDKTLTVRRATASGQSK 378
           +   M  + + +   + +G S 
Sbjct: 75  DKANMQHRYVELFLNSTAGTSG 96

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 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

>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

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 6e-06
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 6/80 (7%)

Query: 293 GPDRVFVGGL-PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           G   + V  L P   T   +  L   +G +    ++ ++              D     +
Sbjct: 1   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQL 55

Query: 352 ACAALNGLKMGDKTLTVRRA 371
           A + LNG K+  K + +  +
Sbjct: 56  AMSHLNGHKLHGKPIRITLS 75

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 8/88 (9%)

Query: 284 ASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
           +SG IG  +     R++VGGL    +   +    + FG++   D VK         + + 
Sbjct: 5   SSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYI 58

Query: 342 VYQDPAVTDIACAALNGLKMGDKTLTVR 369
            Y+       ACA + G  +G     +R
Sbjct: 59  QYESLDAAQAACAKMRGFPLGGPDRRLR 86

>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 = 40.3 bits (93), Expect = 6e-05
 Identities = 17/99 (17%), Positives = 27/99 (27%), Gaps = 11/99 (11%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +    LP      +I+E      T   F  +               + +P     A   L
Sbjct: 13  ILAKNLPAGTLAAEIQE------TFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHL 66

Query: 357 NGLKMGDKTLTVRRA-----TASGQSKTEQESILAQAQQ 390
              K     L +  A      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 NGLKMGDKTLTVRRATASGQSKTEQE 382
           +   MG++ + V   T  G  +    
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 = 2e-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 = 37.9 bits (87), Expect = 3e-04
 Identities = 16/94 (17%), Positives = 28/94 (29%), Gaps = 11/94 (11%)

Query: 284 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G          V V GL     E  + E       L  F  +        K    
Sbjct: 2   SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEA------LEKFGTICYVMMMPFKRQAL 55

Query: 341 CVYQDP--AVTDIACAALNGLKMGDKTLTVRRAT 372
             +++   A   +  AA   + +  +      +T
Sbjct: 56  VEFENIDSAKECVTFAADVPVYIAGQQAFFNYST 89

>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 = 16/106 (15%), Positives = 28/106 (26%), Gaps = 23/106 (21%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
                 +  V+V GL     E  +     +               +  V +   K+ A V
Sbjct: 9   HHKVSVSPVVHVRGLCESVVEADLVEALEKF------------GTICYVMMMPFKRQALV 56

Query: 228 EMRTVEEASNA---MALDGIIFEGVAVRV--------RRPTDYNPT 262
           E   ++ A       A   +   G              RP +  P+
Sbjct: 57  EFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPS 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 = 35.6 bits (81), Expect = 0.002
 Identities = 14/76 (18%), Positives = 23/76 (30%), Gaps = 7/76 (9%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           RV V GLP   +   +K+ +   G +   D+ +D         G   +        A   
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAVRK 54

Query: 356 LNGLKMGDKTLTVRRA 371
           L+  K           
Sbjct: 55  LDNTKFRSHEGETAYI 70

>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	521
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	99.85
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.83
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.82
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.81
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.81
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.81
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.81
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.81
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.8
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.8
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.8
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.79
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.79
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.79
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.79
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.78
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.78
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.78
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.78
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.78
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.77
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.77
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.77
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.76
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.76
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.75
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.75
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.74
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.74
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.74
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.73
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.73
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.73
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.72
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.72
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.71
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.71
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.71
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.71
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.71
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.7
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.7
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.7
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.7
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.69
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.69
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.69
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.68
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.68
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.67
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.67
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.67
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.66
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.66
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.66
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.65
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.64
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.64
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.64
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.64
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.64
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.64
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.63
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.63
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.63
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.62
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.62
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.62
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.61
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.61
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.61
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.61
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.6
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.6
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.59
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.59
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.59
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.59
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.59
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.58
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.58
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.58
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.58
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.57
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.57
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.57
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.57
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.57
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.56
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.56
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.56
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.56
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.56
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.55
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.55
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.55
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.55
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.55
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.55
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.54
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.54
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.54
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.54
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.54
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.54
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.54
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	99.53
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.53
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.53
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.52
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.52
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.51
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.51
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.51
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.51
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.51
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.51
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	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
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.5
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.5
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.5
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.49
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.48
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.48
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.48
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.48
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.48
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.47
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.47
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.47
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.47
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.47
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.46
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.45
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.45
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.44
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.44
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.43
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.43
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.43
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.42
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.4
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.39
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.39
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.37
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.35
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.35
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.33
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.33
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.27
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.14
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.33
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.85
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.79
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.44
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.41
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.81
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	94.8
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	85.36

>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=3.5e-29  Score=222.08  Aligned_cols=171  Identities=22%  Similarity=0.398  Sum_probs=141.9

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~  252 (521)
                      ..++|||+|||+.+|+++|+++|++||.|..+.      .+.+..++.++|||||+|.+.++|.+|+.+++..+.++.+.
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            347899999999999999999999999843210      11122245667999999999999999999888889999888


Q ss_pred             EeCCCCCCccccccCCCCCCCCCcccccccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 009954          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (521)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~  332 (521)
                      +.+.........                       .......++|||+|||..+|+++|+++|+.||.|..+.|+.+..+
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                       111234568999999999999999999999999999999999889


Q ss_pred             CCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       333 g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      |.++|||||+|.+.++|.+||+ +++..|.|+.|.|.+|.+
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 799999999999999865

>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=5.3e-26  Score=201.33  Aligned_cols=167  Identities=20%  Similarity=0.340  Sum_probs=136.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      ++|||+|||+.+|+++|+++|++||.|.++.++.+..+|.++|||||+|.+.++|.+|+. +++..+.++.+.+.+....
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            689999999999999999999999999999999999999999999999999999999998 5778889999998887542


Q ss_pred             CCCchHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCCcceEEE--eeCcCCcccCCChHHHHHHHHHHHHhhcc
Q 009954          375 GQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLC--LTEAITADALADDEEYEEILEDMREECGK  452 (521)
Q Consensus       375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~--l~~~~~~~~~~~~~~~~~~~~dl~~~f~~  452 (521)
                      ......                                .......+|++  |+..++.             ++|+++|+.
T Consensus        86 ~~~~~~--------------------------------~~~~~~~~i~V~~lp~~~te-------------~~L~~~f~~  120 (183)
T d1u1qa_          86 EDSQRP--------------------------------GAHLTVKKIFVGGIKEDTEE-------------HHLRDYFEQ  120 (183)
T ss_dssp             TGGGST--------------------------------TTTCCCSEEEEECCCTTCCH-------------HHHHHHHGG
T ss_pred             cccccc--------------------------------ccccccceeEEccCCCcCCH-------------HHHhhhhcc
Confidence            211000                                00012223333  3333222             599999999


Q ss_pred             ccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCC
Q 009954          453 YGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       453 fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~  511 (521)
                      ||.|..|.|+.+..++..   +|+|||+|.+.++|.+||+ +++..|+|++|+|.++..
T Consensus       121 ~G~v~~~~i~~~~~~~~~---~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         121 YGKIEVIEIMTDRGSGKK---RGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALS  175 (183)
T ss_dssp             GSCEEEEEEEECTTTCCE---EEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCC
T ss_pred             CCceeeeeeecccccCcc---ceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCC
Confidence            999999999998766654   6889999999999999997 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=99.85  E-value=1.6e-21  Score=153.65  Aligned_cols=102  Identities=42%  Similarity=0.821  Sum_probs=94.9

Q ss_pred             CcceEEEeeCcCCcccCCChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhC
Q 009954          417 TLAKVLCLTEAITADALADDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSG  496 (521)
Q Consensus       417 ~~~~v~~l~~~~~~~~~~~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng  496 (521)
                      .|++|++|.|++++++|.++.+|++|++||+++|++||.|++|.|+++..+.. ..+.|+|||+|.+.++|.+|++.|||
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            57899999999999999999999999999999999999999999998764433 35668999999999999999999999


Q ss_pred             CeeCCcEEEEEEcCCCCcccccC
Q 009954          497 RKFGGNTVNAFYYPEDKYFNKDY  519 (521)
Q Consensus       497 ~~~~gr~l~v~~~~~~~~~~~~~  519 (521)
                      +.|+||.|.|.|+++++|.+++|
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=99.83  E-value=7.1e-21  Score=143.57  Aligned_cols=79  Identities=27%  Similarity=0.452  Sum_probs=76.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ++|||+|||+.+++++|+++|++||.|..++|+.++.+|.++|||||+|.+.++|++||+.|||..|.|+.|+|.|+++
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            5899999999999999999999999999999999988999999999999999999999999999999999999999975

>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=99.83  E-value=1.7e-20  Score=143.05  Aligned_cols=81  Identities=28%  Similarity=0.350  Sum_probs=77.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ..+|||+|||..+++++|.++|++||.|.+|+|+.++.+|.++|||||+|.+.++|++|+..|||..|.|+.|.|.||.+
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            36899999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             C
Q 009954          374 S  374 (521)
Q Consensus       374 ~  374 (521)
                      +
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=99.83  E-value=2.8e-20  Score=140.32  Aligned_cols=79  Identities=37%  Similarity=0.606  Sum_probs=76.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ++|||+|||..+++++|+++|++||.|..|+|+.+..+|.++|||||+|.+.++|++|++.|||..|.|+.|.|.||+|
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            5799999999999999999999999999999999988999999999999999999999999999999999999999975

>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=99.82  E-value=2.1e-20  Score=144.09  Aligned_cols=83  Identities=30%  Similarity=0.453  Sum_probs=78.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|+++|++||.|.+|+|+.++.+|.++|||||+|.+.++|++|++.|||..|.|+.|+|.||.
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 009954          373 ASG  375 (521)
Q Consensus       373 ~~~  375 (521)
                      +..
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            743

>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=99.82  E-value=2.5e-20  Score=139.48  Aligned_cols=77  Identities=23%  Similarity=0.327  Sum_probs=75.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      .|||+|||+.+|+++|+++|++||.|.+|+|+.++.+|.++|||||+|.+.++|.+|++.|+|..|.|+.|+|.|++
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

>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=99.82  E-value=1.7e-20  Score=143.48  Aligned_cols=81  Identities=19%  Similarity=0.336  Sum_probs=78.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||.++++++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|+|+.|.|.|+.+
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 009954          374 S  374 (521)
Q Consensus       374 ~  374 (521)
                      .
T Consensus        85 ~   85 (89)
T d2cqba1          85 M   85 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.81  E-value=7e-20  Score=143.76  Aligned_cols=83  Identities=25%  Similarity=0.498  Sum_probs=78.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|..||+.|||..|+|+.|.|.|+.+
T Consensus        18 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~   97 (102)
T d2cpza1          18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS   97 (102)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 009954          374 SGQ  376 (521)
Q Consensus       374 ~~~  376 (521)
                      +..
T Consensus        98 k~~  100 (102)
T d2cpza1          98 KND  100 (102)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            543

>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=141.88  Aligned_cols=82  Identities=29%  Similarity=0.429  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|+|+.|.|.|+.
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 009954          373 AS  374 (521)
Q Consensus       373 ~~  374 (521)
                      +.
T Consensus        87 p~   88 (90)
T d2cq0a1          87 PS   88 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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=5.1e-20  Score=138.99  Aligned_cols=77  Identities=22%  Similarity=0.442  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v  368 (521)
                      .+.++|||+|||..+|+++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|+|
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            33468999999999999999999999999999999999989999999999999999999999999999999999987

>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=5.8e-20  Score=143.67  Aligned_cols=83  Identities=27%  Similarity=0.444  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.++
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             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      ..+
T Consensus        86 ~~~   88 (99)
T d1whwa_          86 TIK   88 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>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=99.81  E-value=8.8e-20  Score=140.55  Aligned_cols=81  Identities=25%  Similarity=0.399  Sum_probs=77.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+|+++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|..|++.|||..|.|+.|.|.|+.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      .
T Consensus        86 ~   86 (93)
T d1h2vz_          86 G   86 (93)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=3.4e-20  Score=140.31  Aligned_cols=80  Identities=56%  Similarity=0.973  Sum_probs=77.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      .+|||+|||..+|+++|+++|++||+|..|+|+.++.+|.++|||||+|.++++|..|++.|||..|.|+.|.|.|+.+.
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            47999999999999999999999999999999999999999999999999999999999999999999999999999763

>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=1.2e-19  Score=137.57  Aligned_cols=78  Identities=26%  Similarity=0.468  Sum_probs=74.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC--eEEEEEEc
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  371 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~  371 (521)
                      .++|||+|||..+++++|+++|++||.|..++|+.++.+|.++|||||+|.+.++|.+||+.|||..+.|  ++|.|.||
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            4679999999999999999999999999999999999999999999999999999999999999999876  88999986

>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=99.80  E-value=1.4e-19  Score=137.02  Aligned_cols=77  Identities=29%  Similarity=0.509  Sum_probs=73.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC--eEEEEEEc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  371 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~~  371 (521)
                      ++|||+|||+.+|+++|+++|++||.|.+++|+.++.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|.|.||
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            579999999999999999999999999999999998899999999999999999999999999999987  55999986

>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=99.80  E-value=1.4e-19  Score=134.46  Aligned_cols=76  Identities=25%  Similarity=0.413  Sum_probs=73.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      +|||+|||+.+++++|+++|++||.|..++|..++ +|.++|||||+|.+.++|.+|++.|||..|.|++|.|.++.
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            69999999999999999999999999999999985 89999999999999999999999999999999999999985

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=3.8e-19  Score=137.04  Aligned_cols=84  Identities=25%  Similarity=0.559  Sum_probs=76.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEE
Q 009954          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       290 ~~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      ....+++|||+|||+.+++++|+++|++||.|..|.|+.+.  +.++|||||+|.+.++|.+|++.|||..|.|+.|.|.
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34556789999999999999999999999999999999884  4479999999999999999999999999999999999


Q ss_pred             EccCCC
Q 009954          370 RATASG  375 (521)
Q Consensus       370 ~~~~~~  375 (521)
                      ||.++.
T Consensus        85 ~A~~r~   90 (93)
T d2cq3a1          85 NATARV   90 (93)
T ss_dssp             ECCSSC
T ss_pred             ecCcCC
Confidence            998743

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.6e-19  Score=136.47  Aligned_cols=82  Identities=23%  Similarity=0.386  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||+++|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.  +..|+|+.|.|.++
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             cCCC
Q 009954          372 TASG  375 (521)
Q Consensus       372 ~~~~  375 (521)
                      .++.
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            7643

>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=99.79  E-value=1.1e-19  Score=136.60  Aligned_cols=79  Identities=16%  Similarity=0.257  Sum_probs=69.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ++|||+|||+.+|+++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.++.|
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

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.8e-19  Score=134.74  Aligned_cols=79  Identities=27%  Similarity=0.518  Sum_probs=74.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++|++||+ +++..|.|+.|.|..|.
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

>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=1.8e-19  Score=138.25  Aligned_cols=82  Identities=28%  Similarity=0.568  Sum_probs=78.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ..+|||+|||+.+++++|.++|++||.|..+.++.+..+|.++|||||+|.+.++|++|++.|+|..|+|+.|.|.|+.+
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~   84 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGK   84 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEEC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999999999888999999999999999999999999999999999999999976


Q ss_pred             CC
Q 009954          374 SG  375 (521)
Q Consensus       374 ~~  375 (521)
                      +.
T Consensus        85 ~~   86 (90)
T d1x5sa1          85 SS   86 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.79  E-value=6.5e-19  Score=134.87  Aligned_cols=80  Identities=26%  Similarity=0.411  Sum_probs=74.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      .+++|||+|||..+++++|+++|++||.|..|.|+.+..+  .+|||||+|.+.++|..|++.|+|..|.|+.|+|.|+.
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            3578999999999999999999999999999999998654  37899999999999999999999999999999999997


Q ss_pred             CC
Q 009954          373 AS  374 (521)
Q Consensus       373 ~~  374 (521)
                      +.
T Consensus        85 ~~   86 (90)
T d2cqia1          85 TP   86 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            63

>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=99.79  E-value=2.6e-19  Score=138.20  Aligned_cols=82  Identities=24%  Similarity=0.468  Sum_probs=76.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC-CCCcceEEEEEEcChHHHHHHHHHH-cCCeeCCeEEEEEE
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVRR  370 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~g~~~g~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~v~~  370 (521)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.+.. +|.++|||||+|.+.++|.+||+.| ||..|.|+.|.|.|
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            346899999999999999999999999999999988754 8999999999999999999999998 89999999999999


Q ss_pred             ccCC
Q 009954          371 ATAS  374 (521)
Q Consensus       371 ~~~~  374 (521)
                      |...
T Consensus        87 A~~~   90 (94)
T d2cpha1          87 ADSE   90 (94)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9763

>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=99.78  E-value=6.3e-20  Score=135.62  Aligned_cols=76  Identities=28%  Similarity=0.496  Sum_probs=73.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ++|||+|||+++|+++|+++|++||.|..+.|+.++.+|.++|||||+|.+.++|.+||+ ++++.|+|+.|.|.+|
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            579999999999999999999999999999999999999999999999999999999997 7999999999999986

>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=99.78  E-value=3.1e-19  Score=135.34  Aligned_cols=78  Identities=24%  Similarity=0.479  Sum_probs=73.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCC---CcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG---NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       297 l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g---~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      |||+|||.++|+++|+++|++||.|.+|.|+.++.++   .++|||||+|.+.++|.+|++.|||..|+|+.|.|.|+..
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            7999999999999999999999999999999887655   4689999999999999999999999999999999999965


Q ss_pred             C
Q 009954          374 S  374 (521)
Q Consensus       374 ~  374 (521)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=4.4e-19  Score=148.08  Aligned_cols=84  Identities=31%  Similarity=0.531  Sum_probs=79.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||.++++++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|+|+.|.|.|+
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            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 009954          372 TASG  375 (521)
Q Consensus       372 ~~~~  375 (521)
                      ....
T Consensus       120 ~~~~  123 (139)
T d1u6fa1         120 ASGH  123 (139)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7643

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=1.9e-19  Score=135.85  Aligned_cols=79  Identities=30%  Similarity=0.513  Sum_probs=74.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCCC
Q 009954          297 VFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASG  375 (521)
Q Consensus       297 l~v~nLp~~~te~~l~~~F~~~G~i~~-v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~~  375 (521)
                      |||+|||+++++++|+++|++||.|.. +.|+.++.+|.++|||||+|.+.++|.+||+.|+|..|.|++|.|.|+.++.
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            799999999999999999999999866 4788898899999999999999999999999999999999999999998643

>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=99.78  E-value=5.2e-19  Score=138.97  Aligned_cols=80  Identities=34%  Similarity=0.634  Sum_probs=75.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||..+++++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|.+||+.+++ .|.|+.|.|.++..
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 79999999999976


Q ss_pred             C
Q 009954          374 S  374 (521)
Q Consensus       374 ~  374 (521)
                      .
T Consensus        89 ~   89 (103)
T d2cqda1          89 G   89 (103)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.78  E-value=2.6e-19  Score=139.74  Aligned_cols=77  Identities=17%  Similarity=0.362  Sum_probs=74.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ++|||+|||..+++++|+++|+.||.|.+|.|+.+..+|.++|||||+|.+.++|.+|++ |||..|.|+.|.|.++.
T Consensus        19 ~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          19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            689999999999999999999999999999999999999999999999999999999995 99999999999999984

>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=2.2e-19  Score=141.73  Aligned_cols=79  Identities=43%  Similarity=0.754  Sum_probs=76.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ++|||+|||.++++++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+..
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            5899999999999999999999999999999999998999999999999999999999999999999999999999865

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=2.5e-19  Score=131.90  Aligned_cols=75  Identities=28%  Similarity=0.570  Sum_probs=71.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      +|||+|||+++++++|+++|++||.|..+.|+.++.+|.++|||||+|.+.++|++||+ +++..|.|+.|.|..|
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

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=6.3e-19  Score=137.90  Aligned_cols=81  Identities=26%  Similarity=0.515  Sum_probs=76.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      ++|||+|||+++++++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|.+||+ ++|..|.|+.|.|.+|.++
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            689999999999999999999999999999999999999999999999999999999997 7999999999999999875


Q ss_pred             CC
Q 009954          375 GQ  376 (521)
Q Consensus       375 ~~  376 (521)
                      .+
T Consensus       100 e~  101 (103)
T d1x4ba1         100 EE  101 (103)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.76  E-value=4.8e-19  Score=135.30  Aligned_cols=78  Identities=23%  Similarity=0.483  Sum_probs=73.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      .+|||+|||+.+++++|+++|++||.|..++|+.+.  +.++|||||+|.+.++|++||+.|||..|+|+.|.|.++.++
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            589999999999999999999999999999999984  457899999999999999999999999999999999999764

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2e-18  Score=128.80  Aligned_cols=76  Identities=22%  Similarity=0.530  Sum_probs=73.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ++|||+|||+++|+++|+++|++||.|..+.+..++.++.++|||||+|.+.++|.+|++ |+|..|+|+.|.|..|
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            689999999999999999999999999999999999999999999999999999999996 8999999999999976

>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=3.3e-19  Score=130.74  Aligned_cols=75  Identities=23%  Similarity=0.432  Sum_probs=71.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      +|||+|||+++|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++||+ +++..|+|+.|.|..|
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 5788999999999865

>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=3.4e-18  Score=133.54  Aligned_cols=84  Identities=29%  Similarity=0.427  Sum_probs=77.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHc------CCeeCCeE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN------GLKMGDKT  365 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~------g~~~~g~~  365 (521)
                      ...++|||+|||..+|+++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+||+.|+      |..|.|+.
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            344689999999999999999999999999999999998899999999999999999999999987      57789999


Q ss_pred             EEEEEccCCC
Q 009954          366 LTVRRATASG  375 (521)
Q Consensus       366 l~v~~~~~~~  375 (521)
                      |.|.|+.++.
T Consensus        86 l~v~~a~~k~   95 (98)
T d1x4ha1          86 LKVDLAVTRD   95 (98)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCC
Confidence            9999997654

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=8.5e-19  Score=129.59  Aligned_cols=75  Identities=25%  Similarity=0.585  Sum_probs=72.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      +|||+|||+++|+++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+||+ |||..|+|+.|.|.+|
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 9999999999999986

>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=1.3e-18  Score=131.84  Aligned_cols=80  Identities=16%  Similarity=0.360  Sum_probs=69.9

Q ss_pred             CCeEEEcCCCCCCC-HHHHHHHHHhcCCeeEEEEeec-CCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          294 PDRVFVGGLPYYFT-ETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       294 ~~~l~v~nLp~~~t-e~~l~~~F~~~G~i~~v~i~~~-~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      .++|||+|||.+++ +++|+++|++||.|..|.|..+ ..+|.++|||||+|.+.++|.+||+ |||..|+|+.|.|.|+
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            36899999999875 5679999999999999998764 4689999999999999999999996 9999999999999999


Q ss_pred             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      .++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            763

>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=99.74  E-value=6.2e-18  Score=135.89  Aligned_cols=78  Identities=22%  Similarity=0.448  Sum_probs=72.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|.++|++||.|.+|.+..   ++.++|||||+|.+.++|..|++.|||..|.|+.|.|.|+.
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            346899999999999999999999999999999876   45679999999999999999999999999999999999986


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      .
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=5.1e-18  Score=133.30  Aligned_cols=82  Identities=22%  Similarity=0.386  Sum_probs=75.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCe
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK  364 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~--------~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~  364 (521)
                      ..++|||+|||..+++++|.++|+.||.|.        .+.+..+..+|.++|||||+|.+.++|.+||+.|||..|.|+
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            346999999999999999999999999874        567778888999999999999999999999999999999999


Q ss_pred             EEEEEEccCC
Q 009954          365 TLTVRRATAS  374 (521)
Q Consensus       365 ~l~v~~~~~~  374 (521)
                      .|.|.|+.++
T Consensus        87 ~i~V~~a~~~   96 (101)
T d2cpea1          87 KLKVSLARKK   96 (101)
T ss_dssp             ECEEECSSCC
T ss_pred             EEEEEEcCCC
Confidence            9999999764

>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=99.74  E-value=2.2e-18  Score=130.90  Aligned_cols=79  Identities=16%  Similarity=0.338  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGF-DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v-~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ...++|||+|||.+++++||+++|+.||.|... .+..+ .+|.++|+|||+|.+.++|.+||+.|||..|+|++|+|.+
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            344679999999999999999999999998764 44444 6899999999999999999999999999999999999987


Q ss_pred             c
Q 009954          371 A  371 (521)
Q Consensus       371 ~  371 (521)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=8.3e-18  Score=129.92  Aligned_cols=75  Identities=19%  Similarity=0.396  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||..+++++|+++|++||.|.+|+|+.+      +|||||+|.+.++|.+|+..|||..|.|+.|+|.|++.
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            368999999999999999999999999999999876      78999999999999999999999999999999999976


Q ss_pred             C
Q 009954          374 S  374 (521)
Q Consensus       374 ~  374 (521)
                      .
T Consensus        92 ~   92 (96)
T d1x4ga1          92 S   92 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=1e-17  Score=126.29  Aligned_cols=76  Identities=22%  Similarity=0.270  Sum_probs=72.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ++|||+|||.++|+++|+++|+.||.|..|.|..+. +|.++|||||+|.+.++|++||+ ++|..|.|+.|.|.|..
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 89999999999999999999997 79999999999999874

>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=99.73  E-value=9.4e-19  Score=137.80  Aligned_cols=84  Identities=20%  Similarity=0.256  Sum_probs=78.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      +.++|||+|||..+++++|+++|++||.|..+.+..+..+|.++|||||+|.+.++|..||+.|||..|.|+.|.|.|+.
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            45789999999999999999999999999999888887789999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 009954          373 ASGQ  376 (521)
Q Consensus       373 ~~~~  376 (521)
                      ++.+
T Consensus        97 ~k~~  100 (102)
T d2cpxa1          97 NKKQ  100 (102)
T ss_dssp             CCSC
T ss_pred             Cccc
Confidence            7543

>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=99.72  E-value=9.8e-19  Score=133.78  Aligned_cols=79  Identities=18%  Similarity=0.341  Sum_probs=73.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ...+|||+|||..+++++|+++|+.||.|..+.|+.+ .+|.++|||||+|.+.++|++||+ |||..|+|+.|.|.++.
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecC
Confidence            3468999999999999999999999999999888755 589999999999999999999996 99999999999999986


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      .
T Consensus        90 ~   90 (91)
T d1fjeb1          90 G   90 (91)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.9e-17  Score=127.93  Aligned_cols=79  Identities=20%  Similarity=0.406  Sum_probs=72.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||+.+++++|+++|+.||.|..+.+..+   +.++|||||+|.+.++|++||+.|||..|.|+.|+|.|+
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            34468999999999999999999999999999987654   456899999999999999999999999999999999999


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      +.
T Consensus        89 ~~   90 (95)
T d1x4aa1          89 RS   90 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=4.9e-18  Score=132.90  Aligned_cols=81  Identities=19%  Similarity=0.440  Sum_probs=75.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ..+++|||+|||.++++++|+++|++||.|..+.+..+. ++.++|||||+|.+.++|.+||+.|||..|.|+++.|.++
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 8999999999999999999999999999999999999877


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      .|
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=99.71  E-value=7.3e-18  Score=128.34  Aligned_cols=76  Identities=20%  Similarity=0.327  Sum_probs=69.8

Q ss_pred             CCeEEEcCCCCCCCHHHH---HHHHHhcCCeeEEEEeecCCCCCc---ceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          294 PDRVFVGGLPYYFTETQI---KELLESFGTLHGFDLVKDRDTGNS---KGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l---~~~F~~~G~i~~v~i~~~~~~g~~---~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      .++|||+|||+.+++++|   .++|++||.|..|.|++++.++.+   .|||||+|.+.++|.+|++.|||..|.|+.|+
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            467999999999999999   678999999999999998776654   49999999999999999999999999999999


Q ss_pred             EE
Q 009954          368 VR  369 (521)
Q Consensus       368 v~  369 (521)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>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=99.71  E-value=7e-18  Score=125.73  Aligned_cols=76  Identities=18%  Similarity=0.303  Sum_probs=69.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCC-eeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL-KMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~-~~~g~~l~v~~~~~  373 (521)
                      ++|||+|||.++++++|+++|++||.|..+.+...      +|||||+|.+.++|.+|++.|||. .|.|+.|.|.|+.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            47999999999999999999999999988776654      789999999999999999999996 69999999999987


Q ss_pred             CCC
Q 009954          374 SGQ  376 (521)
Q Consensus       374 ~~~  376 (521)
                      +.+
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            544

>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=99.71  E-value=3.9e-17  Score=123.74  Aligned_cols=77  Identities=18%  Similarity=0.183  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+++++|+++|++||.|..+.+..      ++|||||+|.+.++|..|+..|||..|.|+.|.|.|+.
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            346899999999999999999999999998887754      37899999999999999999999999999999999998


Q ss_pred             CCC
Q 009954          373 ASG  375 (521)
Q Consensus       373 ~~~  375 (521)
                      +..
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.71  E-value=2e-17  Score=130.43  Aligned_cols=81  Identities=28%  Similarity=0.508  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC-CCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      .++++|||+|||..+++++|+++|+.|| |..+.++.+. .++.++|||||+|.+.++|++|++ |||..|.|+.|+|.|
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            4457899999999999999999999999 7777777654 478899999999999999987775 999999999999999


Q ss_pred             ccCC
Q 009954          371 ATAS  374 (521)
Q Consensus       371 ~~~~  374 (521)
                      +.++
T Consensus        91 a~~~   94 (104)
T d1wi8a_          91 ADQA   94 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9764

>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=99.71  E-value=1.4e-17  Score=125.85  Aligned_cols=75  Identities=35%  Similarity=0.570  Sum_probs=70.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      .++|||+|||..+++++|+++|++||.|.+|.+.++      +|||||+|.+.++|.+|++.|||..|.|+.|+|.||..
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      57999999999999999999999999999999999976


Q ss_pred             C
Q 009954          374 S  374 (521)
Q Consensus       374 ~  374 (521)
                      .
T Consensus        82 ~   82 (86)
T d2cpja1          82 S   82 (86)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.71  E-value=2.5e-17  Score=120.87  Aligned_cols=74  Identities=12%  Similarity=0.188  Sum_probs=68.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ++|||+|||+.+++++|+++|+.||.|..|.|..++.  ..+|||||+|.+.++|.+||. |+|..|+|+.|.|..+
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            4799999999999999999999999999999999853  346899999999999999996 8999999999999876

>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=99.70  E-value=1.3e-17  Score=129.31  Aligned_cols=83  Identities=18%  Similarity=0.303  Sum_probs=74.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeecC-CCCCcceEEEEEEcChHHHHHHHHHHcC--CeeCCeEEEEEE
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDR-DTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVRR  370 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~-i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~v~~  370 (521)
                      ++|||+|||..+++++|+++|+.||. |..|.|+.+. .+|.++|||||+|.+.++|..|++.|++  ..++|+.|.|.|
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 9999998875 3689999999999999999999999965  566899999999


Q ss_pred             ccCCCCC
Q 009954          371 ATASGQS  377 (521)
Q Consensus       371 ~~~~~~~  377 (521)
                      |.++.++
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9875544

>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=1.7e-17  Score=128.50  Aligned_cols=80  Identities=16%  Similarity=0.325  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...++|||+|||.++++++|+++|++||.|..+.     .++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.|+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            3447899999999999999999999999886654     26788999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 009954          372 TASGQ  376 (521)
Q Consensus       372 ~~~~~  376 (521)
                      .++..
T Consensus        89 ~~k~~   93 (96)
T d1fjca_          89 GEKGG   93 (96)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            87543

>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=99.70  E-value=2.8e-17  Score=123.49  Aligned_cols=74  Identities=20%  Similarity=0.329  Sum_probs=68.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee-CCeEEEEEEcc
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-GDKTLTVRRAT  372 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~-~g~~l~v~~~~  372 (521)
                      .++|||+|||..+++++|.++|++||.|..|+++++     .+|||||+|.+.++|..|++.|||..| +|+.|.|.|++
T Consensus         8 ~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           8 NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            468999999999999999999999999999999765     268999999999999999999999888 57999999985

>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=99.70  E-value=3.5e-18  Score=124.98  Aligned_cols=71  Identities=23%  Similarity=0.452  Sum_probs=68.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEE
Q 009954          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (521)
Q Consensus       297 l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (521)
                      |||+|||.++|+++|.++|++||.|..+++..++.++.++|||||+|.+.++|++|++.|||..|.|+.|+
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            79999999999999999999999999999999999999999999999999999999999999999998763

>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=99.69  E-value=2.3e-17  Score=122.60  Aligned_cols=73  Identities=23%  Similarity=0.373  Sum_probs=67.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+||+  +|+++|+++|++||.|.+|.+.++      +|||||+|.+.++|..|+..|||..|.|+.|+|.|+.
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            44799999996  899999999999999999998764      5799999999999999999999999999999999997


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      +
T Consensus        76 ~   76 (79)
T d2bz2a1          76 K   76 (79)
T ss_dssp             S
T ss_pred             C
Confidence            5

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=3.8e-17  Score=128.58  Aligned_cols=82  Identities=13%  Similarity=0.247  Sum_probs=74.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ....+|||+|||+++|+++|+++|..||.|..+.++.+..++.++|||||+|.+.++|++|++ ||+..|+|+.|.|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            344589999999999999999999999999887777776799999999999999999999997 8999999999999999


Q ss_pred             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      ...
T Consensus        92 ~~~   94 (104)
T d1wg5a_          92 SRA   94 (104)
T ss_dssp             CTT
T ss_pred             CHH
Confidence            763

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=4.2e-17  Score=126.34  Aligned_cols=73  Identities=22%  Similarity=0.472  Sum_probs=67.1

Q ss_pred             CCCeEEEcCCC-CCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          293 GPDRVFVGGLP-YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       293 ~~~~l~v~nLp-~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ...+|||+||| ..+++++|+++|++||.|..|.|        ++|||||+|.+.++|++||+.|||..|.|+.|+|.|+
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 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34679999997 56889999999999999999988        3689999999999999999999999999999999999


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      ..
T Consensus        86 ~~   87 (98)
T d1wf2a_          86 AE   87 (98)
T ss_dssp             TS
T ss_pred             CC
Confidence            75

>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=99.68  E-value=3.1e-17  Score=125.61  Aligned_cols=78  Identities=14%  Similarity=0.379  Sum_probs=70.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHH----HHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEE
Q 009954          294 PDRVFVGGLPYYFTETQIKE----LLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~----~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      .++|||+|||..+++++|++    +|++||.|.+|.+..   ++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.
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    689999999988754   56789999999999999999999999999999999999


Q ss_pred             EccCC
Q 009954          370 RATAS  374 (521)
Q Consensus       370 ~~~~~  374 (521)
                      |++.+
T Consensus        80 ~ak~~   84 (91)
T d1nu4a_          80 YAKTD   84 (91)
T ss_dssp             ECSSC
T ss_pred             EeCCC
Confidence            99764

>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=99.68  E-value=6e-17  Score=128.99  Aligned_cols=75  Identities=17%  Similarity=0.272  Sum_probs=69.6

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          294 PDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       294 ~~~l~v~nLp~-~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      .++|||+|||+ .+++++|+++|+.||.|..|.|+.++     +|||||+|.+.++|.+||+.|||..|.|+.|.|.|+.
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 59999999999999999999998873     7899999999999999999999999999999999986


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      .
T Consensus        77 ~   77 (109)
T d2adca1          77 H   77 (109)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=5e-17  Score=127.27  Aligned_cols=80  Identities=16%  Similarity=0.188  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      ....+|||+|||+++|+++|+++|+.||. ..|.++.+. +|.++|||||+|.+.++|++||+ ||+..|+|+.|.|.++
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 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            44568999999999999999999999984 577777774 78999999999999999999987 8999999999999998


Q ss_pred             cCC
Q 009954          372 TAS  374 (521)
Q Consensus       372 ~~~  374 (521)
                      ...
T Consensus        90 ~~~   92 (102)
T d1weza_          90 STA   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.67  E-value=9.8e-17  Score=122.09  Aligned_cols=76  Identities=13%  Similarity=0.106  Sum_probs=68.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee-CCeEEEEEEcc
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-GDKTLTVRRAT  372 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~-~g~~l~v~~~~  372 (521)
                      .++|||+|||.++++++|+++|++||.|..+.+...    ..+|||||+|.+.++|.+|+..|||..| .|+.|+|.|++
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            468999999999999999999999999988876654    3478999999999999999999999988 58999999996


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      .
T Consensus        86 ~   86 (88)
T d2adca2          86 S   86 (88)
T ss_dssp             S
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=99.67  E-value=1.7e-16  Score=121.09  Aligned_cols=80  Identities=20%  Similarity=0.426  Sum_probs=71.8

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ....+|||+|||+.+|+++|+++|..||.|..+.       +.+...+.++|||||+|.+.++|++||+|||..|.|+.|
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            3456899999999999999999999999987653       456678999999999999999999999999999999999


Q ss_pred             EEeCCCC
Q 009954          252 RVRRPTD  258 (521)
Q Consensus       252 ~v~~~~~  258 (521)
                      +|.+++.
T Consensus        84 ~V~~ak~   90 (91)
T d1fjeb1          84 KLEKPKG   90 (91)
T ss_dssp             EEECCCC
T ss_pred             EEEecCC
Confidence            9998653

>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=99.67  E-value=4.2e-17  Score=130.43  Aligned_cols=74  Identities=19%  Similarity=0.177  Sum_probs=69.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccCC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~~  374 (521)
                      ++|||+|||+.+++++|+++|++||.|..|.|..      ++|||||+|.+.++|.+||+.|||..|.|+.|.|.|+...
T Consensus        11 ~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_          11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            5899999999999999999999999999998743      4789999999999999999999999999999999999763

>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=99.66  E-value=7.9e-17  Score=122.23  Aligned_cols=74  Identities=16%  Similarity=0.232  Sum_probs=65.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||+++++++|+++|++||. ..+.+      +..+|||||+|.+.++|++|++.|||..|.|+.|.|.|+.
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 23333      3458899999999999999999999999999999999996


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      .
T Consensus        77 ~   77 (88)
T d1wg1a_          77 T   77 (88)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.7e-17  Score=125.86  Aligned_cols=72  Identities=21%  Similarity=0.249  Sum_probs=67.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      ++|||+|||+.+++++|+++|++||.|..+.|..+       |||||+|.+.++|++||..|||..|.|+.|.|.++..
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            37999999999999999999999999999998654       7999999999999999999999999999999988765

>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=6e-17  Score=127.31  Aligned_cols=79  Identities=14%  Similarity=0.184  Sum_probs=71.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ...+|||+|||+.+|+++|.++|..||.|..+.++....+|.++|||||+|.+.++|++||+ |||..|+|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            34689999999999999999999999999875555555699999999999999999999997 99999999999999884

>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=99.66  E-value=3e-16  Score=121.49  Aligned_cols=76  Identities=25%  Similarity=0.511  Sum_probs=69.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCC--eEEEEEE
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRR  370 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~v~~  370 (521)
                      +.++|||+|||+++++++|+++|++||.|..|++.++      ++||||+|.+.++|.+|++.|||..|.|  +.|+|.|
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            4578999999999999999999999999999998765      5799999999999999999999999976  5899999


Q ss_pred             ccCC
Q 009954          371 ATAS  374 (521)
Q Consensus       371 ~~~~  374 (521)
                      ++..
T Consensus        90 ak~~   93 (97)
T d1whya_          90 AKSG   93 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9763

>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=99.65  E-value=5e-16  Score=121.92  Aligned_cols=78  Identities=17%  Similarity=0.140  Sum_probs=70.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHH--cCCeeCCeEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLTV  368 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l--~g~~~~g~~l~v  368 (521)
                      ..+..+|||+|||..+++++|.++|++||.|..|.+.+.      +|+|||+|.+.++|+.|+..|  ++..++|++|.|
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            345678999999999999999999999999999998764      679999999999999999988  457789999999


Q ss_pred             EEccCC
Q 009954          369 RRATAS  374 (521)
Q Consensus       369 ~~~~~~  374 (521)
                      .|+..+
T Consensus        86 ~~s~~~   91 (104)
T d1wexa_          86 NYSTSK   91 (104)
T ss_dssp             EECSSS
T ss_pred             EEcCCC
Confidence            999763

>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=1.7e-16  Score=125.73  Aligned_cols=76  Identities=21%  Similarity=0.260  Sum_probs=70.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee--CCeEEEEEEc
Q 009954          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVRRA  371 (521)
Q Consensus       294 ~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~--~g~~l~v~~~  371 (521)
                      ..+|||+|||..+|+++|+++|++||.|..|.|..++    .+|+|||+|.+.++|++||..|||..|  .|+.|.|.|+
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s   82 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS   82 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEec
Confidence            4579999999999999999999999999999998774    489999999999999999999999987  6899999999


Q ss_pred             cC
Q 009954          372 TA  373 (521)
Q Consensus       372 ~~  373 (521)
                      .+
T Consensus        83 ~~   84 (108)
T d2adba1          83 KL   84 (108)
T ss_dssp             SS
T ss_pred             CC
Confidence            76

>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=99.64  E-value=5.4e-16  Score=117.85  Aligned_cols=77  Identities=14%  Similarity=0.161  Sum_probs=69.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHH--cCCeeCCeEEEEE
Q 009954          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLTVR  369 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l--~g~~~~g~~l~v~  369 (521)
                      .+.++|||+|||..+++++|.++|++||.|..|.+..+      +|+|||+|.+.++|.+|++.|  ++..+.|+.|.|.
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            44578999999999999999999999999999998865      579999999999999999866  5688999999999


Q ss_pred             EccCC
Q 009954          370 RATAS  374 (521)
Q Consensus       370 ~~~~~  374 (521)
                      |+..+
T Consensus        80 ~sk~~   84 (88)
T d2cq1a1          80 YSNHK   84 (88)
T ss_dssp             ECSCS
T ss_pred             ECCCC
Confidence            99753

>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=8e-17  Score=122.36  Aligned_cols=76  Identities=20%  Similarity=0.426  Sum_probs=68.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ..++|||+|||..+|+++|+++|++||.|..|++..     .++|||||+|.+.++|++||.  +++.|.|+.|.|.++.
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            457999999999999999999999999999997654     357899999999999999985  7889999999999997


Q ss_pred             CCC
Q 009954          373 ASG  375 (521)
Q Consensus       373 ~~~  375 (521)
                      ++.
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.64  E-value=4.9e-16  Score=120.37  Aligned_cols=88  Identities=23%  Similarity=0.388  Sum_probs=79.0

Q ss_pred             CcceEEEeeCcCCcccCC-ChHHHHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHh
Q 009954          417 TLAKVLCLTEAITADALA-DDEEYEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  495 (521)
Q Consensus       417 ~~~~v~~l~~~~~~~~~~-~~~~~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~ln  495 (521)
                      ...+|+.|.|++++.++. +++.|.+|++||.+.|++||.|..|.++.+..       .|+|||+|.+.++|.+|+..||
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            678899999999988774 45679999999999999999999999988642       4789999999999999999999


Q ss_pred             CCeeCCcEEEEEEcCC
Q 009954          496 GRKFGGNTVNAFYYPE  511 (521)
Q Consensus       496 g~~~~gr~l~v~~~~~  511 (521)
                      |+.|+|++|.|.|+..
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            9999999999999854

>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=99.64  E-value=3.3e-16  Score=114.70  Aligned_cols=70  Identities=19%  Similarity=0.358  Sum_probs=63.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEccC
Q 009954          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (521)
Q Consensus       297 l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~~  373 (521)
                      |||+|||+++++++|+++|++|| +..+.+      +.++|||||+|.+.++|.+|++.|||..+.|++|.|+|+..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            79999999999999999999999 444443      34589999999999999999999999999999999999965

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=2.3e-16  Score=122.11  Aligned_cols=74  Identities=22%  Similarity=0.233  Sum_probs=69.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       293 ~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      ...+|||+|||+.+++++|+++|++||.|..+.|..       +|||||+|.+.++|++||+.|||..|.|+.|.|.|+.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            446899999999999999999999999999999864       4799999999999999999999999999999999986


Q ss_pred             C
Q 009954          373 A  373 (521)
Q Consensus       373 ~  373 (521)
                      .
T Consensus        87 ~   87 (98)
T d1wg4a_          87 V   87 (98)
T ss_dssp             E
T ss_pred             c
Confidence            5

>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=99.63  E-value=1e-16  Score=127.76  Aligned_cols=82  Identities=18%  Similarity=0.309  Sum_probs=73.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~  370 (521)
                      ....++|||+|||+.+|+++|.++|+.||.|..+.++.+..+|.++|||||+|.+.++|++||+ |||..|+|+.|.|.+
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            3455789999999999999999999999999776566655799999999999999999999997 899999999999998


Q ss_pred             ccC
Q 009954          371 ATA  373 (521)
Q Consensus       371 ~~~  373 (521)
                      +..
T Consensus        94 ~~~   96 (112)
T d1wela1          94 ITK   96 (112)
T ss_dssp             ECH
T ss_pred             cCh
Confidence            853

>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=99.63  E-value=6.5e-17  Score=123.66  Aligned_cols=86  Identities=49%  Similarity=0.888  Sum_probs=76.7

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEEEe
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVR  254 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v~  254 (521)
                      ++|||+|||..+|+++|+++|+.||.+..+.+. ....+.+..++.++|||||+|.+.++|+.|++|||..+.|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~-~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQA-PGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCS-SSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEe-ccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEEC
Confidence            689999999999999999999999998776543 3445777788899999999999999999999999999999999999


Q ss_pred             CCCCCCc
Q 009954          255 RPTDYNP  261 (521)
Q Consensus       255 ~~~~~~~  261 (521)
                      +++++.+
T Consensus        81 r~k~~~p   87 (90)
T d1u2fa_          81 RPHDYQP   87 (90)
T ss_dssp             CTTCCSC
T ss_pred             CCCCCCC
Confidence            8887654

>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=99.63  E-value=8e-16  Score=118.57  Aligned_cols=75  Identities=25%  Similarity=0.431  Sum_probs=69.5

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||..+++++|+++|++||.            |..+.+..++|||||+|.+.++|..|+ .|||..|.|+.
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 009954          251 VRVRRPTD  258 (521)
Q Consensus       251 i~v~~~~~  258 (521)
                      |+|.|++.
T Consensus        84 l~v~~ak~   91 (96)
T d1x4ga1          84 VKCYWGKE   91 (96)
T ss_dssp             CEEECCCC
T ss_pred             EEEEEcCC
Confidence            99999754

>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=99.62  E-value=8.2e-17  Score=120.87  Aligned_cols=78  Identities=15%  Similarity=0.242  Sum_probs=64.7

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      .++|||+|||+++|+++|+++|++||.|..+.+      +.+...+.++|||||+|.+.++|++|+ .|||..+.|++|+
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i------~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~   75 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRI------MRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLK   75 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEEC------CEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeee------eeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            457999999999999999999999998533211      222233456899999999999999999 6999999999999


Q ss_pred             EeCCC
Q 009954          253 VRRPT  257 (521)
Q Consensus       253 v~~~~  257 (521)
                      |++++
T Consensus        76 v~~a~   80 (82)
T d1b7fa1          76 VSYAR   80 (82)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            99864

>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=7.6e-17  Score=125.87  Aligned_cols=84  Identities=19%  Similarity=0.329  Sum_probs=68.7

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      ....++|||+|||+++|+++|+++|.+||.|....+      +.+..++.++|||||+|.+.++|..|+++++..|.|+.
T Consensus        17 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i------~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~   90 (103)
T d1x4ba1          17 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV------MRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRV   90 (103)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEE------ECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEE
T ss_pred             cCCCCEEEEeCCCCcCCHHHHHHHHHhhCcccceee------cccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEE
Confidence            344578999999999999999999999998543211      11222356789999999999999999999999999999


Q ss_pred             EEEeCCCCCC
Q 009954          251 VRVRRPTDYN  260 (521)
Q Consensus       251 i~v~~~~~~~  260 (521)
                      |.|.++.+..
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

>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=99.62  E-value=1.1e-16  Score=122.87  Aligned_cols=82  Identities=26%  Similarity=0.388  Sum_probs=67.6

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+|||..+|+++|+++|++||.|..+.+      +.+..++.++|||||+|.+.++|..|+ .|||..|.|+.|
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~------~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   81 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHM------PKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   81 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEEC------CBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccce------eecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            3578999999999999999999999998433211      222234567899999999999999999 799999999999


Q ss_pred             EEeCCCCCC
Q 009954          252 RVRRPTDYN  260 (521)
Q Consensus       252 ~v~~~~~~~  260 (521)
                      +|+++....
T Consensus        82 ~V~~A~~~~   90 (93)
T d1x5ua1          82 RVNKASAHN   90 (93)
T ss_dssp             EEEETTTTS
T ss_pred             EEEEcCCCC
Confidence            999976543

>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=3.4e-17  Score=120.67  Aligned_cols=76  Identities=12%  Similarity=0.243  Sum_probs=65.8

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEEEe
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVR  254 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v~  254 (521)
                      |+|||+|||+++|+++|+++|++||.|..+      ..+.+..++.++|||||+|.+.++|++|+++++..|.|+.|.|+
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            689999999999999999999999986432      12344456778999999999999999999999999999999998


Q ss_pred             CC
Q 009954          255 RP  256 (521)
Q Consensus       255 ~~  256 (521)
                      .+
T Consensus        75 ~A   76 (77)
T d1uawa_          75 VA   76 (77)
T ss_dssp             EC
T ss_pred             EC
Confidence            64

>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=99.61  E-value=2.5e-16  Score=117.77  Aligned_cols=77  Identities=16%  Similarity=0.386  Sum_probs=61.9

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEE
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v  253 (521)
                      ++|||+|||+++|+++|+++|++||.+....      .+.+...+.++|||||+|.+.++|.+|+ .|||..+.|++|.|
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 CTLWMTNFPPSYTQRNIRDLLQDINVVALSI------RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVT   75 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEE------ECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeee------eecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            6899999999999999999999999864321      1233455678999999999999999999 69999999999999


Q ss_pred             eCCC
Q 009954          254 RRPT  257 (521)
Q Consensus       254 ~~~~  257 (521)
                      +++.
T Consensus        76 ~~a~   79 (81)
T d2ghpa1          76 KVSN   79 (81)
T ss_dssp             EECC
T ss_pred             EEcc
Confidence            9864

>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=99.61  E-value=6.9e-17  Score=121.39  Aligned_cols=79  Identities=24%  Similarity=0.368  Sum_probs=65.4

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~  252 (521)
                      ..++|||+|||+++|+++|.++|++||.|..+.      .+.+..++.++|||||+|.+.++|.+|+++++..|.|+.|+
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            457899999999999999999999999854311      12222335678999999999999999999999999999999


Q ss_pred             EeCCC
Q 009954          253 VRRPT  257 (521)
Q Consensus       253 v~~~~  257 (521)
                      |+++.
T Consensus        79 V~~A~   83 (84)
T d1l3ka1          79 PKRAV   83 (84)
T ss_dssp             EEECC
T ss_pred             EEeee
Confidence            98753

>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=99.61  E-value=1.5e-16  Score=121.23  Aligned_cols=80  Identities=23%  Similarity=0.345  Sum_probs=68.7

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+|||+++|+++|+++|++||.|..+.+      +.+..++.++|||||+|.+.++|..|+ .|||..|.|+.|
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i------~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l   77 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI------PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI   77 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEEC------CCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEeccc------ccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            3578999999999999999999999998654322      334445778999999999999999999 699999999999


Q ss_pred             EEeCCCC
Q 009954          252 RVRRPTD  258 (521)
Q Consensus       252 ~v~~~~~  258 (521)
                      .|.++.+
T Consensus        78 ~v~~a~p   84 (89)
T d2cqba1          78 RVNLAKP   84 (89)
T ss_dssp             EEEECCC
T ss_pred             EEEEeCC
Confidence            9998754

>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=99.61  E-value=1e-15  Score=116.04  Aligned_cols=77  Identities=14%  Similarity=0.101  Sum_probs=69.1

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHH--cCCeeCCeEEE
Q 009954          291 AEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLT  367 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~-~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l--~g~~~~g~~l~  367 (521)
                      .+..++|||+|||.. +|++||.++|++||.|..|.+..+      +++|||+|.+.++|..|++.|  ++..+.|++|.
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            355678999999986 889999999999999999999876      458999999999999999966  67889999999


Q ss_pred             EEEccC
Q 009954          368 VRRATA  373 (521)
Q Consensus       368 v~~~~~  373 (521)
                      |.|++.
T Consensus        79 V~~s~~   84 (89)
T d1x4da1          79 VHLSQK   84 (89)
T ss_dssp             EEEECC
T ss_pred             EEECCC
Confidence            999975

>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=99.61  E-value=1.1e-16  Score=117.42  Aligned_cols=75  Identities=16%  Similarity=0.352  Sum_probs=62.8

Q ss_pred             eEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEEEeC
Q 009954          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (521)
Q Consensus       176 ~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v~~  255 (521)
                      +|||+|||+++|+++|+++|++||.|..+.+      +.+..++.++|||||+|.+.++|++|+++++..|.|+.|.|++
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            4899999999999999999999998543221      2222345678999999999999999999999999999999975


Q ss_pred             C
Q 009954          256 P  256 (521)
Q Consensus       256 ~  256 (521)
                      +
T Consensus        75 A   75 (75)
T d1hd0a_          75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.9e-15  Score=118.50  Aligned_cols=82  Identities=16%  Similarity=0.266  Sum_probs=72.8

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ++++|||+|||..+|+++|+++|.+||.+..+.+      +.+...+.++|||||+|.+.++|..|+ .|||..|.|+.|
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 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPI------QFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKIL   90 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCC------EEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEe------ecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEE
Confidence            3578999999999999999999999999876533      566677889999999999999999999 799999999999


Q ss_pred             EEeCCCCCC
Q 009954          252 RVRRPTDYN  260 (521)
Q Consensus       252 ~v~~~~~~~  260 (521)
                      +|.|+....
T Consensus        91 ~V~~ak~k~   99 (102)
T d2cpxa1          91 VIEFGKNKK   99 (102)
T ss_dssp             EEEECCCCS
T ss_pred             EEEeCCCcc
Confidence            999986543

>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=7.4e-17  Score=125.56  Aligned_cols=79  Identities=24%  Similarity=0.329  Sum_probs=66.0

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ...++|||+|||+.+|+++|+++|+.||.|..+.      .+.+..++.++|||||+|.+.++|.+|++|||..|.|+.|
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            3457999999999999999999999999853321      1222334667899999999999999999999999999999


Q ss_pred             EEeCC
Q 009954          252 RVRRP  256 (521)
Q Consensus       252 ~v~~~  256 (521)
                      .|+++
T Consensus        90 ~V~~a   94 (101)
T d2cq4a1          90 IVQAS   94 (101)
T ss_dssp             EEEEH
T ss_pred             EEEEC
Confidence            99864

>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=99.59  E-value=1.3e-15  Score=115.27  Aligned_cols=74  Identities=24%  Similarity=0.393  Sum_probs=66.5

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+|||+.+|+++|+++|++||.            +..+.+..++|||||+|.+.++|..|+ .|||..|.|+.|
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             EEeCCCC
Q 009954          252 RVRRPTD  258 (521)
Q Consensus       252 ~v~~~~~  258 (521)
                      .|.|+.+
T Consensus        75 ~V~~akP   81 (86)
T d2cpda1          75 EVTLAKP   81 (86)
T ss_dssp             EEECCCC
T ss_pred             EEEeccC
Confidence            9998764

>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=2.2e-16  Score=120.73  Aligned_cols=80  Identities=26%  Similarity=0.441  Sum_probs=66.5

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      +.++|||+|||+++|+++|+++|.+||.|..+.      .+.....+.++|||||+|.+.++|..|+ .|||..|.|+.|
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            467899999999999999999999999854321      1222234567899999999999999999 799999999999


Q ss_pred             EEeCCCC
Q 009954          252 RVRRPTD  258 (521)
Q Consensus       252 ~v~~~~~  258 (521)
                      +|+++..
T Consensus        78 ~V~~a~~   84 (90)
T d1x5sa1          78 RVDQAGK   84 (90)
T ss_dssp             EEEEEEC
T ss_pred             EEEEcCC
Confidence            9998643

>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=99.59  E-value=3e-15  Score=114.12  Aligned_cols=75  Identities=28%  Similarity=0.426  Sum_probs=65.3

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCCeEEEEecCHHHHHHHH-HccCcee
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~----~~~~g~afV~f~~~~~a~~A~-~l~g~~~  246 (521)
                      ...++|||+|||..+|+++|+++|+.||.            |..+.+    ...+|||||+|.+.++|..|+ .|+|..|
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            44679999999999999999999999998            444443    235789999999999999999 6999999


Q ss_pred             cCceEEEeCCCC
Q 009954          247 EGVAVRVRRPTD  258 (521)
Q Consensus       247 ~g~~i~v~~~~~  258 (521)
                      .|+.|+|.|+..
T Consensus        74 ~g~~i~v~~a~~   85 (90)
T d2cqia1          74 LGKEVKVNWATT   85 (90)
T ss_dssp             TTEEEEEEECCC
T ss_pred             CCEEEEEEEcCC
Confidence            999999998754

>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=2.8e-16  Score=115.74  Aligned_cols=75  Identities=15%  Similarity=0.280  Sum_probs=64.2

Q ss_pred             eEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEEEeC
Q 009954          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (521)
Q Consensus       176 ~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v~~  255 (521)
                      +|||+|||+++|+++|+++|+.||.+..+.+      +.+..++..++||||+|.+.++|.+|+++||..|.|++|+|++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~------~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~   74 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAML------MFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECC------BCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeee------eeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEE
Confidence            4999999999999999999999998654322      2333346678999999999999999999999999999999986


Q ss_pred             C
Q 009954          256 P  256 (521)
Q Consensus       256 ~  256 (521)
                      |
T Consensus        75 A   75 (75)
T d2msta_          75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.59  E-value=1.9e-16  Score=121.56  Aligned_cols=81  Identities=22%  Similarity=0.286  Sum_probs=65.3

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ..+++|||+|||+++|+++|+++|++||.|..+.      .+.+...+.++|||||+|.+.++|..|+ .|||..+.|++
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~------i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~   78 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKII------MGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI   78 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceec------cccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            4578999999999999999999999999843210      0111122445789999999999999999 69999999999


Q ss_pred             EEEeCCCC
Q 009954          251 VRVRRPTD  258 (521)
Q Consensus       251 i~v~~~~~  258 (521)
                      |+|.|+..
T Consensus        79 i~V~~a~~   86 (93)
T d1h2vz_          79 IRTDWDAG   86 (93)
T ss_dssp             CEEEEESC
T ss_pred             EEEEEcCC
Confidence            99998643

>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=99.58  E-value=2.2e-15  Score=125.23  Aligned_cols=83  Identities=16%  Similarity=0.245  Sum_probs=66.7

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||+++|+++|+++|++||.|..+.      .+.+..++.++|||||+|.+.++|..|+ .|||..|.|+.
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      0111123456899999999999999999 69999999999


Q ss_pred             EEEeCCCCCC
Q 009954          251 VRVRRPTDYN  260 (521)
Q Consensus       251 i~v~~~~~~~  260 (521)
                      |+|.++....
T Consensus       114 l~V~~a~~~~  123 (139)
T d1u6fa1         114 LKVALAASGH  123 (139)
T ss_dssp             EEEEESSCCC
T ss_pred             EEEEEcCCCC
Confidence            9999876443

>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=99.58  E-value=4.6e-16  Score=115.68  Aligned_cols=73  Identities=19%  Similarity=0.337  Sum_probs=63.4

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCc-eecCceEE
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI-IFEGVAVR  252 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~-~~~g~~i~  252 (521)
                      .+|||+|||.++|+++|+++|.+||.+            ....+..++|||||+|.+.++|.+|+ .|||. .+.|++|.
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 69986 69999999


Q ss_pred             EeCCCCC
Q 009954          253 VRRPTDY  259 (521)
Q Consensus       253 v~~~~~~  259 (521)
                      |.++.+.
T Consensus        70 V~~a~~k   76 (80)
T d2cqha1          70 VDYSVSK   76 (80)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCc
Confidence            9987653

>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=99.58  E-value=1.9e-16  Score=117.87  Aligned_cols=77  Identities=17%  Similarity=0.292  Sum_probs=63.4

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  253 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v  253 (521)
                      .++|||+|||+++|+++|+++|++||.+..+.      .+.+...+.++|||||+|.+.++|.+|++++|..|.|++|.|
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            47899999999999999999999999854311      011122344679999999999999999999999999999999


Q ss_pred             eCC
Q 009954          254 RRP  256 (521)
Q Consensus       254 ~~~  256 (521)
                      +++
T Consensus        76 ~~A   78 (79)
T d1l3ka2          76 RKA   78 (79)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            864

>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=2.9e-16  Score=114.72  Aligned_cols=74  Identities=18%  Similarity=0.279  Sum_probs=61.7

Q ss_pred             eEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEEEeC
Q 009954          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (521)
Q Consensus       176 ~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~v~~  255 (521)
                      +|||+|||+++|+++|+++|++||.|..+.+      +.+..++.++|||||+|.+.++|++||++++..+.|+.|.|+.
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            5999999999999999999999998533211      2222345678999999999999999998888999999999975

>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=99.58  E-value=1.2e-15  Score=118.31  Aligned_cols=77  Identities=14%  Similarity=0.231  Sum_probs=68.9

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHH--HHcCCeeCCeEEEE
Q 009954          292 EGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA--ALNGLKMGDKTLTV  368 (521)
Q Consensus       292 ~~~~~l~v~nLp~~-~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~--~l~g~~~~g~~l~v  368 (521)
                      ...++|||+|||.+ +|+++|.++|++||.|..|.+..+      +|+|||+|.+.++|..|++  .+++..|.|+.|.|
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            34468999999985 899999999999999999999865      5799999999999999997  57889999999999


Q ss_pred             EEccCC
Q 009954          369 RRATAS  374 (521)
Q Consensus       369 ~~~~~~  374 (521)
                      .|++.+
T Consensus        90 ~~s~~~   95 (99)
T d1x4fa1          90 DLSEKY   95 (99)
T ss_dssp             EEECSC
T ss_pred             EEcCCc
Confidence            999653

>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=99.57  E-value=3e-16  Score=117.87  Aligned_cols=74  Identities=24%  Similarity=0.323  Sum_probs=61.1

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      .++|||+|||+.+|+++|+++|++||.|..+.      .+.+..++.++|||||+|.+.++|..|+ .|||..|.|++|+
T Consensus         9 ~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~   82 (83)
T d2cqca1           9 NCCLGVFGLSLYTTERDLREVFSKYGPIADVS------IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   82 (83)
T ss_dssp             GGCEEEESCCSSCCHHHHHHHHHTTSCEEEEE------EEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCCcccc------ccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeE
Confidence            56899999999999999999999999853211      0112223556789999999999999999 6999999999998


Q ss_pred             E
Q 009954          253 V  253 (521)
Q Consensus       253 v  253 (521)
                      |
T Consensus        83 V   83 (83)
T d2cqca1          83 V   83 (83)
T ss_dssp             E
T ss_pred             C
Confidence            7

>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=3.7e-15  Score=110.17  Aligned_cols=70  Identities=19%  Similarity=0.227  Sum_probs=62.0

Q ss_pred             eEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE-----ecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY-----INHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       176 ~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~-----~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      +|||+|||+.+|+++|+++|++||.|            ..+.     .+.++|||||+|.+.++|..|+ .|||..+.|+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v------------~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~   69 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTL------------KKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR   69 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCE------------EEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCC------------eEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            69999999999999999999999984            3443     3456889999999999999999 6999999999


Q ss_pred             eEEEeCCC
Q 009954          250 AVRVRRPT  257 (521)
Q Consensus       250 ~i~v~~~~  257 (521)
                      +|+|+++.
T Consensus        70 ~l~V~~a~   77 (78)
T d1no8a_          70 PMNIQLVT   77 (78)
T ss_dssp             ECEEEEEC
T ss_pred             EEEEEEee
Confidence            99998753

>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=99.57  E-value=8.1e-16  Score=116.00  Aligned_cols=73  Identities=30%  Similarity=0.520  Sum_probs=67.6

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      .++|||+|||.++++++|+++|++||.            |.++.+..++|||||+|.+.++|..|+ .|||..|.|+.|+
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            467999999999999999999999997            677788889999999999999999999 6999999999999


Q ss_pred             EeCCCC
Q 009954          253 VRRPTD  258 (521)
Q Consensus       253 v~~~~~  258 (521)
                      |+|+..
T Consensus        76 V~~A~~   81 (86)
T d2cpja1          76 VRFACH   81 (86)
T ss_dssp             EEESSC
T ss_pred             EEECCC
Confidence            998654

>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=99.57  E-value=1.9e-15  Score=116.44  Aligned_cols=78  Identities=28%  Similarity=0.434  Sum_probs=65.4

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||+++|+++|+++|..||.|..         +........++||||+|.+.++|..|+ .||+..|.|++
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            34568999999999999999999999987421         222223456899999999999999999 69999999999


Q ss_pred             EEEeCCCC
Q 009954          251 VRVRRPTD  258 (521)
Q Consensus       251 i~v~~~~~  258 (521)
                      |+|.++..
T Consensus        83 l~V~~a~~   90 (95)
T d1x4aa1          83 LRVEFPRS   90 (95)
T ss_dssp             CEEECCCC
T ss_pred             EEEEeccC
Confidence            99998764

>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=6.8e-16  Score=115.99  Aligned_cols=78  Identities=17%  Similarity=0.321  Sum_probs=65.0

Q ss_pred             EEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEEeC
Q 009954          177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRR  255 (521)
Q Consensus       177 l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v~~  255 (521)
                      |||+|||+++|+++|+++|++||.+....     ..+.+..++.++|||||+|.+.++|..|+ .|+|..+.|++|+|.+
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 IFIGNLDPEIDEKLLYDTFSAFGVILQTP-----KIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   75 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCC-----EECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeE-----EEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEE
Confidence            79999999999999999999999864321     11223344677899999999999999999 6999999999999998


Q ss_pred             CCCC
Q 009954          256 PTDY  259 (521)
Q Consensus       256 ~~~~  259 (521)
                      +...
T Consensus        76 a~~k   79 (83)
T d1x5ta1          76 AFKK   79 (83)
T ss_dssp             SCCC
T ss_pred             ecCC
Confidence            7643

>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=99.56  E-value=6.5e-16  Score=117.34  Aligned_cols=81  Identities=21%  Similarity=0.313  Sum_probs=65.5

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ...++|||+|||+++|+++|+++|+.||.|..+.      .+.+..++.++|||||+|.+.++|.+||+ +...|.|+.|
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            3467899999999999999999999999864321      12233346778999999999999999996 3458999999


Q ss_pred             EEeCCCCC
Q 009954          252 RVRRPTDY  259 (521)
Q Consensus       252 ~v~~~~~~  259 (521)
                      .|+++...
T Consensus        79 ~v~~a~~k   86 (90)
T d2cqga1          79 DCKLPNSK   86 (90)
T ss_dssp             EEECCCTT
T ss_pred             EEEeCCCC
Confidence            99987654

>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=99.56  E-value=3e-15  Score=109.52  Aligned_cols=68  Identities=19%  Similarity=0.295  Sum_probs=63.7

Q ss_pred             EEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEEeC
Q 009954          177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRR  255 (521)
Q Consensus       177 l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v~~  255 (521)
                      |||+|||+++|+++|+++|.+||             +..+.++..+|||||+|.+.++|.+|+ .|||..+.|++|.|++
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             566778899999999999999999999 7999999999999998


Q ss_pred             CC
Q 009954          256 PT  257 (521)
Q Consensus       256 ~~  257 (521)
                      +.
T Consensus        68 a~   69 (75)
T d1wi6a1          68 QP   69 (75)
T ss_dssp             CC
T ss_pred             eC
Confidence            64

>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=99.56  E-value=1.5e-15  Score=121.12  Aligned_cols=76  Identities=21%  Similarity=0.153  Sum_probs=69.6

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....++|||+|||+.+|+++|+++|.+||.            |..+.+..++|||||+|.+.++|.+|+ .|||..|.|+
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            344578999999999999999999999997            788888899999999999999999999 7999999999


Q ss_pred             eEEEeCCCC
Q 009954          250 AVRVRRPTD  258 (521)
Q Consensus       250 ~i~v~~~~~  258 (521)
                      .|.|.|+..
T Consensus        75 ~l~v~~a~~   83 (111)
T d1whxa_          75 PLYLEWAPI   83 (111)
T ss_dssp             BCEEEEEET
T ss_pred             eEEEEECCC
Confidence            999998654

>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=99.56  E-value=2.5e-15  Score=120.38  Aligned_cols=76  Identities=17%  Similarity=0.138  Sum_probs=65.3

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      .+++|||+|||..+|+++|.++|++||.|..         |.....+.++|||||+|.+.++|..|+ .|||..|.|+.|
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            3578999999999999999999999998432         333334567899999999999999999 799999999999


Q ss_pred             EEeCCC
Q 009954          252 RVRRPT  257 (521)
Q Consensus       252 ~v~~~~  257 (521)
                      .|.++.
T Consensus        77 ~V~~a~   82 (114)
T d2f9da1          77 VVLYYN   82 (114)
T ss_dssp             EEEECC
T ss_pred             EEEEcC
Confidence            999754

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.56  E-value=4.3e-15  Score=114.05  Aligned_cols=81  Identities=20%  Similarity=0.245  Sum_probs=65.9

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEE-EecCCCCeEEEEecCHHHHHHHH-Hc-cCceecCc
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV-YINHEKKFAFVEMRTVEEASNAM-AL-DGIIFEGV  249 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~-~~~~~~g~afV~f~~~~~a~~A~-~l-~g~~~~g~  249 (521)
                      ...+|||+|||+++++++|+++|.+||.|..+.+      +.+. ..+.++|||||+|.+.++|.+|+ .| |+..|.|+
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i------~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr   80 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRL------PKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR   80 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEC------CCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEE------EeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCE
Confidence            4568999999999999999999999998533211      1111 13557899999999999999999 57 89999999


Q ss_pred             eEEEeCCCCC
Q 009954          250 AVRVRRPTDY  259 (521)
Q Consensus       250 ~i~v~~~~~~  259 (521)
                      +|.|.|+...
T Consensus        81 ~l~V~~A~~~   90 (94)
T d2cpha1          81 RLVLEWADSE   90 (94)
T ss_dssp             BCEEEECCCC
T ss_pred             EEEEEEcCCC
Confidence            9999997654

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=7.3e-17  Score=123.38  Aligned_cols=78  Identities=22%  Similarity=0.439  Sum_probs=69.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEe-----ecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEE
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLV-----KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~-----~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      ++|||+|||..+|+++|+++|+.||.|..+.+.     .+..++.++|||||+|.+.++|++|++ |||..|.|+.|+|.
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            589999999999999999999999988766543     344578899999999999999999996 99999999999998


Q ss_pred             EccC
Q 009954          370 RATA  373 (521)
Q Consensus       370 ~~~~  373 (521)
                      .++.
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            7654

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=4.4e-15  Score=112.86  Aligned_cols=75  Identities=21%  Similarity=0.364  Sum_probs=64.8

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCCeEEEEecCHHHHHHHH-HccCceec
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~----~~~~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      ...+|||+|||+.+|+++|+++|++||.            |..+.+    ..++|||||+|.+.++|.+|+ .|||..|.
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    235799999999999999999 69999999


Q ss_pred             CceEEEeCCCCC
Q 009954          248 GVAVRVRRPTDY  259 (521)
Q Consensus       248 g~~i~v~~~~~~  259 (521)
                      |+.|.|.++...
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

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=1.8e-15  Score=118.03  Aligned_cols=77  Identities=13%  Similarity=0.100  Sum_probs=68.3

Q ss_pred             CCCCeEEEcCCCCCC-CH----HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEE
Q 009954          292 EGPDRVFVGGLPYYF-TE----TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (521)
Q Consensus       292 ~~~~~l~v~nLp~~~-te----~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (521)
                      .+.++|||+||+.++ ++    ++|.++|++||.|.++++.+.      +|+|||+|.+.++|.+|++.|||..|.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            345789999999886 33    569999999999999998754      6799999999999999999999999999999


Q ss_pred             EEEEccCC
Q 009954          367 TVRRATAS  374 (521)
Q Consensus       367 ~v~~~~~~  374 (521)
                      +|.|+...
T Consensus        77 ~v~~a~~~   84 (104)
T d1weya_          77 KLYFAQTL   84 (104)
T ss_dssp             EEECCCCS
T ss_pred             EEeecccC
Confidence            99999763

>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=99.55  E-value=5.3e-16  Score=116.72  Aligned_cols=79  Identities=18%  Similarity=0.237  Sum_probs=64.8

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~  252 (521)
                      ..++|||+|||.++|+++|+++|+.||.|..+.       +.....+.++|||||+|.+.++|.+||++++..+.|+.|.
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            467999999999999999999999999853210       1111224457899999999999999999999999999999


Q ss_pred             EeCCCC
Q 009954          253 VRRPTD  258 (521)
Q Consensus       253 v~~~~~  258 (521)
                      |.+..+
T Consensus        78 v~~~~d   83 (85)
T d1zh5a2          78 ILFKDD   83 (85)
T ss_dssp             EEEGGG
T ss_pred             EEEcCC
Confidence            997544

>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=99.55  E-value=2.1e-15  Score=112.12  Aligned_cols=66  Identities=12%  Similarity=0.247  Sum_probs=60.9

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      ++|+++|+.||+|.+|+|+++..++.+   +|+|||+|.++++|..||+.|||..|+|++|+|.|+..+
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            599999999999999999998877654   689999999999999999999999999999999998653

>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=99.55  E-value=9e-16  Score=115.88  Aligned_cols=81  Identities=12%  Similarity=0.120  Sum_probs=63.2

Q ss_pred             cCCeEEEeCCCccCc-HHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          173 HARRVYVGGLPPLAN-EQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t-~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      +.++|||+|||+++| +++|+++|++||.|..+.+.     ..+...+.++|||||+|.+.++|.+|++||+..|.|+.|
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 56699999999985432110     001123456899999999999999999999999999999


Q ss_pred             EEeCCCC
Q 009954          252 RVRRPTD  258 (521)
Q Consensus       252 ~v~~~~~  258 (521)
                      +|.++..
T Consensus        78 ~V~~a~~   84 (86)
T d2ghpa3          78 SVSLADK   84 (86)
T ss_dssp             EEEECCC
T ss_pred             EEEEcCC
Confidence            9998653

>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=99.54  E-value=4.2e-16  Score=122.60  Aligned_cols=82  Identities=32%  Similarity=0.450  Sum_probs=66.9

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      ...++|||+|||+++|+++|+++|++||.|..+.      .+.+..++.++|||||+|.+.++|..|+ .|||..|.|+.
T Consensus         6 ~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~------i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~   79 (104)
T d1p1ta_           6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFR------LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRA   79 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEE------EEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccccc------cccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            4467899999999999999999999999854311      1122223456799999999999999999 69999999999


Q ss_pred             EEEeCCCCC
Q 009954          251 VRVRRPTDY  259 (521)
Q Consensus       251 i~v~~~~~~  259 (521)
                      |+|.++...
T Consensus        80 i~V~~a~~~   88 (104)
T d1p1ta_          80 LRVDNAASE   88 (104)
T ss_dssp             BEEEETTCT
T ss_pred             EEEEECCCC
Confidence            999987643

>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=99.54  E-value=1.5e-15  Score=115.06  Aligned_cols=72  Identities=24%  Similarity=0.344  Sum_probs=64.7

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      +.+|||+|||+++|+++|+++|.+||.             ..+.+...+|||||+|.+.++|+.|+ .||+..|.|++|.
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            568999999999999999999999972             34556778999999999999999999 7999999999999


Q ss_pred             EeCCCC
Q 009954          253 VRRPTD  258 (521)
Q Consensus       253 v~~~~~  258 (521)
                      |+++..
T Consensus        72 V~~a~~   77 (88)
T d1wg1a_          72 VQLQPT   77 (88)
T ss_dssp             EEECCC
T ss_pred             EEEcCC
Confidence            998654

>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=99.54  E-value=2.3e-15  Score=111.54  Aligned_cols=71  Identities=23%  Similarity=0.376  Sum_probs=65.2

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ..++|||+||+  +|+++|+++|++||.            |.++.+...++||||+|.+.++|..|+ .|||..+.|++|
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            35789999995  899999999999997            667788889999999999999999999 799999999999


Q ss_pred             EEeCCC
Q 009954          252 RVRRPT  257 (521)
Q Consensus       252 ~v~~~~  257 (521)
                      +|.|+.
T Consensus        70 ~V~~a~   75 (79)
T d2bz2a1          70 KVNIAR   75 (79)
T ss_dssp             EEEECC
T ss_pred             EEEEec
Confidence            999875

>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=99.54  E-value=4.8e-15  Score=112.52  Aligned_cols=75  Identities=23%  Similarity=0.372  Sum_probs=64.3

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCcee-cCceE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF-EGVAV  251 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~-~g~~i  251 (521)
                      +++|||+|||..+|+++|+++|.+||.+.          ........++|||||+|.+.++|.+|+ .|+|..+ .|++|
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~----------~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l   79 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVV----------KGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHL   79 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCE----------EEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEE----------EEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEE
Confidence            57899999999999999999999999742          223345567899999999999999999 7999988 58999


Q ss_pred             EEeCCCC
Q 009954          252 RVRRPTD  258 (521)
Q Consensus       252 ~v~~~~~  258 (521)
                      +|.+++.
T Consensus        80 ~v~~sk~   86 (88)
T d2adca2          80 RVSFSKS   86 (88)
T ss_dssp             EEEECSS
T ss_pred             EEEeCCC
Confidence            9998653

>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=99.54  E-value=2.8e-15  Score=117.31  Aligned_cols=89  Identities=21%  Similarity=0.219  Sum_probs=69.7

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCc--eEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDA--VVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~--v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  248 (521)
                      ...++|||+|||..+|+++|+++|..||.|..+........  ..+..++.++|||||+|.+.++|..|+ .|||..|.|
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            45679999999999999999999999998754332211110  111123566899999999999999999 699999999


Q ss_pred             ceEEEeCCCCCC
Q 009954          249 VAVRVRRPTDYN  260 (521)
Q Consensus       249 ~~i~v~~~~~~~  260 (521)
                      +.|+|.++....
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

>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=1.6e-15  Score=118.63  Aligned_cols=81  Identities=17%  Similarity=0.277  Sum_probs=63.8

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHH-ccCceecCce
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVA  250 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~  250 (521)
                      ...++|||+|||+.+|+++|+++|++||.|..+.+      +.+..++.++|||||+|.+.++|.+|++ +|+ .|.|+.
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i------~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~   80 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVV------ITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRK   80 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEE------SCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEE
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceec------cccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEE
Confidence            34568999999999999999999999998432110      1222235678999999999999999995 554 799999


Q ss_pred             EEEeCCCCC
Q 009954          251 VRVRRPTDY  259 (521)
Q Consensus       251 i~v~~~~~~  259 (521)
                      |.|+++...
T Consensus        81 l~V~~a~~~   89 (103)
T d2cqda1          81 ANVNLAYLG   89 (103)
T ss_dssp             CEEEESTTT
T ss_pred             EEEEEcCCC
Confidence            999986543

>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=99.54  E-value=1.3e-15  Score=117.62  Aligned_cols=78  Identities=17%  Similarity=0.261  Sum_probs=67.3

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....++|||+|||+++|+++|+++|.+||.+           ......+.++|||||+|.+.++|..|+ .|||..|.|+
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v-----------~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr   81 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEI-----------RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGR   81 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEE-----------CCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccc-----------eeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCE
Confidence            3456799999999999999999999999874           222345677899999999999999999 6999999999


Q ss_pred             eEEEeCCCCC
Q 009954          250 AVRVRRPTDY  259 (521)
Q Consensus       250 ~i~v~~~~~~  259 (521)
                      +|+|.|+...
T Consensus        82 ~i~V~~a~~k   91 (96)
T d1fjca_          82 SVSLYYTGEK   91 (96)
T ss_dssp             EEEEEECSSS
T ss_pred             EEEEEEeCCC
Confidence            9999987654

>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=99.53  E-value=9.3e-16  Score=119.73  Aligned_cols=75  Identities=13%  Similarity=0.163  Sum_probs=70.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       296 ~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      .++|.+++..++|++|.++|++||.|..|.|+.+ .+|.++|+|||+|.+.++|.+|++.|||.+|+|+.|.|.|+
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 58999999999999999999999999999999999999986

>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=99.53  E-value=3e-15  Score=116.49  Aligned_cols=83  Identities=20%  Similarity=0.284  Sum_probs=65.1

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-Hcc------Cc
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD------GI  244 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~------g~  244 (521)
                      .+.++|||+|||+++|+++|+++|.+||.+....+      +.+...+.++|||||+|.+.++|.+|+ .||      |.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~------~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~   79 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRV------VLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL   79 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEC------CBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeee------ccccccccccceEEEEEcCHHHHHHHHHHcccccccCCc
Confidence            34678999999999999999999999997432111      112223456899999999999999999 454      67


Q ss_pred             eecCceEEEeCCCCCC
Q 009954          245 IFEGVAVRVRRPTDYN  260 (521)
Q Consensus       245 ~~~g~~i~v~~~~~~~  260 (521)
                      .+.|+.|+|.++.+..
T Consensus        80 ~~~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          80 KLDGRQLKVDLAVTRD   95 (98)
T ss_dssp             ESSSCEEEEECCCCCC
T ss_pred             EECCEEEEEEECCCCC
Confidence            8999999999876543

>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=99.53  E-value=1.6e-14  Score=109.35  Aligned_cols=65  Identities=23%  Similarity=0.370  Sum_probs=60.1

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~  511 (521)
                      ++|+++|+.||+|..|.|+++..++.+   +|+|||+|.+.++|+.|+..|||..|+|++|+|.|+..
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            599999999999999999998777654   68899999999999999999999999999999999864

>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=99.52  E-value=1.6e-14  Score=112.25  Aligned_cols=67  Identities=19%  Similarity=0.293  Sum_probs=62.1

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      ++|+++|++||+|..|.|+.+..++.+   +|+|||+|.+.++|+.||+.|||..|+|++|+|.++...+
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            599999999999999999998877765   6888999999999999999999999999999999988764

>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=99.52  E-value=2.2e-14  Score=109.18  Aligned_cols=66  Identities=17%  Similarity=0.311  Sum_probs=60.4

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      ++|+++|+.||+|..|.|+.+..++..   +|+|||+|.+.++|.+||+.|||..|+|+.|+|.|+.+.
T Consensus        23 ~~l~~~f~~~G~v~~v~i~~d~~t~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~   88 (90)
T d2cq0a1          23 TDLQELFRPFGSISRIYLAKDKTTGQS---KGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS   88 (90)
T ss_dssp             HHHHTTSTTTCCEEEEEEEECSSSCSE---EEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCC
T ss_pred             HHHHHHHHHhccccccccccccccccc---ccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCC
Confidence            599999999999999999998766654   688999999999999999999999999999999998653

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.51  E-value=1.1e-14  Score=108.98  Aligned_cols=73  Identities=23%  Similarity=0.335  Sum_probs=64.1

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCCeEEEEecCHHHHHHHH-HccCceec-Cc
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFE-GV  249 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~-~~g~afV~f~~~~~a~~A~-~l~g~~~~-g~  249 (521)
                      ++++|||+|||..+|+++|.++|+.||.            |..+.+.. .+|||||+|.+.++|..|+ .|+|..|. |+
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~------------i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~   74 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPG------------FKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTH   74 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTT------------EEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCcc------------EEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCc
Confidence            4679999999999999999999999997            66666544 5689999999999999999 69998884 68


Q ss_pred             eEEEeCCC
Q 009954          250 AVRVRRPT  257 (521)
Q Consensus       250 ~i~v~~~~  257 (521)
                      .|+|.|++
T Consensus        75 ~i~v~~ak   82 (83)
T d2b0ga1          75 AMKITFAK   82 (83)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEEec
Confidence            99999864

>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=99.51  E-value=4.6e-14  Score=108.01  Aligned_cols=65  Identities=18%  Similarity=0.360  Sum_probs=59.2

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      ++|+++|+.||+|..|.|+.+...     .+|+|||+|.+.++|.+||+.|||..|+|++|+|.|+.+..
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            599999999999999999987632     35888999999999999999999999999999999998764

>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=99.51  E-value=6.1e-15  Score=111.77  Aligned_cols=75  Identities=24%  Similarity=0.392  Sum_probs=64.6

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEE-ecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY-INHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~-~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      .+++|||+|||+.+|+++|+++|.+||.            |.++. ...+++||||+|.+.++|+.|+. ++..|.|++|
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 34578999999999999999995 7889999999


Q ss_pred             EEeCCCCCC
Q 009954          252 RVRRPTDYN  260 (521)
Q Consensus       252 ~v~~~~~~~  260 (521)
                      .|.++....
T Consensus        71 ~v~~a~~k~   79 (88)
T d1wf0a_          71 HISNAEPKH   79 (88)
T ss_dssp             EEECCCCCC
T ss_pred             EEEeCCCCC
Confidence            999876543

>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=99.51  E-value=3e-14  Score=107.93  Aligned_cols=76  Identities=20%  Similarity=0.324  Sum_probs=63.6

Q ss_pred             ceEEEeeCcCCcccCCChHHHHHHHHHH---HHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHh
Q 009954          419 AKVLCLTEAITADALADDEEYEEILEDM---REECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  495 (521)
Q Consensus       419 ~~v~~l~~~~~~~~~~~~~~~~~~~~dl---~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~ln  495 (521)
                      ..|-+|+..++.+             +|   .++|++||+|..|.|+++..++......|+|||+|.+.++|.+||+.||
T Consensus        11 vyV~nLp~~~t~~-------------~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~ln   77 (89)
T d2cpia1          11 VFVVGLSQRLADP-------------EVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVN   77 (89)
T ss_dssp             EEEEEECTTTCCH-------------HHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHT
T ss_pred             EEEECCCCccCHH-------------HHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhC
Confidence            3455565555554             77   7789999999999999998766554456899999999999999999999


Q ss_pred             CCeeCCcEEEEE
Q 009954          496 GRKFGGNTVNAF  507 (521)
Q Consensus       496 g~~~~gr~l~v~  507 (521)
                      |..|+|+.|+|+
T Consensus        78 g~~~~gr~lkvS   89 (89)
T d2cpia1          78 NVVVDGRTLKAS   89 (89)
T ss_dssp             TEEETTEEEEEE
T ss_pred             CCEECCEEEEEC
Confidence            999999999996

>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=99.51  E-value=1.5e-14  Score=108.21  Aligned_cols=65  Identities=25%  Similarity=0.416  Sum_probs=59.6

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~  511 (521)
                      ++|+++|++||+|..|.|+++..++..   +|+|||+|.+.++|+.|++.|||..|+|++|+|.|+.+
T Consensus        17 ~~l~~~f~~~G~v~~v~i~~~~~~~~~---~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          17 EEFRSLFGSIGEIESCKLVRDKITGQS---LGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             HHHHHHHHTTSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHHHHHHhCCcccccceeeccCCCc---eeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            599999999999999999988766554   68899999999999999999999999999999999864

>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=99.51  E-value=2e-14  Score=112.07  Aligned_cols=67  Identities=15%  Similarity=0.198  Sum_probs=61.0

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDK  513 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~  513 (521)
                      ++|+++|+.||.|..|.++.+..++..   +|+|||+|.+.++|+.||+.|||..|+|++|+|.|+....
T Consensus        33 ~~l~~~F~~~G~i~~~~~~~~~~~g~~---kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~   99 (102)
T d2cpza1          33 QDLLQMFMPFGNVVSAKVFIDKQTNLS---KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKN   99 (102)
T ss_dssp             HHHHHHHGGGSCCSEEEEEECSSSCSE---EEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSC
T ss_pred             HHHHHHHHhhccccccceeeecccCCC---ccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCCC
Confidence            599999999999999999998767654   6899999999999999999999999999999999986653

>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=99.51  E-value=2e-14  Score=111.06  Aligned_cols=73  Identities=23%  Similarity=0.414  Sum_probs=67.1

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecC--ce
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--VA  250 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g--~~  250 (521)
                      +++|||+|||+++|+++|+++|++||.            |..+.+..+++||||+|.+.++|..|+ .||+..|.|  ++
T Consensus        17 s~tl~V~nLp~~~t~~~l~~~f~~~G~------------i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~   84 (97)
T d1whya_          17 TTRLWVGGLGPNTSLAALAREFDRFGS------------IRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRR   84 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSC------------EEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCB
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhhcc------------cceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCceE
Confidence            578999999999999999999999987            788888889999999999999999999 799999987  58


Q ss_pred             EEEeCCCC
Q 009954          251 VRVRRPTD  258 (521)
Q Consensus       251 i~v~~~~~  258 (521)
                      |+|.|++.
T Consensus        85 l~v~~ak~   92 (97)
T d1whya_          85 LRVDFAKS   92 (97)
T ss_dssp             CEEEECCC
T ss_pred             EEEEeCCC
Confidence            99998754

>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=2.2e-14  Score=111.77  Aligned_cols=68  Identities=24%  Similarity=0.273  Sum_probs=60.0

Q ss_pred             HHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcC
Q 009954          439 YEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYP  510 (521)
Q Consensus       439 ~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~  510 (521)
                      .+.++++|+++|++||+|.+|.|+++. ++..   +|+|||+|.+.++|.+|++.|||+.|+|++|+|.|.|
T Consensus        37 ~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~---~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~sP  104 (104)
T d1jmta_          37 DEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHL---VGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP  104 (104)
T ss_dssp             HHHHHHHHHHHHHHTCCEEEEEECCSS-SSSS---EEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEECC
T ss_pred             hhhhHHHHHHHhccCCCEEEEEeecCC-CCCE---eeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEECC
Confidence            344557899999999999999998775 5543   6889999999999999999999999999999999975

>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=99.50  E-value=5.8e-14  Score=111.30  Aligned_cols=74  Identities=26%  Similarity=0.307  Sum_probs=65.1

Q ss_pred             CCeEEEeCCCc-cCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCCeEEEEecCHHHHHHHH-HccCceecCce
Q 009954          174 ARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (521)
Q Consensus       174 ~~~l~v~nlp~-~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~-~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~  250 (521)
                      +++|||+|||+ .+|+++|+++|+.||.            |..+.+.. .+|||||+|.+.++|.+|+ .|||..|.|+.
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 5899999999999998            66766554 4799999999999999999 79999999999


Q ss_pred             EEEeCCCCC
Q 009954          251 VRVRRPTDY  259 (521)
Q Consensus       251 i~v~~~~~~  259 (521)
                      |+|.++...
T Consensus        70 l~v~~s~~~   78 (109)
T d2adca1          70 IRITLSKHQ   78 (109)
T ss_dssp             CEEECCSCC
T ss_pred             EEEEECCCC
Confidence            999997643

>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=99.50  E-value=1.5e-14  Score=108.63  Aligned_cols=66  Identities=20%  Similarity=0.268  Sum_probs=61.0

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      ++|+++|+.||+|..|.|+++..+|..   +|+|||+|.++++|..|++.|||..|+|++|+|.|++..
T Consensus        16 ~~l~~~F~~~G~v~~v~i~~d~~tg~~---rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_          16 DQVKELLTSFGPLKAFNLVKDSATGLS---KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             HHHHHHHTSSSCEEEEEEECCCSSSCC---CCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             HHHHHHHHhcCccceEEeecccccccc---ceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            499999999999999999999877764   688899999999999999999999999999999998753

>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=99.50  E-value=1.8e-14  Score=109.27  Aligned_cols=76  Identities=17%  Similarity=0.164  Sum_probs=68.4

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHH---ccCceecC
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIFEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~---l~g~~~~g  248 (521)
                      .++++|||+|||+.+|+++|+++|++||.            |..+.+..+++||||+|.+.++|..|++   +++..+.|
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            34679999999999999999999999987            7888888999999999999999999993   47889999


Q ss_pred             ceEEEeCCCCC
Q 009954          249 VAVRVRRPTDY  259 (521)
Q Consensus       249 ~~i~v~~~~~~  259 (521)
                      ++|+|.+++..
T Consensus        74 ~~l~v~~sk~~   84 (88)
T d2cq1a1          74 QPIYIQYSNHK   84 (88)
T ss_dssp             EECEEEECSCS
T ss_pred             CEEEEEECCCC
Confidence            99999987643

>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=99.49  E-value=4.1e-14  Score=110.81  Aligned_cols=77  Identities=18%  Similarity=0.154  Sum_probs=68.7

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-Hc--cCceecC
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-AL--DGIIFEG  248 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l--~g~~~~g  248 (521)
                      .++++|||+|||..+|+++|.++|.+||.            |..+.+.+.+++|||+|.+.++|+.|+ .+  ++..+.|
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~------------I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g   80 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGT------------ICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAG   80 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhccc------------ceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEee
Confidence            45779999999999999999999999997            788888899999999999999999999 44  6678899


Q ss_pred             ceEEEeCCCCCC
Q 009954          249 VAVRVRRPTDYN  260 (521)
Q Consensus       249 ~~i~v~~~~~~~  260 (521)
                      ++|+|.+++...
T Consensus        81 ~~l~v~~s~~~~   92 (104)
T d1wexa_          81 QQAFFNYSTSKR   92 (104)
T ss_dssp             SBCEEEECSSSS
T ss_pred             EEEEEEEcCCCc
Confidence            999999976543

>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=99.48  E-value=2.3e-15  Score=117.40  Aligned_cols=79  Identities=13%  Similarity=0.260  Sum_probs=64.0

Q ss_pred             hccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCc
Q 009954          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~  249 (521)
                      ....++|||+|||+++|+++|+++|++||.|..+.       +.....+.++|||||+|.+.++|.+|+ .|||..|.|+
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~-------~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr   87 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTR-------ILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTP   87 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEE-------EEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhccccccee-------eecccccccccceeEEeCCHHHHHHHHHHhCCCEECCc
Confidence            34567899999999999999999999999853210       111123455789999999999999999 7999999999


Q ss_pred             eEEEeCC
Q 009954          250 AVRVRRP  256 (521)
Q Consensus       250 ~i~v~~~  256 (521)
                      ++.|.++
T Consensus        88 ~~~v~~~   94 (101)
T d1x5oa1          88 PGVSAPT   94 (101)
T ss_dssp             TTSCCCS
T ss_pred             CCccCCC
Confidence            9988753

>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=99.48  E-value=1.2e-14  Score=109.45  Aligned_cols=69  Identities=19%  Similarity=0.305  Sum_probs=60.8

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPED  512 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~  512 (521)
                      ++|+++|++||.|..|.|+++..++.....+|+|||+|.+.++|..|++.|||..|+|+.|.|.|+...
T Consensus        13 ~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~~   81 (85)
T d2cpfa1          13 ETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERA   81 (85)
T ss_dssp             HHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCS
T ss_pred             HHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            699999999999999999988755543334688999999999999999999999999999999997543

>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=99.48  E-value=8.4e-15  Score=111.80  Aligned_cols=75  Identities=19%  Similarity=0.382  Sum_probs=63.4

Q ss_pred             cCCeEEEeCCCccCcHHHHHH----HHHHHHHhhcCCCCCCCCceEEEEe---cCCCCeEEEEecCHHHHHHHH-HccCc
Q 009954          173 HARRVYVGGLPPLANEQAIAT----FFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGI  244 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~----~f~~~G~~~~~~~~~~~~~v~~~~~---~~~~g~afV~f~~~~~a~~A~-~l~g~  244 (521)
                      ++++|||+|||+.+|+++|++    +|++||.            |..+.+   +.++|||||+|.+.++|..|+ .+||.
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            357999999999999999875    4677776            455554   446899999999999999999 79999


Q ss_pred             eecCceEEEeCCCCC
Q 009954          245 IFEGVAVRVRRPTDY  259 (521)
Q Consensus       245 ~~~g~~i~v~~~~~~  259 (521)
                      .+.|+.|.|.|+...
T Consensus        70 ~~~g~~l~v~~ak~~   84 (91)
T d1nu4a_          70 PFYDKPMRIQYAKTD   84 (91)
T ss_dssp             EETTEECEEEECSSC
T ss_pred             EECCEEEEEEEeCCC
Confidence            999999999997654

>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=99.48  E-value=2.3e-14  Score=104.65  Aligned_cols=69  Identities=19%  Similarity=0.268  Sum_probs=60.5

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec----CCCCeEEEEecCHHHHHHHHHccCceecCce
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~----~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~  250 (521)
                      .+|||+|||+++++++|+++|..||.|            ..+.+.    ..++||||+|.+.++|.+|+.+|+..|.|+.
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            444432    3457999999999999999999999999999


Q ss_pred             EEEeC
Q 009954          251 VRVRR  255 (521)
Q Consensus       251 i~v~~  255 (521)
                      |.|..
T Consensus        69 i~V~~   73 (75)
T d2ghpa2          69 IIVSH   73 (75)
T ss_dssp             CEEEE
T ss_pred             EEEEE
Confidence            99975

>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=99.48  E-value=7.6e-14  Score=107.59  Aligned_cols=75  Identities=25%  Similarity=0.391  Sum_probs=62.3

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-------cCCCCeEEEEecCHHHHHHHH-Hcc--Cc
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVEMRTVEEASNAM-ALD--GI  244 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~-------~~~~g~afV~f~~~~~a~~A~-~l~--g~  244 (521)
                      |+|||+|||..+|+++|+++|++||..           +..+.+       +.++|||||+|.+.++|..|+ .|+  +.
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~-----------i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~   70 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEG-----------VLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRI   70 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTT-----------EEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCS
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCc-----------ceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCe
Confidence            689999999999999999999999862           344443       456899999999999999999 575  45


Q ss_pred             eecCceEEEeCCCCCC
Q 009954          245 IFEGVAVRVRRPTDYN  260 (521)
Q Consensus       245 ~~~g~~i~v~~~~~~~  260 (521)
                      .+.|+.|.|.|+.+..
T Consensus        71 ~~~g~~i~V~~A~p~~   86 (96)
T d2disa1          71 QLWGHQIAVDWAEPEI   86 (96)
T ss_dssp             CBTTBCCEEEESCSSC
T ss_pred             EECCEEEEEEEcCCCC
Confidence            5679999999986543

>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=99.47  E-value=9.9e-15  Score=110.29  Aligned_cols=70  Identities=23%  Similarity=0.257  Sum_probs=62.3

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEEE
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~v  253 (521)
                      ++|||+|||+++|+++|+++|++||.            |..+.+. ..|||||+|.+.++|+.|| .|||..|.|+.|+|
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 79999999999998


Q ss_pred             eCCC
Q 009954          254 RRPT  257 (521)
Q Consensus       254 ~~~~  257 (521)
                      .++.
T Consensus        68 ~~~~   71 (87)
T d3begb1          68 AYIR   71 (87)
T ss_dssp             CBCE
T ss_pred             eEEe
Confidence            7643

>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=99.47  E-value=1.1e-13  Score=106.67  Aligned_cols=61  Identities=23%  Similarity=0.389  Sum_probs=55.8

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCcc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYF  515 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~  515 (521)
                      ++|+++|++||.|+.|.|.+           |+|||+|.+.++|++||+.|||..|.|++|+|.|+.+....
T Consensus        31 ~~L~~~F~~~G~i~~~~i~r-----------g~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~~   91 (98)
T d1wf2a_          31 SDVEAIFSKYGKIVGCSVHK-----------GFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVN   91 (98)
T ss_dssp             HHHHHSSTTSSCEEEEEEET-----------EEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCCCC
T ss_pred             HHHHHHHhhcCCEEEEEEeC-----------CeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            48999999999999999944           89999999999999999999999999999999999765443

>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=99.47  E-value=3.4e-14  Score=106.87  Aligned_cols=63  Identities=24%  Similarity=0.332  Sum_probs=57.9

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCC--cEEEEEEc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYY  509 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~g--r~l~v~~~  509 (521)
                      ++|+++|++||+|..|.|+++..++.+   +|+|||+|.+.++|..||+.|||..+.|  ++|+|.|+
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            599999999999999999998877664   6889999999999999999999999976  88999986

>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=99.47  E-value=2.8e-14  Score=107.23  Aligned_cols=63  Identities=17%  Similarity=0.356  Sum_probs=56.9

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCC--cEEEEEEc
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGG--NTVNAFYY  509 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~g--r~l~v~~~  509 (521)
                      ++|+++|++||+|..|.|+.+..++..   +|+|||+|.+.++|..|++.|||..|+|  ++|+|.|+
T Consensus        21 ~~L~~~F~~~G~v~~v~i~~d~~~g~~---kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          21 KELEQLFSQYGRIITSRILVDQVTGVS---RGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTCCE---EEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHHHHHhCCccccccccccccccC---CCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            599999999999999999998766554   6899999999999999999999999998  55999885

>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=99.47  E-value=8.9e-15  Score=110.53  Aligned_cols=76  Identities=17%  Similarity=0.134  Sum_probs=64.5

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceEE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      ...|||+|||+++++++|+++|..||.+...      ..+.....+.++|||||+|.+.++|.+|+ +||+..+.|++|+
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            3469999999999999999999999876432      12444455677899999999999999999 6999999999999


Q ss_pred             EeC
Q 009954          253 VRR  255 (521)
Q Consensus       253 v~~  255 (521)
                      |..
T Consensus        83 v~l   85 (86)
T d2cqpa1          83 LVL   85 (86)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            974

>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=8.6e-15  Score=114.73  Aligned_cols=79  Identities=13%  Similarity=0.089  Sum_probs=65.7

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~  252 (521)
                      ...+|||+|||+.+|+++|+++|..||.+...      ..+.....+.++|||||+|.+.++|++||++|+..|.|+.|.
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            35679999999999999999999999875321      012233456789999999999999999999999999999999


Q ss_pred             EeCCC
Q 009954          253 VRRPT  257 (521)
Q Consensus       253 v~~~~  257 (521)
                      |.++.
T Consensus        81 V~~~~   85 (103)
T d2cpya1          81 VHVVT   85 (103)
T ss_dssp             EEEEC
T ss_pred             EEECC
Confidence            98754

>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=99.45  E-value=5.7e-14  Score=111.54  Aligned_cols=77  Identities=14%  Similarity=0.135  Sum_probs=67.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCh-HHHHHHHHHHcCCeeCCeEEEEE
Q 009954          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP-AVTDIACAALNGLKMGDKTLTVR  369 (521)
Q Consensus       291 ~~~~~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~-~~A~~Al~~l~g~~~~g~~l~v~  369 (521)
                      ..++..+||+|||..+|+++|+++|++||+|.+|.|+.+      +|||||.|.+. ++|..|+..|++..+.++.+.|.
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            344456799999999999999999999999999999865      68999999996 68999999999998888777777


Q ss_pred             EccC
Q 009954          370 RATA  373 (521)
Q Consensus       370 ~~~~  373 (521)
                      |...
T Consensus        82 ~~~~   85 (113)
T d1owxa_          82 WEVL   85 (113)
T ss_dssp             EEEC
T ss_pred             Eeec
Confidence            7754

>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=99.45  E-value=1e-14  Score=114.41  Aligned_cols=81  Identities=19%  Similarity=0.191  Sum_probs=65.3

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceEE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i~  252 (521)
                      ...+|||+|||+++|+++|+++|..+|.+....      .+.....+..+|||||+|.+.++|++|+++|+..|.|+.|.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v------~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~   87 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGM------TLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIE   87 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEE------ECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEE------EEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEE
Confidence            456799999999999999999999998743210      01222234568999999999999999999999999999999


Q ss_pred             EeCCCCC
Q 009954          253 VRRPTDY  259 (521)
Q Consensus       253 v~~~~~~  259 (521)
                      |.++...
T Consensus        88 V~~~~~~   94 (104)
T d1wg5a_          88 IFKSSRA   94 (104)
T ss_dssp             EEEECTT
T ss_pred             EEECCHH
Confidence            9876543

>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=99.44  E-value=5.7e-14  Score=108.36  Aligned_cols=72  Identities=22%  Similarity=0.265  Sum_probs=63.9

Q ss_pred             cCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceecCceE
Q 009954          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (521)
Q Consensus       173 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~i  251 (521)
                      ...+|||+|||+.+++++|+++|.+||.            |..+.+. .+|||||+|.+.++|++|| .|||..|.|+.|
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            5556554 5799999999999999999 799999999999


Q ss_pred             EEeCCC
Q 009954          252 RVRRPT  257 (521)
Q Consensus       252 ~v~~~~  257 (521)
                      +|.+..
T Consensus        81 ~v~~~~   86 (98)
T d1wg4a_          81 ETSYIR   86 (98)
T ss_dssp             CEEEEE
T ss_pred             EEEEEe
Confidence            998753

>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=99.44  E-value=1.1e-13  Score=107.31  Aligned_cols=64  Identities=23%  Similarity=0.370  Sum_probs=57.3

Q ss_pred             CCCCeEEEc--CCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee
Q 009954          292 EGPDRVFVG--GLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM  361 (521)
Q Consensus       292 ~~~~~l~v~--nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~  361 (521)
                      .+.++|+|.  |||..+|+++|+++|++||.|..|.+..+      +|||||+|.+.++|.+|+..|||..|
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  59999999999999999999999988765      57999999999999999999999887

>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=99.43  E-value=1.1e-14  Score=115.65  Aligned_cols=79  Identities=18%  Similarity=0.178  Sum_probs=66.1

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ....+|||+|||+.+|+++|+++|..||.+...      ..+.....+..+|||||+|.+.++|.+|++||+..|.|+.|
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~------~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i   89 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDS------IYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFI   89 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTT------CEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCB
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccc------eeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEE
Confidence            346689999999999999999999999875432      11333445667899999999999999999999999999999


Q ss_pred             EEeCC
Q 009954          252 RVRRP  256 (521)
Q Consensus       252 ~v~~~  256 (521)
                      .|..+
T Consensus        90 ~V~~~   94 (112)
T d1wela1          90 QVHPI   94 (112)
T ss_dssp             EEEEE
T ss_pred             EEEEc
Confidence            99764

>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=99.43  E-value=6.2e-14  Score=106.05  Aligned_cols=77  Identities=22%  Similarity=0.214  Sum_probs=69.0

Q ss_pred             hccCCeEEEeCCCcc-CcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-H--ccCcee
Q 009954          171 TRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-A--LDGIIF  246 (521)
Q Consensus       171 ~~~~~~l~v~nlp~~-~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~--l~g~~~  246 (521)
                      .+.+++|||+|||.. +|++||.++|++||.            |..+.+..++++|||+|.+.++|..|+ .  +++..+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~------------I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~   72 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGV------------ISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALV   72 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSC------------EEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCC------------eEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCcc
Confidence            456789999999986 899999999999998            888999899999999999999999999 3  478899


Q ss_pred             cCceEEEeCCCCC
Q 009954          247 EGVAVRVRRPTDY  259 (521)
Q Consensus       247 ~g~~i~v~~~~~~  259 (521)
                      .|++|+|.+++.+
T Consensus        73 ~gr~l~V~~s~~~   85 (89)
T d1x4da1          73 FGKPVRVHLSQKY   85 (89)
T ss_dssp             TTEECEEEEECCC
T ss_pred             CCceEEEEECCCc
Confidence            9999999987643

>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=99.43  E-value=3.5e-14  Score=109.89  Aligned_cols=76  Identities=24%  Similarity=0.336  Sum_probs=67.6

Q ss_pred             ccCCeEEEeCCCcc-CcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHH---ccCceec
Q 009954          172 RHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIFE  247 (521)
Q Consensus       172 ~~~~~l~v~nlp~~-~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~---l~g~~~~  247 (521)
                      ...++|||+|||.. +|+++|.++|+.||.            |..+.+..++|||||+|.+.++|..|++   +++..|.
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~------------V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~   83 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGK------------IKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQ   83 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSC------------CSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCSS
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccc------------eeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceEC
Confidence            45678999999985 899999999999997            6777888899999999999999999983   7899999


Q ss_pred             CceEEEeCCCCC
Q 009954          248 GVAVRVRRPTDY  259 (521)
Q Consensus       248 g~~i~v~~~~~~  259 (521)
                      |+.|+|.++..+
T Consensus        84 gr~l~V~~s~~~   95 (99)
T d1x4fa1          84 GRCVKVDLSEKY   95 (99)
T ss_dssp             SSCCEEEEECSC
T ss_pred             CEEEEEEEcCCc
Confidence            999999986543

>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=99.42  E-value=1.1e-14  Score=113.79  Aligned_cols=79  Identities=27%  Similarity=0.139  Sum_probs=63.4

Q ss_pred             ccCCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCceE
Q 009954          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (521)
Q Consensus       172 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~i  251 (521)
                      ....+|||+|||+++|+++|+++|..||.+.-        .+.....+..+|||||+|.+.++|++|+++|+..|.|+.|
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~~~v--------~~~~~~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I   84 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNPMRV--------HIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYV   84 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCSEE--------EEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCccee--------eeEEecCCcceEEEEEEECCHHHHHHHHHcCCCEECCEEE
Confidence            34568999999999999999999998864210        0111123445799999999999999999999999999999


Q ss_pred             EEeCCCC
Q 009954          252 RVRRPTD  258 (521)
Q Consensus       252 ~v~~~~~  258 (521)
                      +|.++..
T Consensus        85 ~V~~s~~   91 (102)
T d1weza_          85 ELFLNST   91 (102)
T ss_dssp             EEEEECC
T ss_pred             EEEEcCC
Confidence            9987554

>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=4.5e-13  Score=103.34  Aligned_cols=78  Identities=18%  Similarity=0.362  Sum_probs=66.9

Q ss_pred             CCCeEEEcCC--CCCCC---------HHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCee
Q 009954          293 GPDRVFVGGL--PYYFT---------ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM  361 (521)
Q Consensus       293 ~~~~l~v~nL--p~~~t---------e~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~  361 (521)
                      ..++|+|.||  |.++.         ++||.+.|++||.|..|.+..+    ..+|+|||+|.++++|.+|+..|||.+|
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            3468999999  54331         2689999999999999988765    3579999999999999999999999999


Q ss_pred             CCeEEEEEEccCC
Q 009954          362 GDKTLTVRRATAS  374 (521)
Q Consensus       362 ~g~~l~v~~~~~~  374 (521)
                      +|++|.|.|+..+
T Consensus        83 ~gr~i~v~~~~g~   95 (99)
T d2dita1          83 GGRQITAQAWDGT   95 (99)
T ss_dssp             TTEECEEEECCSC
T ss_pred             CCEEEEEEEeCCc
Confidence            9999999998653

>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=99.39  E-value=1.5e-13  Score=106.92  Aligned_cols=77  Identities=9%  Similarity=-0.003  Sum_probs=67.1

Q ss_pred             cCCeEEEeCCCccC-c----HHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCcee
Q 009954          173 HARRVYVGGLPPLA-N----EQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (521)
Q Consensus       173 ~~~~l~v~nlp~~~-t----~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~  246 (521)
                      .+.+|||+||+..+ +    +++|.++|+.||.            |+++.+.++++||||+|.+.++|.+|+ .|||..|
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 7999999


Q ss_pred             cCceEEEeCCCCCCc
Q 009954          247 EGVAVRVRRPTDYNP  261 (521)
Q Consensus       247 ~g~~i~v~~~~~~~~  261 (521)
                      .|+.|+|.|+.....
T Consensus        72 ~g~~l~v~~a~~~~~   86 (104)
T d1weya_          72 LGKEMKLYFAQTLHI   86 (104)
T ss_dssp             TTEECEEECCCCSSC
T ss_pred             CCCEeEEeecccCCC
Confidence            999999999865443

>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=99.39  E-value=7.2e-14  Score=110.26  Aligned_cols=75  Identities=17%  Similarity=0.188  Sum_probs=62.6

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCcee--cCce
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF--EGVA  250 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~--~g~~  250 (521)
                      ..+|||+|||+.+|+++|+++|++||.|..          +.+...+++|||||+|.+.++|+.|+ .|||..|  .|..
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~----------~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~   76 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLK----------IITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCT   76 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEE----------EEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEE----------EEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcE
Confidence            457999999999999999999999998421          22233457899999999999999999 7999998  4688


Q ss_pred             EEEeCCCC
Q 009954          251 VRVRRPTD  258 (521)
Q Consensus       251 i~v~~~~~  258 (521)
                      |+|.++..
T Consensus        77 l~v~~s~~   84 (108)
T d2adba1          77 LRIDFSKL   84 (108)
T ss_dssp             CEEEECSS
T ss_pred             EEEEecCC
Confidence            99988654

>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=99.37  E-value=2.6e-13  Score=105.92  Aligned_cols=79  Identities=11%  Similarity=0.215  Sum_probs=67.8

Q ss_pred             CCeEEEcCC--CCCCC--------HHHHHHHHHhcCCeeEEEEeecCCC--CCcceEEEEEEcChHHHHHHHHHHcCCee
Q 009954          294 PDRVFVGGL--PYYFT--------ETQIKELLESFGTLHGFDLVKDRDT--GNSKGYGFCVYQDPAVTDIACAALNGLKM  361 (521)
Q Consensus       294 ~~~l~v~nL--p~~~t--------e~~l~~~F~~~G~i~~v~i~~~~~~--g~~~g~afV~f~~~~~A~~Al~~l~g~~~  361 (521)
                      +++|.|.||  |..+.        .+||++.|++||.|.+|.|+++..+  ....|++||+|.++++|.+|+..|||.+|
T Consensus         4 s~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f   83 (104)
T d1o0pa_           4 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   83 (104)
T ss_dssp             CSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCS
T ss_pred             CcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEE
Confidence            467999999  44432        3679999999999999999886544  34568999999999999999999999999


Q ss_pred             CCeEEEEEEcc
Q 009954          362 GDKTLTVRRAT  372 (521)
Q Consensus       362 ~g~~l~v~~~~  372 (521)
                      +|+.|.|.|..
T Consensus        84 ~gR~v~v~f~~   94 (104)
T d1o0pa_          84 ANRVVVTKYCD   94 (104)
T ss_dssp             SSSCCEEEEEC
T ss_pred             CCeEEEEEEcC
Confidence            99999999985

>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=99.35  E-value=7.5e-13  Score=97.43  Aligned_cols=71  Identities=15%  Similarity=0.199  Sum_probs=61.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeE-EEEEEccC
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT-LTVRRATA  373 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~-l~v~~~~~  373 (521)
                      +.|+|.|+|++++++.| ++|++||.|.++++..      .+|||||+|.+.++|++||+ |||..|+|+. |.|..+..
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            46999999999886545 6899999999998654      36899999999999999996 8999999975 67888864

>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=99.35  E-value=9.6e-13  Score=96.85  Aligned_cols=72  Identities=19%  Similarity=0.287  Sum_probs=62.9

Q ss_pred             CCeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHHHccCceecCce-EE
Q 009954          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA-VR  252 (521)
Q Consensus       174 ~~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~-i~  252 (521)
                      .+.|+|+|+|++++++.| ++|++||.            |.++.+..+++||||+|.+.++|.+||++||..|.|+. |.
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            457999999999986555 68999998            88889999999999999999999999999999999974 67


Q ss_pred             EeCCCC
Q 009954          253 VRRPTD  258 (521)
Q Consensus       253 v~~~~~  258 (521)
                      |.++.+
T Consensus        71 V~~~~~   76 (81)
T d1wwha1          71 VKPCID   76 (81)
T ss_dssp             EEECCC
T ss_pred             EEeCCC
Confidence            876543

>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=99.33  E-value=2.6e-13  Score=98.44  Aligned_cols=59  Identities=17%  Similarity=0.272  Sum_probs=54.0

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEE
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVN  505 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~  505 (521)
                      ++|+++|++||.|..+.+..+..++..   +|+|||+|.+.++|++|++.|||..|+|+.|+
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            599999999999999999998876654   68889999999999999999999999999874

>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=99.33  E-value=2.8e-12  Score=100.32  Aligned_cols=73  Identities=18%  Similarity=0.172  Sum_probs=58.8

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCCCCcccccCC
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPEDKYFNKDYS  520 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~~~~~~~~~~  520 (521)
                      ++|+++|+.|| |+.+.++.+....  ...+|+|||+|.+.++|++|+ .|||..|+|++|+|.|+.+.+-..+.++
T Consensus        30 ~~l~~~f~~~g-~~~~~~~~~~~~~--g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a~~~~~~~~~ps  102 (104)
T d1wi8a_          30 ESIKEFFRGLN-ISAVRLPREPSNP--ERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKDSGPS  102 (104)
T ss_dssp             HHHHHHTTTSC-EEEEECCBCSSCT--TSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCCCCCCCC
T ss_pred             HHHHHHHHHhc-cccceeeeeeccC--CCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEECCCCCCCCCCCc
Confidence            69999999999 7778777665322  234678899999999998776 5999999999999999988776665543

>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=99.27  E-value=4.5e-12  Score=97.91  Aligned_cols=64  Identities=20%  Similarity=0.286  Sum_probs=57.5

Q ss_pred             ccCCeEEEe--CCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCHHHHHHHH-HccCceec
Q 009954          172 RHARRVYVG--GLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       172 ~~~~~l~v~--nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      .+.++|+|.  |||..+|+++|+++|++||.            |..+.+..+++||||+|.+.++|..|+ .|||..+.
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            345688885  59999999999999999997            788888999999999999999999999 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=99.14  E-value=9.7e-12  Score=98.39  Aligned_cols=69  Identities=12%  Similarity=0.048  Sum_probs=60.8

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCCeEEEEecCH-HHHHHHH-HccCceecCceEE
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTV-EEASNAM-ALDGIIFEGVAVR  252 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~~~g~afV~f~~~-~~a~~A~-~l~g~~~~g~~i~  252 (521)
                      ..+||+|||+.+|+++|+++|++||.            |..+.+..++|||||.|.+. ++|..|+ .+++..+.++.+.
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~------------V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~   79 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGE------------IKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKE   79 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCC------------EEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCC------------hheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCceE
Confidence            45799999999999999999999998            88889999999999999995 6788888 7999988877766


Q ss_pred             EeC
Q 009954          253 VRR  255 (521)
Q Consensus       253 v~~  255 (521)
                      |.+
T Consensus        80 v~~   82 (113)
T d1owxa_          80 VTW   82 (113)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            654

>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=98.33  E-value=1.4e-06  Score=58.77  Aligned_cols=67  Identities=15%  Similarity=0.144  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEcCC
Q 009954          439 YEEILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYYPE  511 (521)
Q Consensus       439 ~~~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~~~  511 (521)
                      -.++.+-|.+.|.++|.|.++.|..-. ++.     -.|-|...+..+|..|+..|+.+.||++.|.|++++-
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            356778999999999999999997754 333     4789999999999999999999999999999999863

>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=97.85  E-value=1.6e-05  Score=56.48  Aligned_cols=57  Identities=21%  Similarity=0.373  Sum_probs=50.8

Q ss_pred             HHHHHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHhCCeeCCcEEEEEEc
Q 009954          441 EILEDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALSGRKFGGNTVNAFYY  509 (521)
Q Consensus       441 ~~~~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~lng~~~~gr~l~v~~~  509 (521)
                      .+..+|.+.|..||+|+-|++..+           ..+|.|.+-..|.+|+. |+|..+.|++|+|+.-
T Consensus        36 ~l~~~Llq~l~~~GeViLvRFv~d-----------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          36 DLRTELMQTLGSYGTIVLVRINQG-----------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHHHHSCCSEEEEETT-----------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             HHHHHHHHHHhhCCeEEEEEEeCC-----------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            345688999999999999999884           66999999999999988 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=97.79  E-value=8.4e-05  Score=49.96  Aligned_cols=61  Identities=18%  Similarity=0.192  Sum_probs=53.2

Q ss_pred             HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEcc
Q 009954          309 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (521)
Q Consensus       309 ~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~~  372 (521)
                      +-|.+.|.++|.|.++.|.... .|..  .|-|...+.++|..|+..||-.+|+++.|.|.+++
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            4577889999999999987653 4444  49999999999999999999999999999999985

>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=97.44  E-value=0.00019  Score=50.85  Aligned_cols=54  Identities=15%  Similarity=0.290  Sum_probs=49.3

Q ss_pred             HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHcCCeeCCeEEEEEEc
Q 009954          309 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (521)
Q Consensus       309 ~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~g~~~~g~~l~v~~~  371 (521)
                      .+|.+.|..||.|.-|+++.+        ..+|.|.+-+.|.+|++ |+|.++.|+.|+|+-.
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            468899999999999999887        48999999999999998 8999999999999854

>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=97.41  E-value=0.00032  Score=50.76  Aligned_cols=67  Identities=13%  Similarity=0.229  Sum_probs=57.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCC--cceEEEEEEcChHHHHHHHHHHcCCee
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTDIACAALNGLKM  361 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~--~~g~afV~f~~~~~A~~Al~~l~g~~~  361 (521)
                      ++|.|+.||+.+||+++.+.+...|.+........+.+..  .-.-|||.|.+.++...-.+.++|..|
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F   70 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            5799999999999999999999999998887776554322  224699999999999999999999887

>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=95.81  E-value=0.021  Score=40.93  Aligned_cols=55  Identities=20%  Similarity=0.372  Sum_probs=45.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcChHHHHHHHHHHc
Q 009954          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  357 (521)
Q Consensus       295 ~~l~v~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Al~~l~  357 (521)
                      ..||.-..|..+...||.++|++||.|.-- .+.+.       -|||...+.++|..+++.+.
T Consensus        16 dHVf~~tFP~~Wk~~dI~~lFSpfG~V~Vs-wIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          16 DHVLHVTFPKEWKTSDLYQLFSAFGNIQIS-WIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSCCCE-EEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             ceeEEEeCCcccchhHHHHHhcCCCceEEE-EecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            359999999999999999999999998533 33442       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=94.80  E-value=0.011  Score=42.35  Aligned_cols=64  Identities=16%  Similarity=0.301  Sum_probs=46.0

Q ss_pred             CeEEEeCCCccCcHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-C-----CCeEEEEecCHHHHHHHH-HccCceec
Q 009954          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-E-----KKFAFVEMRTVEEASNAM-ALDGIIFE  247 (521)
Q Consensus       175 ~~l~v~nlp~~~t~~~l~~~f~~~G~~~~~~~~~~~~~v~~~~~~~-~-----~g~afV~f~~~~~a~~A~-~l~g~~~~  247 (521)
                      .+|.|+.||+++||+++.+.+...|.+-          .....-++ +     -.-|||.|.+.++..... .++|..+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d----------~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHD----------YFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEE----------EEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceE----------EEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            4799999999999999998887543310          11111111 1     247999999999998888 68998875


Q ss_pred             C
Q 009954          248 G  248 (521)
Q Consensus       248 g  248 (521)
                      +
T Consensus        72 D   72 (91)
T d1uw4a_          72 D   72 (91)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=85.36  E-value=2.8  Score=29.64  Aligned_cols=41  Identities=15%  Similarity=0.172  Sum_probs=33.4

Q ss_pred             HHHHHhhccccceeEEEecCCCCCCCCCCCccEEEEEecCHHHHHHHHHHHh
Q 009954          444 EDMREECGKYGTLVNVVIPRPDQNGGETPGVGKVFLEYYDAVGCATAKNALS  495 (521)
Q Consensus       444 ~dl~~~f~~fG~I~~v~i~~~~~~~~~~~g~g~afV~F~~~~~A~~Ai~~ln  495 (521)
                      .||+++|++||.|.=-.|.-           --|||.-.+.++|+.+++.++
T Consensus        30 ~dI~~lFSpfG~V~VswIdd-----------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          30 SDLYQLFSAFGNIQISWIDD-----------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             HHHHHHHTTTCSCCCEEEET-----------TEEEEECSCHHHHHHHHHHHH
T ss_pred             hHHHHHhcCCCceEEEEecC-----------ceEEEEecCHHHHHHHHHHhc
Confidence            49999999999887556622           257999999999999988655